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Annual Report 2006

Advanced School for Computing and Imaging

2007 Advanced School for Computing and Imaging p/a DUT / EWI P.O. Box 5031 2600 GA DELFT The Netherlands Phone + 31 15 27 88032 Fax: +31 15 27 86632 [email protected] http://www.asci.tudelft.nl __________________________________________________________________________________ ASCI is a Dutch graduate school established in 1993 and accredited by the Royal Netherlands Academy of Arts and Sciences. Research groups of Delft University of Technology, Vrije Universiteit, University of Amsterdam, Leiden University, University Utrecht, University of Twente, University of Groningen, Eindhoven University of Technology and Erasmus University Rotterdam participate in ASCI.

ASCI Annual Report 2006 3

Contents Preface….…………………………………………………………………………………….……………………………….5

CHAPTER 1 ASCI and its Research ........................................................................................................................ 7 1.1 About ASCI .............................................................................................................................................. 7 1.2 Participating Groups ................................................................................................................................ 7 1.3 ASCI Research Themes ........................................................................................................................ 11

CHAPTER 2 Scientific output ................................................................................................................................ 15 2.1 A: HIGH PERFORMANCE COMPUTING AND COMPUTATIONAL SCIENCE..................................... 15

2.1.1 Contribution of TUD-TNW-tn-qi ...................................................................................................... 15 2.1.2 Contribution of UL-LIACS............................................................................................................... 15 2.1.3 Contribution of UVA-FdNWI-scs .................................................................................................... 17 2.1.4 Contribution of TUD-EWI-me-ce .................................................................................................... 30

2.2 B: LARGE SCALE DISTRIBUTED INFORMATION SYSTEMS AND EMBEDDED SYTEMS ............... 30 2.2.1 Contribution of UVA-FdnWI-csa..................................................................................................... 30 2.2.2 Contribution of UvA-FdNWI-caps................................................................................................... 34 2.2.3 Contribution of UL-LIACS............................................................................................................... 39 2.2.4 Contribution of VU – WI ................................................................................................................. 42 2.2.5 Contribution of UT-EWI-dacs ......................................................................................................... 48 2.2.6 Contribution of TUD-EWI-st-pds .................................................................................................... 52 2.2.7 Contribution of UT-EWI-caes ......................................................................................................... 57 2.2.8 Contribution of TUE-EE-dmes........................................................................................................ 62 2.2.9 Contribution of TUD-me-ce ............................................................................................................ 67

2.3 C: IMAGE & MULTIMEDIA SENSING, PROCESSING, INTERPRETATION AND VISUALISATION.... 70 2.3.1 Contribution of TUD-TNW-tn-qi ...................................................................................................... 70 2.3.2 Contribution of UG-CS-IS............................................................................................................... 72 2.3.3 Contribution of UU-WI-ics .............................................................................................................. 75 2.3.4 Contribution of UG-CS-svcg........................................................................................................... 79 2.3.5 Contribution of TUD-EWI-mm-cgcc................................................................................................ 83 2.3.6 Contribution of TUE-BT-bmia......................................................................................................... 85 2.3.7 Contribution of EUR-RMI-bigr ........................................................................................................ 91 2.3.8 Contribution of UvA-FdNWI-ias...................................................................................................... 94 2.3.9 Contribution of LUMC-lkeb........................................................................................................... 101 2.3.10 Contribution of Tue-WI-vis ........................................................................................................... 105 2.3.11 Contribution of TUD-mm-ict ......................................................................................................... 109 2.3.12 Contribution of UL-LIACS............................................................................................................. 117 2.3.13 Contribution of TUE-EE-dmes...................................................................................................... 118 2.3.14 Contribution of TUD-LR-frs .......................................................................................................... 121 2.3.15 Contribution of UvA- FdNWI-isis .................................................................................................. 121

2.4 D: MULTIMEDIA INFORMATION SYSTEMS ...................................................................................... 125 2.4.1 Contribution of TUD-mm-ict ......................................................................................................... 125 2.4.2 Contribution of UL-LIACS............................................................................................................. 129 2.4.3 Contribution of UVA-FdNWI-isis................................................................................................... 131

3 ASCI-wide Events ...................................................................................................................................... 132 3.1 Cooperation within ASCI ...................................................................................................................... 132 3.2 ASCI 2006 Conference ........................................................................................................................ 136


Preface This is the annual report of the results of ASCI research for 2006. ASCI takes pride in forming the home base for PhD-students in the area of imaging and computation and variations. One of the measures of success is participation in the yearly ASCI conference, another is in the participation in ASCI's educational program. In 2006, thanks to the motivation of its faculty members who receive no compensation, ASCI organised quite a few PhD-level courses distributed over the members of ASCI. In principle, in each course at least two members of ASCI participate to assure quality and diversity of view. In addition, it organized the 2nd edition of the biannual Winterschool addressing the issues related to embedded systems design. The central topic of the 2006 Winterschool was “Nonfunctionals design requirements” addressed at three different levels: application level, compiler level, and architecture level. Like in the 2004 edition of the Winterschool, the last day was reserved for the annual GNARP workshop, the Graduate Network of Applied Research in Parallel systems. The Winterschool and GNARP workshop 2006 were held in Olaertsduyn, Rockanje. Following the good tradition in June the twelfth ASCI conference was held, chaired by Boudewijn Lelieveldt. This time at 'de Vossemeren' Lommel, Belgium. With more than 100 participants to the three day conference including the majority of ASCI's PhD student population present, the conference was a big success. The program offered keynote lectures by Bart de Moor represented by Nathalie Pochet from ESAT-SCD KUL, Bill St Arnaud from CANARIE Inc. and Tim Cootes from the University of Manchester. In addition there was ample room for presentations and poster presentations of PhD-students. On the formal side of things, the number of associated universities, the number of groups from these universities and the number of Ph.D students of ASCI grew again. The number of PhD students in ASCI now has passed the 170 mark. I hope you find the report an interesting read if only by the following key-numbers: 16 PhD degrees were granted, some 610 scientific papers were published in international journals, books and conferences, 40 advanced software packages are described, and some 120 participations in externally funded research programs. For additional information about ASCI, please visit our web page at http://www.asci.tudelft.nl. Prof.dr.ir. Arnold W.M. Smeulders Scientific Director


Chapter 1 ASCI and its Research

1.1 About ASCI ASCI is a national research school on advanced computer and imaging systems. The school was founded in December 1993, and it was approved by the KNAW (Dutch Royal Academy of Sciences) in May 1995. In 2005 ASCI renewed its accreditation for another 6 year period, until 2011. Participants in ASCI are groups from Delft University of Technology, the University of Amsterdam, the Vrije Universiteit, Leiden University and the University of Utrecht; the University of Twente, the University of Groningen, Eindhoven Technical University and the Erasmus University Rotterdam have joined ASCI by association agreements. Research within the school can be characterized as applied, experimental and technical computer science, focussed primarily on parallel and distributed systems and processing, as well as the processing of sensor data, image data and other media. With the emphasis on system development, integration of software and hardware, and the processing of sensory information, it directly addresses the needs in high-performance computing and computing intensive applications, with a special emphasis on computational science, and media-oriented applications such as multimedia, medical imaging, computer vision, industrial automation and CAD/CAM. Other important topics are embedded systems and wide-area systems. The school organizes a graduate program and a research program covering all major subjects concerning parallel, distributed, embedded, and real-time systems, performance analysis, image processing, image analysis, image synthesis, sensor interpretation, pattern recognition and computer vision. Every year ASCI organises the Annual ASCI Conference, the scientific meeting place for all participants in ASCI. Another annual activity is the GNARP workshop (GNARP Graduate Network of Applied Research in Parallel systems) which is organized by PhD students and which is a platform for presenting work in progress. Every two years a winterschool addressing issues related to embedded systems design is organized.

1.2 Participating Groups The following reseach groups participate in ASCI. They are represented together with their abbreviations. For each group the members are listed (situation January 2007). VU-WI-I Vrije Universiteit, Faculty of Sciences, Division of Mathematics and Computer Science,

Dept. of Computer Science http://www.cs.vu.nl/

Prof.dr. A.S. Tanenbaum, Prof.dr. H.E. Bal, Dr. W. de Jonge, Prof.dr. M.R. van Steen, Dr. C.D. Gamage, Dr.ing. T. Kielmann, Dr. G.E.O. Pierre, Dr. B.J. Overeinder, Dr. R. van Nieuwpoort, Dr. J. Maassen, Dr.ir. H.J. Bos, Dr. B. Crispo, Dr.ir. C. van Reeuwijk, B.C. Popescu MSc., Drs. M.D. den Burger, Drs. A.M. Dobber, Drs. N. Drost, Drs. T. van der Schaaf, S. Sivasubramanian M.Sc, Drs. M. Szymaniak, Drs. S. Voulgaris, Drs. J.M.S. Wams, Drs. M. Wrzesinska; D. Gavidia Simonetti, MSc, M.R. Rieback MSc, Drs. W.J. de Bruijn, S. Krishnan Nair, Drs. M.H.J. Nijhuis, Drs. G. Portokalidis, Drs. J.N. Herder, J.Slowinska.

UvA-FdNWI-caps University of Amsterdam, Department of Computer Science, System and Network

Engineering http://www.science.uva.nl/research/sne/

Prof.dr. L.O. Hertzberger, Dr. A. Belloum, Prof.drs. M. Boasson, Dr. C.T.A.M. de Laat, C. Erbas MSc, Drs. J.J. van der Ham.

UvA-FdNWI-ias University of Amsterdam, Faculty of Science, Informatics Institute, Intelligent Autonomous

Systems http://www.science.uva.nl/research/isla/


Prof.dr. F.C.A. Groen, Prof.dr. D.M. Gavrila, Dr. B.J.A. Kröse, Dr. L. Dorst, Dr. N. Vlassis, Dr. Z. Zivkovic, Drs. W. van der Mark, Drs. J.J. Verbeek, Drs. J.R. Kok, Drs. M.T.J. Spaan, Drs. W.P. Zajdel, Drs. S. van Gosliga, O. Booij MSc, ir.J.A. van Kleef, M. Hofmann, Th. Noulas MSc., Drs. J.R.J. Nunnink.

UvA- FdNWI-isis University of Amsterdam, Faculty of Sciences, Informatics Institute, Intelligent Sensory

Information Systems Group http://www.science.uva.nl/research/isis Prof.dr. A.W.M. Smeulders, Dr. R. van den Boomgaard, Dr. M. Worring, Dr.Ing. J.M. Geusebroek, Dr. T. Gevers, Dr. C.J. Veenman, R.F. Aldershoff, Dr. V.T. Pham, Dr. F.J. Seinstra, A. Diplaros MSc., Drs. C.G.M. Snoek ,ir. G.J. Burghouts, Mw. G.P. Nguyen, S. Mehra M.A., Drs. J.C. van Gemert, T.K. Dang MSc.

UvA-FdNWI-scs University of Amsterdam, Faculty of Science, (Informatics Institute/CSP Laboratory),

Section Computational Science. http://www.science.uva.nl/research/scs Prof.dr. P.M.A. Sloot, Dr. G.D. van Albada, Dr. A.G. Hoekstra, Dr. J.A. Kaandorp, Dr.

R.G. Belleman, K. Iskra MSc, Drs. M. Scarpa.

UvA-FdNWI-csa University of Amsterdam, Faculty of Sicence, Informatics Institute, Computer Systems Architecture Group http://www.science.uva.nl/research/csa/ Prof.dr. C. Jesshope, Dr. P.M.W. Knijnenburg, Dr. A. Pimentel, Drs. T.B. Bernard, K. Bousias, Guang Liang MSc, Drs. M. Thompson, Drs. Li Zhang.

TUD-EWI-isa-pds Delft University of Technology, Faculty of Electrical Engineering, Mathematics &

Computer Science, Parallel and Distributed Systems Group http://www.pds.ewi.tudelft.nl

Prof.dr. H.J. Sips, Dr. D.H.J. Epema, Prof.dr.ir. A.J.C. van Gemund, Prof.dr. C. Witteveen, Dr. K. Langendoen, Dr. A.G. Baggio, P.J. Garbacki MSc, Ir. G.P. Halkes, I. Haratcherev MSc., Ir. J. Pietersma, Ir. A. Iosup, A.L. Varbanescu MSc, ir. J.D. Mol, O.O. Sonmez.

TUD-EWI-me-ce Delft University of Technology, Faculty of Electrical Engineering, Mathematics &

Computer Science, Computer Engineering Group http://ce.et.tudelft.nl

Prof.dr. S. Vassiliadis, Dr. B.H.H. Juurlink, Ir. P.J. de Langen. TUD-EWI-mm-cgcc Delft University of Technology, Faculty of Electrical Engineering, Mathematics &

Computer Science, Computer Graphics and CAD/CAM Group http://graphics.tudelft.nl

Prof.dr. F.W. Jansen, Dr. W.F. Bronsvoort, Ir. F.H. Post, Dr. W. Pasman, M. Koutek, C.P. Botha MSc., Ir. B. Vrolijk, Ir. H.A. van der Meiden, L. Zhao MSc, E.J. Griffith MSc, Ir. G. de Haan.

TUD-EWI-mm-ict Delft University of Technology, Faculty of Electrical Engineering, Mathematics &

Computer Science, Department of Mediamatics, Information and Communication Theory Group http://www.ict.ewi.tudelft.nl

Prof.dr.ir. J. Biemond, Prof.dr.ir. R.L Lagendijk, Dr.ir. R.P.W. Duin, Dr. E.A Hendriks, Dr.ir. J.C.A. van der Lubbe, Prof.dr.ir. M.J.T Reinders, Dr. A. Hanjalic, Dr. L.F.A. Wessels, Dr.ir. D. de Ridder, Dr.ir. E.P. van Someren, Dr. E.M. Pekalska, Ir. R.J.M. den Hollander, MTD A.I. Deac, Ir. P.J.O. Doets, P. Juszczak MSc, C. Lai MSc, Ir. J.F. Lichtenauer, Ir. M. van Staalduinen, Ir. J.R. Taal, A. Harol MSc, Ir. Th.A. Knijnenburg, S.A. Verzakov MSc, J. Wang, Ir. R.J.P. van Berlo, H. Celik MSc, Drs. G.A. ten Holt, B. Kroon, Yunlei Li, Drs. W. Meuleman, U. Naci MSc, Ir. M.H. van Vliet, Ir. R.P. Westerlaken.


TUD-TNW-tn-qi Delft University of Technology, Faculty of Applied Physics, Imaging Science &

Technology, Quantitative Imaging Group http://www.qi.tnw.tudelft.nl/

Prof.dr. I.T. Young, Prof.dr. L.J. van Vliet, Dr. P.P. Jonker, Prof.dr. A.M. Vossepoel, J. Caarls, Drs. F.G.A. Faas, B.E. Tuan Quang Pham, I.W.O. Serlie, Ir. G.O.F. Parikesit, Ir. C. van Wijk, B.J. Vermolen.

UL-LIACS/LERC Leiden University, Faculty of Mathematics and Natural Sciences, Leiden Institute of

Advanced Computer Science (LIACS) Computer & Software Systems Division- Leiden Embedded Research Center (LERC)

http://www.liacs.nl/ Prof.dr. H.A.G. Wijshoff, Prof.dr. E.F. Deprettere, Prof.dr. F.J. Peters, Dr. M.S. Lew, Dr.

A.A. Wolters, Dr. D.P. Huijsmans, Dr. E.M. Bakker, Dr.ir. T.P. Stefanov, Drs. J.T. Rijsdam, C. Zissulescu-Ianculescu MSc, M. Haneda MSc, A. Turjan, Drs. M.L. Cristea, Drs. V. Zivkovic, Drs. I. Cimpian, Drs. Hui Li, H. Nikolov MSc, Rs.ing. J.H.T. Rohling, Drs. Bin Jiang, J. Lemaitre, Drs. S. Meijer, Drs. A.A.J. Oerlemans.

UU-WI-ics Utrecht University, Faculty of Science, Department of Information and Computing

Sciences, Center for Geometry, Imaging and Virtual Environments http://www.give.nl Prof.dr. M.H. Overmars, Dr. M. van Kreveld, Dr. F. van der Stappen, Dr. R. Veltkamp, Dr. R.W. van Oostrum, Dr. P. Min, Dr. O. Grigore, Drs. R. Geraerts, Drs. A. Kamphuis, Dipl.ing. I. Reinbacher, Drs. J.P. van den Berg, Drs. E.J. Moet, Dipl.Inform. R. Typke, O.C. Goemans MSc, Ir. R. van Gulik, Drs. M. Bosma, Drs. F.B. ter Haar, Drs. R.H. van Leuken, M. Vahedi.

TUD-L&R-frs Delft University of Technology, Faculty of Aerospace Engineering Department of Earth Observation and Space systems (DEOS)

Optical and Laser Remote Sensing Group http://www.lr.tudelft.nl/olrs Dr. B.G.H. Gorte, Dr.ir. F. van den Heuvel, T.R. Shah MSc, F. Karimi Nejadasl.

UG-CS-svcg University of Groningen, Faculty of Mathematics and Physical Sciences, Institute of

Mathematics and Computing Science, Scientific Visualization and Computer Graphics. http://www.cs.rug.nl/informatica/onderzoek/programmas/svcg Prof.dr. J.B.T.M. Roerdink, Dr. G. Vegter, Dr. H. Bekker.

UG-CS-IS University of Groningen, Faculty of Mathematics and Natural Sciences, Institute of

Mathematics and Computing Science, Intelligent Systems. http://www.cs.rug.nl/

Prof.dr. N. Petkov, Dr. M.H.F. Wilkinson.

TUE-EE-dmes Technische Universiteit Eindhoven, Faculty of Electrical Engineering, Design Methodology for Electronic Systems http://www.es.ele.tue.nl/ Prof.dr.ir. R.H.J.M. Otten, Dr.ir. T. Basten, Prof.dr. H. Corporaal, Dr.ir. M.C.W. Geilen, Prof.dr.ir. G. de Haan, Dr.ir. J.P.M. Voeten, A. Beric MSc, S.H. Fatemi MSc, S. Stuijk, M. Zhao MSc; Dipl.Ing. O. Florescu, Dipl.Eng. S.V. Gheorghita, A.H. Ghamarian Msc., H. Hu MSc.

TUE-WI-vis Technische Universiteit Eindhoven, Department of Mathematics and Computer Science,

Visualization Group http://www.win.tue.nl/vis Prof.dr.ir. J.J. van Wijk, Dr. R. van Liere, Dr.ir. A.J.F. Kok, Dr. A.C. Telea, Dr.ir. H.M.M.


van de Wetering, Ir. F.J.J. van Ham, A.J. Pretorius MSc, PD.Eng. S.L. Voinea, Ir. D. Reniers.

TUE-BMT-bmia Technische Universiteit Eindhoven, Department of Biomedical Engineering Biomedical Image Analysis http://www.bmi2.bmt.tue.nl/image-analysis/ Prof.dr. B.M. ter Haar Romeny, Prof.dr. F.A. Gerritsen, Dr. L.M.J. Florack, Dr. A. Vilanova Bartroli, Dr.ir. J.M. Hofman, H. Bouma, Dr.ir. R. Duits, F. Kanters, P. Sereda MSc, E. Balmachnova MSc, Ir. E.M. Franken, Ir. T.H.J.M. Peeters, Ir. B. Platel, Ir. F. Kanters.

UL-LUMC-lkeb Leiden University Medical Center, division of Image Processing, laboratorium voor klinische en Experimentele Beeldverwerking www.lkeb.nl Prof.dr.ir. J. H.C. Reiber, Dr.ir. F.A. Behloul, Ir. J.G. Bosch, Dr.ir. B.P.F. Lelieveldt, I.M. Adame MSc, L. Ferrarini MSc, Drs M. van Stralen, Drs. A. Suinesiaputra, Drs. A.E.H. Scheenstra.

UT-EEMCS-dacs University of Twente, Faculty of Electrical Engineering, Mathematics and Computer Science, Design and Analysis of Communication Systems http://dacs.ewi.utwente.nl Prof.dr. B. Haverkort, Dr.ir. G.J. Heijenk, Dr.ir. A. Pras, Dr.ir. P.T. de Boer, Dr.ir. G. Karagiannis, Ir. P. Goering, A. Jehangir MSc, Ir. M. Kamilova, Ir. Fei Liu, A. Remke Dipl.-Inf.

EUR-RMI-bigr Erasmus MC, Departments of Radiology and Medical Informatics, Biomedical Imaging Group Rotterdam http://www.bigr.nl/ Prof.dr. W.J. Niessen, Prof.dr.ir. A. Vossepoel, Dr.ir. E. Meijering, Dr. J. Veenland, Dr.ir. H. Vrooman, Dr.ir. Th. van Walsum, Dr. R. Stokking, L. Alic MSc, Drs. F. van der Lijn, E. Rollano MSc, I. Smal MSc.


1.3 ASCI Research Themes In this report the scientific output of ASCI over the year 2006 has been collected and categorized along the two main research lines of ASCI, Computing and Imaging. These are divided into research themes (A,B,C and D – see matrix). ASCI research historically comprises two main themes: Computing and Imaging. Within these themes, activities can be divided into methods & algorithms and systems & architecture. Methods & algorithms deals with the development of models and tools for scientific and industrial applications. Systems & architecture deals with the large scale integration in areas like telematics, embedded systems, communication and networks. Both types of activity are targets for fundamental and applied research within ASCI. These themes and target areas make it possible to construct the following matrix, in which four fields can are defined. These fields are indicated as A, B, C and D and are made more specific in the following paragraphs.

Methods & Algorithms

Systems & Architecture

Computing

A High Performance Computing and Computational Science

B Large scale distributed Information Systems and Embedded Systems

Imaging

C Image and Multimedia Sensing, Processing, Interpretation and Visualisation

D Multimedia Information Systems

A: High Performance Computing and Computational Science

A1: High Performance Computing

High Performance Computing (HPC) is the collective name of large scale and/or real-time calculations on state-of-the-art computers. These computers are the very tools used in computational science to allow thrusting back the frontiers of knowledge. The Computing branch of ASCI is interested in HPC to develop, improve, and study program models and programming tools for different HPC architectures. Of special interest to ASCI is research on distributed HPC architectures, which will form the basis of future Grid computing. To this purpose ASCI has a research distributed HPC system available: the DAS (Distributed ASCI Supercomputer). The research in distributed HPC comprises applications, algorithm design, languages and compilers, run-time systems, and scheduling techniques.

A2: Computational Science

Besides theoretical and experimental research, modeling and simulation has become the powerful third paradigm of scientific inquiry in the natural sciences. Here, models of natural phenomena are analyzed through (in many cases large-scale) simulations executed on state-of-the-art computing system, ranging from desktop workstations to heterogeneous distributed (grid-based) environments or massively parallel computers. Over the years, researchers have realized that modeling and simulation has many generic elements, not connected to a specific application field. Furthermore, it became clear that successful modeling and simulation requires multidisciplinary teams, where computer scientists, numerical mathematicians and researchers from application fields work closely together. These developments led to the evolution of the field of computational science. Here, research focuses on computational methods, models, and tools, using new insight from computer science and (numerical) mathematics, with the goal to facilitate the study of processes, through simulation, that was hitherto not possible. Within ASCI a number of groups are active in the field of Computational Science. Their embedding in ASCI provides necessary input from basic computer science, especially from the computing theme. Computational Science within


ASCI is basic research (as opposed to application driven computational science), focusing on generic models, enabling tools and problem solving environments. Generic Models : Capable to capture many natural systems, allowing for formal study (using e.g. concepts from theoretical computer science), and preserving inherent parallelism. Examples include Cellular Automata, particle based models, and natural solvers. Also, study of fundamental issues related to e.g. synchronous vs. asynchronous execution in generic (parallel) models. Enabling Tools : Examples include Virtual labs, grid based computing environments, automatic load balancing and scheduling systems, scientific visualization and virtual reality environments, data analysis and data retrieval systems (e.g. for BioInformatics), web based computing, etc. Problem Solving Environments : Tailored towards specific application fields (e.g. climate models) or generic environments for e.g. interactive simulation. The main challenge for computational science within ASCI lies in obtaining a true fundamental understanding of all issues related to the modeling and simulation chain. This can be achieved by thorough study of generic models and execution environments, and through detailed analysis of (possibly application oriented) case studies, in combination with realization of specific tools and problem solving environments.

B: Large-scale Distributed Information Systems and Embedded Systems

With the advent of the Internet, a new dimension has been added to the notion of computing. Computing not only concerns high-performance computations, but includes collecting, processing, and communicating information across large-scale networks. These developments are leading to a next generation of distributed computer systems that are characterized by their mixed scale, interconnectivity, and heterogeneity. Examples include traffic control systems and large-scale computational grids. The number of embedded system applications is growing explosively and parallels the rapidly emerging systems-on-silicon paradigm and the explosive expansion of networked applications, both wired and wireless. Considerable research is needed by multidisciplinary teams of experts. Research topics include the following: B1: Operating systems Simply using existing operating systems to build the type of applications mentioned above will not do. Existing operating systems are tailored for general use and often require significant CPU power and main memory. In addition, they are still optimized for using local resources, and provide only traditional networking support. What is often needed are specialized operating systems that exploit the available networking facilities such as programmable network interfaces. In addition, the trend to customize operating systems to specific applications requires that new avenues to flexibility are explored. B2: Distributed Systems An important area of research covers middleware, also known as distributed systems. Middleware provides a layer of abstraction by which the underlying network infrastructure is mostly transparent to applications. Such a layer handles issues such as failure masking, resource management, caching and replication, automated storage, security, and so on. It provides applications with a convenient communication interface while hiding the intricacies related to issues such as performance and reliability. Developing scalable distributed systems is a major multifaceted research topic and includes subjects such as adaptive large-scale replication, worldwide directory services, and high-performance communication infrastructures. B3: Embedded systems An embedded system is a (not self-contained) part of a larger unit that provides service(s) to, or controls that unit. It typically consists of a heterogeneous collection of autonomous subsystems (ASICs, FPGAs, microcontrollers and DSPs) that require co-operation to perform (complex) tasks. They can be part of a geographically distributed system, locally distributed systems (in-home networks), or lumped systems (such as TV receivers). Reactive real-time embedded systems are becoming ubiquitous. Such systems react continuously to their environment at the speed of the environment. Research in this area ranges from the development of hardware and software components for digital signal processing to the development of advanced communication software. Formal methods must be called for to


guarantee time-to-market, correctness and safety. However formal specifications, verifications and synthesis of software and hardware from high levels of abstraction have been demonstrated only for small, specialized languages with restricted semantics. This is at odds with the complexity and heterogeneity found in typical embedded systems of tomorrow. One challenge is to base the approach of designing heterogeneous reactive embedded systems on the use of appropriate formal models to describe the behavior of the system at a high level of abstraction, before a decision on its decomposition into hardware and software components is taken. Another challenge is the systematic development of embedded applications such as networked embedded applications. In the same way as embedded system design is a hardware/software co-design effort, embedded application and embedded system should be specified and explored in concert. Important issues here are scalability, robustness, re-use, quality of service, adaptive resource contracts, balancing processing load and data allocation over available processing and storage resources, both local and distributed. C: Image and Multimedia Sensing, Processing, Interpretation, and Visualization On the junction of Imaging and Methods and Algorithms we deal with the development and evaluation of generic models, methods, algorithms and tools for image sensing, processing, interpretation, and visualization that can be used in many concrete applications. The past decade has witnessed a huge increase in the amount of digital visual data that is generated, processed, and stored. Because humans are good in the processing of visual information, and computers are strong in the fast processing of huge amounts of data, the best of both worlds can only be combined if computers can adequately process visual data for analysis and visualisation. Many theoretical and technological breakthroughs are required before we reach that goal. New fundamental insight into the inherent complexity of problems, new algorithms with proven practical behaviour are required. Research topics include: C1: Image and multimedia sensing The sensing of the real world with satellites, cameras, all kinds of (medical) scanners etc. The resulting data streams are typically large amounts of digital still images and video. Important aspects of research are the development of technology for image acquisition, image sensors and other media, motion capturing, image filtering, image coding, restoration, high quality image compression, and conversion. C2: Image processing Taking an image as input, process the digital image data, and output data either as an image, or as geometrical, numerical, or statistical data. Fundamentally difficult issues are topics such as: representation of images, segmentation, digital geometry, measurement, and mathematical morphology. C3: Image interpretation Classification and recognition of information in images. The problem is often ill-posed, and the image data often ambiguous. Challenging research questions are the development of new models for sensor data fusion, parameter estimation, adaptive control, statistical and geometrical pattern recognition, neuro computing, learning, goal directed computation, model-based interpretation, image database techniques. C4: Visualization and modeling The (interactive) modeling of complex objects and whole scenes, and the generation of images from these descriptions. Relevant research aspects are multi-modal data integration, 3D modelling and feature recognition, motion and path planning, computational geometry, data and information visualisation, rendering, 3D interaction, virtual environments, levels of detail. This list is not complete, and the classification of topics is not strict, there is much overlap between various topics. Each of the techniques plays a natural role in many applications, including bio-medical imaging, industrial inspection, image and video archiving and retrieval, document analysis, geographic information systems, earth observation, computer-aided design and reverse engineering, robotics and manufacturing, robot vision and path planning. See also multimedia information systems at the junction of Imaging and Communication and Systems.


D: Multimedia Information Systems Multimedia systems are systems that are concerned with the handling of multimedia. It includes the acquisition, representation, composition, interaction, architecture, analysis, retrieval and distribution of one or multiple information streams like images, video, speech, sound, free text, language, and graphics. New uses of information require new ways of representing the information, not only because of the availability of multiple information streams but also because of their interaction and the way they can support one another. New methods, techniques and means for the manipulation and architecture of the information are required. It will not only influence the user and the use of information, extensive use of multimedia will also fire back at the internals of the computer, the computer organization and the networks connecting them. Research topics include: D1: Multimedia repositories The processing of multimedia information relies on new designs of the system architectures. Research questions are directed towards data and storage structures for multimedia data. Efficient use of storage space is necessary. Indexing multimedia data based on a higher, more abstract level are to be investigated. New search techniques to handle the large databases efficiently and to uncover information are to be developed. D2: Image, video and audio compression Although substantial progress has been achieved in efficient representation (compression) of images and video, it is no longer studied as an isolated problem, but is considered as one of the components of an entire system. Compression optimization is now investigated in relation with overall performance, including limited or adaptive bandwidth, quality of service, scaling of information and the ability to analyze and to manipulate content in the compressed domain directly. To interact with multimedia data, techniques are investigated to describe the data as coherent spatio-temporal objects. D3: Multimedia understanding At the multimedia level, understanding the information is reached by fusing the information of different modalities and sources. The main issue is how to combine multiple information streams to facilitate a better understanding. Learning from multimedia repositories is a challenging problem. Multimedia mining covers the conversion of the content of large databases into generic rules on the content. D4: Multimedia editing systems For the design of multimedia products the availability of multimedia editing systems is indispensable. Research questions are how to make these systems work on a sufficient level of abstraction in order not to obstruct the designer, but which are - at the same time - intuitive to understand. D5: Delivery To secure multimedia data through e.g. the Internet, watermarking, security and encryption techniques are inevitable for copy protection, authentication or hiding of data. Research issues are for instance the development of watermarking techniques that are resistant to various deformations and privacy guaranteed exchange of multimedia data. D6: Multi-modal man-machine interaction The need grows for personalized video delivery, that is, for developing systems able to filter the incoming programs, to analyze them and prepare them for retrieval according to user preferences. This is only possible if such systems are capable of learning about the user profile. An important research multimedia files. The management of data in bio-informatics, especially in the area of bio-diversity and microscopic analysis and the spatial location of metabolic processes invariably are multimedia of nature. Exploring the depth of the content is an important task for the development of new knowledge. In the Internet based tele-working and other aspects of professional life, multimedia transport of information to escape human transportation is of great societal relevance.issue here is to find ways of characterizing, quantifying and measuring emotions. D7: Multimedia applications Multimedia applications are found in many different circumstances. To mention a few examples, disciplines such as the textile branch, detective work and the medical profession drive on multimedia files. The management of data in bio-informatics, especially in the area of bio-diversity and microscopic analysis and the spatial location of metabolic processes invariably are multimedia of nature. Exploring the depth of the content is an important task for the development of new knowledge. In the Internet based tele-working and other aspects of professional life, multimedia transport of information to escape human transportation is of great social relevance.


Chapter 2 Scientific output

2.1 A: HIGH PERFORMANCE COMPUTING AND COMPUTATIONAL SCIENCE

2.1.1 Contribution of TUD-TNW-tn-qi Architectures and Algorithms, Embedded Imaging Systems The work encompassed projects on embedded systems that incorporate real-time computer vision subsystems. The theoretical work was on the establishment of a parallel programming environment where heterogeneous architectures can be programmed within a single parallel programming language but use various programming paradigms, such as dataflow and data parallel. This is performed within the context of the Progress project SMARTCAM; with TUE, Philips Research and Philips CFT as main industrial partners. Data-parallelism is hidden in “algorithmic skeletons, while task parallelism is scheduled at run time over a Smartcam processor configuration incorporating TriMedia, Xetal-SIMD, FPGA with embedded PowerPC; and controller PC. Hardware design space exploration is part of the project. A real-time stereo vision camera was developed in cooperation with Philips Research and Philips Applied Technologies. Equivalent problems, navigation using cameras and encoders, are encountered in augmented reality applications. Within the Mobile & Wireless project of the Telematica Institute and with TUD-ITS, the positioning of virtual objects exactly in overlay with the real world, is obtained by determining the position and orientation of the human head in relation with the real world. An embedded imaging system closely coupled in a fast loop with the graphics animation system determines from visual cues, fused with information from gyros, accelerometers, magnetometers and tilt sensors, the position and orientation in 3D space with an update rate of 10ms. A demonstrator helmet was developed. A collaboration project with the Royal Academy of Art in the Hague to require Augmented Reality content was successfully applied for and started in 2006. A more or less equivalent problem can be found in the "ROBOCUP" project, in which two teams of four autonomous robots play soccer on an indoor field of about 10x6 meter. Positioning of the robot, interception of the ball, and collision avoidance of the other robots, is performed using odometry and real time image sensing and processing. This project was done in cooperation with the TU-Eindhoven. Similarly robot soccer with Sony AIBO dogs is played in cooperation with the UvA, UU and the Decis lab. A collaboration regarding humanoid robots is started up with the faculty of 3ME at the TU-Delft. A focus in these projects is on reinforcement learning of robots to walk and dribble with the ball. Much effort was put into the set-up of the Dutch Initiative for Cure and Care Technology, a 3TU- initiative together with Erasmus MC, AMC and LUMC. Its focus is on the effectiveness of the entire cure and care chain as well as on automatic systems that sense-think-act. External projects SmartCam Period: 2002-2006; funding STW-Progress, with: TU/e Embedded Systems

2.1.2 Contribution of UL-LIACS Analysis and modeling of the circadian pacemaker at the cellular level The project for developing computer models and performing large-scale simulation of the circadian pacemaker at the cellular level started in 2004 as collaboration between the Leiden Institute of Advanced Computer Science (LIACS) and the Leiden University Medical Center (LUMC). A simulation model has been developed to investigate the effects of the single unit activities (SUAs) on the activity of populations in the biological clock, more precisely the Suprachiasmatic Nuclei (SCN). The simulations use a limited number of neurons and contain different light-dark regimes. Performance predictions and resource management in a Grid To deliver nontrivial quality of service is one of the most challenging problems in the Grid. Specifically, mining performance data on Grid resources to extract useful information, helps to improve performance or manage the system itself. The main research questions are: 1. How to define a set of performance metrics and efficiently predict it using statistical data mining techniques?


2. How resource brokers can incorporate prediction information in an intelligent way to improve throughput and response time on a meta-level? 3. How dynamic prediction information can be efficiently published or routed to the interested brokers/parties? Another research topic is workload characterization and modeling in a Grid environment, specifically in Markov Arrival Processes and Markov Modulated Poisson Processes (MMPP) in modeling job arrival patterns at the Grid level. Cyttron Bio-Computing Search Project The Cyttron (www.cyttron.nl) consortium wants to implement a comprehensive, integrated infrastructure for bio-imaging and modeling cells down to atomic detail. We would like to provide a generic tool for identifying the molecular causes of disease, essential for the prevention of disease and the development of new drug and therapies, and to establish a platform for advanced diagnosis and tuning of individualized therapy, increasing effectiveness in health care. The consortium is highly multidisciplinary including (bio-)physicists, chemists, mathematicians, bio-informatics and image processing specialists, cell biologists, microscopists and medical researches from various research institutes. This sub-project of Cyttron focuses on image search algorithms and methods for bio-image data bases. HIRLAM on a grid environment We investigate how the operational numerical weather forecast system HIRLAM could be made grid-enabled, meaning what kind of adaptions are required to execute the system efficiently on a grid. As grid platform we use the DAS-2 system, which consists of five clusters located on five different universities. For the experiments on a single cluster, we found that more compute processors result in a better performance. However, we cannot obtain more improvement by only increasing the number of computer processors due to communication overhead. We also found that an additional one or two IO processors is an ideal number for the forecast model, more IO processors do not result in a better performance. For the experiment on a multi-cluster, we varied the distribution of processors over two clusters to investigate the performance of the forecast model. The distribution over two clusters increases the elapsed time: the more processors are distributed over the two clusters the larger the elapsed time becomes. Our experiment shows that running the forecast model on a multi-cluster does not result in a better performance than on a single cluster. However, using grid technology may give an advantage if the in- and output files are not located on the main compute server. Iterative Compilation In iterative compilation we search for the best program transformations by profiling many variants and selecting the one with the shortest execution time. Since this approach is extremely time consuming one has to incorporate static models. We show that a highly accurate model as a filter to profiling can reduce the number of executions by 50%. We also show that using a simple model to rank transformations and profiling only those with highest ranking can reduce the number of executions even further, in case we have a limited number of profiles at our disposal. We conclude that a production compiler might perform best using the last approach. Exterrnal Projects Cyttron Bio-Computing Search Project 2004-2008, Bsik, 8.8 MEuro. The Cyttron consortium wants to implement a comprehensive, integrated infrastructure for bio-imaging and modeling cells down to atomic detail. We would like to provide a generic tool for identifying the molecular causes of disease, essential for the prevention of disease and the development of new drug and therapies, and to establish a platform for advanced diagnosis and tuning of individualized therapy, increasing effectiveness in health care. Distributed ASCI Supercomputer 3 (DAS 3) 2005-2009, NWO-EW, 900 KEuro, cooperation with all partners of the ASCI graduate school. Flexible Application Mapping Environments (FAME) 2002-2006, NWO-EW, 270 KEuro, TUE The FAME project aims at developing a novel approach to program optimization, namely, iterative compilation in which the transformation space is searched and profiling is used to measure the impact of transformations. One of the most important goals of this project is to develop heuristics to control the complexity of the search by using analytical models and domain specific knowledge. Lateral boundary conditions for nested models – mathematical and computational aspects 2005-2009, NWO-ALW/EW, 300 KEuro.


The aim of this project is to formulate and implement good lateral boundary conditions, both mathematically ("well-posed") and meteorologically (i.e., properly transferring information from the global into the local domain). The reseach should result in a production code, implying that the code implements the developed algorithms efficiently on massively parallel and/or GRID computers.

2.1.3 Contribution of UVA-FdNWI-scs Biomedical Informatics Complex Systems Problem Solving Environments and Visualisation

Within each of the three main themes in our research, a number of projects are being pursued. Sometimes these projects intersect more themes. We will start this section with the two PhD theses defended in 2006, by K.J. Rycerz and by A. Gualandris, and then move on to a thematic report on the projects that were active in 2006. Other important highlights for 2006 were the appointment of Marian Bubak as Professor in Distributed System Engineering at our institute and the granting of a HC Doctorate to Karl Kesselman on the occasion of the 274th Dies Natalis of the UvA. Besides the many projects that were active in 2006, a large number of proposals were written and granted in 2006. These include the EU projects MORPHEX, the nationally funded VIEW programme project VEARD, the ESF funded project ASTROSIM, the NWO STARE project Dutch Distributed GRAPE Grid. Much of our research is performed in close international collaborations. Within the framework of a formal agreement between the Universiteit van Amsterdam and the Saint Petersburg State University, Russian Federation, a joint laboratory for computational science is operated in Saint Petersburg. This lab works on problem solving environments and applications. We formally collaborate with CYFRONET, Krakow, Poland, through joint Ph.D. students in the field of monitoring and scheduling for scientific computing on the Grid. In the framework of a NATO Science for Peace program we collaborate with institutes of the Siberian Branch of the Russian Academy of Science in the field of biomedical diagnostic systems. Finally, strong research cooperation is established with a number of USA based universities. PhD Theses In 2006 PhD theses were defended by Katarzyna Rycerz (externally prepared at AGH in Krakow, Poland) and by Alessia Gualandris (internally prepared). In her thesis "Grid-based HLA Simulation Support", Katarzyna Rycerz develops a grid-service based implementation of HLA (G-HLAM) that supports complex simulations, including run-time steering in a Grid environment. In her thesis "Simulating self-gravitating systems on parallel computers," Alessia Gualandris first investigates the performance of parallel and wide-area distributed systems for the simulation of N-body systems. She finds that communication latencies become relatively unimportant for large N. Subsequently she reports on studies of a number of challenging dynamical problems in astronomy, using parallel and distributed N-body simulations. BioMedical Informatics The bioinformatics group is collaboration between researchers from SILS-UVA, IvI-UvA and Academic Medical Center Amsterdam working on bioinformatics and is a continuation of the Amsterdam Genomics Center (AmGC) initiative. In 2004 three projects related to modelling and simulation of biological networks has been started up within the Section Computational Science (Mesoscale simulation paradigms for biological systems, Simulation of developmental regulatory networks, Mathematics and Computation for the System Biology of Cells). In November 2005 the project Modelling and inferring developmental regulatory networks was started up. In May 2006 the bioinformatics group organised the third international symposium on networks in bioinformatics in Amsterdam. In 2006 two new projects received funding: MORPHEX, ``Morphogenesis and gene regulatory networks in plants and animals: a complex systems modelling approach” and ``A Visual Exploration environment for Analyzing gene Regulation in Developmental processes (VEARD)”. The MORPHEX project is funded by the EU, the VEARD project by the Dutch Science foundation Mesoscale simulation paradigms for biological systems In this proposed project we want to develop and compare computational models of parts of the living cell that can calculate in detail system properties from experimentally obtained molecular and physical-chemical data. Such a model


is as close as possible to the biological experiments and therefore can be used not only for understanding the principles of function but also to steer further biological experiments. Simulation of developmental regulatory networks In this project we will develop a model for simulating regulatory networks that are capable of quantitatively reproducing spatial and temporal expression patterns in developmental processes. The model is a generalisation of the standard connectionist model used for modelling genetic interactions. The model will be coupled with a biomechanical model of cell aggregates and used to study the formation of spatial and temporal expression patterns of gene products during development in cellular systems (sponges and scleractinian corals). Mathematics and Computation for the System Biology of Cells (Cell.Math.) The aim of the project is to develop, implement, and validate mathematical and computational techniques for the systems biology of the cell. Biologists and mathematicians together will formulate realistic mathematical models of metabolic and regulatory networks including intrinsic spatial non-homogeneity. Depending on the cellular phenomenon considered, models and methods of appropriate temporal and spatial scales will be developed and can then be applied: models in the form of ordinary differential equations and methods for system reduction; multi-adaptive computational methods for partial differential equations (PDEs) for moderate spatial and temporal variability within a cell or an organelle; particle models describing the interaction of individual molecules and computational methods for the evaluation of the dynamic behaviour; and methods for integration of these different approaches into a single simulation. Modelling and inferring developmental regulatory networks The project is collaboration with Prof. A. Samsonov (Ioffe Institute Russian Academy of Sciences, St Petersburg). And Prof. M. Samsonava (St Petersburg State Polytechnical University) In this project we will develop mathematical models of regulatory networks that are capable of quantitatively reproducing spatial and temporal expression patterns in developmental processes. The second aim of the project is to develop new statistical techniques for the analysis of temporal and spatial gene expression patterns, model driven optimisation methods, based on simulated annealing in combination with semi parametric statistical techniques, to infer regulatory networks from actual data sets. To demonstrate the effectiveness of our models we are planning to apply these methods to analyze the developmental process in organisms with a relatively simple body plan (for example sponges and scleractinian corals). MORPHEX, ``Morphogenesis and gene regulatory networks in plants and animals: a complex systems modelling approach” The main objective of the project is to obtain via a modelling and simulation approach a better understanding of the structure and dynamics of metabolic pathways of gene regulatory networks involved in the morphogenesis of animals and plants. We will concentrate on the development of two kinds of sponges and on the organogenesis of carpel and anthers of a flowering plant. We will tackle the complexity involved in these processes by using concepts and tools arising from complex systems science. On the one side morphogenesis of sponges and organogenesis in flowering plants share many common concerns and approaches that justify the feasibility of tackling them within a common complex systems framework. On the other side they consider distinguished features and methods of analysis that will guarantee a minimal genericity in the tools designed for the modelling process. The following problems will be addressed: provide a general model allowing describing the underlying complex systems at different hierarchical levels in the same formalism; provide tools to extract concrete models description from experimental data; provide a way to conduct in-silico experiments. These tools will be applied on real data in order to significantly progress on the initial biological problems and will also be used to develop a model guided data collection process. Moreover, the simulation tools will be modular enough to be customised or extended in the future for modelling complex systems arising from other fields. Our global goals can be summarised by three measurable and verifiable objectives: to build spatiotemporal atlases of gene expression for flowering plants (for carpel and anther) and one for sponges; to design, implement and finely tune models of development for reproductive organs in flowering plants and for sponges; to develop a customisable modelling and simulation platform adapted to the study of complex systems in the context of development biology. A Visual Exploration environment for Analyzing gene Regulation in Developmental processes (VEARD) Funding was obtained in 2006 for this project. Understanding the development of complex-shaped biological structures in space and time is a major visualisation problem. Investigating these structures requires an interactive visualisation environment which can be used for quantitative research on complex shaped and variable biological objects and


model-based research on these objects. An important characteristic of model-based studies on biological objects is that the models are usually characterised by a relatively large number of (usually unknown) parameters. An important visualisation issue here is the exploration of these parameter spaces, investigation of these parameter spaces can provide crucial information about the structure of these spaces. In many model-based studies on biological objects these parameter spaces are investigated using optimisation methods to extract model parameters, frequently this optimisation is very expensive, a visual exploration of parameter spaces may be used here to guide the optimisation process. In this project we propose to develop visualisation techniques for quantitative research on complex shaped and variable biological and simulated objects and techniques for the visualisation of abstract n-dimensional parameter spaces in models of gene regulatory networks. The project aims to develop methods and tools to extract and present geometrical information from spatial measurements and simulation, to develop visualisation methods to compare simulation models and measured data, and techniques for the navigation of morphometric parameter spaces (morphospaces) and model parameter spaces. We will focus on a prototypical case study: gene regulation of development in metazoans with a relatively simple body plan (sponges and scleractinian corals).

Figure – Chain of cause/effect relationships considered by Virolab Virolab The goal of Virolab is to provide researchers and medical doctors in Europe with a virtual laboratory for infectious diseases. To this end a virtual laboratory will be developed enabling easy access to distributed resources as well as sharing, processing and analysing virological, immunological, clinical and experimental data. As a prototype for this virtual laboratory for infectious diseases, the problem of HIV drug resistance will be used. The virtual laboratory will integrate the biomedical information from viruses (proteins and mutations), patients (e.g. viral load) and literature (drug resistance experiments) resulting in a rule-based distributed decision support system for drug ranking. In addition ViroLab will include advanced tools for (bio) statistical analysis, visualization, modelling and simulation, enabling prediction of the temporal virological and immunological response of viruses with complex mutation patterns for drug therapy.


Complex Systems In the Complex Systems research theme we study a variety of complex natural systems using a range of computational methods. Optics of Biological Particles In the context of the Science for Peace program of Nato we collaborate with institutes in Minsk (Belarus) and Novosibirsk (Russian Federation) on new sensitive methods for cytological analysis of haematological samples. We concentrate on the computational science aspects and HPC simulations in the field of computational electromagnetics. We delivered ADDA, a public domain code for Computational Light Scattering, capable to simulate scattering from particles as large as real biological particles. In effect, this code is capable to solve sets of linear equations with O(10^7) unknowns. ADDA is a highly efficient parallel code that was ported to many parallel computers, including the USA ASCI computers, and the Dutch ASCI Supercomputer DAS 2. An international benchmark was organised, and the DDA method was also compared to another method that solves Maxwell’s equations from scratch, the FDTD method. Scattering by Red Blood Cells and granulated particles was studied in detail. In collaboration with the AMC (Dr. Rienk Nieuwland) we have started to look into the possibilities to detect biological nano-particles, the so-called microparticles, exosomes and P4 particles, using optical methods. LBM The work on mesoscopic modelling and simulation concentrated on adapting the LBM method, and specifically the L-BGK method, for unsteady flow, and to apply this to modelling flow of blood during a full heart beat in the lower abdominal aorta. We also initiated research to adapting the models to take advantage of state of the art (parallel) numerical algorithms (such as multi grids). In collaboration with Prof. Reiber of LUMC we have developed a problem-solving environment for image-based computational haemodynamics. Moreover, we have studied in detail the stability of time harmonic LBM simulations and addressed the question of optimally choosing simulations parameters, by targeting at a specified wanted accuracy and minimizing execution time. Finally, in collaboration with a number of German institutes, we have developed a next generation LBM code capable of handling nested grids. We have realised a state-of-the-art decomposition tool to aid parallelisation of this unstructured LBM code, and demonstrated efficiencies as high as 80% on a 128 node NEC SX8. In effect this code is currently the by far fastest LBM code available. PECVD In this project a grid-based PSE to study the plasma enhanced chemical vapour deposition of thin films is being developed. Internally funded project in close collaboration with the IHPCIS in St. Petersburg. The research was conducted with financial support from the Dutch National Science Foundation NWO and the Russian Foundation for Basic Research. Computational Astrophysics The research group for computational astrophysics at the University of Amsterdam is an interdisciplinary group of astronomers and computer scientists with as main objective to understand the Galaxy as a stellar system by computation. The main interest of the computational astrophysics group is to study the ecology of dense stellar systems. This work combines the developments of numerical algorithms and theoretical tools to study the gravitational, chemical, nuclear and photonic evolution of solar systems, star clusters and galaxies. In this context the development of an advanced particle integration methodology plays a prominent role. Our recent research activities are related to the study the formation and evolution of the Nuclear Bulge and of dense star clusters are summarized. Each of the main themes is relevant for computational science and astrophysics. The Galactic centre welcomes black hole immigrants In a collaborative effort with Japanese, European and American researchers we have proposed a self-consistent scenario for the formation of the Galactic bulge. Our results are published in the astrophysical journal (Portegies Zwart et al, 2006, ApJ 641, 319). The researchers calculate that about half the total mass of the supermassive black hole in the Galaxy centre can be the result of the coalescence of intermediate mass black holes, which are produced in nearby star clusters. An attractive 'side' effect of their model is that these star clusters, as they sink towards the Galactic centre, transport their massive stars to close proximity of the central black hole. They predict that there are about 50 intermediate mass black holes within a distance of about 10 light years of the Galactic centre, and the majority of these will collide with the


supermassive black hole in the next 10 million years. Mergers between two black holes will lead to a surge in gravitational wave energy, sufficient to be detected by the next generation of gravitational wave detectors, which are currently being designed.

Figure: Snapshot of a simulated star cluster near the moment of dissolution. The age of the cluster is about 400,000 years and it is located at a distance of about 6 light years from the Galactic centre. The cluster was born in a circular orbit around the central black hole in the Galactic centre but has spiralled in toward the black hole in the course of its evolution. In the mean while the cluster has experienced an exotic evolutionary phase during which about 100 stars have collided to form an unusually massive star, that later collapses to a black hole with a mass of about 1000 times the mass of the Sun. This intermediate mass black hole continues to spiral inwards towards the Galactic centre to eventually collide with the supermassive black hole. The symbol sizes in the figure are proportional to the surface area of each star and colour runs from red (cool low-mass stars) to blue (hot massive stars). The origin of hypervelocity stars Hypervelocity stars (HVS) are star which travel through space with an unusually high velocity, often exceeding the escape speed of the Galaxy. We have performed N-body simulations of the formation of hyper-velocity stars in the centre of the Milky Way due to inspiralling intermediate-mass black holes (IMBHs). Our simulations show that HVS are generated in short bursts that last only a few Myrs until the IMBH is swallowed by the supermassive black hole (SMBH). After the HVS have reached the galactic halo, their escape velocities correlate with the distance from the Galactic centre in the sense that the fastest HVS can be found furthest away from the centre. Finally, our simulations show that the presence of an IMBH in the Galactic centre changes the stellar density distribution inside r < 0.02 pc into a core profile, which takes at least 100 Myrs to replenish.


Problem Solving Environments and Visualisation In the area of visualisation the Section Computational Science has formed an alliance with the Insight visualisation group of SARA Computing and Networking Services to combine their visualisation resources and expertise. As of 2006, Robert Belleman has rejoined the SCS group as a tenured researcher to lead this research on interactive visualisation and virtual reality. Token2000 Token2000 is a nationally funded project (NWO), where we collaborate closely with the Universities of Leiden and Twente on the development of an interactive medical application, somewhat similar to the work in CrossGrid. This application is intended for training of surgeons. In collaboration with Leiden University Medical Centre we have created Hemosolve, a problem-solving environment for image based computational Haemodynamics. Hemosolve includes our L-BGK solver, but also a FEM Navier-Stokes solver. Moreover, it contains a 3D editing tool and powerful visualisation modules. Complex Automata Simulation Techniques (COAST) We recently proposed Complex Automata (CxA) as a modelling paradigm for multi-scale multi-science applications. A CxA is a hierarchical composition of Cellular Automata and Agent Based models, each operating on specific length and time scales. Within the EU FP6 project COAST (that we coordinate), and in collaboration with 4 European partners, we further develop the CxA concept. Using the idea of a scale separation map we have identified a small set of multi-scale classes, and have identified how to map them to a CxA. Moreover, we have found basic ways of multi-scale coupling within CxA for each of these classes. Moreover, as a proof of concept, we started to develop a multi-scale Lattice Boltzmann model for blood rheology, applying the concept of Hierarchical Model Coupling. Special purpose computing for Cellular Automata In this project we aim to develop an three dimensional generic CA implementation on FGPA hardware, and to investigate the speedup that may be achieved by using special purpose co-processing for CA simulations. So far we have realised a 2D implementation using a ‘pipelining in time’ paradigm. The next step will be to assess its performance and compare with a performance model that was also developed this year. ACGT The project "Advancing Clinico-Genomic Trials on Cancer" (ACGT) has the aim to provide open grid services for improving medical knowledge discovery. In this project we work together with the In-Silico Oncology Group of the National Technical University of Athens (NTUA) to combine interactive Virtual Reality visualisation with in-silico tumour simulation models to better comprehend tumour growth and optimise the planning of treatment schemes. McScatter: A simple three-body scattering package with stellar evolution In collaboration with UK and Australian astronomers and mathematicians the computational astrophysics group has developed a multi purpose software environment for astrophysical applications in which different existing numerical codes will be incorporated to a single framework. In this first initiative to combine stellar evolution and stellar dynamics we opted for a Monte-Carlo stellar dynamics solver combined with two stellar and binary evolution packages. The packages of choice are SeBa, developed by Portegies Zwart and BSE, developed by Hurley.


Figure: Using a tablet PC to enrich a real environment with data from a virtual environment. The object library allows scientists to use combinations of codes to solved coupled problems without the need to write new codes or significantly alter existing codes. The generic, homogeneous library combines the two regimes with a transparent interface, which enables the user to add new stellar end binary evolution modules to the library with relatively little effort. High Performance Simulation on the GRID In this project we study the use of Grid systems for High Performance Simulations. The project is a collaboration between Amsterdam, St. Petersburg, Moscow and Novosibirsk. Dynamite The Dynamite project (now internally funded) is the continuation of work on the dynamic scheduling and migration of tasks in parallel programs started in the ESPRIT project Dynamite. In 2006 work continued on the single task checkpointer (ironing out some smaller remaining defects) and on developing support for MPI and grid environments. Virtual Schoollab In this VL-e funded dissemination project, we are offering high school students a peek into e-Science and the way in which modern computer and network systems affect the ways in which we can collect, process and understand data about our environment.


External projects Projectname period Funding agency Total funding partners in ASCI Brief description Mesoscale simulation paradigms for biological systems

2003-2007 NWO Applied Mathematics

k€ 329 See report

Simulation of developmental regulatory networks

2003-2007 NWO Computational Life Sciences

k€ 328 See report

Mathematics and Computation for the System Biology of Cells

2003-2007 NWO Computational Life Sciences

k€ 487 See report

Modelling and inferring developmental regulatory networks

2006-2009 Dutch-Russian Research Cooperation 2004

k€ 123 See report

MORPHEX 2007-2009 EU k€ 282 See report A Visual Exploration Environment for Analysing gene Regulation in Developmental processes (VEARD)

2007-2011 NWO-VIEW k€ 471 See report

Virolab 2006-2009 EU-FP6 k€ 1000 See report ASTROSIM ESF See report Dutch Distributed GRAPE

NWO Stare See report

Complex Automata Simulation Techniques (COAST)

2006-2009 EU-FP6 See report

Special purpose computing for cellular automata

See report

ACGT 2006-2010 EU-FP6 k€ 500 See report Token 2000 2002 – 2007 NWO - EW k€ 150 LKEB/LUMC (P.I.:

Reiber) Mesoscopic bloodflow simulation

Doctoral Degrees A. Gualandris: Simulating self-gravitating systems on parallel computers, PhD thesis, University of Amsterdam, (Promotores: Prof. Dr. E.P.J. van den Heuvel and Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. S.F. Portegies Zwart) September 2006. ISBN-10: 9064640246 ISBN-13: 9789064640247. K.J. Rycerz: Grid-based HLA Simulation Support, PhD thesis, University of Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. M.T. Bubak) June 2006.


Books V.N. Alexandrov; G.D. van Albada; P.M.A. Sloot and J.J. Dongarra: in Computational Science - ICCS 2006: 6th International Conference, Reading, UK, Proceedings, Part I, in series Lecture Notes in Computer Science, vol. 3991, . Springer, Berlin, Heidelberg, May 2006. ISBN 3-540-34379-2. V.N. Alexandrov; G.D. van Albada; P.M.A. Sloot and J.J. Dongarra: in Computational Science - ICCS 2006: 6th International Conference, Reading, UK, Proceedings, Part II, in series Lecture Notes in Computer Science, vol. 3992, . Springer, Berlin, Heidelberg, May 2006. ISBN 3-540-34381-4. V.N. Alexandrov; G.D. van Albada; P.M.A. Sloot and J.J. Dongarra: in Computational Science - ICCS 2006: 6th International Conference, Reading, UK, Proceedings, Part III, in series Lecture Notes in Computer Science, vol. 3993, . Springer, Berlin, Heidelberg, May 2006. ISBN 3-540-34383-3. V.N. Alexandrov; G.D. van Albada; P.M.A. Sloot and J.J. Dongarra: in Computational Science - ICCS 2006: 6th International Conference, Reading, UK, Proceedings, Part III, in series Lecture Notes in Computer Science, vol. 3994, . Springer, Berlin, Heidelberg, May 2006. ISBN 3-540-34385-7. G. Lee; D. Slezak; T.H. Kim; P.M.A. Sloot; H.-K. Kim; I.S. Ko and M. Szczuka: IEEE Proceedings of the 2006 International Conference on Hybrid Information Technology, (IEEE Computer Society Order Number P2674) . IEEE, November 2006. ISBN 13:978-0-7695-2674-4, ISBN 10: 0-769-2674-8. P.M.A. Sloot; G.D. van Albada; M.T. Bubak and A. Trefethen: 2nd IEEE International Conference on e-Science and Grid Computing, (CD Only) IEEE, . IEEE, 12 2006. ISBN 0-7695-2734-5.

Papers in international journals A.M.M. Artoli; A.G. Hoekstra and P.M.A. Sloot: Mesoscopic simulations of systolic flow in the Human abdominal aorta, Journal of Biomechanics, vol. 39, nr 5 pp. 873-884. 2006. (DOI: 10.1016/j.jbiomech.2005.01.033). A.M.M. Artoli; A.G. Hoekstra and P.M.A. Sloot: Optimizing lattice Boltzmann simulations for unsteady flows, Computers & Fluids, vol. 35, nr 2 pp. 227-240. February 2006. (DOI: 10.1016/j.compfluid.2004.12.002). H. Baumgardt; A. Gualandris and S.F. Portegies Zwart: "Ejection of hypervelocity stars from the Galactic Centre by intermediate-mass black holes", Mon. Not. Royal Astr. Soc., vol. 372, pp. 174-182. October 2006. (DOI: 10.1111/j.1365-2966.2006.10818.x). H. Baumgardt; A. Gualandris and S.F. Portegies Zwart: "Ejection of Hyper-Velocity Stars by Intermediate-Mass Black Holes", Journal of Physics Conference Series, vol. 54, pp. 301-305. dec 2006. (DOI: 10.1088/1742-6596/54/1/047). H. Baumgardt; C. Hopman; S.F. Portegies Zwart and J. Makino: "Tidal capture of stars by intermediate-mass black holes", Mon. Not. Royal Astr. Soc., vol. 372, pp. 467-478. oct 2006. (DOI: 10.1111/j.1365-2966.2006.10885.x). M.B. Davies; P. Amaro-Seoane; C. Bassa; J. Dale; F. de Angeli; M. Freitag; P. Kroupa; D. Mackey; M.C. Miller and S.F. Portegies Zwart: "The MODEST questions: Challenges and future directions in stellar cluster research", New Astronomy, vol. 12, pp. 201-214. dec 2006. (DOI: 10.1016/j.newast.2006.09.004). M. Gieles; S.F. Portegies Zwart; H. Baumgardt; E. Athanassoula; H.J.G.L.M. Lamers; M.S. Sipior and J. Leenaarts: "Star cluster disruption by giant molecular clouds", Mon. Not. Royal Astr. Soc., vol. 371, pp. 793-804. sep 2006. (DOI: 10.1111/j.1365-2966.2006.10711.x). M. Gieles; H.J.G.L.M. Lamers and S.F. Portegies Zwart: "The Oort problem solved", Modelling Dense Stellar Systems, 26th meeting of the IAU, Joint Discussion 14, 22-23 August 2006, Prague, Czech Republic, JD14, \#20, vol. 14, . aug 2006.


Y.E. Gorbachev; A.I. Zhmakin; M.A. Zatevakhin; V.V. Krzhizhanovskaya and M.S. Ramm: From Electronic Textbooks to Virtual Laboratories, Telecommunications and Informatization in Education, (In Russian) nr 5(36) . SGU, Moscow, 2006. Grindlay; S.F. Portegies Zwart and S.L.W. McMillan: "Short gamma-ray bursts from binary neutron star mergers in globular clusters", Nature Physics, vol. 2, pp. 116-119. feb 2006. (DOI: 10.1038/nphys214). D.C. Heggie; S.F. Portegies Zwart and J.R. Hurley: "McScatter: A simple three-body scattering package with stellar evolution", New Astronomy, vol. 12, pp. 20-28. oct 2006. (DOI: 10.1016/j.newast.2006.04.005). A.G. Hoekstra; V.P. Maltsev and G. Videen: Preface to special issue dedicated to the Optical Properties of Biological Cells, J. Quant. Sectr. Rad. Transf., vol. 102, nr 1 pp. 1-2. Nov. 2006. C. Hopman; D. Guetta; E. Waxman and S.F. Portegies Zwart: "The Redshift Distribution of Short Gamma-Ray Bursts from Dynamically Formed Neutron Star Binaries", Astronomical Journal Let., vol. 643, pp. L91-L94. jun 2006. (DOI: 10.1086/505141). J. Cui and J.A. Kaandorp: Mathematical modeling of calcium homeostasis in yeast cells, Cell Calcium, vol. 39, nr 4 pp. 337-348. Elsevier Science, April 2006. (DOI: doi:10.1016/j.ceca.2005.12.001). J.A. Kaandorp: Groei en vorm van koralen & de invloed van atmosferische CO2 en stijgende zeetemperaturen, Ecologie & Ontwikkeling, (in Dutch) vol. 71, pp. 13-15. 2006. I.V. Kolesnikova; S.V. Potapov; M.A. Yurkin; A.G. Hoekstra; V.P. Maltsev and K.A. Semyanov: Determination of volume, shape and refractive index of individual blood platelets, J. Quant. Spectr. Rad. Transf., vol. 102, nr 1 pp. 37-45. Nov. 2006. J. Kromkamp; D. van den Ende; B.D. Kandhai; R.G.M. Sman and R.M. Boom: Lattice Boltzmann simulation of 2D and 3D non-Brownian suspensions in Couette flow, Chem. Eng. Sc, vol. 61, nr 2 pp. 858-873. January 2006. (DOI: 10.1016/j.ces.2005.08.011). V.V. Krzhizhanovskaya; B. Chopard and Y.E. Gorbachev: Simulation of Multiphysics Multiscale Systems, Special Issue of International Journal for Multiscale Computational Engineering, (Guest editorship and Preface) vol. 4, nr 2 pp. 207. (V.V. Krzhizhanovskaya; B. Chopard and Y.E. Gorbachev, editors), Begell House, 2006. ISSN 1543-1649. (DOI: 10.1615/IntJMultCompEng.v4.i2). V.V. Krzhizhanovskaya; B. Chopard and Y.E. Gorbachev: Simulation of Multiphysics Multiscale Systems, Special Issue of International Journal for Multiscale Computational Engineering, (Guest editorship and Preface) vol. 4, nr 3 pp. 305-306. (V.V. Krzhizhanovskaya; B. Chopard and Y.E. Gorbachev, editors), Begell House, 2006. ISSN 1543-1649. (DOI: DOI: 10.1615/IntJMultCompEng). R.M.H. Merks; A.G. Hoekstra; J.A. Kaandorp; P.M.A. Sloot and P. Hogeweg: Problem-Solving Environments for Biological Morphogenesis, Comput. Sci. Eng, vol. 8, nr 1 pp. 61-72. 2006. (DOI: 10.1109/MCSE.2006.11). M. Min; J.W. Hovenier; C. Dominik; A. de Koter and M.A. Yurkin: Absorption and scattering properties of arbitrarily shaped particles in the Rayleigh domain: A rapid computational method and a theoretical foundation for the statistical approach, J. Quant. Spectr. Rad. Transf., vol. 97, nr 2 pp. 161-180. 2006. (DOI: 10.1016/j.jqsrt.2005.05.059). W.E.G. Müller; O.V. Kaluzhnaya; S.I. Belikov; M. Rothenberger; H.C. Schröder; A. Reiber; J.A. Kaandorp; B. Manz; D. Mietchen and F. Volke: Magnetic resonance imaging of the siliceous skeleton of the demosponge Lubomirskia baicalensis, Journal of Structural Biology, vol. 153, nr 1 pp. 31-41. 2006. (DOI: 10.1016/j.jsb.2005.09.008). M.P. Muno; J.S. Clark; P.A. Crowther; S.M. Dougherty; R. de Grijs; C. Law; S.L.W. McMillan; M.R. Morris; I. Negueruela; D. Pooley; S.F. Portegies Zwart and F. Yusef-Zadeh: "A Neutron Star with a Massive Progenitor in Westerlund 1", Astrophys. J. Let., vol. 636, pp. L41-L44. jan 2006. (DOI: 10.1086/499776)


M.P. Muno; C. Law; J.S. Clark; S.M. Dougherty; R. de Grijs; S.F. Portegies Zwart and F. Yusef-Zadeh: "Diffuse, Nonthermal X-Ray Emission from the Galactic Star Cluster Westerlund 1", Astronomical Journal, vol. 650, pp. 203-211. oct 2006. (DOI: 10.1086/507175). M.P. Muno; B.M. Gaensler; J.S. Clark; S.F. Portegies Zwart; Pooley, D.; R. de Grijs; I. Stevens and I. Negueruela: "XMM Observations of AXP CXO J167410.2-455216 Four Days Prior to Outburst", The Astronomer's Telegram, vol. 902, pp. 1-+. sep 2006. L.A. Naumov: An Overview of Cellular Automata Modeling Software, Telecommunications and Informatization of Education, (in Russian) vol. 33, nr 2 pp. 114-125. 2006. ISSN: 1609-4670. A. Patruno; S.F. Portegies Zwart; J. Dewi and C. Hopman: "The ultraluminous X-ray source in M82: an intermediate-mass black hole with a giant companion", Mon. Not. Royal Astr. Soc., vol. 370, pp. L6-L9. jul 2006. (DOI: 10.1111/j.1745-3933.2006.00176.x). S.F. Portegies Zwart; H. Baumgardt; S.L.W. McMillan; J. Makino; P. Hut and T. Ebisuzaki: "The Ecology of Star Clusters and Intermediate-Mass Black Holes in the Galactic Bulge", Astronomical Journal, vol. 641, pp. 319-326. apr 2006. (DOI: 10.1086/500361). J. Vidal Rodríguez; J.A. Kaandorp; M. Dobrzyński and J.G. Blom: Spatial Stochastic Modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli, Bioinformatics, vol. 22, nr 15 pp. 1895-1901. 2006. (DOI: 10.1093/bioinformatics/btl271). M. Scarpa; R.G. Belleman; P.M.A. Sloot and C.T.A.M. de Laat: Highly interactive distributed visualization, Future Generation Computer Systems, vol. 22, pp. 896-900. May 2006. (DOI: 10.1016/j.future.2006.03.004.). P.M.A. Sloot; A. Tirado-Ramos; I. Altintas; M.T. Bubak and C.A. Boucher: From Molecule to Man: Decision Support in Individualized E-Health, IEEE Computer, (Cover feature) vol. 39, nr 11 pp. 40-46. November 2006. E. Vesperini; S.L.W. McMillan and S.F. Portegies Zwart: "Mass segregation in young star clusters", Modelling Dense Stellar Systems, 26th meeting of the IAU, Joint Discussion 14, 22-23 August 2006, Prague, Czech Republic, JD14, \#36, vol. 14, . aug 2006. J.A. Vrugt; H.V. Gupta; B. Ó Nualláin and W. Bouten: Real-time data assimilation for operational ensemble streamflow forecasting, Journal of Hydrometeorology, vol. 7, nr 3 pp. 548-565. June 2006. (DOI: 10.1175/JHM504.1). J.A. Vrugt; B. Ó Nualláin; B.A. Robinson; W. Bouten; S.C. Dekker and P.M.A. Sloot: Application of parallel computing to stochastic parameter estimation in environmental models, Computers & Geosciences, vol. 32, nr 8 pp. 1139-1155. January 2006. (DOI: 10.1016/j.cageo.2005.10.015). R. Wiersma; A. Sills and S.F. Portegies Zwart: The Effect of Pre-Main-Sequence Stars on Star Cluster Dynamics, Astrophys. J., vol. 637, pp. 838-849. Feb 2006. (DOI: 10.1086/498562). L.R. Yungelson; J.P. Lasota; G. Nelemans; G. Dubus; E.P.J. van den Heuvel; J. Dewi and S.F. Portegies Zwart: "The origin and fate of short-period low-mass black-hole binaries", Astron. Astrophys., vol. 454, pp. 559-569. aug 2006. (DOI: 10.1051/0004-6361:20064984). M.A. Yurkin; V.P. Maltsev and A.G. Hoekstra: Convergence of the discrete dipole approximation. I. Theoretical analysis, Journal of Optical Society of America A, vol. 23, nr 10 pp. 2578-2591. 2006. M.A. Yurkin; V.P. Maltsev and A.G. Hoekstra: Convergence of the discrete dipole approximation. II. An extrapolation technique to increase the accuracy, Journal of Optical Society of America A, vol. 23, nr 10 pp. 2592-2601. 2006. E.V. Zudilova-Seinstra: Combining desktop and virtual realities. Addressing demands of real life clinical environments, Interfaces, vol. 67, pp. 11-13. British HCI Group, 2006. ISSN 1351-119X.


Contributions to international conference proceedings L. Abrahamyan; J. Bernsdorf; T. Zeiser; P. Lammers; A.G. Hoekstra and P.M.A. Sloot: MPI parallelization and performance aspects of a graph based LB flow solver, in Proceedings Discrete Simulation of Fluid Dynamics DSFD2006, Geneva, Switserland, 2006. Abrahamyan; A.G. Hoekstra and P.M.A. Sloot: Choosing Optimal L-BGK Simulation Parameters for Time Harmonic Flows, in Proceedings Discrete Simulation of Fluid Dynamics DSFD2006, Geneva, Switserland, 2006. A.G. Hoekstra; B. Chopard; P. Lawford; R. Hose; M. Krafczyk and J. Bernsdorf: Introducing Complex Automata for Modelling Multi-Scale Complex Systems, in proceedings European Complex Systems Conference 2006, (CD) . European Complex Systems Society, Oxford, UK, September 2006. ISBN 0-9554123-0-7. V.V. Korkhov and V.V. Krzhizhanovskaya: Benchmarking and Adaptive Load Balancing of the Virtual Reactor Application on the Russian-Dutch Grid, in Proceedings of the 6th International Conference on Computational Science, in series Lecture Notes in Computer Science, vol. 3991, pp. 530-538. Springer Berlin, Heidelberg, Reading, UK, 2006. ISBN: 3-540-34379-2. (DOI: 10.1007/11758501). V.V. Korkhov and V.V. Krzhizhanovskaya: Workload Balancing in Heterogeneous Grid Environment: A Virtual Reactor Case Study, in Book of abstracts of the Second International Conference on Distributed Computing and Grid Technologies in Science and Education, pp. 93. JINR, Dubna, Russia, 2006. ISBN 5-9530-0117-7. V.V. Korkhov and V.V. Krzhizhanovskaya: Workload Balancing in Heterogeneous Grid Environment: A Virtual Reactor Case Study, in Second International Conference on Distributed Computing and Grid Technologies in Science and Education, pp. 103-113. JINR, Dubna, Russia, 2006. M.B.N. Kouwenhoven; A.G.A. Brown; S.F. Portegies Zwart and L. Kaper: "Finding the Primordial Binary Population in Sco OB2: on the interpretation of binary star observations", in IAU Symposium 240, . Prague, Czech Republic, aug 2006. K. Kruszynski; R. van Liere and J.A. Kaandorp: An Interactive Visualization System for Quantifying Coral Structures, in T. Ertl; K. Joy and B. Santos, editors, Eurographics/ IEEE-VGTC Symposium on Visualization, pp. 1-8. Benidorm, Spain, January 2006. V.V. Krzhizhanovskaya; P.M.A. Sloot and Y.E. Gorbachev: Modeling of Plasma Chemical Deposition and Degradation of Silicon Thin Films, in E.E. Gdoutos, editor, Proceedings of the 16th European Conference of Fracture, Alexandroupolis, Greece, July 3-7, 2006, (abstract) pp. 1347-1348. Springer, Alexandroupolis, Greece, 2006. ISBN-10 1-4020-4971-4. V.V. Krzhizhanovskaya; V.V. Korkhov; A. Tirado-Ramos; D.J. Groen; I.V. Shoshmina; I.A. Valuev; I.V. Morozov; N.V. Malyshkin; Y.E. Gorbachev and P.M.A. Sloot: Computational Engineering on the Grid: Crafting a Distributed Virtual Reactor, in P.M.A. Sloot; G.D. van Albada; M.T. Bubak and A. Trefethen, editors, 2nd IEEE International Conference on e-Science and Grid Computing, (full paper on CD) pp. 101. IEEE, Amsterdam, The Netherlands, December 2006. (DOI: 10.1109/E-SCIENCE.2006.42) V.V. Krzhizhanovskaya; V.V. Korkhov and P.M.A. Sloot: Virtual Reactor: a distributed computing environment for simulation of plasma chemical processes on heterogeneous resources of the Grid, in All-Russian conference "Scientific services on the Internet: Parallel Programming Technologies", . Novorossiysk, Russia, September 2006. V.V. Krzhizhanovskaya and V.V. Korkhov: Problem-Solving Environments for Simulation and Optimization on Heterogeneous Distributed Computational Resources of the Grid, in Third International Conference on Parallel Computations and Control Problems PACO, pp. 917-932. V.A. Trapeznikov Institute of Control Sciences RAS, Moscow, Moscow, Russia, October 2006. ISBN 5-201-14990-1. V.V. Krzhizhanovskaya: Software Environment for Simulation of Plasma-Chemical Deposition Reactors on Heterogeneous Computational Resources of the Grid, in Conference on Computer Technologies in Modern


Researches, Polytechnic Symposium "Young Scientists to the industry of Northwest Russia", (Best presentation award) pp. 81-82. St. Petersburg State Polytechnic University, St.Petersburg, Russia, December 2006. ISBN 5-7422-1365-4. L.A. Naumov: Comparision of Specialized Netwoking Protocols CTP (Commands Transfer Protocol) and IL (Internet Link), in Proceedings of XIII All-Russian Guidance Conference "Telematics-2006", (in Russian) pp. 266-267. SPbSU ITMO, Saint-Petersburg, 2006. ISBN 5-7577-0192-7. S.D. Olabarriaga; A. Nederveen; J.G. Snel and R.G. Belleman: Towards a Virtual Laboratory for fMRI Data Management and Analysis, in HealthGrid 2006, Valencia, June 2006. S.D. Olabarriaga; A. Nederveen; J.G. Snel and R.G. Belleman: A Virtual Laboratory for fMRI Data Management and Analysis, in Human Brain Mapping 2006, Florence, June 2006. A. Penttilä; E. Zubko; K. Lumme; K. Muinonen; M.A. Yurkin; Y. Shkuratov and A.G. Hoekstra: Comparison between discrete dipole and exact techniques, in Proceedings of the 9th Conference on Electromagnetic and Light Scattering by Nonspherical Particles: Theory, Measurement and Applications, pp. 227-230. St.Petersburg, Russia, June 2006. ISBN 5-9651-0210-0. K.J. Rycerz; M.T. Bubak; M. Malawski and P.M.A. Sloot: A Grid Service for Management of Multiple HLA Federate Processes, in R. Wyrzykowski; J.J. Dongarra; N. Meyer and J. Wasniewski, editors, Parallel Processing and Applied Mathematics: 6th International Conference (PPAM) 2005, Revised selected papers, in series Lecture Notes in Computer Science, vol. 3911, pp. 699-706. Springer, 2006. ISBN: 3-540-34141-2. (DOI: 10.1007/11752578_84). K.J. Rycerz; M.T. Bubak; P.M.A. Sloot and V.S. Getov: Problem solving environment for distributed interactive applications, in S. Gorlatch; M.T. Bubak and T. Priol, editors, Integrated Research in Grid Computing, Integration Workshop, pp. 129-140. Academic Computing Centre CYFRONET AGH, Krakow, Poland, October 2006. ISBN 83-915141-6-1. J.G. Snel; S.D. Olabarriaga; J. Alkemade; H.G. van Andel; A.J. Nederveen; C.B. Majoie; G.J. den Heeten; M. van Straten and R.G. Belleman: A Distributed Workflow Management System for Automated Medical Image Analysis and Logistics, in IEEE CMBS, special track on Grids for Biomedical Informatics, . Salt Lake City, June 2006. A. Tirado-Ramos and P.M.A. Sloot: A Conceptual Grid Architecture for Interactive Biomedical Applications, in 19th IEEE International Symposium on Computer-Based Medical Systems (CBMS'06), pp. 762-767. IEEE, Salt Lake City, USA, 2006. ISBN 0-7695-2517-1. M.A. Yurkin; V.P. Maltsev and A.G. Hoekstra: Can the Discrete Dipole Approximation Simulate Scattering of Particles with Size Parameter equal to 100?, in Proceedings of 9th International Conference on Electromagnetic and Light Scattering by Non-Spherical Particles, pp. 279-282. Saint Peterburg, Russia, June 2006. ISBN 5-9651-0210-0. M.A. Yurkin and A.G. Hoekstra: An Extrapolation Technique to Increase the Accuracy of The Discrete Dipole Approximation, in Proceedings of 9th International Conference on Electromagnetic and Light Scattering by Non-Spherical Particles, pp. 283-286. Saint Peterburg, Russia, June 2006. ISBN 5-9651-0210-0. E.V. Zudilova-Seinstra and T. Adriaansen: Combining Visualisation and Interaction to Facilitate Scientific Exploration and Discovery, in Proc. of the 20th BCS HCI Group conference in co-operation with ACM "HCI 2006: Engage!", pp. 260-263. London, UK, September 2006. ISSN 1470-5559.

Experimental software The Dynamite software package for the checkpointing of PVM programs is available through http://www.science.uva.nl/research/scs/Software


Development of "Roche" binary evolution web interface: http://carol.wins.uva.nl/~spz/act/roche/roche.html Development of "McScatter" hybrid software package for Monte-Carlo dynamics with binary evolution. http://manybody.org/McScatter.html MODESTA is a dedicated parallel computer platform for MOdeling DEnse STellar systems in Amsterdam. The machine became available for production on 2 October 2004 and is now working full time. Current performance is 1.01 TFLOPs sustained speed. MODESTA has a dedicated web site: http://modesta.science.uva.nl/

Patent

US SOFTWARE PATENT: Retrogram: A decision support system for HIV drugs ranking, Trademark world coverage: 713908: US Software Patent 10/058622, 2006.

2.1.4 Contribution of TUD-EWI-me-ce ARCHitectural enhancements for Image and VIdeo REtrieval (ARCHIVIRE) In the past decades, image and video retrieval was based on textual annotations. Manual annotation is a tedious and time-consuming process. Therefore, multimedia retrieval has been shifting to Content-Based Image and Video Retrieval (CBIVR) systems. There are many features and algorithms in the context of the multimedia retrieval systems. The aim of this project is design of a new programmable processor with a new ISA. The feature extraction is performed in the transform domain, in particular using the discrete wavelet transform. Different parallelisms are exploited for feature extraction and feature matching algorithms in the transform domain by using micro-architectural techniques. Contributions to international conference proceedings A. Shahbahrami, B. Juurlink, and Stamatis Vassiliadis. Accelerating Color Space Conversion Using Extended Subwords and the Matrix Register File" Proceeding of 8th IEEE International Symposium on Multimedia (ISM2006), pp.37- 46, December, 2006, California, USA. A. Shahbahrami, B.H.H Juurlink, S.Vassiliadis, Limitations of Special-Purpose Instructions for Similarity Measurements in Media SIMD Extensions, Proceeding of ACM International Conference on Compilers, Architecture and Synthesis for Embedded Systems (CASES2006), pp.293-303, October, Seoul, Korea. A. Shahbahrami, B. Juurlink, S. Vassiliadis. SIMD Vectorization of Histogram Functions. Proc. 18th IEEE Int. Conf. on Application-Specific Systems, Architectures and Processors (ASAP07), pp. 174-179, July 2007.

2.2 B: LARGE SCALE DISTRIBUTED INFORMATION SYSTEMS AND EMBEDDED SYTEMS

2.2.1 Contribution of UVA-FdnWI-csa Computer architecture, thread-level parallelism, micro-grids, system-level design, design space exploration. In the MicroGrid project, we are developing a novel approach to micro-architecture that supports massive on-chip concurrency, which is scalable, flexible and amenable to analysis. It has the potential to provide for the management of on-chip resources (processors etc.) so as to autonomously configure a system for performance, power dissipation or fault tolerance. To this end, we have introduced the concept of microthreads. Microthreading is an execution model that breaks code down into fragments that can execute simultaneously, on a single micro-threaded micro-processor or distributed over different processors. Our work on this project embraces compilers, operating systems, simulators and


implementation issues, which are being investigated using FPGAs. Within the Aether project, we extend the above concepts to develop computer systems that support self-adaptation in their software, architecture and implementation. In the scope of the Artemisia project, the CSA group also investigates more generic methods and techniques for system-level design and analysis of (future) system-on-chip based computer architectures. This work focuses on architectural design space exploration (DSE) during the very early stages of design, where design decisions have great impact on (the success of) the final product. To this end, we study both analytical modeling methods as well as simulation methods for system-level (performance) analysis. These methods and techniques are incorporated in our Sesame simulation framework for system-level DSE. External projects MicroGrid, 2005-2009, NWO, 500KEur. This project aims at developing architectures that support massive on-chip concurrency. AETHER, 2006-2009, EU-IST-FET, 4MEur. This project aims at developing techniques to support self-adaptation in the software, architecture and implementation of computer systems. Artemisia, 2005-2009, STW-Progress, 750KEur, UL-WI-I, TUD-EWI-me-ce. In this project, we develop methods and techniques for the system-level design of Network-on-Chip based Systems-on-Chip. Doctoral Degrees C. Erbas, November 2006, "System-Level Modeling and Design Space Exploration for Multiprocessor Embedded System-on-Chip Architectures", PhD thesis, Department of Computer Science, University of Amsterdam. Amsterdam University Press, The Netherlands. ISBN: 90-5629-455-5. 2e geldstroom (STW-Progress). Books Jesshope, C. R., and Shafarenko, A. (Eds.). INT J PARALLEL PROG, 34(4), 2006. Pimentel, A.D. and Vassiliadis, S., editors, Special Issue of the Journal of VLSI Signal Processing-Systems for Signal, Image, and Video Technology, Vol. 43 (No. 2-3), May 2006.

Knijnenburg, P. M. W. (Ed.). (2006). Concurrency and Computation: Practice and Experience (18, 11). UK: John Wiley & Sons, Ltd.

Papers in international journals

Bell, I., Hasasneh, N., and Jesshope, C. R., “Supporting Microthread Scheduling and Synchronisation in CMPs”. International Journal of Parallel Programming, 34(4), 343-381, 2006.

Jesshope, C. R., “Microthreading, a Model for Distributed Instruction-level Concurrency”. Parallel Processing Letters, 16(2), 209-228, 2006. Cazorla, F. J., Knijnenburg, P. M. W., Sakellariou, R., Fernandez, E., Ramirez, A., and Valero, M., “Predictable Performance in SMT processors: Synergy Between the OS and SMTs”. IEEE Transactions on Computers, 55(7), 785-799, 2006. Heydeman, K., Bodin, F., Knijnenburg, P. M. W., and Morin, L., “UFS: a Global Trade-off Strategy for Loop Unrolling for VLIW Architectures”. Concurrency and Computation: Practice and Experience, 18(11), 1413-1434, 2006.


Pimentel, A.D., Erbas, C., and Polstra, S., “A Systematic Approach to Exploring Embedded System Architectures at Multiple Abstraction Levels'', in IEEE Transactions on Computers, pp. 99-112, Vol. 55 (No. 2), Feb. 2006. Erbas, C., Cerav-Erbas, S., and Pimentel, A.D., “Multiobjective Optimization and Evolutionary Algorithms for the Application Mapping Problem in Multiprocessor System-on-Chip Design”. IEEE Transactions on Evolutionary Computation, 10(3), 358-374, 2006. Contributions to international conference proceedings Bernard, T., Bousias, K., Geus, B. de, Lankamp, M., Zhang, L., Pimentel, A.D., Knijnenburg, P.M.W., and Jesshope, C.R., “A Microthreaded Architecture and its Compiler”. In Proc. of the Int. Workshop on Compilers for Parallel Computers (pp. 326-340), 2006. Haneda, M., Knijnenburg, P. M. W., and Wijshoff, H.A.G., “Code Size Reduction by Compiler Tuning”. In Proc. of the Int. Workshop on Embedded Computer Systems: Architectures, Modeling, and Simulation (SAMOS), 2006 . Haneda, M., Knijnenburg, P.M.W., and Wijshoff, H.A.G., “On the Impact of Data Input Sets on Statistical Compiler Tuning”. In Proc. of the Workshop on Performance Optimization of High-Level Languages and Libraries (POHLL), 2006. Hasasneh, N., Bell, I., and Jesshope, C.R., “Scalable and Partitionable Asynchronous Arbiter for Micro-threaded Chip Multiprocessors”. In Proc. of Architecture of Computing Systems (ARCS 2006) (pp. 252-267), 2006. Jesshope, C.R., “uTC: an intermediate language for programming chip multiprocessors”. In Proc. of the Asia-Pacific Computer Systems Architecture Conference, 2006. Pimentel, A.D., Thompson, M., Polstra, S., and Erbas, C., “On the Calibration of Abstract Performance Models for System-level Design Space Exploration”. In Proc. of the Int. Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation (IC-SAMOS 2006) (pp. 71-77), 2006. Thompson, M., Pimentel, A.D., Polstra, S., and Erbas, C.,“A Mixed-level Co-simulation Method for System-level Design Space Exploration”. In Proc. of the IEEE Workshop on Embedded Systems for Real-Time Multimedia (ESTIMedia'06) (pp. 27-32), 2006. Experimental software Pimentel, A.D. et al., As part of Artemis, we have developed a prototype modeling and simulation environment called Sesame (Simulation of Embedded System Architectures for Multi-level Exploration). See http://sesamesim.sourceforge.net/ for the software. Highlight The increasing complexity of modern embedded systems, which are more and more based on heterogeneous MultiProcessor-SoC (MP-SoC) architectures, has led to the emergence of system-level design. A key ingredient of system-level design is the notion of high-level modeling and simulation in which the models allow for capturing the behavior of system components and their interactions at a high level of abstraction. As these high-level models minimize the modeling effort and are optimized for execution speed, they canbe applied at the very early design stages to perform, for example, architectural Design Space Exploration (DSE). Such early DSE is of eminent importance as early design choices heavily influence the success or failure of the final product.


Developing system-level models for DSE purposes usually still requires a significant effort. It typically involves the decomposition and parallelization of applications so that they can be mapped onto an MP-SoC, the HW/SW partitioning of the application(s), the modeling of the MP-SoC platform architecture, and the efficient evaluation (e.g., by means of simulation) of a multitude of design options. To this end, the use of various different tools and toolflows is often needed, potentially leaving the designer with all kinds of interoperability problems. Moreover, there typically remains a large gap between the resulting system-level models and actual implementations of the system under study. In the scope of the Artemisia project, we are developing the Daedalus toolflow, which addresses these issues. The toolflow, which is being developed by the Leiden Embedded Research Center (LERC) in cooperation with the University of Amsterdam (UvA), provides a single environment for rapid system-level exploration, programming and prototyping of MP-SoC architectures that are constructed from a library of pre-determined and pre-verified IP components. With respect to the term "rapid", we target timeframes in the order of hours. The Figure below depicts the Daedalus toolflow. Starting from a sequential application specification (in C or Matlab), the KPNgen tool (developed by LERC) allows for automatically converting the application into a parallel Kahn Process Network (KPN) specification. By means of automated source-level transformations, KPNgen is also able to produce different input-output equivalent KPNs, in which for example the degree of parallelism can be varied. The structural description of these KPNs can

subsequently be used by our Sesame modeling and simulation environment to perform system-level architectural DSE (see also: http://sesamesim.sourceforge.net/). To this end, it uses (high-level) architecture model components from the IP component library. Sesame allows for quickly evaluating the performance of different application to architecture mappings, HW/SW partitionings, and target platform architectures. Such DSE should result in a number of promising candidate system designs, of which their specs (platform description, application-architecture mapping description, and application description) act as input to the ESPAM tool (developed by LERC). This tool uses these specs, together with RTL versions of the IP model components (from the IP component library), to automatically generate synthesizable VHDL that implements the candidate platform architecture. In addition, it also generates the C/C++ code for those application processes that are mapped onto programmable cores (microprocessors). Using commercial synthesis tools, this implementation can be readily mapped onto an FPGA for prototyping purposes. Such prototyping also allows for calibrating and validating Sesame's system-level models, and as a consequence, improving the trustworthiness of these models.


To summarize, the Daedalus user can traverse the path from sequential application to a working MP-SoC prototype (in FPGA technology) with the application mapped onto it in a matter of hours. During this traversal, guidance is provided by the integrated system-level DSE environment. Such a unique toolflow clearly offers incredible potentials for quickly experimenting with different MP-SoC architectures and exploring design options during the very early stages of design.

2.2.2 Contribution of UvA-FdNWI-caps Advanced Networking Authorization Concepts and Architectures Security Grid Middleware en Workflow Management Sensor Grids Advanced Networking Network modeling: We continued our research on modeling of optical networks. Models suitable for provisioning light paths need to include description of the multi-layer components and the capabilities for all the devices present in the network. Furthermore such models need to provide mechanisms for information discovery and exchange, given the provisioning of the connection happens among different administrative domains. For this purpose we further extended our both model based on the ITU G.805 used for the functional description of the network and NDL – Network Description Language used for the actual syntax. We participated in SC2006 with a demonstration on light path finding based on NDL. NDL has been adopted by the GLIF – the Global Lambda Integrated Facility – an organization of optical exchanges around the world as the language for topology information Network monitoring and fault isolation: We focused our network monitoring and management on further evaluation of the performance of SURFnet6 and on the development of an expert system for fault isolation in hybrid optical networks. On SURFnet6 we conducted extensive tests to look at the impact of packet reordering on their international links. To isolate faults in network connections we developed proof-of-concept software called lmon. lmon gathers as much information as possible from devices along the network connection, and based on that information, determines where the error is. The idea is that the expert system closely follows the manual process of fault isolation as observed in practice in the GLIF community, but automates this process DAS-3 and StarPlane: Our research for StarPlane whose goal is to enable application-specific management of photonic networks was started. The control plane software in StarPlane allows the dynamic creation of connections among the DAS-3 clusters: a separate portion of the SURFnet6 network and the WAN connections on the DAS-3 cluster nodes form the architecture of the project. We contributed to the selection procedure, the installation and the validation of the DAS-3 nodes. We started to design the web services interfaces between application and control plane together with collaborators at the VU. We also researched the use of authorization and policy tokens in a GMPLS environment: this policy mechanism could be used in StarPlane to provision the photonic devices. Authorization Concepts and Architectures In the year 2006 our work focused on the concept of using tokens to enable access control and facilitate resource management for optical networks. To proof the concept we decided to implement the token concept as part of the signaling mechanism of a Generalized Multi Protocol Label Switching (GMPLS) based optical network control plane. Tokens or token-keys are issued by a scheduling system, which is considered the authority deciding who can use what connection when. In collaboration with USC, we adapted their elastic scheduler such that a request for a certain amount of bandwidth could be fitted into a lager timeframe with some flexibility. After finding a fit, a Generic AAA server - a development of our group - will issue a token-key to both the requestor and the GMPLS network. This key is subsequently used to generate a token by the requesting host. This token is placed in a standards based way in a RSVP-TE signaling message, which is received by the edge node of the GMPLS optical network. The edge node will use the key to recognize the validity of the token and subsequently decide to create or maintain the optical connection.


To demonstrate the principle, we adapted the US NSF-funded DRAGON project GMPLS code to support tokens. The result was demonstrated during SuperComputing 2006, which attracted significant attention from several international network research and development projects. Security Started in 2006 this research subgroup focuses on security research. Grid Middleware en Workflow Management Grid-based Virtual Laboratory: We have started to investigate the Distributed Services Discovery of services for Grid-based Virtual Laboratory based on Peer-to-Peer Networks, we started by looking into the problem of classifying the services that have to be distributed and discovered by the targeted system. There are several ways to achieve the classification of the services using pattern recognition, Natural Languages, or Ontology based classifiers. We have decomposed this work into a number of steps: Survey the existing classifiers, model the targeted services, and evaluating the classifiers. Currently, we are investigating the classification problem in both structured and unstructured network Workflow in Virtual Laboratory for e-Science: We developed a grid-based workflow engine. The workflow engine, called WS-VLAM, has been implemented as a WSRF compliant web service, which can submit jobs to grid computing using GT4 core services. The WS-VLAM engine subscribes to a number of GT4 standard events and reflects them to the monitoring interface, allowing to follow the status of the jobs submitted to the grid resources. The WS-VLAM engine is a stateful WSRF resources and thus has the advantage of allowing the detach/attach feature, the client application used which request the execution of the workflow can be stopped and restarted later without disturbing the execution of the workflow, an important feature for long lasting workflows. WS-VLAM engine is a standard WSRF web service and thus can be invoked from any client application which supports WSRF services. This feature makes the WS-VLAM suitable to be used in conjunction with other workflow management systems such as Taverna, or Kepler. Currently, we are investigating the interoperability between Taverna and WS-VLAM, the objective of this research is to allow the composition of workflows where part of it will be executed by the WS-VLAM. The second research activity we have started in 2006 is the idea of workflow bus. The basic idea of a workflow bus is to wrap a number of popular and relative mature legacy SWMSs as federated components, and to loosely couple them as one meta workflow system using a software bus. Fig. 1. shows the basic idea of workflow bus, in which Taverna, Triana, Kepler and VLAM-G are coupled. Among other research topic we are focusing on is the interoperability and integration between workflow systems. In this line, we mainly focus on two issues: 1) study different levels of interoperability issues between existing workflow management systems, 2) evaluate existing technologies and propose an efficient solution to realize these interoperability issues. The final output will be answers to why, what and how related questions of workflow system interoperability and more importantly will guide the first prototype of the workflow bus.

Generic Grid middleware

Workflow bus: provide services for

1) Interoperability and integration, 2) composition, 3) provenance, 4) Enactment, 5) Human in the loop computing

Taverna Kepler Triana VLAMG

Sub workflow 1

Sub workflow 2

Sub workflow 3

Scientific experiment: a meta workflow

Sub workflow 4

Generic Grid middleware

Workflow bus: provide services for

1) Interoperability and integration, 2) composition, 3) provenance, 4) Enactment, 5) Human in the loop computing

Taverna Kepler Triana VLAMG

Sub workflow 1

Sub workflow 2

Sub workflow 3

Scientific experiment: a meta workflow

Sub workflow 4


Sensor Grids It is already a mainstream vision that orders of magnitude more sensors and actuators than humans will use the internet and interact through the net with themselves or with applications. With this vision in mind the SNE group started research into the area of sensor (and actuator) networking. Complementary to the popular studies of battery saving, self organizing sensor-to-sensor and sensor-to sink communications SNE embarked on the field of sensor telecommunications. In this field one studies the development of internet technologies that allow an application specific behavior of the internet. Here one strives to program a part of the Internet in such a way that it optimizes, in an application specific manner, the way how groups of sensors communicate to groups of traditional internet access points (that connect to applications). Typically the programmable part of the internet is most likely a set of autonomous systems with mobile links, forming a wireless networks that span huge geographic distances. These networks will not be over dimensioned much as costs will inhibited that. In this situation the behaviors and topologies of sensors, applications and networks must be optimized as a system. SNE addresses the system optimization issue through Grid concepts. In this case network elements, sensors and applications are regarded as resources and are represented by objects in computer programs that interact with them. In 2006 SNE started this research, concentrating on the creation of a concept that represents ("virtualizes") network elements as objects in computer programs. This resulted in the publication of a paper "User programmable virtualized networks" that showed the potential and implementation of the concept. As there is ample overlap with work of SNE on high speed optical mentioned elsewhere in this report the progress of SNE in the field of sensor networks is fast and natural. In 2006 a collaboration on the theme of "Intelligent Sensor Networks" with the Dutch Institute for applied research TNO lead to a joint knowledge centre on this topic. In the Centre for Intelligent Observation Systems (CIOS) the research of programmable networks will be continue where a PhD study starts on the subject of ICT system programming. This R&D activity develops methods how specifications of the time behavior of sensors, applications, computers and network elements can be translated in actions of system elements to contribute to that behavior. Closely related to the work of sensor networks, intelligent observation systems is the subject of decision making on basic of sensor and human inputs. In the Bsik project Interactive Collaboration Information Systems, Robert Meijer of SNE, headed the chair of the ICIS Architecture group (www.icis.decis.nl). External projects GigaPort-NG Research on Networks 2004-2008. Sponsored via Bsik GigaPort is a national project, in which a new generation Internet for education and research is realised. The project combines the interests of science, government and businesses. GigaPort develops a sophisticated network, which will act as an engine for innovation for education, research and other social sectors between 2004 and 2008 Phosphorus 2006-2009. Integrated Project under FP6, sponsored by the EU. Phoshorus is a European and Global alliance of partners to develop advanced solution of application-level middleware and underlying management and control plane technologies. The project will address some of the key technical challenges in enabling on-demand end-to-end network services across multiple heterogeneous domains. In the Phosphorus' implementation the underlying network will be treated as first class Grid resource. Phosphorus will demonstrate solutions and functionalities across a test-bed involving European NRENs, GÈANT2, Cross Border Dark Fibre and GLIF. VL-e: Sponsored via Bsik, 2004-2009. The virtual laboratory for eScience aims to bridge the gap between the technology push of the high performance networking and the Grid and the application pull of a wide range of scientific experimental applications.


Nextgrid: 2005 - 2008 NextGRID is part of a major initiative to ensure that Europe is a world leader in this technology, central to the new knowledge-based economy. StarPlane:2006-2009. StarPlane is a NWO funded project with major contributions from SURFnet and NORTEL. The vision is to allow part of the photonic network infrastructure of the Dutch National Research and Education Network SURFnet6 to be manipulated by Grid applications to optimize the performance of specific e-Science applications.

Contributions to Books Franco Travostino, Joe Mambretti, Gigi Karmoes-Edwards, Grid Networks, ISBN-10: 0-470-01748-1_Cees de Laat, Freek Dijkstra and Joe Mambretti, Chapter 14, "Grid Network Services Infrastructure". Papers in international journals Gommans, L., Dijkstra, F., Laat, C.T.A.M. de, Taal, A., Wan, A., Lavian, T., Monga, I., & Travostino, F.; Applications drive secure lightpath creation across heterogeneous domains. IEEE Communications Magazine, volume 44, 2006, 3, pp. 100-106. Gommans, L., Oudenaarde, B. van, Wan, A., Laat, C.T.A.M. de, Meijer, R.J., Travostino, F., & Monga, I.; Token based networking: Experiment. Future Generation Computer Systems, volume 22, 2006, 8, pp. 1025-1031. P. Grosso , P. de Boer and L.Winkler; The network infrastructure at iGrid2005: lambda networking in action. Future Generation Computer Systems, volume 22, 2006, 8, pp. 915-919. Freek Dijkstra, Jeroen van der Ham, Cees de Laat; Using Zero Configuration Technology for IP addressing in Optical Networks. Future Generation Computer Systems, volume 22, 2006, 8, pp. 908-914. Jeroen van der Ham, Freek Dijkstra, Franco Travostino, Bert Andree, Cees de Laat; Using RDF to Describe Networks Future Generation Computer Systems, volume 22, 2006, 8, pp. 862-867. V.V. Korkhov, V.V. Krzhizhanovskaya and P.M.A. Sloot; A Grid Based Virtual Reactor: Parallel Performance and Adaptive Load Balancing. Submitted (second review) to Journal of Parallel and Distributed Computing. 2006. Leon Gommans, Bas van Oudenaarde, Cees de Laat, Tal Lavian, Inder Monga, Arie Taal, Franco Travostino, Fred Wan; Applications Drive Secure Lightpath Creation across Heterogeneous Domains. Accepted for publication in IEEE Communications Magazine, Feature topic Optical Control Planes for Grid Networks: Opportunities, Challenges and the Vision, March 2006. Contributions to international conference proceedings Zhao, Z., Booms, S., Belloum, A.S.Z., Laat, C.T.A.M. de, & Hertzberger, L.O.; VLE-WFBus: a scientific workflow bus for multi e-Science domains. Proceedings of the 2nd IEEE International conference on e-Science and Grid computing 2006 (pp. 11-19). IEEE Computer Society Press. Experimental software Dijkstra, F. and vd. Ham J.; Utilities for NDL 2005-2007 Various programming languages. We have created several tools to aid in the development of NDL descriptions. All tools that can be downloaded from the SNE under the BSD license.


Gommans, L., Taal, A., Wan, A., Hoekstra, M.; Generic AAA toolkit 2005-2007 Java – Unix compatible OS. The Generic AAA toolkit is our prototype implementation of the Generic AAA framework as outlined in RFC-2903 and subsequent. The latest version of these components is available via: http://www.science.uva.nl/research/sne/gaaatk/ Experimental hardware ASCI, O.Z.S.; Distributed ASCI Supercomputer 3. 2006. We contributed to the selection procedure, the installation and the validation of the DAS-3 nodes. We started to design the web services interfaces between application and control plane together with collaborators at the VU: DAS-3 (The Distributed ASCI Supercomputer 3) is a five-cluster wide-area distributed system designed by the Advanced School for Computing and Imaging (ASCI). DAS-3 is funded by NWO/NCF (the Netherlands Organization for Scientific Research), the VL-e project, and the participating universities and organizations (see below). As one of its distinguishing features, DAS-3 employs a novel internal wide-area interconnect based on light paths. Cooperation within ASCI

- StarPlane, in collaboration with group of H. Bal at VU - DAS-III, in collaboration with groups at VU, Leiden and Delft.

High-light DAS-3 and StarPlane StarPlane has the goal is to enable application-specific management of photonic networks. The control plane software in StarPlane allows the dynamic creation of connections among the DAS-3 clusters: a separate portion of the SURFnet6 network and the WAN connections on the DAS-3 cluster nodes form the architecture of the project. We contributed to the selection procedure, the installation and the validation of the DAS-3 nodes. We started to design the web services interfaces between application and control plane together with collaborators at the VU. We also researched the use of authorization and policy tokens in a GMPLS environment: this policy mechanisms could be used in StarPlane to provision the photonic devices.


2.2.3 Contribution of UL-LIACS Research themes Performance analysis and design space exploration of embedded multi-processor Systems-on-chip and large-scale distributed embedded systems. Short description Given a number of relevant industrial media applications, and a media platform of type on-chip networked heterogeneous multiprocessor platform, model and program platform based architectures on a high level of abstraction, and with a high level of confidence in a reasonable time. External projects Project Artemisia, 2004-2008, PROGRESS/STW, €132 K + AIO + PostDoc, UVA CSA, TUD EWI-CE, TUD EWI –ST, TUE E-ESA. The project includes the following: Firstly, translate given applications input-output equivalent process networks (an automated translator does exist for a restricted class of applications and is called Compaan). Secondly, model the platform, the architecture templates derived from it as well as the instantiation of these to architectures. Modeling takes place on a high level of abstraction. Thirdly, provide low-level performance/cost numbers for the processing units on the architecture so that high-level performance/cost numbers are well calibrated and, hence, sufficiently accurate (a calibration tool/platform does exist for a restricted class processing units and is called Laura. A more advanced calibration tool/platform is to be developed/designed within Artemisia. Project MASSIVE, 2000-2007, PROGRESS/STW, €242 K + 4 AIO. The aim of this project is to develop methods and tools to master the complexity of large scale embedded signal processing systems. The dataflow part of such a system (in particular distributed radio telescopes), has been modeled and analyzed with respect to performance in previous years. Currently the dataflow is modeled in an independent way, and the interfacing between dataflow and control flow is being modeled. Project TRADER, 2004-2008, Embedded Systems Institute/BSIK, €169k, TUD EWI. Modern systems such as household appliances, DVD players, PCs, medical X-ray imaging systems, printers, advanced vehicles, and airplanes rely increasingly on software, in particular for system integration. Embedded software monitors the whole system taking care that the system accomplishes more than its parts would. In such software intensive systems, reliability is of prime importance.


Project NEVA, 2005-2009, MEDEA+/IS, EU, €447k. Is a European MEDEA+ collaboration between ACE, Bull Certess, LETI/CEA, Universiteit Leiden, Philips, Silicomp, STMicroelectronics, TIMA/INPG, and VERIMAG/UJF (Project 2A703: Networks on Chip Design Driven by Video and Distribution Applications). Circuits for electronic devises are becoming so complex that they are expected to reach a billion transistors by the end of 2008. Traditional silicon chip architectures are nearing the limit of their performance in such applications, so the NEVA project was set up to introduce innovative network-on-chip designs, based on multiple processors and asynchronous circuitry. The goal is to allow designers and application engineers to cope with emerging applications resulting from multimedia/communications convergence. In first instance, datastream applications – mainly from video environments – will be used as drivers, with a targeted computing power of around one-giga operations per second per chip. Scientific publications Hristo Nikolov, Todor Stefanov, and Ed Deprettere, "Multi-processor System Design with ESPAM", In Proc. "4th IEEE/ACM/IFIP Int. Conf. on HW/SW Codesign and System Synthesis CODES-ISSS'06)", pp. 211-216, Seoul, Korea, Oct. 22-25, 2006. Ed Deprettere, Todor Stefanov, Shuvra Bhattacharyya, and Mainak Sen, "Affine Nested Loop Programs and their Binary Parameterized Dataflow Graph Counterparts", In Proc. "17th IEEE Int. Conf. on Application-specific Systems, Architectures and Processors (ASAP'06)", pp. 186-190, Steamboat Springs, Colorado, USA, Sep. 11-13, 2006. Hristo Nikolov, Todor Stefanov, and Ed Deprettere, "Efficient Automated Synthesis, Programming, and Implementation of Multi-processor Platforms on FPGA Chips", In Proc. "16th Int. Conference on Field Programmable Logic and Applications (FPL'06)", pp. 323-328, Madrid, Spain, Aug. 28-30, 2006. Sven Verdoolaege, Hristo Nikolov, and Todor Stefanov, "Improved Derivation of Process Networks", In Proc. "4th Int. Workshop on Optimizations for DSP and Embedded Systems (ODES'06)", pp., New York, NY, USA, Mar. 26, 2006. Experimental Software Nikolov, H., Stefanov, T., ESPAM, 2005-2006, Java, Linux The ESPAM tool was developed to close the gap between HW/SW abstract specification of multi-core systems and implementation-level specification. The ESPAM system design methodology takes as input a platform description, an application description in KPN format generated by Compaan, and a mapping file that specifies what KPN process is mapped where in the platform. ESPAM automatically generates the RTL needed to synthesize the multi-core architecture in a FPGA using Microblaze microprocessors and dedicated IP cores. Software and manuals are available. Kienhuis, Bart, Meijer, Sjoerd, David Snuijf, Johan Walters, IMCA, 2006, Java, Linux/Windows. Intel provides a multiprocessor platform in the form of the Intel IXP2400 Network Processor. This platform consists of 8 RICS Micro-engines and one XScale processor. Programming these platforms is a tedious, slow and error-prone process. To make programming the IXP simpler, we development the IMCA tool that performs an automatic mapping and implementation of a KPN specification onto the Intel IXP2400. The KPN is obtained using the Compaan tool flow. The Compaan tool flow converts sequential Matlab programs into parallel running Kahn Process Networks (KPN). Cooperation within ASCI. Within the ARTHEMISIA project the following ASCI groups participate: CSA, TUD EWI-CE, TUD EWI –ST, TUE E-ESA


Highlight Maximum Likelihood based Interactive Object Tracking; Ard Oerlemans, Michael S. Lew Abstract. We present a video tracking system which uses interactive relevance feedback to improve motion detection and tracking. For visual matching, we propose the Multi-Dimensional Maximum Likelihood (MDML) similarity measure, a multidimensional generalization of previous work which has been shown to consistently outperform the standard L1 & L2 similarity measures. Keywords: Visual similarity, video analysis, motion detection, object tracking, relevance feedback.

1. INTRODUCTION

This article presents an interactive video tracking system that includes user feedback in both motion detection and object tracking. The feedback from the user is applied in real-time, so the effect on the tracking results is immediately visible. Tracking and identifying moving objects in images from a stationary camera, such as people walking by or cars driving through a scene, has gained much attention in the recent years. It can be a very useful technique for human-computer interaction, the next generation games, and for surveillance applications [1,4]. We developed an object tracking system that can analyze live input streams from any video input device and which is able to output the locations, unique identifiers and pictorial information of the moving objects in the scene. Object detection and identification however is a topic that has its unique set of problems that still are not fully addressed. Multiple object tracking is complicated by the fact that objects can touch or interact with each other, can occlude another, even leave the scene and come back again. And the usual problems with single object tracking, like illumination changes, partial occlusion or object deformation, still apply as well. To get improved object tracking results, we investigate methods to include user feedback for detecting moving regions and to ignore or focus on specific tracked objects. Our object tracking framework includes relevance feedback functionality at both the segmentation and tracking level. Furthermore, we are investigating new similarity metrics that are applied to the object tracking framework, but are applicable in general visual similarity matching as well. We propose the Multi-Dimensional Maximum Likelihood (MDML) similarity measure which is the 2 dimensional generalization of the 1 dimensional maximum likelihood work done by Sebe, et al.[2,3]. In this higher dimensional measure, we both remove the previous constraint[2] on measuring similarity as the difference of two values; and we propose a smooth transitional function which allows the user to address the problem of small training sets in that the function below interpolates between the L1 and the true MDML measure.

2. OBJECT-LEVEL FEEDBACK

Below is an example of using feedback for the tracking algorithm. Figure 1 shows a frame from a sequence in which a person is leaving an object behind and where the user selects a positive example for the object tracking algorithm. In this case, objects with similar color will always remain marked as foreground and they will not be added to the background model, which is the normal behaviour for adaptive object tracking algorithms. Figure 2 shows the object being classified as a foreground object based on the user feedback.


Fig 1. One frame from a sequence where someone leaves an object behind, together with the object tracking results. The user selects a positive example for the object tracking algorithm.

Fig 2. The object tracking using the positive example. The object will not be added to the background model and stays visible as a tracked object. Negative examples for the object tracking algorithm are useful for marking objects that are not interesting to the user. The tracking algorithm will ignore objects that are similar to the examples supplied by the user. The MDML metric is trained using information on the tracked object from each frame in which it is still tracked.

5. CONCLUSIONS

The interactive video tracking system has shown that including relevance feedback in the motion detection and object tracking process is intuitive and effective in our experiments. The strong point of the MDML metric is that it generalizes the 1D maximum likelihood metric, which already has shown to outperform other commonly used similarity measures. As mentioned before, estimating visual similarity is improved by a thorough knowledge of the probability density of the similar examples. A weak point is that a large number of training samples is typically required to obtain a representative estimate to the true joint probability density function. REFERENCES [1] M.S. Lew, N. Sebe, C. Djeraba and R. Jain, "Content-based Multimedia Information Retrieval: State of the Art and Challenges", ACM Transactions on Multimedia Computing, Communications and Applications, volume 2, issue 1, pages 1-19, February 2006. [2] N. Sebe, M.S. Lew, D.P. Huijsmans, "Toward Improved Ranking Metrics", IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 22, No. 10, pp. 1132-1141, October, 2000 [3] N. Sebe, M.S. Lew , "Robust Computer Vision - Theory and Applications", Kluwer Academic Publishers, ISBN 1-4020-1293-4, April 2003 [4] A. Yilmaz, O. Javed, M. Shah, "Object tracking: A survey", ACM Computing Surveys, Volume 38, Issue 4 (2006), Article no. 13.

2.2.4 Contribution of VU – WI Ibis is a Java-centric grid programming system that exploits Java's 'write once, run anywhere' portability to run applicationson heterogeneous grids. Ibis (and the JavaGAT described below) arepart of the BSIK project VL-e (Virtual Laboratory for e-Science).Ibis has been used to develop parallel Grid applications that runon large numbers of resources distributed across Europe,including DAS-3 and Grid'5000Ibis has been used to implement several high-level programming models. In particular, our divide-and-conquer system (Satin) is highly suitable for writing parallel Grid applications.Using DAS, we have shown that this model can be made fault-tolerant and can even automatically adapt to changing conditions in the grid,like overloaded CPUs or networks.Ibis and Satin are used by several institutes, for applications (many from VL-e) like analyzing brain images, protein identification, and grammar learning.


The Scalp project (together with TU Delft) aims at the creationof an efficient and effective programming methodology for the next generationhigh performance architectures in Consumer Electronic products.We have developed an efficient and portable runtime system called Hinchthat can exploit both task and data parallelism. Hinch was initially designed for the Philips SpaceCake architecture, but also has beenported to multiprocessors and the Cell architecture. As part of the latter work,we have developed a library called Gordon that handles the data transfers and synchronization within the Cell. Grid computing Our focus in the grid computing field are environments providingaccess to grid resources like data repositories (files) and computing resources to, mostly scientific, distributed supercomputing applications.We have developed the Java-GAT (the Java version of the Grid Application Toolkit), based on our previous work in the EC-funded projectGridLab. Since 2004, the Java-GAT development is taking place in thecontext of the BSIK project "Virtual Laboratory for e-Science" (VL-e).By now, the Java-GAT provides a high-level, middleware-independent and site-independent interface to the grid. It is using intelligent dispatching of its API calls to existing middlewares to overcome configuration and version incompatibilities as well as transient errors. Based on our experiences with the Java-GAT, our group is leading the efforts towards standardization of the "Simple API for Grid Applications"(SAGA) within the Open Grid Forum (OGF). Having a world-wide accepted standard for grid application interfaces will leverage the applicabilityof the Java-GAT (and related systems) even beyond its current, already widely international, user base. In the context of the OMII-SAGA project, funded by OMII-UK, we are developing a Java language binding to the SAGAAPI, together with an implementation based on the Java-GAT.Within the EC-funded project XtreemOS, we are deploying SAGA as the general API for the XtreemOS grid operating system. The AstroStream project (together with TU Delft and Astron)is funded by NWO's STARE program. It aims atcreating an application-development environment for stream-based astronomy applications tailored to the needs of the next-generation radio telescopes Lofar and Ska. Within the project, we are investigating grid-based stream coordination for processing sensor data originating from widely distributed telescope sensors. Challenging aspects arise from network quality of service and from the rather high fault probabilities of systems with ten thousands of sensor and processing elements. Given the rapidly increasing importance and volume of multimedia data,automatic analysis of the content of such information is becoming a problem of phenomenal proportions. Consequently, for urgent and scientifically challenging problems in multimedia content analysis, Grid computing is rapidly becoming indispensable. As emerging multimedia applications often must meet strict time constraints, multimedia Gridapplications must be made variability-tolerant by way of controlled adaptive resource utilization. This raises the need for new stochastic runtime performance control methodologies that react to the continuously changing circumstances in large-scale Grid systems. The JADE-MM project (together with UvA) aims to develop stochastic control schemes that make time-constrained multimedia applications tolerant to the dynamics of large-scale Grid environments, and to integrate these control schemes into a software framework for large-scale multimedia content analysis. Operating systems Our work on reliable and secure operating systems is continuing.The MINIX 3 project has been focused on building a fault-tolerant, self-repairing operating system. In particular, we have carefully designed the system to allow as many system components as possible to run in user space. Some of these components need special powerto do their work. We have carefully located the precise powersthat various components may need and determined how to carefully allocate the precise minimum to each component. Large-scale distributed systems We have been gradually diverting our attention to peer-to-peer systems (also in collaboration with TU-Delft) and wireless sensor networks. A main theme in this work is that we seek to apply gossip-based solutions for (1) disseminating results and (2) taking local-only decisions. We have looked into two specific areas. First, we have been applying gossiping to automatically group nodes in a large network, depending on criteria such as similarity, locla properties, etc. The problem to address is to make sure that the resulting overlay networks are not partitioned, which may lead to halting the discovery of new pairs. Our solution is to run a gossiping protocol as a peer-sampling service, which effectively organizes all nodes in a dynamically changing, strongly connected random graph. The automated grouping is then run a as a separate protocol functionally placed above the peer-sampling service. The second area concerns large-scale wireless networs. In 2006, we have just started this work and have concentrated on efficient dissemination schemes. A wireless environment is completely different in comparison to a


wired one, as the underlying topology precludes random peer sampling, while at the same time we need to take into account that links are generally highly unreliable. Internet and webtechnology The work on Globule is continuing. In this context, we worked on anumber of related issues. The first line of research is to develop new techniques to host dynamic Web applications in a scalable fashion. We proposed several techniques based on database query caching and on partial database replication. A similar type of research is also being pursued in the context of collaborative content delivery networks. In particular, we are working at designing a fully decentralized platform to host the popular Wikipedia Website. Finally, we started two new projects. The first one is a collaboration with Tsinghua university from Beijing, China. This collaboration is implemented in the form of two chinese PhD students who work on their PhD alternatively at both universities. Supersision is also done collaboratively by researchers from the two universities. These students work on scalable hosting infrastructures for Web services. The second new project is realized in the context of the XtreemOS European project. We started working at building scalable service infrastructures to allocate computing resources to application in very large-scale grid environments. The second line of research concerns seamless access to distributed resources. We built mechanisms that allow to consider a group of machines, possibly distributed worldwide, as a single entity. Communication between clients and nodes of the this 'distributed server' can be controled in a very flexible and efficient way, by exploiting properties of the Mobile IPv6. Third, we finalized the research that was being conducted on scalable network latency estimation. We demonstrated the scalability of our approach thanks to an internship done at Google, where an implementation of our network localization system was implemented and successfully deployed. Security We do research on RFIDs, remote policy enforcement, access control, and intrusion detection. Our work on RFID security is also continuing. One notable result obtained during 2006 was our discovery that it is possible to put a virus on an RFID chip, thus opening the backend database used in the system to attack. We presented a paper on this at the IEEE PerCom conference and won the Best paper award. The story also hit the media and was featured in hundreds of media outlets, including the front page of the New York Times Website, BBC, CNN, and others. We also did about 15 radio interviews the day the story broke. In other work we built a second version of our RFID personal firewall, the RFID Guardian and presented a paper at the USENIX LISA conference in Dec. 2006, where it also won a Best Paperaward. Work on remote policy enforcement is also continuing, with a first design finished. The idea is to make it possible for a piece of data to be tagged with a policy and then sent to a remote machine, where the policy will be enforced locally. We assume that trusted software is running remotely, so our concern is how the policy can be enforced. In addition, we are working in the area of access control for distributed systems. In particular we pointed out some shortcomings in some of the existing standard policy languages for access control (e.g. XACML) to capture requirements typical of distributed systems and propose how to address these limitations. We are also working in the area of policy enforcement, thus building systems that can give guarantees that the specified security policy is indeed enforced or otherwise detect where and why it has been violated. We are addressing this problem at the level of a single machine and in a distributed system (Grids) for the specific case of usage control policies. We also did some work on digital rights management by designing and prototyping a solution for peer-to-peer networks of physical devices (e.g. music players). Furthermore, the system allows implementing new business models were consumers can (legally) at their will act asdistributors of the content they purchase. The threat of botnets and other attacks on the Internet is increasing, and the time between the discovery of a vulnerability, and the appearance of attacks that exploit the vulnerability is decreasing. Moreover, the attacks are often polymorphic, mutating themselves as they spread. For these reasons, traditional security measures such as virusscanners and firewalls are no longer adequate. Instead, we need tools to detect and 'fingerprint' entirely new ('zero-day') attacks. For this reason, we work on very accurate intrusion detection technology for next-generation honeypots. The system, known as Argos, is based on a hardware emulator which keeps track of what data comes from suspect sources (e.g., the network) and triggers an alert when such data is used in ways that violate the security policy. The system is intended to not just detect the attack, but also generate signatures of the attack. Such signatures can then be used to block attacks elsewhere on the Internet. Moreover, since attackers are targetting client software as well as servers, we also investigate the integration of Argos-like technology in production machines. In recent years, the Argos honeypot has grown to be quite popular. To date, it has been downloaded 1500 times and it is in use in both research and production networks in several institutes worldwide.


Networking High-speed network traffic processing is difficult due to bottlenecks in bothsoftware and hardware. Problems include excessive copying and contextswitching, caching, and lack of support for integrating new hardware. To deal with these and other issues, we are developing the Streamline framework. By means of aggressive copy avoidance, minimal context switching, andjudicious use of the cache, Streamline significantly improves performance of modern operating systems. In addition, Streamline takes a 'structured operating systems' whereby simple components can be clicked together in straightforward way in order to build complex applications. As a result, the architecture offers more flexibility to the end-user, and facilitates incorporation of advanced hardware (such as network processor boards, or FPGAs). The framework is sufficiently flexible to allow for distributed traffic processing whereby a high-speed link is split among several nodes (perhaps on several levels) which each node performs part of the processing. As the two-level hierarchy easily extends to more levels, the system is inherently scalable. We also do networking research with DAS-3. The most novel part of DAS-3 is its optical wide-area interconnect, which is provided by SURFnet, as part of its Gigaport project. An extra band of the optical SURFnet-6 network is allocated to DAS-3, with up to 8 lambda's of 10 Gb/s each, giving DAS-3 its own dedicated optical network, separate from the university backbone. DAS does not support the high degree of reconfiguration that Grid'5000 allows, but DAS-3 was designed to allow reconfiguration of the optical wide-area network. Using Wavelength Selective Switches (WSS), the topology of the optical interconnect can be changed dynamically, giving DAS-3 a unique reconfigurable optical network, called StarPlane (see www.starplane.org). As part of this project (together with the (University of Amsterdam), we investigate how data-intensive applications (e.g., from e-Science or multimedia) can benefit from this flexibility. Doctoral Degrees Spyros Voulgaris, Epidemic-Based Self-Organization in Peer-to-Peer Systems, 3 October, (promoters: van Steen, Tanenbaum) Contributions to Books Thilo Kielmann. Journal of Grid Computing, Special Issue on Grid Applications, Volume 4, Issue 2, 2006. Editorial . David Wallom and Thilo Kielmann (Editors). Workshop on Grid Applications: From Early Adopters to Mainstream Users, Published as GGF document GFD.68, Global Grid Forum, 2006. Thilo Kielmann and Wilson Rivera. Concurrency & Computation: Practice & Experience, Special Issue on Adaptive Grid Middleware, Vol. 18,No. 13, 2006. Editorial. Rosa Badia, Francoise Baude, Vladimir Getov, Thilo Kielmann, Ian Taylor(Editors). Workshop on Grid Systems, Tools and Environments, October2005, Sophia Antipolis, France, Published as CoreGRID Technical Report. TR-0043, 2006. Latency-Driven Replica Placement (extended version). G. Pierre, M. Szymaniak, M. van Steen. IPSJ Journal, 47(8), August 2006. Globule: A Collaborative Content Delivery Network.G. Pierre, M. van Steen. IEEE Communications Magazine, vol. 44(8), August 2006. Managing Clouds: A Case for a Fresh Look at Large Unreliable DynamicNetworks. O. Babaoglu, M. Jelasity, A.-M. Kermarrec, A. Montresor, M. van Steen. Dynamically extending the Corral with native code for high-speed packetprocessing (Elsevier Computer Networks, Special Issue on Active andProgrammable Networks, 50(14), pp. 2444-2461, October 2006)


Papers in international journals Tom Goodale, Shantenu Jha, Hartmut Kaiser, Thilo Kielmann, Pascal Kleijer, Gregor von Laszewski, Craig Lee, Andre Merzky, Hrabri Rajic,John Shalf. SAGA: A Simple API for Grid Applications, High-Level Application Programming on the Grid, Computational Methods in Scienceand Technology, Vol. 12, No. 1, 2006, pp. 7-20, Scientific Publishers N, Poznan. Jason Maassen, Rob V. van Nieuwpoort, Thilo Kielmann, Kees Verstoep,Mathijs den Burger. Middleware Adaptation with the Delphoi Service,Concurrency and Computation: Practice and Experience, Vol. 18, No. 13,pp. 1659-1679, November 2006. Gosia Wrzesinska, Rob V. van Nieuwpoort, Jason Maassen, Thilo Kielmann,Henri E. Bal. Fault-tolerant Scheduling of Fine-grained Tasks in GridEnvironments , International Journal of High Performance ComputingApplications (IJHPCA), Vol. 20, No. 1, pp. 103-114, Spring 2006. Thilo Kielmann, Andre Merzky, Henri Bal, Francoise Baude, DenisCaromel, Fabrice Huet. Grid Application Programming Environments. InFuture Generation Grids, pp. 283-306, Springer Verlag, 2006. Ivo H. M. van Stokkum and Henri E. Bal: "A Problem Solving Environmentfor interactive modelling of multiway data", Concurrency andComputation: Practice and Experience (Special Issue: Computational Frameworks), Volume 18, Issue 2, pp. 263- 269, February 2006. Contributions to international conference proceedings Gosia Wrzesinska, Jason Maassen, Kees Verstoep, and Henri E. Bal:Satin++: Divide-and-Share on the Grid, 2nd IEEE InternationalConference on e-Science and Grid Computing, Amsterdam, The Netherlands, 4-6 Dec. 2006 Ana Lucia Varbanescu, Maik Nijhuis, Arturo Gonzalez Escribano, HenkSips, Herbert Bos and Henri Bal: SP@CE - An SP-based Programming Model for Consumer Electronics Streaming Applications, 19th Intl. Workshop onLanguages and Compilers for Parallel Computing (LCPC), 2-4 Nov. 2006,New Orleans, Louisiana. Maik Nijhuis, Herbert Bos, Henri E. Bal: Supporting Reconfigurable parallel Multimedia Applications (distinguished paper), Euro-PAR '06,Dresden, Germany, pp. 765-776, Aug. 2006. Tom van der Schaaf, Michal Koutek, Desmond Germans and Henri Bal:ICWall: a Calibrated Stereo Tiled Display from Commodity Components,ACM International Conference on Virtual Reality Continuum and Its Applications (VRCIA), Hong Kong, 14-17 June 2006. Niels Drost, Rob V. van Nieuwpoort, and Henri E. Bal: Simplelocality-aware co-allocation in peer-to-peer supercomputing. SixthInternational Workshop on Global and Peer-2-Peer Computing (GP2P), May 2006, Singapore. Tom van der Schaaf, Michal Koutek and Henri Bal: Parallel particlerendering: A performance comparison between Chromium and Aura,Eurographics Symposium on Parallel Graphics and Visualization (EGPGV'06), Braga, Portugal, 11-12 May 2006. Pieter Adriaans and Ceriel Jacobs. Using MDL for grammar induction. In8th International Colloquium on Grammatical Inference (ICGI '06),Tokyo, Japan, September 2006. Thilo Kielmann. Programming Models for Grid Applications and Systems:Requirements and Approaches, 2006 IEEE John Vincent AtanasoffInternational Symposium on Modern Computing (JVA 2006), Sofia, Bulgaria, October 2006, pp. 27-32. Grid Services for Adaptive Content Delivery,Guillaume Pierre. In Proceedings of the Workshop on the Use of P2P, GRID and Agents for the Development of Content Distribution Networks (UPGRADE-CDN), June 2006.


An Analysis of Interest Community Facilitated P2P Search.E. Ogston, Fifth International Workshop on Agents and Peer-to-Peer Computing (AP2PC) 2006. Versatile Anycasting with Mobile IPv6. M. Szymaniak, G. Pierre, M. van Steen. Proc. ICST Int'l Workshop on Advanced Architectures and Algorithms for Internet Delivery and Applications (AAA-IDEA), Pisa, Italy, October 2006. 2Fast: Collaborative Downloads in P2P Networks.P. Garbacki, A. Iosup, D. Epema, M. van Steen. Proc. Sixth Int'l Conf. Peer-to-peer Computing, Cambridge, UK, September 2006. From Web Servers to Ubiquitous Content Delivery. G. Pierre, M. van Steen, M. Szymaniak, S. Sivasubramanian. In Baldoni et al., Global Data Management, IOS Press, July 2006. Towards Autonomic Hosting of Multitier Internet Applications S. Sivasubramanian, G. Pierre, M. van Steen. Proc. First Workshop on Hot Topics in Autonomic Computing. Dublin, Ireland, June 2006. A Distributed Shared Data Space for Personal Health Systems.W. Stut, F. Wartena, M. van Steen. Proc. 20th IEEE Int'l Congress of the European Federation for Medical Informatics (MIE 2006), Maastricht, The Netherlands, August 2006. A Wide-Area Distribution Network for Free Software. A. Bakker, M. van Steen, A.S. Tanenbaum. ACM Transactions on Internet Technology, vol. 6(3), August 2006. Gossip-based Clock Synchronization for Large Decentralized Systems.K. Iwanicki, S. Voulgaris, M. van Steen. Proc. 2nd IEEE Int'l Workshop on Self-Managed Networks, Systems & Services (SelfMan 2006), Dublin, Ireland, June 2006. On the Value of Random Opinions in Decentralized Recommendation.E. Ogston, A. Bakker, M. van Steen. Proc. 6th IFIP Int'l Conf. on Distributed Applications and Interoperable Systems (DAIS), Bologna, Italy, June 2006. Tribler: A Social-Based Peer-to-Peer System.J. Pouwelse, P. Garbacki, J. Wang, A. Bakker, J. Yang, A. Iosup, D. Epema, M. Reinders, M. van Steen, H. Sips. Proc. 5th Int'l Workshop on Peer-to-Peer Systems (IPTPS), Santa Barbara, CA, February 2006. SUB-2-SUB: Self-Organizing Content-Based Publish and Subscribe for Dynamic and Large Scale Collaborative Networks.S. Voulgaris, E. Riviere, A.-M. Kermarrec, M. van Steen. Proc. 5th Int'l Workshop on Peer-to-Peer Systems (IPTPS), Santa Barbara, CA, February 2006. A Gossip-based Distributed News Service for Wireless Mesh Networks.D. Gavidia, S. Voulgaris, M. van Steen. Proc. 3rd IEEE Conference on Wireless On demand Network Systems and Services (WONS), Les Menuires, France, January 2006. Argos: an Emulator for Fingerprinting Zero-Day Attacks (ACM SIGOPS EUROSYS 2006, Leuven, Belgium, April 2006). SweetBait: Zero-Hour Worm Detection and Containment Using Low- and High-Interaction Honeypots (Elsevier Computer Networks, Special Issue on Security through Self-Protecting and Self-Healing Systems, 2006?, accepted for publication). SafeCard: a Gigabit IPS on the network card (RAID'06, Hamburg, Germany, September 2006). Experimental software We released the Ibis and JavaGAT software


Cooperation within ASCI Many publications are part of the VL-e project, which involves ASCI groups from the UvA and TU Delft. Within the AstroStrem project, we collaborate with TU Delft. The Jade-MM project is pursued in collaboration with the UvA. Both the VU and TU Delft are partners of CoreGRID, the EU-funded Network of Excellence on Foundations, Software Infrastructures and Applications for large scale distributed, GRID and Peer-to-Peer Technologies.

2.2.5 Contribution of UT-EWI-dacs

Management and measurement of operational networks: In this activity, we work on methods and techniques to improve networkperformance, dependability and security, based on measurements taken in a life network.Today, the network we focus on is primarily the fixed internet. Using activeand passive measurement techniques, critical network parameters are derived (using statistical techniques). Simple models are fed with these parameters;model evaluations help in decision making in order to improve networkperformance, dependability, and security. Decisions are put into effect using networkmanagement techniques (e.g. SNMP or web-services based). Anomaly-based intrusion detectionis a new activity we started in 2006. Mobile and wireless communications: This activity focuses on the development of architectures, protocols, algorithms for future wireless networks. Aspects that play a role here are forinstance access mechanisms, routing, service discovery, and all kinds of traffic control aspects, such as scheduling, congestion control, power control, etc. Newechanisms are designed, and the designs are analyzed using analytical models,simulation models, and prototype implementations. The current work concentrateson self-organizing ad hoc networks, that optimize their operation based on information regarding other nodes in the network and the environment. Design and analysis of networked embedded systems: Networked embedded systems are starting to appear as real systems.Networked embedded systems typicallly have to operate under severeresource constraints; furthermore, best effort services are typically not appropriate. Hence, new lightweight protocols have to be designed and validated for their correctness and performance and dependability properties. Our research in this area primarily focusses on specifications of such systems, followed by numerical evaluation of critical performance and dependability parameters. Our specification and evaluation techniques use classical techniques known from queueing theory, but also more advanced techniques pairing stochastic analysis with model checking. We started work on using the DAS machine for distributed evaluation of these very largemodels (relates to Theme A.1). External projects MC=MC, 2004-2008, NWO, 350 kEU, -. This project focusses on specification and numerical evaluation of infinite-state systems, using stochastic model checking technique. Techniques own for finite-state systems model checking, will be adapted and enhanced for nfinite-state systems. This is a cooperation project between the UT-EWI-FMT group (Katoen, now at RWTH Aachen) and us. VOSS2, 2005-2007, NWO, 55 kEU, -. This project facilitates the cooperation between two universities in the Netherlands (UT (Haverkort, Katoen), RUN (Vaandrager)) and 3 universities in Germany (Bonn (Baier), Saarbruecken (Hermanns) and Muenchen (Siegle)). MoQS, 2006-2008, NWO, 500 kEU, -. Cooperation project (NWO/FOCUS) with the UT-EWI-FMT group (Stoelinga), in which work on component-based design and evaluation of large systems is being erformed. Tool support for that purpose is being developed as well.


Verigem, 2006-2008, NWO, 500 kEU, -. Cooperation project (NWO/FOCUS) between TU/e (Groote), CWI (Van der Pol) and UT, in which large-scale distributed algorithms are developed for model checking purposes, in order to increase the size of the systems that can be practically analysed with these techniques by at least one order of magnitude. Use of the ASCI DAS-3 is foreseen. QoSPN@Home, 2004-2008, EZ/Senter, 400 kEuro (DACS budget), -. Cooperation project between TUDelft (Niemegeers/Van Mieghem) and UT, on the design and analysis of QoS-aware personal networks. Such networks are overlay networks consisting of ad hoc nodes (such as in a personal area network) and potentially fixed nodes. Freeband/Awareness, BSIK, 500 kEuro (DACS budget), ?. Cooperation project between UT and Lucent Tehnologies, Telematica Instituut, Ericsson, Roessingh R&D, Yucat, TMS, and WMC, researching and developing context-aware services and networks. The DACS group investigates context discovery for ad hoc networks in this project. Freeband/PNP2008, BSIK, 500 kEuro (DACS budget), ?. Cooperation project between UT and TUDelft, Philips, KPN, WMC,and TNO, to research and develop a Personal Network, focussing on the prototyping of a Personal Mobile Gateway. Gigaport NG---Research on Networks, 2005-2007, BSIK, 150KE, UvA & TUD. Within this project the UT investigates self-management of hybrid IP/ Optical networks, and the measurement of traffic flows within such networks. The project is managed by SURFnet, and supports the introduction of SURFnet6. Emanics, 2006-2009, EU, 310 KE, -. European Network of Excellence (NoE) for the Management of Internet Technologies and Complex Services. This NoE addresses the scalability, dynamics, security and automation challenges that emerge towards the management plane of the future Internet and complex services running on top of it. UT coordinates the research within this NoE. Papers in international journals Pavlou, G. and Pras, A. (2006) Editorial Network and service management. IEEE communications magazine, 44(10). pp. 58-59. ISSN 0163-6804. Pavlou, G. and Pras, A. (2006) Editorial network and service management. IEEE communications magazine, 44(3). pp. 132-132. ISSN 0163-6804. Arlat, J. and Bondavalli, A. and Haverkort, B.R.H.M. and Verissimo, P., ed. (2006) Guest Editorial for the Special Issue on the 2005 IEEE/IFIP Conference on Dependable Systems and Networks, including the Dependable Computing and Communications and Performance and Dependability Symposia. IEEE Transactions on Dependable and Secure Computing, 3 (3). pp. 169-171. ISSN 1545-5971. Gijsen, B.M.M. and van der Mei, R.D. and van den Berg, J.L. and van Wingerden, K.M.C. (2006) Sojourn-time approximations in queueing networks with feedback. Performance evaluation, 63 (8). pp. 743-758. ISSN 0166-5316. Heijenk, G.J. and Liu, F. (2006) Interference-based routing in multi-hop wireless infrastructures. Computer Communications, 29 (13-14). pp. 2693-2701. ISSN 0140-3664. Roijers, F. and van den Berg, J.L. and Fan, X. and Fleuren, M. (2006) A performance study on service integration in IEEE 802.11E wireless LANs. Computer Communications, 29 (13-14). pp. 2621-2633. ISSN 0140-3664. de Boer, P.T. (2006) Analysis of State-Independent Importance-Sampling Measures for the Two-Node Tandem Queue. ACM transactions on modeling and computer simulation, 16 (3). pp. 225-250. ISSN 1049-3301. van den Berg, J.L. and Mandjes, M.R.H. and van de Meent, R. and Pras, A. and Roijers, F. and Venemans, P.H.A. (2006) QoS aware bandwidth provisioning of IP links. Computer networks, 50 (5). pp. 631-647. ISSN 1389-1286.


Abendroth, D. and van den Berg, J.L. and Mandjes, M.R.H. (2006) A versatile model for TCP bandwidth sharing in networks with heterogeneous users. AEU : International journal of electronics and communications, 60 (4). pp. 267-278. ISSN 1434-8411. Bell, A. and Haverkort, B.R.H.M. (2006) Distributed Disk-Based Solution of Very Large Markov Chains. Formal Methods in System Design, 29 (2). pp. 177-196. ISSN 0925-9856. Contributions to international conference proceedings Kuntz, G.W.M. and Siegle, M. (2006) CASPA: Symbolic Model Checking of Stochastic Systems. In: Proceedings of the 13th GI/ITG Conference Measureing, Modelling and Evaluation of Computer and Communication Systems, March 27-29, 2006, Nuernberg, Germany. pp. 465-468. VDE Verlag. ISBN 3-800-72945-8. Martinez Verdugo, J.M. and Haverkort, B.R.H.M. (2006) MathMC: A mathematica-based tool for CSL model checking of deterministic and stochastic Petri nets. In: Proceedings of the Third Int'l. Conference on the Quantitative Evaluation of Systems, September 11-14, 2006, Riverside, CA, USA. pp. 133-134. IEEE Computer Society Press. ISBN 978-0-7695-2665-2. Remke, A.K.I. and Haverkort, B.R.H.M. and Cloth, L. (2006) Uniformization with Representatives - comprehensive transient analysis of infinite-state QBDs. In: First International Conference on Performance Evaluation Methodologies and Tools, 10 Oct 2006, Pisa, Italy. 7. ACM. ISBN 1-59593-506-1. Fioreze, T. and Pras, A. (2006) Using Self-management for Establishing Light Paths in Optical Networks: an Overview. In: Proceedings of the 12th Open European Summer School, 18-20 Sept 2006, Stuttgart, Germany. pp. 17-20. Institut für Kommunikationsnetze und Rechnersysteme, Universität Stuttgart. ISBN 3-938965-02-9. Remke, A.K.I. and Haverkort, B.R.H.M. and Cloth, L. (2006) A versatile infinite-state Markov reward model to study bottlenecks in 2-hop ad hoc networks. In: Third International Conference on the Quantitative Evaluation of Systems, 11-14 Sept 2006, Riverside, CA. pp. 63-72. IEEE Computer Society Press. ISBN 0769526659. El Allali, H. and Heijenk, G.J. and Lo, A. and Niemegeers, I.G.M.M. (2006) A measurement-based admission control algorithm for resource management in diffserv IP networks. In: Proceedings 17th Annual IEEE International Symposium on Personal, Indoor and Mobile Radio Communications (PIMRC'06)., 11-14 September 2006, Helsinki, Finland. pp. 1-5. IEEE Computer Society Press. ISBN 1-4244-0330-8. Jehangir, A. and Heemstra de Groot, S.M. (2006) A Security Architecture for Personal Networks. In: First International Workshop on Personalized Networks, 21 July 2006, San Jose, California, USA. IEEE. ISBN 0-7803-9792-4. Coenen, T.J.M. and Goering, P.T.H. and Jehangir, A. and van den Berg, J.L. and Boucherie, R.J. and Heemstra de Groot, S.M. and Heijenk, G.J. and Dhillon, S.S. and Lu, W. and Lo, A. and van Mieghem, P.F.A. and Niemegeers, I.G.M.M. (2006) Architectural and QoS aspects of Personal Networks. In: Proceedings of First International Workshop on Personalized Networks, PerNets 2006, 21 July 2006, San Jose, CA, USA. IEEE. ISBN 0-7803-9792-4. Taniman, R.O. and Sikkes, B. and van Bochove, A.C. and de Boer, P.T. (2006) Stable-matching-based subcarrier assignment method for multimode PON using a multicarrier variant of subcarrier multiplexing. In: 11th European Conference on Networks & Optical Communications, 10-13 July 2006, Berlin, Germany. pp. 442-449. Fraunhofer Institute for Telecommunications. ISBN 3-923613-40-7. van de Meent, R. and Mandjes, M.R.H. and Pras, A. (2006) Gaussian traffic everywhere? In: Proceedings of the 2006 IEEE International Conference on Communications, 10-14 Jun 2006, Istanbul, Turkey. pp. 573-578. IEEE Computer Society. ISBN 1-4244-0355-3. Cloth, L. and Haverkort, B.R.H.M. (2006) Five Performability Algorithms. A Comparison. In: MAM 2006: Markov Anniversary Meeting, 12-14 Jun 2006, Charleston, SC, USA. pp. 39-54. Boson Books. ISBN 1 932482 34 2.


Liu, F. and Heijenk, G.J. (2006) Context discovery using attenuated Bloom filters in ad-hoc networks. In: Proceedings 4th International Conference on Wired/Wireless Internet Communications, WWIC 2006, May 9-12, 2006, Bern, Switzerland. pp. 13-25. Lecture Notes in Computer Science 3970. Springer-Verlag. ISSN 0302-9743 ISBN 3-540-34023-8. Timmer, M. and de Boer, P.T. and Pras, A. (2006) How to Identify the Speed Limiting Factor of a TCP Flow. In: Fourth IEEE/IFIP Workshop on End-to-End Monitoring Techniques and Services, 3 April 2006, Vancouver, Canada. pp. 17-24. IEEE. ISBN 1-4244-0145-3. Martinez Verdugo, J.M. and Haverkort, B.R.H.M. (2006) CSL model checking of deterministic and stochastic Petri nets. In: Proceedings 13th GI/ITG conference on measuring, Modelling and Evaluation of Computer and Communication Systems, March 27-29, 2006, Nuernberg, Germany. pp. 265-282. Springer Verlag. ISBN 978-3-8007-2945-6. Kuntz, G.W.M. and Siegle, M. (2006) Symbolic Model Checking of Stochastic Systems: Theory and Implementation. In: Proceedings of the 13th International SPIN Workshop, March 30 - April 1, Vienna, Austria. pp. 89-107. Lecture Notes in Computer Science 3925. Springer Verlag. ISSN 0302-9743 ISBN 978-3-540-33102-5. Kalden, R.A. and Haverkort, B.R.H.M. (2006) Measuring and modelling of application flow length in commercial GPRS networks. In: Third International Conference on the Quantitative Evaluation of Systems, 11-14 september 2006, Riverside, CA, USA. pp. 83-92. IEEE Computer Society. ISBN 0769526659. van den Berg, J.L. and Roijers, F. and Mandjes, M.R.H. (2006) Performance Modeling of a Bottleneck Node in an IEEE 802.11 Ad-hoc Network. In: Ad Hoc Now 2006, 5th International Conference on Ad hoc Networks & Wireless, 17-19 August 2006, Ottawa, Canada. pp. 321-336. Lecture Notes in Computer Science 4104. Springer Verlag. ISSN 0302-9743 ISBN 3-540-37246-6. Fioreze, T. and Neisse, R. and Granville, L.Z. and Almeida, M.J. and Pras, A. (2006) A policy-based hierarchical approach for management of grids and networks. In: Application session proceedings of the 10th IEEE/IFIP Network Operations & Management Symposium (NOMS 2006), 3-7 Apr 2006, Vancouver, Canada. pp. 1-14. IEEE. ISSN 1542-1201 ISBN 1-4244-0143-7. Timmer, M. and de Boer, P.T. and Pras, A. (2006) How to Identify the Speed Limiting Factor of a TCP Flow. In: Fourth IEEE/IFIP Workshop on End-to-End Monitoring Techniques and Services, 3 April 2006, Vancouver, Canada. pp. 17-24. IEEE. ISBN 1-4244-0145-3. Experimental software An experimental version of the AHOY discovery protocol for ad-hoc networks has been delivered, as well as of a protocol suite for QoS-signalling in theinternet (NSIS, see RFC 4080: www.ietf.org/rfc4080). Patents Heijenk, G.J. (2006) System and method for fair, channel-dependent scheduling for wireless systems. Patent US7126927 (Assigned). Products of scientific research as a result of cooperation within ASCI In 2005 we joined ASCI and are starting cooperations in this context,e.g., in the Gigaport NG project on optical networking, and in thecontext of gossiping protocols (after the Lorentz workshop organised by Van Steen et al.). Highlights Development and analysis of a scheduling mechanism for wireless CDMA-based systems. Various papers have been published on the idea over the last few years, and a patent for the mechanism (Fair Channel Dependent Scheduling) has been granted in 2006. The idea has been implemented in Ericssons W-CDMA base-stations.


2.2.6 Contribution of TUD-EWI-st-pds In the area of embedded systems, we have developed a performance estimator for MPSoC systems. Furthermore, we have developed a stream programming model for MPSoCs called SP@CE. In the area of grids, we have added components to our KOALA grid scheduler which has been deployed in the Distributed ASCI Supercomputer (support for different applications types and communication-aware scheduling policies), we have investigated the dynamics of the availability of grid resources, we have extended the Grenchmark tool for grid benchmarking, and we have created the Grid Workload Archive. In peer-to-peer systems, we have released the first version of the Tribler p2p client as an extension to Bittorrent with as a final goal TV distribution across the Internet, which includes a novel buddycast algorithm for peer and content discovery and a mechanism (called 2Fast) for improving the downloading performance by means of so-called helper peers. In addition, we have designed an algorithm for building multicast trees for video distribution in p2p systems, and we have investigated the performance improvement due to semantic clustering. In the area of wireless sensor networks, we have carried out a second deployment within the LOFAR-agro project measuring the micro-climate (temperature and humidity) within a potato field during the growing season, we have developed a new energy-efficient MAC protocol (Crankshaft) targeted at dense deployments, and we have enhanced our localization algorithms to handle scenarios involving mobile nodes. External projects ASTROSTREAM, 2006-2010, NWO, Euro 180.000 The Astrostream project aims at creating an application development environment for stream-based astronomy applications tailored to the needs of the next-generation radio telescopes LOFAR and SKA. The Astrostream software architecture will be optimized for high productivity, high efficiency, multi-platform support, and flexibility in run-time behavior. Astrostream is intended for challenging applications with many Tera-bits/s of streaming input data and tens of Teraflops of processing power, typically on large cluster computers. CONSENSUS, 2002 – 2006, NWO, Euro 155.000. The CONSENSUS project will develop collaborative algorithms for Wireless Sensor Networks to overcome the limited capabilities of individual sensor nodes. TUD focuses on algorithms for communications and networking, including distributed wireless access, ad-hoc routing protocols, and reliable end-to-end transport. CoreGRID, 2004-2008, EU (Network of Excellence), EURO 38.000, ASCI partners VU-EW-cs-i. This network integrates the grid research of 42 universities in Europe. GUARanteed Delivery in Grids (GUARD-G), 2006-2010, NWO, Euro 295.274, ASCI partner UL-WI-I. This project aims to research mechanisms and policies to provide performance guarantees for applications submitted to grids, which now only give best-effort service. I-SHARE (part of Freeband), 2004-2008, EZ (BSIK program), EURO 800.000, ASCI partners TUD-EWI-mm-ict, VU-EW-cs-i. This projects researches sharing technology in distributed systems, particularly for video. As a research vehicle, we have chosen P2P-TV, a system for sharing live and recorded TV programs of 10,000+ TV channels and web cams among millions of users. LOFAR-agro, 2004 - 2008, NN (Stichting Samenwerking Noord Nederland), Euro 200.000. The LOFAR-Agro project carries out a pilot project in which ensor nodes will measure the conditions in a potato field; this detailed information (1 reading per 150m2) will be used to improve the advice on how to fight the fungous Phytophtora infestans disease within a crop. MilSens, 2003 – 2007, TNO-FEL (AIO fonds), Euro 160.000. The key objective is to develop an integrated approach to operate large ad-hoc networks of wireless sensor nodes. We will take a practical approach and start from some well-defined application scenarios (to be developed at the start of the project), derive the requirements on the network, and integrate and develop the necessary algorithms.


RELATE, 2005-2008, EU (FP6-IST), EURO 400.000 This project will investigate an approach wherein spontaneously networked mobile objects perform collaborative sensing and communication to collectively determine their relative positions and spatial arrangement. SCALP, 2004-2008, STW, EURO 220.000, ASCI partners VU-EW-cs-i. This project deals with high-productivity methods for programming parallel systems on a chip. Smart Surroundings, 2004 – 2008, EZ (BSIK program), Euro 800.000. The overall mission of the Smart Surroundings project is to investigate, define, develop, and demonstrate the core architectures and frameworks for future ambient systems. TUD focuses on two important aspects at the middleware layer: service discovery and localization. These two are related through the ServiceGRID approach, in which location serves as an index in a database of cached service providers. Two-level Peer-to-Peer Systems, 2003-2007, NWO, EURO 147.000, ASCI partner VU-EW-cs-i. This project aims at exploring the notion of superpeers in p2p systems in order to improve the performance of such systems. Virtual Laboratory for e-Science (VL-e), 2004-2008, EZ (BSIK program), EURO 1.000.000 (TUD-EWI-st-pds part), ASCI partners TUD-EWI-mm-cgcc, VU-EW-cs-I, UvA-FdNWI-caps, UvA-FdNWI-scs. This projects aims at designing and implementing grid technology (schedulers, communication libraries, problem-solving and visualization environments, etc) for virtual laboratories (e.g., for simulations in the sciences) on top of the basic grid fabric. Doctoral Degrees Haratcherev, I.J.; March 14 2006; Application-oriented Link Adaptation for IEEE 802.11. TU Delft, Delft 2006, ix + 110pp, ISBN-13: 978-90-9020513-7, External project (2e or 3e geldstroom). Scientific publications over 2006 A. Iosup and D.H.J. Epema and C. Franke and A. Papaspyrou and L. Schley and B. Song and R. Yahyapour (2006). On Grid Performance Evaluation using Synthetic Workloads. In E. Frachtenberg and U. Schwiegelshohn (Eds.). Proc. of the 12th Workshop on Job Scheduling Strategies for Parallel Processing (JSSPP). Lecture Notes in Computer Science.

K.G. Langendoen (2006). Apples, Oranges, and Testbeds. In 3rd IEEE Conf. on Mobile Ad-hoc and Sensor Systems (MASS 2006), pp. 367--396.

A. Baggio and K.G. Langendoen (2006). Monte-Carlo Localization for Mobile Wireless Sensor Networks. In 2nd Int. Conf. on Mobile Ad-hoc and Sensor Networks (MSN 2006), pp. 317--328.

C.L. Dumitrescu and D.H.J. Epema and J. Dunnweber and S. Gorlatch (2006). Reusable Cost-Based Scheduling of Grid Workflows Operating on Higher-Order Components. In Proc. of the Second IEEE International Conference on e-Science and Grid Computing (e-Science'06), pp. 87-94. IEEE Computer Science.

O. Sonmez and H.H. Mohamed and D.H.J. Epema (2006). Communication-Aware Job Placement Policies for the KOALA Grid Scheduler. In Proc. of the Second IEEE International Conference on e-Science and Grid Computing (e-Science'06), pp. 79-86. IEEE Computer Science.

Javier Bustos-Jim'enez and Denis Caromel and Jose Miguel Piquer and Alexandru Iosup (2006). The Rocking Chair


and the Grid: Balancing Load Across Project Grids. In Sergei Gorlatch and Marian Bubak and Theirry Priol (Eds.). Proc. of the CoreGRID Workshop on Integrated Research in Grid Computing, pp. 117--128.

A. Iosup and P. Garbacki and D.H.J. Epema (2006). Provisioning and Scheduling Resources for World-Wide Data-Sharing Services. In Proc. of the Second IEEE International Conference on e-Science and Grid Computing (e-Science'06), pp. 84-91. IEEE Computer Science.

J. Wang and J. Pouwelse and R. Lagendijk and M.J.T. Reinders (2006). Distributed Collaborative Filtering for Peer-to-Peer File Sharing Systems. In 21st Annual ACM Symposium on Applied Computing, pp. 1026-1030.

J. Wang and J. Pouwelse and J. Fokker and M.J.T. Reinders (2006). Personalization of a peer-to-peer television system. In 4th European Conference on Interactive Television, pp. 147-155, Athens, Greece.

J.A. Pouwelse and P. Garbacki and J. Wang and A. Bakker and J. Yang and A. Iosup and D.H.J. Epema and M. Reinders and M. van Steen and H.J. Sips (2006). Tribler: A social-based peer-to-peer system. Technical Report 2006-002 (presented at IPTPS'06), Delft University of Technology.

A.L. Varbanescu (2006). PAM-SoC Experiments and Results. Technical Report PDS-2006-001, Delft University of Technology.

Ivaylo J. Haratcherev (2006). Application-oriented Link Adaptation for IEEE 802.11. PhD Thesis, TU-Delft.

J.J.D. Mol, D.H.J. Epema, H.J. Sips (2006). The Orchard Algorithm: P2P Multicasting without Free-Riding. In Proc. of the Twelfth Annual Conference of the Advanced School for Computing and Imaging (ASCI 2006), pp. 82-89, Lommel, Belgium.

Jenneke Fokker and Johan Pouwelse and Wray Buntine (2006). Tag-Based Navigation for Peer-to-Peer Wikipedia. In Collaborative Web Tagging Workshop held in conjuction with the 15th International World Wide Web Conference (WWW2006), pp. CDROM, Edinburgh, Scotland.

A.L. Varbanescu and H.J. Sips and A.J.C. van Gemund (2006). A performance prediction methodology for MPSoCs. In Proc. of the ASCI 2006 Conference, pp. 211-218.

Iosup and D.H.J. Epema (2006). GrenchMark: Towards a Generic Framework for Analyzing, Testing, and Comparing Grids. In J.W.J. Heijnsdijk and K.G. Langendoen (Eds.). 12th Annual Conference of the Advanced School for Computing and Imaging (ASCI'06), pp. 21--29.

Iosup and D.H.J. Epema (2006). GrenchMark: Towards a Generic Framework for Analyzing, Testing, and Comparing Grids. In J.W.J. Heijnsdijk and K.G. Langendoen (Eds.). 12th Annual Conference of the Advanced School for Computing and Imaging (ASCI'06), pp. 21--29.

P. Garbacki and A. Iosup and D.H.J. Epema and M. van Steen (2006). Collaborative Downloads in File-Sharing P2P Networks. In 12th Annual Conference of the Advanced School for Computing and Imaging (ASCI'06), pp. 90--98.

Iosup and D.H.J. Epema (2006). GrenchMark: A Framework for Analyzing, Testing, and Comparing Grids. In Proc. of the 6th IEEE/ACM Intl. Symposium on Cluster Computing and the Grid (CCGrid06), pp. 313-320. IEEE Computer Society.

K.G. Langendoen and A. Baggio and O.W. Visser (2006). Murphy Loves Potatoes: Experiences from a Pilot Sensor Network Deployment in Precision Agriculture. In 14th Int. Workshop on Parallel and Distributed Real-Time Systems (WPDRTS), pp. 1-8.


Dumitrescu and D.H.J. Epema and J. Duennweber and S. Gorlatch (2006). User-Transparant Scheduling of Structured Parallel Applications in Grid Environments. In Workshop on HPC Grid Programming Environments and Components and Component and Framework Technology in High-Performance and Scientific Computing (HPC-GECO+COMPFRAME). IEEE Computer Society Press.

A. Iosup and P. Garbacki and J. Pouwelse and D.H.J. Epema (2006). Correlating Topology and Path Characteristics of Overlay Networks and the Internet. In Proc. of the the 6th Intl. Workshop on Global and Peer-to-Peer Computing (GP2PC06), pp. 10, CDROM. IEEE Computer Society.

A.I.D. Bucur and D.H.J. Epema and H.H. Mohamed (2006). Co-Allocation in Grids: Experiences and Issues. In V. Getov and D. Laforenza and A. Reinefeld (Eds.) Proc. of the Workshop on Future Generation Grids. Springer-Verlag.

M. Ali and U. Saif and A. Dunkels and T. Voigt and K. R"omer and K.G. Langendoen and J. Polastre and Z. Uzmi (2006). Medium Access Control Issues in Sensor Networks. ACM SIGCOMM Computer Communication Review 36(2):33--36.

Jun Wang and Johan Pouwelse and Jenneke Fokker and Arjen P. de Vries and Marcel J.T. Reinders (2006). Personalization on a Peer-to-Peer Television System. Multimedia Tools and Applications to appear.

A. Iosup and C. Dumitrescu and D.H.J. Epema and H. Li and L. Wolters (2006). How Are Real Grids Used? The Analysis of Four Grid Traces and its Implications. In The 7th IEEE/ACM International Conference on Grid Computing (Grid2006), pp. 262-269. IEEE Computer Society.

G.P. Halkes and A. Baggio and K.G. Langendoen (2006). A Simulation Study of Integrated Service Discovery. In Paul Havinga and Maria Lijding and Nirvana Meratnia and Maarten Wegdam (Eds.). Proceedings of the 1st European Conference on Smart Sensing and Context (EuroSCC 2006), pp. 39--53. LNCS 4272

J.J.D. Mol and D.H.J. Epema and H.J. Sips (2006). The Orchard Algorithm: P2P Multicasting without Free-riding. In 6-th IEEE International Conference on Peer-to-Peer Computing, pp. 275-282. IEEE Society Press.

V. K. Naik and P. Garbacki and A. Mohindra (2006). Architecture for Service Oriented Solution Delivery Using Grid Systems. In IEEE International Conference on Services Computing (SCC'06), pp. 414-422.

V. K. Naik and P. Garbacki and K. Kummamuru and Y. Zhao (2006). On-line Evolutionary Resource Matching for Job Scheduling in Heterogeneous Grid Environments. In 2nd International Workshop on Scheduling and Resource Management for Parallel and Distributed Systems (SRMPDS'06), pp. 103-108.

P. Garbacki and A. Iosup and D.H.J. Epema and M. van Steen (2006). 2Fast: Collaborative Downloads in P2P Networks (Best Paper Award). In 6-th IEEE International Conference on Peer-to-Peer Computing, pp. 23-30. IEEE Computer Society.

A.L. Varbanescu and M. Nijhuis and A. Gonzalez-Escribano and H.J. Sips and H. Bos and H.A. Bal (2006). SP@CE - An SP-based Programming Model for Consumer Electronics Streaming Applications. In LCPC 2006, pp. 33-48. LNCS 4382.

A.L. Varbanescu and M. Nijhuis and A. Gonzalez-Escribano and H.J. Sips and H. Bos and H.A. Bal (2006). SP@CE - An SP-based Programming Model for Consumer Electronics Streaming Applications. In LCPC 2006, pp. 33-48. LNCS 4382.

A.L. Varbanescu and H.J. Sips and A.J.C. van Gemund (2006). Semi-Static Performance Prediction for MPSoC Platforms. In CPC 2006, pp. 1-15.


A.L. Varbanescu and H.J. Sips and A.J.C. van Gemund (2006). PAM-SoC: a Toolchain for Predicting MPSoC Performance. In Europar 2006, pp. 111-123. LNCS 4128.

I. Haratcherev and J. Taal and K.G. Langendoen and R.L. Lagendijk and H.J. Sips (2006). Optimized video-streaming over 802.11 by cross-layer signalling. IEEE Communications Magazine 44(1):115-121. Experimental software J.A. Pouwelse, M. ten Brinke, D.H.J. Epema, J.-D. Mol, J. Roozenburg, J. Yang (TUD), and A. Bakker (VU), Tribler, an open-source P2P client, Version 4.0 This software, which is freely available from www.tribler.org, is a result of the I-Share project, and constitutes a P2P client implemented in Python and based on BitTorrent with fundamental additions for social-based notions (friends, taste buddies), for recommendations, for improving the download performance (cooperative downloading), and for video distribution. The core of Tribler is the epidemic buddycast algorithm for disseminating information about peers and content in, and about the operation of, the Tribler P2P system. High-light For our P2P system Tribler, we have developed a collaborative download protocol called 2Fast, in which a user invokes the help of his friends to speed up downloads. Early downloading protocols (e.g., Gnutella) have no incentives for donating upload bandwidth, which has serious limitations in real environments, because unconstrained bandwidth sharing is sensitive to freeriding. The Bittorrent tit-for-tat mechanism was the first system which offered an incentive for uploading. The current Bittorrent mechanism also has its disadvantages, because without enough seeding peers (i.e, peers which possess the complete file in question), the download speed of a peer is restricted by Bittorrent's tit-for-tat bartering protocol to its upload link capacity. Hence, peers with asymmetric Internet access, such as ADSL or ADSL-2, cannot fully use their download capacity. The 2Fast protocol makes use of social groups, where members who trust each other collaborate to improve their download performance (see Figure 1). In the idea of downloading with the help of others, altruistic peers contribute their bandwidth by joining a swarm even if they are not interested in the content being distributed in this swarm. The inherent assumption of sufficient altruism in the network without any incentives makes this simple approach impractical in real-world environments. Our 2Fast protocol solves this problem by introducing social-group incentives.

Figure 1: Overview of collaborative downloading. In 2Fast, peers from a social group that decide to participate in a collaborative download take one of two roles: they are either collectors or helpers. A collector is the peer that is interested in obtaining a complete copy of a particular file, and a helper is a peer that is recruited by a collector to assist in downloading that file. Both the collector and the helpers start downloading the file using the classical Bittorrent tit-for-tat and the collaborative download extensions. As in Bittorrent, a helper selects a chunk of the file for downloading based on the rarest-first policy among the chunks in


possession of its bartering partners. However, before actually downloading this chunck, it asks the collector for approval, which will only be granted when the chunk is unique, that is, when no other helper already downloads the same chunk. After downloading a file chunk, the helper sends the chunk to the collector without requesting anything in return. In addition to receiving file chunks from its helpers, the collector also optimizes its download performance by dynamically selecting the best available data source from the set of helpers and other peers in the Bittorrent network using the default mechanisms of Bittorrent, which prefer peers that upload at higher rates. As helpers give priority to collector requests, they are preferred as data sources. We have implemented and tested 2Fast in a real environment. For this we have selected a middle-sized swarm of around 1,900 peers with only 6% seeds, distributing a 1.2 GB file. These numbers remained almost unchanged during our experiments. We have performed tests for three download-to-upload bandwidth ratios from standard Internet package offerings: low-end ADSL with a ratio of 512:128 Kbps, high-end ADSL with a ratio of 2048:512 Kbps, and ADSL-2 with a ratio of 8:1 Mbps. It should be noted that we could only impose these bandwidths on the collector and the helpers, which were under our control, but not on the peers in the Internet that they selected as their bartering partners. As a performance metric of our system, we use the ratio between the download time achieved by a peer obtaining a file all by itself versus the corresponding time for a collaborative group (speedup). The theoretical maximum speedup is achieved when a peer can fully use its download bandwidth, and so it is equal to the ratio between the download and upload link capacities. Thus, for ADSL and ADSL-2 the maximum achievable speedup is 4 and 8, respectively. Figure 2 shows the obtained speedups for the number of helpers in the range from 0 to 32. The total download time was decreased with a factor of almost 2 for low-end ADSL, of more than 3 for high-end ADSL, and of almost 6 for ADSL-2. The difference between the theoretical and achieved speedups is mainly due to the influence of the seeders (when there are many seeders to begin with, the potential speedup is restricted) and of the delays experienced by helpers when requesting unique file chunks from peers. The more helpers are involved, the more restrictive the unique file chunk selection method is, and consequently, the longer the time needed to find a bartering partner for such a chunk. This time is further increased in the case of low-end ADSL by the fact that then the collector and the helpers were discriminated as peers with an upload bandwidth which is below average.

Figure 2: The impact of the helpers on the download speedup.

2.2.7 Contribution of UT-EWI-caes The main emphasis of the group is on efficient architectures for dependable networked embedded systems. Within this theme the chair performs research on three related key areas: 1. efficient architectures for streaming applications,


2. wireless networked embedded systems and 3. dependability issues of networked embedded systems. Energy-efficiency and dependability are the main drivers of our research. Energy-efficiency is important for streaming applications found in battery powered mobile devices (e.g. PDAs and portable multimedia players), and is of crucial importance for wireless sensor networks. Dependability plays an important role in sensor networks (nodes may fail or run out of energy unexpectedly), but due to the abundance of nodes distributed applications continue despite of failing nodes. In MPSoC (Multi Processor Systems-on-Chip) systems for streaming applications dependability techniques also play an important role. One of the problems in manufacturing a MPSoC with millions of transistors using deep-submicron technologies (90 nm and below), is an increase in the probability of defects in silicon, which results in decreasing manufacturing yield. To effectively deal with this increased defect density, we need efficient methods for fault detection, localization, and fault tolerant architectures implemented on-chip. External projects Gecko, 2001-2006, NWO, 500kE High2, 2001-2006, STW Progress, 250 kE Micro-CHP, 2007-2011, Essent, Gasterra, EO.N UK, 250kE NXP projects, 2005-2009, NXP, 750 kE CMOS Beamforming, 2007-2010, STW, 250 kE Beam Force, 2007-2010, Thales, 250 kE 4S, 2004-2007, EU FP6, 500kE A4, 2005-2008, STW, 125kE AAF, 2005-2008, BSIK Freeband, 250kE AWGN, 2002-2006, BSIK Freeband, 250kE For more information on the projects we refer to the website of the group: caes.ewi.utwente.nl. Doctoral Degrees Guo, Y. (2006) Mapping Applications to a Coarse-Grained Reconfigurable Architecture. PhD thesis, Univ. of Twente. ISBN 978-90-365-2390-5, funding NWO. Joseph, A.A. (2006) Defect-based testing of LTS digital circuits. PhD thesis, University of Twente. ISBN 90-365-2362-1, funding STW. Mansour, O. (2006) High level synthesis for non-manifest digital signal processing applications. PhD thesis, University of Twente. ISBN 90-365-2321-4, funding STW. Contributions to Books Rauwerda, G.K. and Potman, J. and Hoeksema, F.W. and Smit, G.J.M. (2006) Adaptation in the physical layer using heterogeneous reconfigurable hardware. In: Adaptation Techniques in Wireless Multimedia Networks. Wireless Networks and Mobile Computing. Nova Science Publishers, USA. ISBN 1-59454-883-8. Zhang, Q. and Hoeksema, F.W. and Kokkeler, A.B.J. and Smit, G.J.M. (2006) Towards Cognitive Radio for emergency networks. In: Mobile Multimedia: Communication Engineering Perspective. Nova Publishers, U.S.A. ISBN 1-60021-207-7. Papers in international journals Chatterjea, S. and Havinga, P.J.M. (2006) A Taxonomy of Distributed Query Management Techniques for Wireless Sensor Networks. International Journal of Communication Systems. ISSN 1099-1131.


Chatterjea, S. and Kininmonth, S. and Havinga, P.J.M. (2006) Sensor networks. GeoConnexion, 5 (9). pp. 20-22. ISSN 1476-8941. Dulman, S.O. and Rossi, M. and Havinga, P.J.M. and Zorzi, M. (2006) On the hop count statistics for randomly deployed wireless sensor networks. International Journal of Sensor Networks, 1 (1/2). pp. 89-102. ISSN 1748-1287. Contributions to international conference proceedings Havinga, P.J.M. and Lijding, M.E.M. and Meratnia, N. and Wegdam, M., ed. (2006) Smart Sensing and Contex, First European Conference, EuroSSC 2006. Lecture Notes in Computer Science 4272. Springer Verlag, Heidelberg. ISBN 978-3-540-47842-3. Bijlsma, T. and Jansen, P.G. (2006) Energy Conservation with EDFI scheduling. In: First European Conference, EuroSSC 2006, 25-27 Oct 2006, Enschede. pp. 259-262. Lecture Notes in Computer Science 4274. Springer Verlag. ISBN 3-540-47842-6. Bijlsma, T. and Wolkotte, P.T. and Smit, G.J.M. (2006) An Optimal Architecture for a DDC. In: Proceedings of the 20th IEEE International Parallel and Distributed Processing Symposium (IPDPS'06) - 12th Reconfigurable Architecture Workshop (RAW 2006), 25-29 Apr 2006, Rhodes Island, Greece. pp. 192-200. IEEE Computer Society. ISBN 1-4244-0054-6. van de Burgwal, M.D. and Smit, G.J.M. and Rauwerda, G.K. and Heysters, P.M. (2006) Hydra: an Energy-efficient and Reconfigurable Network Interface. In: Proceedings of the 2006 International Conference on Engineering of Reconfigurable Systems & Algorithms, 26-29 June 2006, Las Vegas, USA. pp. 171-177. CSREA Press. ISBN 1-60132-011-6. Chatterjea, S. and van Hoesel, L.F.W. and Havinga, P.J.M. (2006) A Framework for a Distributed and Adaptive Query Processing Engine for Wireless Sensor Networks. Transactions of the Society of Instrument and Control Engineers, E-S-1 (1). pp. 58-67. ISSN 0453-4654. Chatterjea, S. and di Luigi, S. and Havinga, P.J.M. (2006) DirQ: A Directed Query Dissemination Scheme for Wireless Sensor Networks. In: IASTED International Conference on Wireless Sensor Networks 2006, WSN 2006, 3-4 July 2006, Banff, Canada. Wireless and Optical Communication. ACTA Press. ISBN 0-88986-563-9. Chatterjea, S. and Luigi, S.d. and Havinga, P.J.M. (2006) An Adaptive Directed Query Dissemination Scheme for Wireless Sensor Networks. In: 9th IEEE International Conference on Parallel Processing Workshops 2006, ICPPW 2006, 14 Aug 2006, Columbus, USA. pp. 181-188. International Conference on Parallel Processing Workshop. IEEE Computer Society Press. ISBN 0-7695-2637-3. Dam, A.C. and Lammertink, M.G.J. and Rovers, K.C. and Slagman, J. and Wellink, A.M. and Rauwerda, G.K. and Smit, G.J.M. (2006) Hardware/Software Co-design Applied to Reed-Solomon Decoding for the DMB Standard. In: Proceedings of the 9th EUROMICRO Conference on DIGITAL SYSTEM DESIGN Architectures, Methods and Tools (DSD 2006), August 30 - September 1, 2006, Dubrovnik, Croatia. pp. 447-455. IEEE Computer Society. ISBN 0-7695-2609-8. Dil, B. and Dulman, S.O. and Havinga, P.J.M. (2006) Range-Based Localization in Mobile Sensor Networks. In: Proceedings of Third European Workshop on Wireless Sensor Networks, 13-15 Feb 2006, Zurich, Switzerland. pp. 164-179. Lecture notes in computer science 3868. Springer Verlag. ISBN 3-540-32158-6. Durmaz Incel, O. and Dulman, S.O. and Jansen, P.G. (2006) Multi-channel Support for Dense Wireless Sensor Networking. In: Proceedings of the First European Conference on Smart Sensing and Context, EuroSSC 2006, 25-27 Oct 2006, Enschede, the Netherlands. pp. 1-14. Lecture Notes in Computer Science 4272. Springer. ISBN 978-3-540-47842-3.


Guo, Y. and Hoede, C. and Smit, G.J.M. (2006) A Pattern Selection Algorithm for Multi-Pattern Scheduling. In: Proceedings of the 20th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - 12th Reconfigurable Architecture Workshop (RAW 2006), 25-29 Apr 2006, Rhodes Island, Greece. pp. 198-205. IEEE Computer Society. ISBN 1-4244-0054-6. Guo, Y. and Hoede, C. and Smit, G.J.M. (2006) A Column Arrangement Algorithm for a Coarse-grained Reconfigurable Architecture. In: Proceedings of the International Conference on Engineering of Reconfigurable Systems and Algorithms (ERSA'06), 26-29 Jun 2005, Las Vegas, Nevada, USA. pp. 117-122. CSREA Press. ISBN 1-932415-74-2. Jacobs, J.W.M. and Bond, W. and Pouls, R. and Smit, G.J.M. (2006) High Volume Colour Image Processing with Massively Parallel Embedded Processors. In: Parallel Computing: Current & Future Issues of High-End Computing, 13 - 16 September 2005, Malaga, Spain. pp. 583-590. NIC Series 33. John von Neumann Institute for Computing. ISBN 3-00-017352-8. Jacobs, J.W.M. and Dai, R. and Smit, G.J.M. (2006) Mining Dynamic Document Spaces with Massively Parallel Embedded Processors. In: 6th International Workshop on Embedded Computer Systems: Architectures, Modeling, and Simulation, SAMOS 2006, 17-20 July 2006, Greece. pp. 69-78. Lecture Notes in Computer Science 4017. Springer Verlag. ISSN 0302-9743 ISBN 3-540-36410-2. Kavaldjiev, N.K. and Smit, G.J.M. and Jansen, P.G. and Wolkotte, P.T. (2006) A Virtual Channel Network-on-Chip for GT and BE traffic. In: IEEE Computer Society Annual Symposium on Emerging VLSI Technologies and Architectures (ISVLSI'06), 2-3 March 2006, Karlsruhe, Germany. pp. 211-216. IEEE Computer Society. ISBN 0769525334. Kavaldjiev, N.K. and Smit, G.J.M. and Wolkotte, P.T. and Jansen, P.G. (2006) Providing QoS Guarantees in a NoC by Virtual Channel Reservation. In: International Workshop on Applied Reconfigurable Computing (ARC 2006), 1-3 March 2006, Delft, the Netherlands. pp. 299-310. Lecture Notes in Computer Science 3985. Springer-Verlag. ISBN 354036708X. Köbben, B. and van Bunningen, A.H. and Muthukrishnan, K. (2006) Wireless Campus LBS - Building campus-wide Location Based Services based on WiFi technology. In: Geographic Hypermedia: Concepts and Systems, 4-5 Apr 2005, Denver, Colorado, USA. pp. 399-408. Lecture Notes in Geoinformation and Cartography. Springer. ISBN 978-3-540-34237-3. Kerkhoff, H.G. (2006) Testable Design and Testing of Microsystems. In: Design of Systems on a Chip. Springer, Berlin - Heidelberg - New York, pp. 203-219. ISBN 978-0-387-32499-9. Kerkhoff, H.G. and Barber, R.W. and Zhang, X. and Emerson, D.R. (2006) Fault Modelling and Co-Simulation in FlowFET-Based Biological Array Systems. In: Proceedings of third IEEE International Workshop on Electronic Design, Test & Applications DELTA 2006, 17 - 19 jan 2006, Kuala Lumpur, Malaysia. pp. 177-182. Conference Publishing Services. IEEE Computer Society Press. ISBN 0-7695-2500-8. Kerkhoff, H.G. and Zhang, X. (2006) Fault simulation of heterogeneous integrated biological systems. In: Proceedings of the 12th IEEE International mixed signal testing workshop, 21-23 jun 2006, Edinburgh, United Kingdom. pp. 129-134. ISBN not assigned. Khatib, M.G. and van der Zwaag, B.J. and van Viegen, F.C. and Smit, G.J.M. (2006) Striping Policy as a Design Parameter for MEMS-based Storage Systems. In: The 2nd International Workshop on Software Support for Portable Storage, 26 Oct 2006, Seoul, Korea. Informal proceedings. ISBN not assigned. Law, Y.W. and Havinga, P.J.M. (2006) How to Secure a Wireless Sensor Network. Technical Report TR-CTIT-06-06 Centre for Telematics and Information Technology, University of Twente, Enschede. ISSN 1381-3625. Liu, Hongyuan and Dumas, N. and Richardson, A. and Heal, R. and Kerkhoff, H.G. (2006) Built-in test of electrode degradation of multi-electrode array biosensors. In: Proceedings of the 12th IEEE International mixed signal testing


workshop (IMSTW'06), 21-23 jun 2006, Edinburgh, United Kingdom. pp. 136-141. ISLI en Lancaster University. ISBN not assigned. Marin-Perianu, M. and Havinga, P.J.M. (2006) RMD: Reliable Multicast Data Dissemination within Groups of Collaborating Objects. In: First IEEE International Workshop on Practical Issues in Building Sensor Network Applications, SenseApp 2006, 14-16 Nov 2006, Tampa, Florida, USA. pp. 656-663. IEEE Computer Society Press. ISSN 0742-1303 ISBN 1-4244-0418-5. Marin-Perianu, M. and Hofmeijer, T.J. and Havinga, P.J.M. (2006) Assisting Business Processes through Wireless Sensor Networks. In: 13th International Conference on Telecommunications (ICT 2006), 9-12 May 2006, Funchal, Madeira Island, Portugal. IEEE Portugal. ISBN 972-98368-4-1. Marin-Perianu, M. and Hofmeijer, T.J. and Havinga, P.J.M. (2006) Implementing Business Rules on Sensor Nodes. In: 11th IEEE International Conference on Emerging Technologies and Factory Automation (ETFA 2006), 20-22 Sept 2006, Prague, Czech Republic. pp. 292-299. IEEE Computer Society Press. ISBN 1-4244-0681-1. Marin-Perianu, R.S. and Scholten, J. and Havinga, P.J.M. and Hartel, P.H. (2006) Energy-Efficient Cluster-Based Service Discovery in Wireless Sensor Networks. In: Sixth International Workshop on Wireless Local Networks, 14-16 Nov 2006, Tampa, Florida. pp. 931-938. IEEE Computer Society Press. ISBN 1-4244-0418-5. Muthukrishnan, K. and Meratnia, N. and Lijding, M.E.M. and Koprinkov, G.T. and Havinga, P.J.M. (2006) WLAN location sharing through a privacy observant architecture. In: 1st Int. Conf. on Communication System Software and Middleware (COMSWARE), Jan 8-12, 2006, New Delhi, India. IEEE Computer Society. ISBN 0-7803-9575-1. Rauwerda, G.K. and Smit, G.J.M. and van Benthem, C.R.W and Heysters, P.M. (2006) Reconfigurable Turbo/Viterbi Channel Decoder in the Coarse-Grained Montium Architecture. In: Proceedings of the International Conference on Engineering of Reconfigurable Systems and Algorithms (ERSA'06), 26-29 June 2006, Las Vegas, Nevada, USA. pp. 110-116. CSREA Press. ISBN 1-60132-011-6. Smit, G.J.M. and Kokkeler, A.B.J. and Wolkotte, P.T. and van de Burgwal, M.D. and Heysters, P.M. (2006) Efficient architectures for streaming applications. In: Dynamically Reconfigurable Architectures, Apr 2006, Dagstuhl, Germany. pp. 1-7. Dagstuhl Seminar Proceedings 06141. Internationales Begegnungs- und Forschungszentrum fuer Informatik (IBFI). ISSN 1862-4405. Wiggers, M.H. and Bekooij, M.J.G. and Jansen, P.G. and Smit, G.J.M. (2006) Efficient Computation of Buffer Capacities for Multi-Rate Real-Time Systems with Back-Pressure. In: Proceedings of the Internal Conference on Hardware/Software Codesign an System Synthesis (CODES+ISSS), 22-25 Oct 2006, Seoul, Korea. pp. 10-15. ACM. ISBN 1-59593-370-0. Wolkotte, P.T. and van de Burgwal, M.D. and Smit, G.J.M. (2006) Non-Power-of-Two FFTs: Exploring the Flexibility of the MONTIUM. In: Proceedings of the International Symposium on System-on-Chip (SoC 2006), 13-16 Nov 2005, Tampere, Finland. pp. 167-170. IEEE Computer Society. ISBN 1-4244-0621-8. Zhang, Q. and Kokkeler, A.B.J. and Smit, G.J.M. (2006) Adaptive OFDM System Design For Cognitive Radio. In: 11th International OFDM-Workshop, 30th - 31st Aug. 2006, Hamburg, Germany. pp. 91-95. IEEE Communications Society, Germany Chapter. ISBN not assigned. Zhang, Q. and Kokkeler, A.B.J. and Smit, G.J.M. (2006) Cognitive Radio for Emergency Networks. In: Global Mobile Congress 2006, 09-11 Oct 2006, Beijing, China. pp. 32-37. Delson Group. ISSN 1557-0622. Zhang, Q. and Kokkeler, A.B.J. and Smit, G.J.M. (2006) A reconfigurable radio architecture for Cognitive Radio in emergency networks. In: European Conference on Wireless Technology, 10-15 September 2006, Manchester, UK. pp. 35-38. IEEE Communication Society. ISBN 2-9600551-5-2.


Zhang, Y. and Wu, J. and Havinga, P.J.M. (2006) Implementation of an On-Demand Routing Protocol for Wireless Sensor Networks. In: 13th International Conference on Telecommunications, 9-12 May 2006, Funchal, Madeira island, Portugal. pp. 1-4. IEEE Portugal Section. ISBN 972-98368-4-1.

2.2.8 Contribution of TUE-EE-dmes Embedded multi-media systems: architectures, models, programming and design The focus of our work is on mapping applications onto multiprocessor systems. System level design methods allow the systematic development of abstract executable models. These models are used to verify correctness and performance properties of the system, or to synthesise systems or system components. The results allow system designers to take well-founded design decisions about the architecture of the system, hardware/software partitioning, the choice of processors, etc. Multiprocessor implementation platforms also require novel programming techniques, mapping, and synthesis techniques. These techniques must optimize execution time, memory usage, and energy usage and allow trade-offs. Platform development is necessary to provide hardware and software components with predictable behaviour.

We continued the development of a mapping trajectory for multi-media applications targeting multiprocessor architectures. As a basic model of computation, we take Kahn process networks (KPN) and its derivates such as synchronous dataflow (SDF). We developed efficient analysis techniques for SDF graphs, and made them available in a publicly available tool SDF3 (http://www.es.ele.tue.nl/sdf3). Building upon the concept of application scenarios that capture common execution modes of a system implementation from the resource usage point of view, we developed Scenario-Aware Dataflow Graphs. We also continued our work on property preserving synthesis of concurrent real-time embedded control systems. The modeling and analysis techniques have been extended to deal with mixed hard and soft real-time components. We further developed our hybrid VLIW/SIMD processor template, realizing a prototype in FPGA and extending the architecture to handle dynamic communication. External Projects Betsy: BEing on Time Saves energy Continuous multimedia experiences on networked hand-held devices, 2004-2007. EU/IST/FP6, M€ 4.4, Philips research, CSEM, IMEC, ISI, MDH/TU Kaiserslautern, Siemens C-lab, TUE, en de University of Cyprus The aim of the BETSY project is to have multimedia streams on wireless hand-held devices seamlessly adapted to fluctuating network conditions and available terminal resources while reducing the energy consumption of the stream processing. This way the user can enjoy true multimedia experiences with freedom of movement in a networked home or at any hot-spot. To achieve this, we need to be able to make trade-offs between the use and consumption of


network and terminal resources, such as bandwidth use, CPU consumption, memory needed and power consumption by the terminal, while guaranteeing end-to-end timeliness - required for streaming data. PreMaDoNa Predictable Matching of Demands on Networked Architectures, 2004-2009, Progress/STW, M€ 1.97, Philips, CMG The PreMaDoNa project focuses on the design and implementation of NoC-based platforms for multi-media applications. The research challenges mainly originate from the increasing complexity of multi-media applications and the ever-shortening design time to realise multi-media systems. The major research objective is the following: Being able to design NoC-based real-time system in a predictable way such that non-functional properties can be guaranteed, while still being able to dynamically match quality with the available resources. PROgramming Multi-processor Embedded multi-media Systems (PROMES) 2002-2008, NWO, k€ 295 PROMES focuses on the development of both a sound theoretical framework and a programming environment for multi-media applications building on top of multi-processor systems. Important is the study of task-level analysis techniques that provide insight in concurrency-, timing-, and energy-related properties at the specification level without fully implementing an application. SmartCam 2002-2007. STW/progress, 1.4 M€, Philips Natlab, Philips CFT, TNO-FEL, In3D, HP Bristol labs, TUD-TNW-tn-ph The SmartCam project investigates low-cost one-chip Smart Camera solutions, contributing to a quantitatively guided design trajectory. In particular, we investigate the impact of current applications, and we try to define relevant architectural parameters and to develop an architectural template. Other aims are to enhance and integrate existing application mapping environments for SIMD and ILP processors. Fexible Application Mapping Environment (FAME) 2003-2007, NWO, 250 k€, Leiden University, Delft University of Technology, TUD-ITS-me-ce FAME aims to obtain low power solutions when mapping applications on processor platforms. We like to achieve this goal by creating a compiler infrastructure capable of performing source-code transformations. We propose a dynamic approach in combination with analytic pruning of the transformation search space in order to find the best low-power optimizations. Beyond the Ordinary: Design of Embedded Real-time Control (BODERC) 2003-2007. Senter, 2.5 M€, Océ Technologies, Philips CFT, AAS, Imtech ICT, Chess iT, Katholieke Universiteit Nijmegen, Universiteit Twente The Boderc project focuses on distributed embedded real-time controllers of complex systems. An Océ printer is taken as a case-study and acts as a driver for the project. The target is an integral approach for a systematic architectural design, modeling, analysis, and validation methodology for such heterogeneous systems. PUSH: Practical Use of Software/Hardware Engineering 2006-2008, STW/PROGRESS, k€ 50, Chess, DevLab The purpose of this PROGRESS+ project is to improve the industrial use of the SHE (Software Hardware Engineering) method, the POOSL language, and the supporting tools, in particular in the Netherlands. Papers in international journals Aa, T. van der; Jayapala, M.; Barat, F.; Deconinck, G.; Lauwereins, R.; Corporaal, H.; Catthoor, F.: Instruction buffer exploration for low energy embedded processsors. JEC 1, nr. 3, 2006, pp. 341-351. Fatemi, S.H.; Mesman, B.; Corporaal, H.; Basten, A.A.; Kleihorst, R.: RC-SIMD: Reconfigurable Communication SIMD Architecture for Image Processing Applications. JEC 2, nr. 2, 2006, pp. 167-179. Jess, J.A.G.; Kalafala, K.; Naidu, S.R.; Otten, R.H.J.M.; Visweswariah, C.: Statistical Timing for parametric Yield Prediction of Digital Integrated Circuits. IEEE Trans. Comput.-Aided Des. Integr. Circuits Syst. 25, nr. 11, 2006, pp. 2376-2392.


Palkovic, M.; Brockmeyer, E.; Vanbroekhoven, P.; Corporaal, H.; Catthoor, F.: Systematic preprocessing of data dependent constructs for embedded systems. Journal of Low Power Electronics 2, nr. 1, 2006, pp. 9-17. Reymen, I.M.M.J.; Hammer, D.K.; Kroes, P.A.; Aken, J.E. van; Dorst, C.H.; Bax, M.F.Th.; Basten, T.: A domain-independent descriptive design model and its application to structured reflection on design processes. Research in Engineering Design 16, nr. 4, 2006, pp. 147-173 Contributions to international conference proceedings Aa, T. van der; Jayapala, M.; Corporaal, H.; Deconinck, G.: Efficient Architecture Exploration of a Clustered Loop. Proceedings of the Internation Workshop on Optimizations for DSPS and Embedded Sytems, 26-29 March 2006. Aa, T. van der; Jayapala, M.; Catthoor, F.; Deconinck, G.; Corporaal, H.: Instruction Transfer and Storage Exploration for Low Energy VLIWS. Proceedings of IEEE 2006 Workshop on Signal Processing Systems, 1-3 October 2006; IEEE Computer Society, Los Alamitos, 2006, pp. 313-318. Bartels, Ch.; Huisken, J.; Goossens, K.; Groeneveld, P.R.; Meerbergen, J.L. van: Comparison of An Aethereal Network on Chip and A Traditional Interconnect for a Multi-Processor DVB-T System on Chip. Proceedings of the 14th IFIP WG10.5 International Conference on Very Large Scale Integration and System-on-Chip VLSI-SOC 2006, 16-18 October 2006, ISBN 3-901882-19-7; IFIP, Nice, 2006 Caarls, W.; Jonker, P.P.; Corporaal, H.: Algorithmic Skeletons for Stream Programming en Embedded Heterogeneous Parallel Image Processing Applications. Proceedings of the 20th IEEE International Parallel and Distributed Processing Symposium, 26-29 April 2006; IEEE Computer Society, Los Alamitos, 2006. Ciordas, C.; Hansson, A.; Goossens, K.G.W.; Basten, T.: A Monitoring-aware NoC Design Flow. Proceedings of the 9th EUROMICRO Conference, DSD 2006, 30 August - 1 September 2006, ISBN 0-7695-2609-8, ed. V. Muthukumar; IEEE Computer Society Press, Los Alamitos, USA, 2006, pp. 97-104. Ciordas, C.; Goossens, K.G.W.; Radulescu, A.; Basten, T.: NoC Monitoring: Impact on the Design Flow. Proceedings the IEEE International Symposium on Circuits and SYStems, 2006, 21-24 May 2006, ISBN 0-7803-9390-2; IEEE Computer Society Press, Los Alamitos, USA, 2006, pp. 1981-1984. Ciordas, C.; Goossens, K.G.W.; Basten, T.; Radulescu, A.; Boon, A.G.: Transaction Monitoring in Networks on Chip: The On-Chip Run-Time Perspective. Proceedings of IEEE Symposium on Industrial Embedded Systems, 18-20 October 2006, ISBN 1-4244-0777-X; IEEE Computer Society Press, Los Alamitos, 2006. Couvreur, C.; Nollet, V.; Catthoor, F.; Corporaal, H.: Fast Multi-Dimentsion Multi-Choice Knapsack Heuristic for MP-SoC Run-Time Management. Proceedings of the International Symposium on System-on-Chip, 13-16 November 2006, ISBN 1-4244-0621-8, 2006, pp. 195-198. Couvreur, C.; Nollet, V.; Marescaux, T.; Brockmeyer, E.; Catthoor, F.; Corporaal, H.: Pareto-Based Application Specification for MPSoC Customized Run-Time Management. Proceedings of the Internation Conference on Embedded Computer Systems: Architectures, Modeling and Simulation, 17-20 July 2006, ISBN 1-4244-0155-0, 2006, pp. 78-84. Fatemi, S.H.; Mesman, B.; Corporaal, H.; Basten, T.; Jonker, P.: Run-Time Reconfiguration of Communication in SIMD Architectures. Proceedings of the 20th International Parallel and Distributed Processing Symposium 20006, 13th Reconfigurable Architectures Workshop, RAW 2006, 25-26 April 2006, ISBN 1-4244-0054-6; IEEE Computer Society Press, Los Alamitos, USA, 2006. Florescu, O.; Hoon, M. de; Voeten, J.P.M.; Corporaal, H.: Probabilistic Modelling and Evaluation of Soft Real-Time Embedded Systems. Proceedings of the Embedded Computer Systems: Architectures, Modeling and Simulation., 17-20 July 2006, ISBN 3-540-36410-2, 2006, pp. 206-215.


Florescu, O.; Voeten, J.P.M.; Corporaal, H.: Property-Preserving Synthesis for Unified Conrol- and Data-Oriented Models. Applications of Specification and Design Languages for SoCs., ISBN 1-4020-4997-8, ed. Alain Vachoux; Springer, 2006, pp. 247-262. Florescu, O.; Voeten, J.P.M.; Verhoef, M.; Corporaal, H.: Reusing Real-Time Systems Design Eperience Through Modelling Patterns. Proceedings of the Forum on Specification & Design Languages 2006, 19-22 September 2006, ISBN 3-00-019710-9, 2006, pp. 375-380. Florescu, O.; Huang, J.; Voeten, J.P.M.; Corporaal, H.: Strengthening Property Preservation in Concurrent Real-Time Systems. Proceedings of the IEEE International Conference on Embedded and Real-Time Computing Systems and Applications., 16-18 August 2006, ISBN 0-7695-2676-4; IEEE Computer Society, Los Alamitos, USA, 2006, pp. 106-109. Ghamarian, A.H.; Geilen, M.C.W.; Basten, T.; Theelen, B.D.; Mousavi, M.R.; Stuijk, S.: Liveness and Boundedness of Synchronous Data Flow Graphs. Proceedings of the 6th International Conference on Formal Methods in Computer-Aided Design, 12-16 November 2006, ISBN 0-7695-2707-8; IEEE Computer Society, Los Alamitos, USA, 2006, pp. 68-75. Ghamarian, A.H.; Geilen, M.C.W.; Stuijk, S.; Basten, T.; Moonen, A.J.M.; Bekooij, M.J.G.; Theelen, B.D.; Mousavi, M.R.: Throughput analysis of synchronous data flow graphs. Application of Concurrency to System Design (Proceedings 6th International Conference, ACSD 2006, Turku, Finland, June 28-30, 2006), ISBN 0-7695-2556-3; IEEE, 2006, pp. 25-34. Gheorghita, S.V.; Basten, T.; Corporaal, H.: Application Scenarios in Streaming-Oriented Embedded Systems Design. Proceedings of the International Symposium on System-on-Chip 2006, 13-16 November 2006, ISBN 1-4244-0621-8; IEEE, Piscataway, USA, 2006, pp. 175-178. Gheorghita, S.V.; Basten, T.; Corporaal, H.: Handling Dynamism in Embedded system Design by Application Scenarios. Proceedings of Architecture and Compilers for Embedded Systems Symposium 2006, 3-4 October 2006, ISBN 90-382-1016-7, 2006, pp. 5-8. Gheorghita, S.V.; Basten, T.; Corporaal, H.: Profiling Driven Scenario Detection and Prediction for Multimedia Applications. Proceedings of Embedded Computer Systems: architectures, modelling and simulation, International Conference, IC-SAMOS, 17-20 July 2006, ISBN 1-4244-0155-0; IEEE Computer Society Press, Los Alamitos, USA, 2006, pp. 63-70. Huang, J.; Geilen, M.C.W.; Voeten, J.P.M.; Corporaal, H.: Branching-time Property Preservation between Real-Time Systems. Proceedings of the International Symposium on Automated Technology for Verification and Analysis, 23-26 October 2006, ISBN 3-540-47237-1, ed. Susanne Graf; Wenhui Zhang; Springer-Verlag, Berlin, Germany, 2006, pp. 260-275. Huang, J.; Voeten, J.P.M.; Corporaal, H.: Correctness-preserving Synthesis for Real-Time Control Software. Proceedings of the International Conference on Quality Software., 27-28 October 2006, ISBN 0-7695-2718-3, ed. Mei Hong; IEEE Computer Society, Los Alamitos, USA, 2006, pp. 65-73 Kumar, A.; Mesman, B.; Corporaal, H.; Meerbergen, J.L. van; Ha, Y.: Global Analysis of Resource Arbitration for MPSoC. Proceedings of the 9th Euromicro Conference on Digital Systems Design., 30 August - 1 September 2006, ISBN 0-7695-2609-8; IEEE Computer Society, Dubrovnik, Croatia, 2006, pp. 71-78. Kumar, A.; Theelen, B.D.; Mesman, B.; Corporaal, H.: On Composability of MPSoC Applications. Advanced Computer Architecture and Compilation for Embedded Systems., 22-27 July 2006, ISBN 90-382-0981-9; Academia Press, Ghent, Belgium, 2006, pp. 149-152. Kumar, A.; Mesman, B.; Theelen, B.D.; Corporaal, H.; Ha, Y.: Resource Manager for Non-preemptive Heterogeneous Multiprocessor System-on-chip. Proceedings of the IEEE Workshop on Embedded Systems for Real-Time Multimedia., 26-27 October 2006, ISBN 0-7803-9783-5; IEEE Computer Society, Los Alamitos, USA, 2006, pp. 33-38.


Mesman, B.; Fatemi, S.H.; Corporaal, H.; Basten, T.: Dynamic-SIMD for lens distortion compensation. Proceedings of Application-specific Systems, Architectures and Processors, 11-13 September 2006, ISBN 0-7695-2682-9; IEEE Computer Society Press, Los Alamitos USA, 2006, pp. 261-264 Nollet, V.; Avasare, P.; Verkest, D.; Corporaal, H.: Exploiting Hierarchical Configuration to Improve Run-Time MPSoC Task Assignment. Proceedings of the Internation Conference on Engineering of Systems and Algorithms., 26-29 June 2006, pp. 49-55. Palkovic, M.; Catthoor, F.; Corporaal, H.: Automatic Model Generation for Evaluation of Scenario Creation Heuristics. Proceedings of the 6th Symposium on Architecture and Compilers for Embedded Systems., 2006, pp. 1-4. Palkovic, M.; Catthoor, F.; Corporaal, H.: Dealing with variable trip count loops in system level exploration. Proceedings of the 4th Workshop on Optimizations for DSP and Embedded Systems, 2006, pp. 19-28. Pastrnak, M; With, P.H.N. de; Stuijk, S.; Meerbergen, J.L. van: Parallel Implementation of Arbitrary-Shaped MPEG-4 Decoder for Multiprocessor Systems. Proceedings of Visual Communications and Image Processing, 15-19 January 2006, ISBN 0-8194-6117-2, ed. John G. Apostolopoulos; Amir Said; IS&T Society for Imaging Science and Technology, Bellingham, USA, 2006, pp. 60771-1-60771-10 Stuijk, S.; Geilen, M.C.W.; Basten, T.: Exploring Trade-offs in Buffer Requirements and Throughput Constraints for Synchronous Dataflow Graphs. Proceedings of the 43rd Design Automation Conference 2006, 24-28 July 2006, ISBN 1-59593-381-6; ACM Press, New York, USA, 2006, pp. 899-904. Stuijk, S.; Basten, T.; Geilen, M.C.W.; Ghamarian, A.H.; Theelen, B.D.: Resource-efficient Routing and Scheduling of Time-constrained Network-on-Chip Communication. Proceedings of 9th EUROMICRO Conference, DSD 2006, 30 August - 1 September 2006, ISBN 0-7695-2609-8, ed. V. Muthukumar; IEEE Computer Society Press, Los Alamitos, USA, 2006, pp. 45-52. Stuijk, S.; Geilen, M.C.W.; Basten, T.: SDF3: SDF For Free. Proceedings of the 6th International Conference ACSD 2006, 27-30 June 2006, ISBN 0-7695-2556-3, ed. K.G.W. Goossens; L. Petrucci; IEEE Computer Society Press, Los Alamitos, USA, 2006, pp. 276-278. Theelen, B.D.; Geilen, M.C.W.; Basten, T.; Voeten, J.P.M.; Gheorghita, S.V.; Stuijk, S.: A Scenario-Aware Data Flow Model for Combined Long-Run Average and Worst-Case Performance Analysis. Proceedings of the ACM-IEEE International Conference on Formal Methods and Models for Codesign., 27-29 July 2006, ISBN 1-4244-0421-5; IEEE Computer Society, Los Alamitos, USA, 2006, pp. 185-194 Other products of scientific research Stuijk, S; Multiprocessor design flow 2002 - now, C++/JAVA, Linux/Windows. Next-generation embedded multi-media systems will often be built on multi-processor systems to obtain high compute power at relatively low energy cost. Work is ongoing to implement a design flow to map streaming applications specified as synchronous dataflow (SDF) graphs to a heterogeneous multi-processor systems. We aim at predictability with respect to timing behavior, while minimizing energy consumption. An important component of this design-flow is a tool to analyze SDF graphs, called SDF3. The tool also allows the generation of random test graphs, and it supports the visualization of graphs. The tool is available via http://www.es.ele.tue.nl/sdf3. Geilen, M.C.W.; Pareto Calculator 2006 – now, C++/Visual Studio .Net C++/XML, Linux/Windows Pareto Algebra is an algebraic method to compositionally specify and compute trade-offs in multi-dimensional optimization problems. The approach is particularly designed to allow for describing incremental design decisions and composing sets of Pareto-optimal configurations. The Pareto Calculator implements the algebra. It is available via http://www.es.ele.tue.nl/pareto.


Gheorghita, S.V.; Scenario-based DVS compilation flow 2006 – now, C, Linux/Windows Application scenarios group together operation modes of an application that are similar from the resource usage perspective. If possible operation modes in which a system may run, together with information about their resource consumption, are known at design time, specific and aggressive design decisions can be made for each operation mode in different design steps. The software realizes an automated scenario-based design trajectory for reducing the energy consumption of a streaming application running on a single processor platform via dynamic voltage and frequency scaling, under both soft and hard real-time constraints. More information on scenario-based design is available via http://www.es.ele.tue.nl/scenarios. Cooperation within ASCI TUD-TNW-tn-ph: Caarls, W.; Jonker, P.P.; Corporaal, H.: Algorithmic Skeletons for Stream Programming en Embedded Heterogeneous Parallel Image Processing Applications. Proceedings of the 20th IEEE International Parallel and Distributed Processing Symposium, 26-29 April 2006; IEEE Computer Society, Los Alamitos, 2006. Fatemi, S.H.; Mesman, B.; Corporaal, H.; Basten, T.; Jonker, P.: Run-Time Reconfiguration of Communication in SIMD Architectures. Proceedings of the 20th International Parallel and Distributed Processing Symposium 20006, 13th Reconfigurable Architectures Workshop, RAW 2006, 25-26 April 2006, ISBN 1-4244-0054-6; IEEE Computer Society Press, Los Alamitos, USA, 2006.

2.2.9 Contribution of TUD-me-ce Arachne The general goal of the project is to investigate novel processor architectures that enables a ubiquitous (i.e., anywhere and anytime) and unobtrusive (i.e., without much user intervention) communication environment. In order to achieve this, we focus on the following (intertwined) research topics: Arachne network processor This entails the specification of the Arachne network processor. In a truly ubiquitous communication environment, the communication devices are not located in a fixed geographical location and therefore may encounter different communication settings during their utilization. For example, moving from a GSM/UMTS network to a Wi-fi network to a Bluetooth network. Instead of incorporating a multitude of heterogeneous and application-specific network processors, we seek to provide a single solution that adapts itself depending on its surroundings in order to lower design complexity and costs of such devices. Herein, we focus on the design of complex hardware units that are able to perform the required functions and on the utilization of reconfigurable hardware technologies, e.g. field-programmable gate arrays (FPGAs). Furthermore, we focus on low-power implementations of the Arachne network processor that are intended to be incorporated in battery-powered handheld devices. Finally, the research in this project also focus on other communication devices other than wireless handheld devices as suggested previously. Examples of such devices include wireless base stations, network routers, network gateways, etc.. Therefore, we investigate the possibility of a single and scalable solution that can be incorporated in these devices. This means covering bandwidths from several kilobits to several tens of Gigabits. Internet and protocol processing This entials the investigation into the functional and temporal requirements of Internet-related applications, such as web-based databases, database mining, content-based processing (e.g., multimedia stream processing), voice-over-IP, videoconferencing, e-learning. In addition, we investigate the requirements associated with the processing of protocols, e.g., IPv4/IPv6, TCP, RTP/RTCP, SIP, etc. and their derivatives that govern and enable the previously mentioned applications on top of the internet. The research performed entails ranging from the modeling and profiling of applications to modeling of the Arachne processor to the design of specialized hardware units.


Software and design tools The research performed entails the development of software tools that allow (faster) modeling and profiling of Internet applications and the Arachne network processor with the purpose of investigating the attainable performance and power requirements/consumption. Related research topics include: simulation tools development, benchmarking, application and processor modeling. In addition, special attention must be paid in the integration of these tools as they provide a valuable source of information prior to the definition of the Arachne network processor (targeting a specific network environment or application set) or to the actual design of specialized hardware units. Finally, design tools must be developed that incorporate the earlier determined profiling information. Molen The MOLEN proposition is that reconfigurable processors, i.e. processors that adapt (dynamically or statically) their microarchitecture to fit application "design requirements", are the answer to the processor (embedded or not) hardware design challenges. To prove the viability of the proposition, we are working on multiple design aspects of (single and multi) processors on a chip using reconfigurable fabric. More specifically our team is working on the following: The MOLEN reconfigurable microcoded processor The main idea for the MOLEN reconfigurable processors is to utilize microcode and custom configured hardware to improve embedded system computing. The reconfigurable hardware execution of code (ranging from a single instruction to a piece of application code) is divided into two logical phases. In the first phase the reconfigurable hardware is being configured. In the second phase the execution of the code is being performed. In both phases, microcode is utilized to perform both the reconfiguration process and the execution of the code. Frequently utilized microcode resides permanently within the fixed part of an on-chip storage facility and non-frequently utilized microcode are paged into the pageable part of the same or another storage facility. The approach is generic, therefore, different applications can utilize the proposed processing capabilities. Our experimentation thus far has involved multimedia operations. In the multimedia experimentation, we investigate processing elements that are capable of performing operations and algorithms found in generating, coding, and displaying multimedia formats, i.e., pictures, video, audio, and graphics. At the current stage, the multimedia processor architecture has targeted multimedia standards including JPEG, MPEG-1/2, MPEG-4, and H.261. Currently, we consider graphic operations and power consumption. We have implemented a Molen processor prototype on the Virtex-II Pro FPGA family from Xilinx Corp. The Virtex-II Pro devices incorporate up to four PowerPC 405 GPP cores, FPGA reconfigurable fabric hardware, dedicated RAM blocks, and dedicated high-speed I/O blocks. In the future of the project we intend to consider lossless compression. Reconfigurable arithmetic and logic processor units The first basic goal is to speed up scientific (mostly vector based) code. Arithmetic (mostly complex to design in hardware) units normally are not present in general purpose processor instruction sets. Such operations include matrix multiplication, sparse matrix operations (such as transpose) etc. They can be implemented in reconfigurable hardware speeding up the execution of scientific programs. A second goal is to design a router and network related reconfigurable hardware. Reconfigurable processor units can be added to general purpose processors for domains (such us switches, networks, packet processing, protocols), that have not been envisioned for the general purpose processor paradigm providing substantial speed-ups. Embedded IP execution units We analyze embedded system computational requirements in order to determine the feasibility of hardwired accelerator units and propose implementations for such units. We have considered JPEG, MPEG-1/2, MPEG-4, H.261, and lossless compression algorithms and we have proposed numerous specialized units including DCT/IDCT, sum of absolute differences (SAD), variable length decoding (VLD), Paeth encoding for portable network graphics (PNG), filters, entropy decoders, repetitive padding units, saturated arithmetic units, accepted quality function (AQF), color space convertors. For our experimentation, we have utilized various FPGA technologies and applied the Molen processor framework to the Philips Trimedia, the IBM's PowerPCs (processors integrated on the Xilinx Virtex-II Pro devices) and the ARM (processors integrated on the Altera Excalibur devices). We will keep on exploring embedded applications for potential hardwired IP units. Memory architecture and implementations Multimedia and embedded processing has specific requirements for memory accesses. For high performance processing, it is required that the memory is accessed in a rectangular manner implying that to be efficient, mechanisms are needed that access memory in a two-dimensional manner. We propose mechanisms for media reconfigurable processors utilizing special addressed memory organizations and an implementation of two-dimensional


memory cores that substantially improve the memory performance of the Molen FPGA implemented processor. In addition, because memory may require a significant amount of power, we propose a cache organization that reduces the number of off-chip accesses thus decreasing main memory power consumption of the reconfigurable processor architecture. Compiler and design space exploration tools We have defined a programming paradigm that target the Molen reconfigurable microcoded processor engine and we are developing a backend compiler and a design space exploration toolset. The programming paradigm is based on sequential consistency. It provides mechanisms for parallel and concurrent hardware execution and it is intended (currently) for single program execution. In order to conform to the Molen programming paradigm, an existing compiler has been extended to support the required instruction set and register set extensions. Moreover, a specific mechanism has been developed for passing parameters/results in the case of parallel executions. The compiler and the design space exploration tools are developed in the project The Delft Workbench. Low-Power High-Performance Graphics Architectures We are designing a low-power 2D/3D graphics hardware accelerator for mobile terminals equipped with an ARM processor core. The purpose of using a graphics accelerator is to move some of the graphics-related computations, in particular the rasterization, from the CPU to this dedicated hardware device in order to improve the rendering speed for graphics applications. One important concern for a graphics accelerator meant to be employed in mobile terminals is a low power consumption figure since the most current graphics accelerators are notorious for their high power consumption. Therefore, algorithmic- and circuit-level techniques for low-power graphics need to be studied and evaluated. GraalBench Low-Power Graphics benchmark. The GraalBench is a 3D graphics benchmark suite suitable for 3D graphics on low-power mobile systems, in particular mobile phones. These benchmarks were collected to facilitate our studies on low-power 3D graphics accelerators in the Graal (GRAphics AcceLerator) project. It includes traces of several games as well as virtual reality applications such as 3D museum guides. Applications were selected on the basis of several criteria such as resolution, polygon count, pixel rate, and relevance to mobile devices. For example, 3D FPS games or 3D virtual guides were considered relevant while CAD/CAM applications, such as contained in the Viewperf package, were excluded because it is unlikely that they will be offered on mobile devices (they often have high polygon count and require high resolution). More information and downloads can be found in The GraalBench Benchmark Suite. System on Chip (SoC). Clustered Torus The underlining assumption of this research is that entire systems are migrating onto single chips and that a single chip incorporates numerous heterogeneous IPs. We further assume that the entire system comprises of a network that provides communications among chiplet IPs (processors). In essence, we consider embedded multiprocessor systems and networks on a chip (NoC). We believe that for such systems the interconnection networks have to be regular, expendable, and that they have to provide fast interconnections for some but not all communications between processors. Additionally, networks have to be reliable and avoid lifelock and deadlocks. In our research, we have been proposing a network topology, denoted as the clustered torus, having the properties discussed above and we examine the properties, performance, design issues, and feasibility of such a network. The Delft Java processor We have developed a processor which is a parallel multi-threaded engine optimized for the Java language. Since Java bytecodes are interpreted, the interpretation of the program achieves a performance level that meets or exceeds natively compiled code. The multi-threaded processor architecture is currently being utilized by Sandbridge Technologies to develop cost-effective low-power broadband wireless processor technology. The processor, a 3G digital wireless multi-threaded processor architecture, is intended to meet demands for services such as web browsing, MP3 audio, MPEG-4 video, and video telephony for handheld devices.


2.3 C: IMAGE & MULTIMEDIA SENSING, PROCESSING, INTERPRETATION AND VISUALISATION

2.3.1 Contribution of TUD-TNW-tn-qi Multidimensional Image Analysis We have continued our efforts in developing novel strategies for the processing, analysis and interpretation of multi-dimensional images, including time-series, color images and hyper-spectral images. The work focuses on the detection and subsequent characterization of geometric image structures rather than specific intensity patterns. This approach yields generic tools for image description that can be applied in a wide variety of applications. The methods are largely independent of the physical imaging technique used or the intrinsic image resolution. The theoretical component in this work has focused on - Interactive 3D segmentation using connected orthogonal contours; - Model based segmentation of material mixtures near boundaries using an analytical scale-invariant model for the relation between intensity and gradient magnitude; - Model based segmentation of three-material mixtures near generalized T-junctions; - Level set PDE’s for modeling single-curved surfaces; - Segmentation and size measurements of bumps; - Improved wave-front modeling for fast marching; - Decomposition of the structure tensor near multi-model neighborhoods; - Quantitative evaluation of dynamic superresolution methods; - Characterization of pore spaces and network structures in tablets; - Motion and flow analysis of liquid flow in micro-machined nanoliter wells; - Design of orientation selective filters for lines, planes, edges in 3D space; - An addressable multi-resolution sampling grid for 3D orientation; - Dynamic super-resolution in image sequences based on adaptive (scale, orientation and curvature) data fusion of registered local image data; - Partial volume effects estimation in 3-D CT based on density and gradient trajectories; - Computer aided diagnosis by automatic screening for polyps in colonography; - Inter and intra patient registration of DTI images applied to atlas building, tractography and patient studies; - Using line segments as structuring elements for sampling-invariant measurements; - The generalized Radon transform: sampling, accuracy and memory considerations. The aforementioned developments have been applied in numerous industrial collaborations and medical applications. - Analysis of micro-structures formed by complex networks of bio-polymers; - Detection of channels and faults in 3D seismic images; - Analysis of liquid flow and diffision using tracer particles; - Analysis of perceptual image quality of printed materials using local image features, scale and color; - Analysis, transformation, visualization and registration of diagnostic and surgical images for use in minimally invasive surgery and placement of endoprostheses; - Virtual endoscopy; - Detection and progression analysis of glaucoma; - MRI thermography; - Diffusion Tensor MRI; - Characterizing the Three- Dimensional Organization of Telomeres. External projects 4D image processing for analyzing motion patterns of the wrist Period: 2005-2009; Funding STW. In this project we will develop image processing and analysis methods for 4D characterization of the wrist. The extracted information will be combined with biomechanical models for diagnosis and treatment planning. Processing and analysis of Diffusion Tensor MRI at 3Tesla Period: 2005-2008; Funding VL-e through AMC Amsterdam In this project we will develop image processing and analysis methods for Diffusion Tensor MRI images.


Dynamic superresolution of small moving objects Period: 2004-2007; Funding: TNO Investigating techniques for detection, registration and subsequent superresolution of small moving objects Intelligent image interpretation for automated quality grading of young tomato plants in horticulture Period: 2003-2006; Funding: IOP beeldverwerkingOntology driven image processing and analysis for the quality grading of young tomato plants in horticulture. Detection and progression analysis of glaucoma Period: 2002-2005; Funding: LDT (Laser Diagnostic Technologies, recently taken over by Carl Zeiss Meditec). Early detection of glaucoma and its progression in images acquired through scanning laser polarimetry, by means of the GDx apparatus. Cyttron Period: 2003-2007; Funding: Bsik Nanophoresis Period: 2002-2010; Funding: FOM Superresolution in undersampled image sequences Period: 2002-2005; Funding: IOP beeldverwerking Increasing the spatial resolution in exchange for temporal resolution through adaptive techniques. Automatic polyp detection in 3D CT Period 2002-2006; Funding IOP beeldverwerking Image processing, analysis and recognition to facilitate automatic screening for polyps in 3D CT of the colon. Multi-dimensional measurement techniques Period: 2002-2006; Funding: FOM Fundamental techniques for multi-dimensional image processing and analysis. Improved techniques for virtual endoscopy Period: 2001-2005; Funding: Philips Medical Systems; Doctoral degrees Pekalska, E.; (cum laude) 17 January 2005; Dissimilarity representations in pattern recognition, TU Delft, Delft 2005, 322 pp., ISBN 90-9019021-X, External project (=2e geldstroom). Contributions to Books Vos, F.M., R.E. van Gelder, I.W.O. Serlie, J. Florie, Y.C. Nio, F.H. Post, R. Truyen, A.M. Vossepoel, and J. Stoker; Virtual Colonoscopy (Ch.9), in: J. Dankelman, C.A. Grimbergen, H.G. Stassen (eds.), Engineering for Patient Safety: Issues in Minimally Invasive Procedures, Lawrence Erlbaum Associates, Mahwah, NJ, 2005, 206-225. Papers in international journals Bouma, H., A. Vilanova, L.J. van Vliet, and F.A. Gerritsen; Correction for the dislocation of curved surfaces caused by the PSF in 2D and 3D CT images, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 27, no. 9, 2005, 1501-1507. Bruin, P.W. de, V.J. Dercksen, F.H. Post, A.M. Vossepoel, G.J. Streekstra, and F.M. Vos; Interactive 3D segmentation using connected orthogonal contours, Computers in Biology and Medicine, vol. 35, no. 4, 2005 (@2004), 329-346.


Doel, L.R. van den, P.T. Nagy, L.J. van Vliet, and G.P. Neitzel; Regularized phase-tracker with iso-phase scanning strategy for analysis of dynamic interferograms of nonwetting droplets under excitation, Applied Optics (Optical Society of America), vol. 44, no. 14, 2005, 2695-2704. Contributions to international conference proceedings Blaas, J., C.P. Botha, B. Peters, F.M. Vos, and F.H. Post; Fast and Reproducible Fiber Bundle Selection in DTI Visualization, IEEE Visualization 2005 (Proc. Conf. Mineapolis, MN, USA, Oct.23-25), ACM Press, 2005, p. accepted. Dietrich, H.R.C., L.R. v.d. Doel, W. Hoyer, W. van Oel, G. Liqui Lung, Y. Garini, T. Jovin, and I.T. Young; Adaptation of Nanoarrays for the Study of a-synuclein aggregation - preliminary results, in: D.V. Nicolau, J. Enderlein, R.C. Leif, D.L. Farkas, R.Raghavachari (eds.), Imaging, Manipulation, and Analysis of Biomolecules and Cells: Fundamentals and Applications III (Proc. SPIE Photonics West: Biomedical Optics (BiOS) San Jose, California, USA, Jan.22-27), Proc. SPIE, vol. 5699, 2005, 395-402. Dietrich, H.R.C., E. van IJsseldijk, S. de Vries, I.T. Young, and Y. Garini; Advances in the Development of a Novel Method to be used in Proteomics using Gold Nanoparticles, Proc. Int. Conf. on Biopartitioning and Purification (SL, June 20-24), 2005, 17-18 Dietrich, H.R.C., I.T. Young, and Y. Garini; Gold nanoparticles: A novel application of spectral imaging in proteomics - preliminary results, in: G.H. Bearman, Anita Mahadevan-Jansen, Richard M. Levenson (eds.), Spectral Imaging: Instrumentation, Applications, and Analysis III (Proc. SPIE Photonics West: Biomedical Optics (BiOS) San Jose, California, USA, Jan.22-27), Proc SPIE, vol. 5694, 2005, 82-89. Cooperation within ASCI With : TUD-EWI-mm-cgcc, TUD-EWI-mm-ict, UL-LUMC-lkeb and with EU-EMCR-bigr. Highlight Our publication in PNAS in 2005 (see below) represented a clear illustration of the power of applying quantitative, multi-dimensional image analysis tools that we developed to the study of cell replication in normal and malignant cell lines. Having participated in the discovery of the “telomeric disc” (published in BMC Biology in 2004), we showed in this work how this disc’s development is altered by the protein c-Myc and how this is related to chromosomal rearrangement. Relevant publication: Louis, S.F., B.J. Vermolen, Y. Garini, I.T. Young, A. Guffei, Z. Lichtensztejn, F. Kuttler, T.C.Y. Chuang, S. Moshir, V. Mougey, A.Y.C. Chuang, P.D. Kerr, T. Fest, P. Boukamp, and S. Mai; c-Myc induces chromosomal rearrangements through telomere and chromosome remodeling in the interphase nucleus, Proceedings of the National Academy of Sciences USA, vol. 102, no. 27, 2005, July 5, 9613-9618.

2.3.2 Contribution of UG-CS-IS Models of the visual cortex are developed and used in computer algorithms. This research is relevant for the areas of image processing, computer vision, pattern recognition, visual perception, and computational neuroscience. Our goal is to understand how humans see and deploy principles of natural vision in artificial vision systems. Using facts from neuroscience and visual perception, we build models of visual neurons and use them in computer simulations to obtain insights and derive practicalcomputer vision algorithms.


One example is the model of a grating cell that we developed [Petkov and Kruizinga: 1997 Biological Cybernetics 76 (2) 83-96] and used in a texture operator [Kruizinga and Petkov: 1999 IEEE Transactions on Image Processing 8 (10) 1395-1407], [Grigorescu, Petkov and Kruizinga: 2002 IEEE Trans. on Image Processing 11 (10) 1160-1167]. By means of computer simulations we demonstrated that grating cells may play an important role in the disambiguation of edge information in early vision (texture vs. contours). In contrast to traditional texture operators used in image processing, the texture operator derived from a computational model of a grating cell responds only to texture and does not respond to non-textural features, such as object contours. Another example is our model of non-classical receptive filed inhibition, also called surround suppression, in groups of orientation selective neurons [Petkov and Westenberg: 2003 Biological Cybernetics 88 236-246]. This biological mechanism was simulated and applied to a large number of natural images. We demonstrated that the biological role of this inhibitory mechanism is quick pre-attentive detection of object contours and region boundaries in natural images that are rich in texture. We proposed various contour detection algorithms that deploy this mechanism and showed that they are more effective in detecting object contours and region boundaries than traditional computer vision algorithms for edge detection [Grigorescu, Petkov, Westenberg: 2003 IEEE Trans. on Image Processing 12 (7) 729-739], [Grigorescu, Petkov, Westenberg: 2004 Image and Vision Computing 22 609-622]. A new direction in our research that is inspired by psychological research on the human visual system is the development of a method for the evaluation of the robustness of shape recognition algorithms to incompleteness of contours [Ghosh and Petkov, 2005 IEEE Trans. on Pattern Analysis and Machine Intelligence 27 (11) 1793-1804]. Currently we extend our research on the use of Gabor filters to the area of motion analysis. We also develop algorithms that mimic perceptual grouping by humans. One envisaged application is texture analysis. Shape analysis In shape analysis we study geometrical approaches in which a feature point is characterized by the spatial arrangement of other feature points around it. The collection of local geometrical descriptors for the different feature points of an object is used as a shape characteristics of that object. We study the potential of this approach for object segmentation and classification in natural scenes in practical applications such as traffic sign recognition and image database retrieval [Grigorescu and Petkov: 2003 IEEE Trans. on Image Processing 12 (10) 1274-1286]. We also study the robustness of shape recognition algorithms to incomplete contour representations [Ghosh and Petkov, 2005 IEEE Trans. on Pattern Analysis and Machine Intelligence 27 (11) 1793-1804]. On the applications side, we collaborate with researchers from the University of Leon, Spain, in the area of automatic sperm classification. Connected filters and morphological operators Connected filters are a comparatively new field of research within mathematical morphology. They are edge preserving operators which have found use in noise removal, texture analysis, image compression and description, and feature extraction. Research on connected operators in our group entails algorithm development (including parallelization), development of new classes of filters, applications to 2-D and 3-D medical images, and the development of new connectivity measures for these filters for increased robustness. One line of this research links to visual cortex modelling: developing morphological analogues of texture operators based on models of certain visual cortical cells. It is hoped these morphological counterparts will be an order of magnitude faster, whilst retaining the useful properties of the cortical cell models. Finally, fast visualization based on connected attribute filters is being explored. Segmentation is a core problem in image analysis, and methods based on both simple thresholding methods and more advanced methods such as watersheds and deformable models are being explored. Application areas are many, but the focus lies on biomedical imaging, both macroscopic (MRI, CT) and microscopic. Machine learning and neural networks Neural networks and other adaptive information processing systems can be applied in classification or regression problems. Such systems can be trained from example data which facilitates the implementation of tasks which cannot be formulated as a simple set of rules in a straightforward way.


Currently, prototype based learning schemes for distance based classification are in the center of our interest. We aim at a theoretical understanding of such systems in terms of model situations. The obtained insights allow to understand and predict phenomena which are also relevant in real world learning problems. Furthermore, they enable us to systematically develop and improve practical training algorithms. As an important example we have investigated so-called Learning Vector Quantization (LVQ) systems. This heuristic approach to distance based classification is widely used in practice, but lacks through theoretical understanding. Our framework allows for a systematic comparison of training prescriptions in terms of their typical behavior. Applications of LVQ and similar methods, for instance in the area of medical image analysis, serve as a testing ground for theoretical results and newly developed algorithms. We are furthermore studying networks of so-called Integrate-and-Fire units which model the behavior of biological spiking neurons. We aim at understanding of, for instance, masking effects in the first few layers of the visual system. Systems of adaptive information processing, such as neural networks, can be applied in variety of classification or regression problems. Their ability to learn from example data makes it possible to implement tasks which are not easily formulated as a simple set of rules, but for which example data are available. External projects Dynamical Systems Approach to Texture Analysis, 2004-2008, NWO, 110 kEuro. Generalized Connected Morphological Operators for Robust Shape Extraction, 2003-2007, NWO, 150 kEuro. Books M.H.F. Wilkinson (ed.). Fifth Quinquennial Review 2001-2006. CD-ROM, Dutch Society for Pattern Recognition and Image Processing, Amsterdam, 2006. Papers in international journals M. Biehl, A. Ghosh, and B. Hammer: Learning Vector Quantization: the dynamics of Winner-Takes-All algorithms, Neurocomputing 69 (7-9), 2006, 660-670. A. Ghosh, M. Biehl, and B. Hammer: Performance analysis of LVQ algorithms: a statistical physics approach, Neural Networks 19, 2006, 817. A. Ghosh and N. Petkov: A cognitive evaluation procedure for contour based shape descriptors, Int. J. Hybrid Intelligent Systems, 2 (4), 2005, 237-252. A. Ghosh and N. Petkov: Effect of high curvature point deletion on the performance of two contour based shape recognition algorithms, Int. J. Pattern Recognition and Artificial Intelligence, 27 (11), 2006, 913-924. L. Sanchez, N. Petkov and E. Alegre: Statistical approach to boar semen evaluation using intracellular intensity distribution of head images, Cellular and Molecular Biology, 52 (6), 2006, 38-43. A.C. Jalba, M.H.F. Wilkinson, and J.B.T.M. Roerdink: Shape representation and recognition through morphological curvature scale spaces. IEEE Trans. Image Proc., 15, 2006, 331-341. Contributions to international conference proceedings G. Papari, P. Campisi, N. Petkov and A. Neri: Multiresolution contour detection using two-level surround inhibition, in Proc. Int. Conf. on Computers and Devices for Communication CODEC 2006, Calcutta, India, December 18-20, 2006, N. Petkov:untry, 2006) 6 pages.


Contour detection by surround suppression of texture, in J.M.R.S. Tavares and R.M. Natal Jorge (eds.): Computational Modelling of Objects Represented in Images - Fundamentals, Methods and Applications; Proc. Int. Symp. CompImage 2006, Coimbra, Portugal, 20-21 Oct. 2006 (Taylor and Francis Group London, 2007) pp. 29-32 (keynote speech). N. Petkov, E. Alegre, M. Biehl and L. Sanchez:LVQ acrosome integrity assesment of boar sperm cells, in J.M.R.S. Tavares and R.M. Natal Jorge (eds.): Computational Modelling of Objects Represented in Images - Fundamentals, Methods and Applications;Proc. Int. Symp. CompImage 2006, Coimbra, Portugal, 20-21 Oct. 2006 (Taylor and Francis Group London, 2007) pp. 337-342. G. Papari, P. Campisi, N. Petkov and A. Neri Contour detection by multiresolution surround inhibition, in L. Cotton (ed.): Proc. Int. Conf. on Image Processing ICIP 2006, Atlanta, GA, October 8-11, 2006, (IEEE, 2006) pp. 749 - 752 (IBM best student paper award to G. Papari). G. Papari, P. Campisi, N. Petkov and A. Neri:Contour detection by surround inhibition in the CHF domain, in E. Bagnoli and M. Casula (eds):Proc. 14th European Signal Processing Conference EUSIPCO 2006, Florence, Italy, September 4-8, 2006,CD-ROM (EURASIP, 2006) 5 pages. N. Petkov:Contour detection by surround suppression of texture, Visualization, Imaging, and Image Processing - VIIP 2006, Palma de Mallorca, Spain, 28-30 Aug. 2006(keynote speech). M. Biehl, P. Pasma, M. Pijl, L. Sanchez and N. Petkov:Classification of boar sperm head images using learning vector quantization, in M. Verleysen (Ed.), Proc. European Symposium on Artificial Neural Networks ESANN 2006, Brugge, April 26-28, 2006(d-side, Evere, Belgium, 2006) pp.545-550. G. Papari, P. Campisi, N. Petkov and A. Neri:A multiscale approach to contour detection by texture suppression, in E. R. Dougherty, J. T. Astola, K. O. Egiazarian, N. M. Nasrabadi and S. A. Rizvi (eds.): Image Processing: Algorithms and Systems, Neural Network, and Machine Learning; Proc. SPIE-IS\&T Electronic Imaging 2006, San Jose, CA, USA, January 16-18, 2006, vol. 6064, CID 60640D, 2006, pp. 60640D-1 -- 60640D-12, (SPIE, Bellingham, Washington; IS\&T, Springfield, Virginia, 2006). G.K. Ouzounis and M.H.F. Wilkinson. Filament enhancement by non-linea volumetric filtering using clustering-based connectivity. International Workshop on Intelligent Computing in Pattern Analysis/Synthesis (IWICPAS) 2006, Xi'an, China, August 26-27, Lecture Notes in Computer Science, 4153, (Springer-Verlag Berlin Heidelberg),2006, pp 317-327. E.R.Urbach and M.H.F. Wilkinson. Efficient 2-D gray-scale dilations and erosions with arbitrary flat structuring elements. Int. Conf. Image Procesing (ICIP) 2006, Atlanta, GA, October 8-11 2006, pp 1573-1576.

2.3.3 Contribution of UU-WI-ics Geometry, Imaging and Virtual Environments The advances in information and communication technology have led to an enormous amount of spatial and image data. There are many application domains where one needs to analyze, process, or visualize such data. Examples include computer-aided training and simulation, multimedia, medical imaging, molecular modeling, automated cartography, 3D web design, virtual reality, and computer games. The research program is concerned with the design, analysis, and implementation of algorithms and data structures for spatial data, and their application in the above mentioned domains. The type of research ranges from theoretical algorithms research leading to the design and analysis of fundamental geometric algorithms and data structures, to application-oriented research leading to new systems applying algorithmic results in domains like geographic information systems, automated cartography, navigation and manipulation for robots and virtual characters, and content-based image retrieval and multimedia. The program has the following main lines of research:


Computational geometry The field of computational geometry studies fundamental algorithmic techniques and data structures for geometric problems. The main goal is to design correct and provably efficient algorithms and data structures for generic algorithmic questions dealing with collections of points, lines, polygons, and more complicated geometric primitives in the plane and in higher-dimensional space. The robust implementation of such algorithms has become another key research question in this line of research. We also study geometric algorithmic questions that are derived from particular application domains, in particular from geographic information systems (dealing with terrain data), automated cartography (for example map labeling), robotics, and manufacturing. Multimedia In this line of research we study algorithmic questions related to the interpretation of images, 3D models, music, and video. The topics we work on include segmentation, feature extraction, matching of objects and organization of media in index structures. The research is concerned with the algorithmic aspects of shape analysis, perceptually relevant retrieval of shapes and music, 3D object modeling and recognition, 3D face and gesture recognition, and searching in large databases of 3D scenes, music, and images. Navigation and Manipulation Navigation (or motion) and interaction (often in the form of manipulation) are key issues in games virtual environments. The research concentrates on algorithms for planning and simulation of motion and manipulation in complex environments, such as models of industrial installations and computer games. Path planning and collision detection are crucial underlying algorithmic techniques for this. Motion is often not a goal in itself but a means of reaching a target area where a manipulation task is to be performed, such as the assembly of a spare part in a virtual factory or the removal of a tissue sample in virtual minimal-invasive surgery. For realistic simulation of these tasks we apply knowledge of techniques from robotics such as kinematics and the mechanics of manipulation, in combination with sophisticated models of physical behavior. Animation We have started a new line of research in the area of animation. Here we study new techniques for automatically creating appropriate animations for avatars and computer-controlled characters performing tasks in virtual environments. We in particular study the relation between navigation, manipulation and the corresponding animations. The goal is to achieve natural motions, that is, the virtual characters should make the same motions as real people would. To this end we have obtained a motion-capture facility in which we can record and analyse the motions by real people. In all theses lines of research we aim both for new fundamental algorithms and data structures, and for techniques that have been verified on practical problem instances and can be used in the different application domains. External projects MOVE-ME, 2002-2007, NWO, 150 KEuro. This project studies motion planning for large groups of entities in huge virtual environments. We will try to combine flocking techniques with motion planning techniques to let groups move together in realistic ways. Clamp, 2003-2007, NWO, 280 KEuro This project studies manipulation problems from an algorithmic perspective. The goal is to devise new algorithms to fixtures 2- and 3-dimensional objects and to reorient those using passive devices. BRICKS, 2004-2008, subproject Modelling, Simulation and Visualization, 320 KEuro Our subproject concentrates on interaction with virtual environments. In particular we work on navigation through virtual environments and manipulation of objects in virtual environments. ASCI groups in Delft and CWI are involved in this project as well. AIM@SHAPE, 2004-2007, EU Sixth Framework, Utrecht part: 450 Keuro.


Doctoral degrees Geraerts, R.; 8 May 2006; Sampling-based motion planning: analysis and path quality, Utrecht University, Utrecht, 185 pp., Project: MOCCAM, 2e geldstroom. Reinbacher, I; 20 June 2006; Geometric algorithms for delineating geographic regions, Utrecht University, Utrecht, 138 pp., Project: SPIRIT, 3e geldstroom. Cheong, J-S.; 6 November 2006; Immobilizing grasps for two- and three-dimensional objects, Utrecht University, Utrecht, 150 pp., 1e geldstroom. Books Oosterom, P.J.M. van & Kreveld, M.J. van (Eds.). (2006). Geo-information and Computational Geometry. Delft: NCG. Contributions to books Kreveld, M.J. van (2006). Computational Geometry: Its objectives and relation to GIS. In P.J.M. van Oosterom & M.J. van Kreveld (Eds.), Geo-information and Computational Geometry (pp. 1-8). Delft: NCG. Veltkamp, R.C., J.W.H. Tangelder (2006). Content Based 3D Shape Retrieval. In: Encyclopedia of Multimedia, Borko Furht (Ed.), ISBN: 0-387-24395-X, Springer. Veltkamp, R.C., F. Wiering, R. Typke (2006). Content Based Music Retrieval. In: Encyclopedia of Multimedia, Borko Furht (Ed.), ISBN: 0-387-24395-X, Springer. Papers in international journals Agarwal, P., M.H. Overmars, M. Sharir (2006). Computing maximally separated sets in the plane.SIAM J. Computing, 36, 815-834. Arampatzis, A., Kreveld, M.J. van, Reinbacher, I., Jones, C.B., Vaid, S., Clough, P., Joho, H. & Sanderson, M. (2006). Web-based delineation of imprecise regions. Computers, environment and urban systems, 30, 426-459. Bose, J., Cabello, S., Cheong, O., Gudmundsson, J., Kreveld, M.J. van & Speckmann, B. (2006). Area-preserving approximations of polygonal paths. J. of Discrete Algorithms, 4, 554-566. Cheong, J.S., Haverkort, H.J. & Stappen, A.F. van der (2006). On computing all immobilizing grasps of a simple polygon with few contacts. Algorithmica, 44, 117-136.

Geraerts, R., M.H. Overmars (2006). Sampling and node adding in probabilistic roadmap planners. Robotics and Autonomous Systems Journal, 54, 165-173. Goemans, O.C., Goldberg, K. and Stappen, A.F. van der (2006). Blades for feeding 3D parts on vibratory tracks. Assembly automation, 26, 221-226. Kreveld, M.J. van & Stappen, A.F. van der (2006). Approximate unions of lines and Minkowski sums. Algorithmica, 45, 91-107. Song, D., Stappen, A.F. van der & Goldberg, K. (2006). Exact algorithms for single frame selection on multi-axis satellites. IEEE Transactions on Automation Science and Engineering, 3, 16-28.


Wiering, F. (2006). Comment on Huron and Veltman: Does a Cognitive Approach to Medieval Mode Make Sense? Empirical Musicology Review, vol. 1, nr. 1, 56-60. Contriubutions to international conference procedures Ahn, H.K., Berg, M.T. de, Cheong, O., Haverkort, H.J., Stappen, A.F. van der & Toma, L. (2006). River networks and watershed maps of triangulated terrains revisited. In I. Emiris, I. Emiris, M. Karevalas, M. Karevalas, L. Palios & L. Palios (Eds.), Abstracts of the 22nd European Workshop on Computational Geometry (EWCG'06). Bosma, M., R.C. Veltkamp, F. Wiering (2006). Muugle: A Modular Music Information Retrieval Framework. In: Proceedings of the Sixth International Conference on Music Information Retrieval (ISMIR 2006). Bosma, M., R.C. Veltkamp, F. Wiering (2006). Muugle: A Music Retrieval Experimentation Framework. In: Proceedings of the 9th International Conference on Music Perception and Cognition, 1297-1303. Cabello, S., Haverkort, H., Kreveld, M.J. van & Speckmann, B. (2006).Algorithmic Aspects of Proportional Symbol Maps. In Proc. 14th Europ. Symp. on Algorithms (720-731). Berlin: Springer. Garbers, J. (2006). An Integrated MIR Programming and Testing Environment. In: Proceedings of the Sixth International Conference on Music Information Retrieval (ISMIR 2006). Geraerts, R., M.H. Overmars (2006). Creating high-quality roadmaps for motion planning in virtual environments. Proceedings IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS'06), 4355--4361. Goemans, O.C., Goldberg, K. & Stappen, A.F. van der (2006). Blades: a new class of geometric structures for feeding 3D parts on vibratory tracks. In Proceedings of the IEEE International Conference on Robotics and Automation (1730-1736). Gudmundsson, J. & Kreveld, M.J. van (2006). Computing longest duration flocks in trajectory data. In Proc. 14th ACM Symp. on the Advances in GIS(35-42). Gudmundsson, J., Kreveld, M.J. van & Narasimhan, G. (2006). Region-restricted clustering for geographic data mining. In Proc. 14th Europ. Symp. on Algorithms (399-410). Berlin: Springer. Löffler, M. & Kreveld, M.J. van (2006). Largest and Smallest Tours and Convex Hulls for Imprecise Points. In Proc. 10th Scandinavian Workshop on Algorithm Theory (375-387). Berlin: Springer. Moet, E.J., Knauer, C. & Kreveld, M.J. van (2006). Visibility Maps of Segments and Triangles in 3D. In M. Gavrilova et al. (Ed.), Proc. ICCSA'2006, 6th International Workshop on Computational Geometry and Applications (CGA'06) Vol. 3980. LNCS (20-29). Berlin Heidelberg: Springer-Verlag. Moet, E.J., Kreveld, M.J. van & Stappen, A.F. van der (2006). On Realistic Terrains. In N. Amenta & O. Cheong (Eds.), Proceedings of the 22nd ACM Symposium on Computational Geometry (pp. 177-186). Sedona, Arizona, USA. Moet, E.J., Kreveld, M.J. van & Stappen, A.F. van der (2006). On Realistic Terrains. In I. Emiris, M. Karevalas & L. Palios (Eds.), Abstracts of the 22nd European Workshop on Computational Geometry (EWCG'06) (169-172). Nieuwenhuisen, D., A.F. van der Stappen, M.H. Overmars (2006). Pushing using compliance. Proceedings of the IEEE International Conference on Robotics and Automation (ICRA '06), 2010-2016. Nieuwenhuisen, D., A.F. van der Stappen, M.H. Overmars (2006). Path planning among movable obstacles. Proceedings Workshop on Algorithmic Foundations of Robotics (WAFR 2006).


Reinbacher, I., Kreveld, M.J. van & Benkert, M. (2006). Scale dependent definitions of gradient and aspect and their computation. In A. Riedl, W. Kainz & G. Elmes (Eds.), Progress in Spatial Data Handling, 12th Int. Sympos. on Spatial Data Handling (pp. 863-879). Berlin: Springer. Speckmann, B., Kreveld, M.J. van & Florisson, S. (2006). A Linear Programming Approach to Rectangular Cartograms. In A. Riedl, W. Kainz & G. Elmes (Eds.), Progress in Spatial Data Handling, 12th Int. Sympos. on Spatial Data Handling (529-546). Berlin: Springer. Typke, R., Frans Wiering, Remco C. Veltkamp (2006). MIREX Symbolic Melodic Similarity and Query by Singing/Humming. Proceedings MIREX 2006. Typke, R., Remco C. Veltkamp, Frans Wiering (2006). A Measure for Evaluating Retrieval Techniques Based on Partially Ordered Ground Truth Lists.In: Proceedings International Conference on Multimedia & Expo (ICME) 2006. Van den Berg, J., D. Ferguson, J. Kuffner (2006).Anytime Path Planning and Replanning in Dynamic Environments. Proc. IEEE Int. Conf. on Robotics and Automation - ICRA'06, 2366-2371. Van den Berg, J., M.H. Overmars (2006).Computing shortest paths amidst growing discs in the plane. Proceedings European Workshop on Computational Geometry, 59-62. Van den Berg, J., M.H. Overmars (2006).Path planning in repetitive environments. Proceedings IEEE Int. Conf. on Methods and Models in Automation and Robotics (MMAR'06), 657-662. Van den Berg, J., M.H. Overmars (2006). Planning the shortest safe path amidst unpredictably moving obstacles. Proceedings Workshop on Algorithmic Foundations of Robotics (WAFR 2006). Van Leuken, R.H., R.C. Veltkamp, R. Typke (2006).Selecting Vantage Objects for Similarity Indexing. In: Proceedings of the 18th International Conference on Pattern Recognition (ICPR '06), 453-456. Van Kranenburg, P. (2006).Composer Attribution by Quantifying Compositional Strategies.In: Proceedings of the Sixth International Conference on Music Information Retrieval (ISMIR 2006). Veltkamp, R.C., L.J. Latecki (2006).Properties and Performances of Shape Similarity Measures. In: Batagelj et al. (eds.), Data Science and Classification, Spinger, 47-56. (Proceedings of the IFCS06 conference.) Wein, R., van den Berg, J., Halperin, D. (2006).Planning Near-Optimal Corridors amidst Obstacles.Proc. Workshop on Algorithmic Foundations of Robotics - WAFR'06. Whitmarsh, T., R.C. Veltkamp, M. Spagnuolo, S. Marini, Frank ter Haar (2006). Landmark Detection on 3D Face Scans by Facial Model Registration.In Proc. 1st Int. Workshop on Shapes and Semantics, 71-76. Experimental software Muugle – Musical Utrecht University Global Look-up Engine. This software package is to compare and search notated music. Component of this package are used at Meertens Instituut for musicological research.

2.3.4 Contribution of UG-CS-svcg 3D Morphological shape analysis In 3D Morphological shape analysis we improved Euclidean skeletonization of 3D data sets in linear time by the integer medial axis transform. We developed a GPU implementation of multiresolution representation for maximum intensity projection (MIP) volume rendering based on morphological pyramids which allows progressive refinement.


Surface and volume visualization In the project "Particle systems for image segmentation and visualisation" a new volumetric technique based on regularized-membrane potentials for aggregating the input sample points was introduced, which gives improved noise tolerability and outlier removal, without sacrificing much with respect to detail (feature) recovery. We also introduced a novel, physically-motivated deformable model for image segmentation and shape recovery, which is inspired by fluid dynamics and is based on a flooding simulation similar to the watershed paradigm. Perception-based visualisation I Perception-based visualisation we carried out a series of experiments investigating crowding in the elementary feature dimensions size, hue, and saturation. Our primary finding is that all features show clear signs of crowding. We are studying how theories and models of crowding could be able to accommodate these differences in crowding effects, and what the relevance is for information visualisation Visualisation in functional neuroimaging In our work on visualization in functional neuroimaging, a new approach to the visualisation of coherence in multichannel EEG data was developed. Existing high-density EEG coherence visualizations are generally either hypothesis-driven, or data-driven with a large amount of visual clutter. A new method has been developed for data-driven visualization of high-density EEG coherence, which strongly reduces clutter and is referred to as functional unit map (FU). FU maps can be used as a preprocessing step for hypothesis-driven conventional analysis. Gene regulatory network identification and visualization A software framework to visualize gene expression time series data in a gene regulatory network context has been developed. It has features that are currently lacking in existing tools, such as mapping of expression value and corresponding confidence value to a single visual attribute, multiple time point visualization, and visual comparison of multiple time series. A small case study, carried out by members of the Molecular Genetics group (RUG), has shown that the application provides a valuable addition to the analysis methods currently in use, and makes it easier to identify biologically relevant trends. Computational Geometry and Object Modeling In Computational Geometry and Object Modeling, we introduced envelope surfaces, a new class of tangent continuous surfaces based on finite collections of balls. Earlier work on certified meshing was extended to the context of excursion sets, where a whole family of isosurfaces can be meshed, with little overhead compared to the cost of meshing a single isosurface. Work on the approximation of the Medial Axis (MA) of 2D objects with smooth boundaries is in progress. Our approximation method yields topological guarantees, in the sense that the approximation of the MA lies within a given Hausdorff distance from the true MA. External projects Visualization of regulatory gene networks NWO-CW, 2002-2005, 239 keuro, 1 PhD and 1 Postdoc, part of the project Computational Genomics of Prokaryotes, NWO-BMI program (Biomolecular Informatics). Partners: WU, RU, RUG-Molecular Biology, RUG-Computing Science. Certified Shape Reconstruction NWO-EW, 2005-2009, 90 kEuro, 1 PhD. IMOVIS: Interactive morphological and wavelet-based volume processing and visualisation NWO-EW, 2005-2009, 500 kEuro, 2 PhD and 1 Postdoc, part of the NWO program VIEW (Visual Interactive Effective Worlds). Pathway and Network Visualisation Bioinformatics Centre (NBIC), 2005-2008, 175 kEuro (excluding matching of 50% by the University of Groningen), 1 postdoc. Part of the SPX - Project Integrative Bioinformatics of the BioRange program.


Algorithms for Complex Shapes with certified topology and numerics (ACS) EU, 2005-2008, 246 kEuro, 1 PhD and 1 postdoc. Vegter is coordinator of this project, in which seven European universities and research institutes and one industrial partner participate. ASTROVIS: Scalable analysis and visualisation of high-dimensional, astronomical data sets NWO-EW, 2006-2010, 500 kEuro, 2 PhD and 1 Postdoc, part of the NWO program STARE (STAR E-Science). Jointly with prof. van der Hulst, Kapteyn Astronomical Institute, RUG. Doctoral Degrees N. G. H. Kruithof: Envelope Surfaces. Surface Design and Meshing. Groningen, March 13, 2006. Supervisor: G.Vegter. Scientific publications over 2006 A. Pizurica, A.M. Wink, E. Vansteenkiste, W. Philips and J.B.T.M. Roerdink. A review of wavelet denoising in MRI and ultrasound brain imaging. Current Medical Imaging Reviews, 2 (2), pp. 247-260, 2006. S. Plantinga, G. Vegter, Computing contour generators of evolving implicit surfaces, ACM Transactions on Graphics, vol. 25, 2006, pp. 1243--1280. A.M. Wink and J.B.T.M. Roerdink. BOLD noise assumptions in fMRI. Intern. J. Biomedical Imaging, 2006, Article ID 12014, 2006. doi:10.1155/IJBI/2006/12014. Contributions to Books H.W. Broer, A.L. Hagen, G. Vegter, A versatile algorithm for computing invariant manifolds", in: Model Reduction and Coarse-Graining Approaches for Multiscale Phenomena, ed. by A.N. Gorban, N. Kazantzis, Y.G. Kevrekidis, H.C. Ottinger and C. Theodoropoulos. Springer series on Complexity. (Springer, Berlin--Heidelberg--New York), page 17--38, 2006. J.-D. Boissonnat, D. Cohen-Steiner, B. Mourrain, G. Rote, G. Vegter, Meshing of Surfaces, in: Effective Computational Geometry for Curves and Surfaces, ed. by J.-D. Boissonnat and M. Teillaud, Springer series on Mathematics and Visualization, (Springer, Berlin--Heidelberg--New York), Chapter 5, page 181--230, 2006. G. Rote and G. Vegter, Computational Topology: an Introduction, in: Effective Computational Geometry for Curves and Surfaces, ed. by J.-D. Boissonnat and M. Teillaud, Springer series on Mathematics and Visualization, (Springer, Belin--Heidelberg--New York), Chapter 7, 277-315, 2006. Papers in international journals D.W.J. Bosman, E.-J. Blom, P.J. Ogao, O.P. Kuipers and J.B.T.M. Roerdink, MOVE: A Multi-level Ontology-based Visualization and Exploration framework for genomic networks. In Silico Biology, 2006 (7), 0004. http://www.bioinfo.de/isb/2006/07/0004/. S. Ghosh and J.H. Rieger, Singularities of secant maps of immersed surfaces, Geometriae Dedicata, vol. 121, 2006, pp. 73--87. A. Hannus, R. van den Berg, H. Bekkering, J.B.T.M. Roerdink and F.W. Cornelissen. Visual search near threshold: some features are more equal than others. Journal of Vision, 6 (4), pp. 523-540, 2006. A.C. Jalba, M.H.F. Wilkinson and J.B.T.M. Roerdink. Shape representation and recognition through morphological curvature scale spaces. IEEE Trans. Image Processing, 15 (2), pp. 331-341, 2006.


A. Pizurica, A.M. Wink, E. Vansteenkiste, W. Philips and J.B.T.M. Roerdink. A review of wavelet denoising in MRI and ultrasound brain imaging. Current Medical Imaging Reviews, 2 (2), pp. 247-260, 2006. S. Plantinga, G. Vegter, Computing contour generators of evolving implicit surfaces, ACM Transactions on Graphics, vol. 25, 2006, pp. 1243--1280. A.M. Wink and J.B.T.M. Roerdink. BOLD noise assumptions in fMRI. Intern. J. Biomedical Imaging, 2006, Article ID 12014, 2006. doi:10.1155/IJBI/2006/12014. Contributions to international conference proceedings A.C. Jalba and J.B.T.M. Roerdink. A physically-motivated deformable model based on fluid dynamics. In: ECCV 2006, A. Leonardis, H. Bischof and A. Pinz (eds.), 2006, LNCS 3951, pp. 496-507, Proceedings, Part I. A.C. Jalba and J.B.T.M. Roerdink. Efficient Surface Reconstruction from Noisy Data using Regularized Membrane Potentials. In: Data Visualization Eurovis 2006. Eurographics/IEEE VGTC Symposium on Visualization, May 8-10, Lisbon, Portugal, B. Sousa Santos and T. Ertl and K. Joy (eds.), 2006, The Eurographics Association, pp. 83-90. N.G.H. Kruithof and G. Vegter, Envelope Surfaces, Proceedings 22nd ACM Symposium on Computational Geometry, Sedona, Arizona, USA, 2006, pp. 411-420. W.J. van der Laan and J.B.T.M. Roerdink. MIP rendering using adjunction pyramids accelerated on graphics hardware. SIREN: Scientific ICT Research Event Netherlands, 12 October 2006, Utrecht (poster). M.A. Westenberg, S.A.F.T. van Hijum, O.P. Kuipers, and J.B.T.M. Roerdink. Gene expression and network visualization. \textit Netherlands Bioinformatics Conference, Ede-Wageningen, April 24, 2006 (poster). M.A. Westenberg, S.A.F.T. van Hijum, O.P. Kuipers, and J.B.T.M. Roerdink. GENeVis: Gene expression and network visualization. \textit 3rd Int. Symposium on Networks in Bioinformatics - ISNB 206, Amsterdam, May 29-31, 2006 (poster). High-light Gene network visualization A software framework to visualize gene expression time series data in a gene regulatory network context has been developed. It has features that are currently lacking in existing tools, such as mapping of expression value and corresponding confidence value to a single visual attribute, multiple time point visualization, and visual comparison of multiple time series. Various interaction mechanisms, such as panning, zooming, regulator and target highlighting, data selection, tooltips, and subnetwork views support data analysis and exploration. A small case study, carried out by members of the Molecular Genetics group (RUG), has shown that the application provides a valuable addition to the analysis methods currently in use, and makes it easier to identify biologically relevant trends, see Fig. 1.


(a) (b) Fig. 1 Visualisation of gene regulatory network information from thepublicly available DBTBS (database of transcriptional regulation in Bacillus subtilis) database, which contains information on transcription factors and regulated target genes. A force directed layout algorithm was used to lay out the DBTBS graph. Graph complexity management is used to emphasize the essential graph structure by collapsing leaf nodes (i.e., nodes with only incoming edges) into their parent node. (a): before collapse; (b): after collapse. From: D.W.J. Bosman, E.-J. Blom, P.J. Ogao, O.P. Kuipers and J.B.T.M. Roerdink,“MOVE: A Multi-level Ontology-based Visualization and Exploration framework for genomic networks”, In Silico Biology, 2006(7), 0004.

2.3.5 Contribution of TUD-EWI-mm-cgcc Research on geometric modelling is directed towards feature modelling, which allows modelling of 3D objects with features, i.e. parametric shapes with a functional meaning. The most important research issues are feature validity maintenance, constraint solving, multiple-view feature modelling and conversion, freeform feature modelling, mesh generation, and collaborative design. Scientific visualisation Research on visualisation is focused on the development of algorithms and data structures for extracting information from large scientific and engineering data sets, and visualizing this information with computer graphics and virtual reality techniques. Main application areas are flow visualization and medical visualization. Virtual reality Interaction techniques for exploring and manipulating data in 3D virtual environments, and techniques for collaborative visualization. Important applications are in atmospheric research and molecular biophysics. External projects Semantics of families of objects, NWO-EW, 2003-2007, 1 OIO, ir. R. van der Meijden Techniques for defining and classifying objects as member of a family of parametric objects. These methods will be based on semantic feature modelling, in which shapes with well-defined semantics and constraints are used to model objects. Of particular interest are techniques to compute the ranges of parameters that correspond to members of a family.

Visualization of Cumulus Clouds in Virtual Reality, NWO-EW, 2004-2008, 1 OIO, E.J. Griffith MSc. Joint project with the Physics Department on visualiszation of Large-Eddy Simulations (LES) for atmospheric research to help resolve important research questions on cloud dynamics, cloud mixing phenomena, and precipitation. Our contribution is data handling and interactive visualization for very large time-varying data sets from cloud simulations.

Techniques for Collaborative Visualization in Virtual Environments, Bsik VL-e, 2004-2007, post-doc, dr. M. Koutek. Techniques for distributed and collaborative visualization in virtual environments, and 3D interaction; design of software architectures for multi-platform collaborative VR support. Cooperation with CWI (van Liere), VU (Bal) and TUD-PGS (Epema).

Interaction techniques for virtual environments, Bsik BRICKS-MSV2, 2004-2008, 1 OIO, ir. G. de Haan. Research on generic Virtual Reality software architecture and interaction techniques for navigation, object manipulation, and exploration, to make 3D interaction more comfortable, fast, and effective. Interaction metaphors such as pseudo-haptic visual force feedback are investigated.Cooperation with CWI (van Liere) and UU (van der Stappen).


Surface and volume geometry processing for lesion detection and segmentation in virtual colonoscopy, Philips Medical Systems, 2004-2008, 1 AIO, Lingxiao Zhao MSc.Research on the determination and use of geometric properties of the inner surface of the human colon for automatic pre-detection of colonic polyps. Invertigation of higher-order geometric properties (curvature) for claculation of distinctive features for polyp detection. Cooperation with TUD-TNW-QI (van Vliet).

Integration of design and analysis, NWO-EW, 2005-2009, 1 OIO, drs. M. Sypkens Smit. The goal of this project is to develop efficient meshing methods for finite element analysis. For 3D meshes, a method will be developed to only locally update the mesh where the design model has actually been modified. For cases in which it is unfeasible to analyse a full 3D model, methods will be developed to generate meshes for idealised (simplified) models, and to automatically propagate changes in such a model to the design model.

Multifield Medical Visualization, NWO-VIEW, 2005-2010, 2 OIO, ir. J. Blaas and S. Busking, MSc. An increasing number of medical acquisition and processing techniques are generating large amounts of multi-field data, such as data from different imaging modalities. Many of these datasets are also time-varying, for example in heart motion studies. In this project, we want to transfer knowledge and techniques from closely related fields such as vector and tensor field visualization in scientific visualization, to medical visualization applications. Joint project with TUE-BME (ter Haar-Romeny, Vilanova). Scientific publications over 2006 Papers in international journals

Bronsvoort, WF, Bidarra, AR, & Nyirenda, PJ . Developments in feature modelling. Computer-aided design and applications, (ISSN 1686-4360), 3(5), 655-664. Haan, AB de, Willekens, B, Klooster, J, Los, AA, Zwieten, JE van, Spekreijse, H, Botha, CP, IJskes, SG, & Simonsz, H.J. The prenatal development of the human orbit. Strabismus, (ISSN 0927-3972), 14(1), 51-56. Lourenco, D, Oliveira, P, Noort, A, & Bidarra, AR. Constraint solving for direct manipulation of features. Ai edam-artificial intelligence for engineering design analysis and man, (ISSN 0890-0604), 20, 369-382. Meiden, HA van der, & Bronsvoort, WF. A constructive approach to calculate parameter ranges for systems of geometric constraints. Computer-aided design, (ISSN 0010-4485), 38(4), 275-283. Nyirenda, PJ, Mulbagal, M, & Bronsvoort, WF. Definition of freeform surface feature classes. Computer-aided design and applications, (ISSN 1686-4360), 3(5), 665-674. Olabarriaga, SD, Snel, JG, Botha, CP, & Belleman, RG. Integrated support for medical image analysis methods: from development to clinical application. IEEE Transactions on information technology in biomedicine, (ISSN 1089-7771). Pasman, W, & Lindenberg, J. Human-agent service matching using natural language queries: system test and training. Personal and ubiquitous computing, (ISSN 1617-4909), 10(6), 393-399. Vrolijk, B, & Post, FH. Interactive out-of-core isosurface visualisation in time-varying data sets. Computers & graphics-UK, (ISSN 0097-8493), 30(2), 265-276. Contributions to international conference proceedings

Haan, G de, Griffith, EJ , Koutek, M , & Post, FH . Hybrid interfaces in VE's: Intent and Interaction. In D Fellner & S Spencer (Eds.), Virtual Environments 2006 (pp. 109-118). Aire-la-Ville Switzerland: Eurographics Association (ISBN 3-905673-33-9).


Krekel, PR , Botha, CP, Valstar, E, Bruin, PW de, Rozing, PM, & Post, FH. Interactive simulation and comparative visualisation of the bone-determined range of motion of the human shoulder. In T Schulze, G Horton, B Preim, & S Schlechtweg (Eds.), Simulation und Visualisierung 2006 (pp. 275-288). Erlangen: SCS Publishing House e.v. (ISBN 3-936150-46). Loke, RE, Jansen, FW, & Buf, JMH du. A background-priority discrete boundary triangulation. In J Jorge & V Skala (Eds.), Proceedings WSCG'2006 (pp. 53-60). Plzen: University of West Behemia (ISBN 80-86943-05-4). Meiden, HA van der, & Bronsvoort, WF. Solving topological constraints for declarative families of objects. In S.N. Spencer (Ed.), Proceedings SPM2006 (pp. 63-72). New York USA: The Association for Computing Machinery, Inc. (ISBN 1-59593-358-1). Schaaf, A van, Koutek, M, Germans, DM, & Bal, HE. ICWall: a calibrated stereo tiled display from commodity components. In SN Spencer (Ed.), VRCIA2006 (pp. 289-296). New York: The Association for Computing Machinery (ISBN 1-59593-324-7). Schaaf, A van, Koutek, M, & Bal, H. Parallel particle rendering: a performance compasison between chromium and aura. In A Heirich & L.P. dos Santos (Eds.), Parallel graphics and visualization 2006 (pp. 137-144). Aire-la-Ville, Switzerland: Eurographics Association (ISBN 3-905673). Warmerdam, J, Knepfle, M, Bidarra, AR, Bekebrede, G, & Mayer, I. SimPort: a multiplayer management game framework. In Q Mehdi, F Mtenzi, B Duggan, & H McAtamney (Eds.), Proceedings of CGames'2006 (pp. 219-224). Wolverhampton, UK: University of Wolverhampton School of Computing (ISBN 0-9549016-2-2). Zlatanova, S, Pu, S, & Bronsvoort, WF. Freeform curves and surfaces in DBMS: a step forward in spatial data integration. In S Nayak, SK Pathan, & JK Garg (Eds.), Proceedings of the ISPRS (pp. 407-412). Ahmedabad, India: ISPRS Archives (ISBN 1682-1777).

2.3.6 Contribution of TUE-BT-bmia The group Biomedical Image Analysis, headed by prof. B.M. ter Haar Romeny, started in 2001 in the department of Biomedical Engineering (BME) at the TUE. The group is part of the BME Master track Biomedical Imaging and Modeling (BioMIM), and collaborates closely with Philips Medical Systems and the Maastricht University Hospital. The aim of the group is to develop high quality algorithms and applications in (bio-) medical image analysis and visualization, based on fundamental computer vision research, and to offer an interesting teaching environment for BME students. The applications areas are computer-aided diagnosis applications, diffusion tensor imaging, microscopic life-sciences image analysis, and image-guided (neuro-) surgery. Multi-scale computer vision Analysis and exploitation of the deep (i.e. over scale) structure of images. This is biologically inspired, fundamental research into singularities and toppoints in images, to come to a hierarchical representation. In 2005 an NWO VICI grant was rewarded to dr. Luc Florack. In a EU-funded project (‘Deep Structure Singularities in Computer Vision’, DSSCV) we explore multiple research aspects of the toppoints, such as stability, feasibility for image retrieval, image editing and image reconstruction. See fig. 3. Together with Oce BV we develop a toppoint-based document analysis and -retrieval system for the IOP project “Intelligent Scanners”. Perceptual grouping and context operators. This biologically inspired research focuses on the exploitation of the multi-orientation structure of images. Applications focus on the detection of dim elongated structures (contours, catheters, bloodvessels, electrodes) in images. Diffusion tensor imaging analysis and 3D visualization: 3D visualization techniques for MR diffusion tensor imaging (DTI) data have been investigated in an interactive setting, in close collaboration with the TUE Dept. of Computing Science. Clinical studies focus on neonatal brain fiber development, muscle fiber orientations in the heart and skeletal muscle, and the extraction of grouped bundles in DTI. We program the visualization on modern GPU graphics cards.


Methods were developed to automatically extract transfer functions from the data itself, i.e. from LH histograms (fig. 2). Illustrative rendering techniques have been developed for medical 3D volume datasets, in the style of drawing in classical anatomy books.

Fig. 2. Iso-surface rendering of a vessel lumen in the lung. The concave shape of the ‘elliptical hole’ indicates the presence of a pulmonary embolism, and is automatically detected. Data courtesy Philips Medical Systems. From [Bouma et al. 2006].

Clinical image analysis & applications: This research theme is in close collaboration with Philips Medical Systems, Best. Automated detection of pulmonary emboli in spiral 3D CT acquisitions of the lung. A computer-aided diagnosis system is developed, based on second order shape and intensity features. A detailed analysis was carried out on the dislocation of highly curved surfaces such as of small blood vessels. See fig. 2. Molecular Imaging of Ischemic Heart Disease Segmentation of short-axis cardiac MR using active contours. We collaborate with the Medical Imaging and Computer Aided Diagnosis group of the Catholic University Nijmegen on mammographic image analysis (MSc student exchanges). In 2004 a major (22.4 M€) BSIK grant “Molecular Imaging of Ischemic Heart Disease” was rewarded to Univ. of Maastricht, TU/e, Philips and Organon. The BMIA group participates in the visualization of multi-spectal and tensor-based image data (see fig. 4), classification of atherosclerotic plaque from multispectral MRI data, and the quantitative analysis of heart motion (multi-scale optic flow). Neurosurgical navigation In 2005 the Dept. of Neurosurgery at the Maastricht University Hospital acquired the first open low-field (0.15 Tesla) intra-operative MRI in the Netherlands. We collaborate with projects focused on the nonlinear warping of pre-operative MRI and CT data onto the intra-operative data, the integrated and interactive 3D visualization of DTI, fMRI and atlas data, and the optimization of image quality. These projects are carried out in collaboration with Medtronic Inc.

Fig. 3. So-called toppoints of an image, defined as singularity points in the multi-scale structure, can efficiently be exploited for image-based content retrieval, i.e. subscene retrieval from a complex scene. [Platel, Balmashnova et al., 2006]


The development of a Mathematica software library for rapid symbolic and numerical prototyping, ‘MathVisionTools’. A general Import format to deal with a wide spectrum of image formats, such as DICOM 3.0, FDF MRI data, 3D US data etc.; A symbolic and numerical generalized and speed-optimized toolbox for doing high order differential geometry advanced image analysis functions on multi-dimensional images: MathVisionTools (see www.mathvisiontools.net);

Fig. 4. Visualization of heart fibers crossing a single transversal plane in the heart, extracted by fiber tracking from Diffusion Tensor Imaging MRI data. Data courtesy TU/e-MRL, 2006. From [Peeters et al. 2006].

External projects The Problem of Scale in Biomedical Image Analysis. VICI grant of 1.25 M€ rewarded to dr. Luc Florack, dossier number NWO: 016.053.605, 01-01-2005 till 01-01-2010. Hemodyn Period: September 2002 – September 2006 Funding: Philips Medical Systems (1 PhD student) The prediction of the chance of rupture for the abdominal aorta is calculated by cardiovascular flow calculations. The data are specific for each patient, and derived from high resolution CT scans of the patient. Advanced methods in volume visualization Period: September 2002 – September 2006 Funding: Philips Medical Systems (2 PhD students) New algorithms are designed in the PMS Easy-Vision environment, particularly focusing on automated transfer function settings from the data, and the detection of pulmonary emboli in high resolution multi-slice CT scans. Robust multi-scale operators for optic flow Period: June 1 2006 – June 1 2010 Funding: STW project number: STW/ENN6760 (2 PhD students) This project focuses on a new, biologically-inspired, paradigm for motion detection, based on the motion of the scale-space toppoints (see VICI project Florack) of images. It promises to lead to a more robust method than conventional methods. The main application area is cardiac dynamics Deep Structure and Singularities in Computer Vision Period: June 1 2002 – June 1 2006 Funding: EC project (2 PhD students) This project is a collaboration between the University of Copenhagen (project leader), University of Manchester and the Eindhoven University of Technology. Goal is to explore the mathematical underpinning and applications for the use of multi-scale singularity points (‘toppoints’) in the deep structure of images.


Intelligent Scanners Period: June 1 2003 – June 1 2007 Funding: Senter/Novem IOP Beeldverwerking This project is a collaboration with Océ BV, in order to come to an automated document analysis by a hierarchical multi-scale description of images by means of ‘toppoints’. Molecular Imaging for the Ischemic Heart Period: November 1 2004 – November 1 2008 Funding: BSIK Molecular Imaging of the Ischemic Heart (2 PhD students and 1 postdoc) The project focuses on the realistic and interactive visualization of fiber tracts in the heart measured by diffusion tensor imaging, on the exploitation of multi-orientation contextual filters for the enhancement and quantitative analysis of line-like structures, and op new optic flow methods for quantitative motion analysis of the heart. Diffusion Tensor Imaging - Feature Extractuin Period: February 1 2006 –February 1 2010 Funding: Portuguese Science Foundation (1 PhD student) Diffusion Tensor Imaging - Segmentation Period: January 1 2006 – January 1 2010 Funding: NWO-VENI (dr. A. Vilanova) (1 PhD student) Diffusion Tensor Imaging - Visualization Period: January 1 2006 – January 1 2010 Funding: NWO-VIEW (1 PhD student) This project is a collaboration with TU Delft, and focuses on DTI visualization and bundle extraction. Dynamic contrast enhanced CAD for breast MRI Period: December 1 2005 – December 1 2009 Funding: Center for Molecular Medicine (1 PhD student & 1 postdoc) The project is a collaboration with Philips Medical Systems and focuses on radiation-free dynamic MRI CAD methods for screening breast cancer. Biomechanical models are developed for two-compartment models of the vessel structure in the tumor, parameter optimization and the statistical analysis and validation from the bulk data. Doctoral degrees May 10, 2006: H.C.van Assen, 3D Active Shape Modeling for Cardiac MR and CT Image Segmentation, PhD. Thesis, 2006, Leiden University. Papers in international journals H.. van Assen, M.G. Danilouchkine, A.F. Frangi, S. Ordás, J.J.M. Westenberg, J.H.C. Reiber, B.P.F. Lelieveldt, SPASM: a 3D-ASM for Segmentation of Sparse and Arbitrarily Oriented Cardiac MRI Data, Med. Image Analysis, 10(2), 286-303, (2006). E.J.L. Brunenberg, O. Pujol, B.M. ter Haar Romeny, P. Radeva, Automatic IVUS segmentation of atherosclerotic plaque with Stop & Go snake, Lecture notes in computer science, 4191(-), 9-16, (2006). E.M. Franken, M.A. van Almsick, P.M.J. Rongen, L.M.J. Florack, B.M. ter Haar Romeny, An Efficient Method for Tensor Voting using Steerable Filters, Lecture notes in computer science, 3954, 228-240, (2006). E.M. Franken, P.M.J. Rongen, M.A. van Almsick, B.M. ter Haar Romeny, Detection of Electrophysiology Catheters in Noisy Fluoroscopy Images, Lecture notes in computer science, 4191(2), 25-32, (2006).


C..A. Guerrero Sanchez, T. Erdmenger, P. Sereda, D. Wouters, U.S. Schubert, Water-soluble ionic liquids as novel stabilizers in suspension polymerizations: engineering polymer beads, Chem. Eur. J., 12(35), 9036-9045, (2006). J.M.A. Hofman, W.J. Branderhorst, H.M.M. ten Eikelder, V.C. Cappendijk, S. Heeneman, ME. Kooi, P.A.J. Hilbers, B.M. ter Haar Romeny, Quantification of atherosclerotic plaque components using in-vivo MRI and supervised classifiers, Magn Reson Med, 55, 790-799, (2006). B.J. Janssen, L.M.J. Florack, R. Duits, B.M. ter Haar Romeny, Optic Flow from Multi-scale Dynamic Anchor Point Attributes, Lecture notes in computer science, 4141, 767-779, (2006). B. Platel, E. Balmachnova, L.M.J. Florack, B.M. ter Haar Romeny, Top-Points as Interest Points for Image Matching, Lecture notes in computer science, 3951, 418-429, (2006). C. van Pul, J. Buijs, A. Vilanova, F.G. Roos, P.F.F. Wijn, Fiber tracking in newborns with perinatal hypoxic-ischemia at birth and at 3 months, Journal Radiology, 240(1), 203-214, (2006). S. de Putter, F. Laffargue, M. Breeuwer, F.N. van de Vosse, F.A. Gerritsen, Computational mesh generation for vascular structures, Int J CARS, 1, 1-11, (2006). P. Sereda, A. Vilanova, I.W.O. Serlie, F.A. Gerritsen, Visualization of Boundaries in Volumetric Datasets Using LH Histograms, IEEE TVCG, 12(2), 208-218, (2006). Contributions to international conference proceedings H.C. van Assen, A.F. Frangi, M.G. Danilouchkine, S. Ordás, J.J.M. Westenberg, J.H.C. Reiber, B.P.F. Lelieveldt, Efficient Reconstruction of Cardiac LV Surfaces Using a 3D Sparse ASM, in Biomedical Imaging: Macro to Nano, 2006. 3rd IEEE International Symposium on; Arlington, United States, 117-120, (2006). H.E. Bennink, J.M. Korbeeck, B.J. Janssen, B.M. ter Haar Romeny, Warping a Neuro-Anatomy Atlas on 3D MRI Data with Radial Basis Functions, in Proc. Intern. Conf. on Biomedical Engineering (Biomed) 2006; Editors: F. Ibrahim, Kuala Lumpur, Malaysia, 214-218, (2006). E.J.L. Brunenberg, O. Pujol, B.M. ter Haar Romeny, P. Radeva, Automatic IVUS segmentation of atherosclerotic plaque with Stop & Go snake, in Proc. ASCI Conf. 2006; Editors: B. Lelieveldt, B. Haverkort, C. de Laat, Lommel, Belgium, (2006). F. Daniels, B.M. ter Haar Romeny, M.P. Rubbens, H.C. van Assen, Quantification of Collagen Orientation in 3D Engineered Tissue, in Proc. Intern. Conf. on Biomedical Engineering BioMed 2006; Editors: F. Ibrahim, Kuala Lumpur, Malaysia, 344-348, (2006). L.M.J. Florack, B.J. Janssen, F.M.W. Kanters, R. Duits, Towards a New Paradigm for Motion Extraction, in Lecture Notes in Computer Science, vol. 4141; Editors: Campilho and Kamel, Povoa de Varzim, Portugal, 743-754, (2006). E.M. Franken, J. Sporring, S. Kreiborg, Visualization of Tooth Eruption in CT-Scans, in Cranofacial Image Analysis for Biology, Clinical Genetics, Diagnostics and Treatment; Editors: T. Darvan, N. Hermann, P. Larsen, and S. Kreiborg, Copenhagen, Denmark, 33-39, (2006). M. Gangeh, R.P.W. Duin, C. Eswaran, B.M. ter Haar Romeny, Scale Space Texture Classification Using Combined Classifiers With Application To Ultrasound Tissue Characterization, in IFMBE Proc. Vol. 15, Intern. Conf.on Biomedical Engineering BioMed 2006; Editors: F. Ibrahim, Kuala Lumpur, Malaysia, 303-306, (2006). F.M.W. Kanters, L.M.J. Florack, B. Platel, B.M. ter Haar Romeny, Multi-Scale Differential Error: A Novel Image Quality Assessment Tool, in Proc. 8-th International Conference on Signal and Image Processing; Honolulu, Hawaii, United States, pp 188--194, (2006).


M. Mlejnek, P. Ermes, A. Vilanova, R. van der Rijt, H. van de Bosch, F.A. Gerritsen, E. Gröller, Application-Oriented Extensions of Profile Flags, in EuroVis - Eurographics/IEEE-VGTC Symposium on Visualization; Lissabon, Portugal, -, (2006). T.H.J.M. Peeters, A. Vilanova, G.J. Strijkers, R.B.M. ter Haar Romeny, Visualization of the Fibrous Structure of the Heart, in VMV 2006; Aachen, Germany, (2006). T.H.J.M. Peeters, A. Vilanova, R.B.M. ter Haar Romeny, Visualization of DTI fibers using hair-rendering techniques, in ASCI 2006; Editors: B.P.F. Lelieveldt, B. Haverkort, C.T.A.M. de Laat, J.W.J. Heijnsdijk, Lommel, Belgium, 66-73, (2006). D. Ruijters, D. Babic, B.M. ter Haar Romeny, P. Suetens, Silhouette fusion of vascular and anatomical volume data, in IEEE International Symposium on Biomedical Imaging: From Nano to Macro; Editors: J. Kovacevic, Arlington, VA, United States, 40-44, (2006). D. Ruijters, M. Vermeer, A. Vilanova, P. Suetens, Robustness of mutual inforin SPIE -Medical Imaging; Editors: to appear, San Diego, United States, (2006). P. Sereda, A. Vilanova, F.A. Gerritsen, Automating Transfer Function Design for Volume Rendering Using Hierarchical Clustering of Material Boundaries, in Eurographics/IEEE VGTC Symposium on Visualization (EuroVis); Editors: B. Sousa Santos, T. Ertl, K. Joy, Lisboa, Portugal, 243–250, (2006). P. Sereda, F.A. Gerritsen, A. Vilanova, Mirrored LH Histograms for the Visualization of Material Boundaries, in VMV; Editors: L. Kobbelt, T. Kuhlen, T.Aach, R. Westermann, Aachen, Germany, 237-244, (2006). P. Sereda, A. Vilanova, F.A. Gerritsen, Automating Transfer Function Design for Volume Rendering Using Hierarchical Clustering of Material Boundaries, in Proc. 12th ASCI conf.; Editors: B. P. F. Lelieveld, B. Haverkort, C. T. A. M. de Laat, J. W. J. Heinsdijk, Lommel, Belgium, 187-194, (2006). W. Timm, S. Boecker, T. Twellmann, T.W. Nattkemper, Peak Intensity Prediction for PMF Mass Spectra Using Support Vector Regression, in Proc. of the International FLINS conference on Applied Artificial Intelligence; Genova, Italy, (2006). T. Twellmann, O. Lange, T.W. Nattkemper, A. Meyer-Baese, Visualizations of Suspicious Lesions in Breast MRI Based on Intelligent Neural Systems, in Proc. of SPIE Vol. 5818; Editors: Harold H. Szu, Orlando, Florida, United States, 38-49, (2006). A. Vilanova, D. Ruijters, Optimizing GPU Volume Rendering, in WSCG - Winter School of Computer Graphics; Pilzen, Czech Republic, (2006). Books and book chapters Twellmann, Data-driven Analysis of Dynamic Contrast-Enhanced Magnetic Resonance Imaging Data in Breast Cancer Diagnosis, BieSOn, Bielefeld University, ISBN (2006). Highlights Some highlights in 2006 were: 13 November 2006: The Biomedical Image Analysis group was invited to give a demonstration of their work at the 'Imagine' exhibit at the European Congress of Radiology. This congress was held on March 9-13, 2007, in Vienna, where our group was represented by approximately 25 people. 12 November 2006: The lectures of the ASCI Front-End Vision course (a8), given by prof. Bart ter Haar Romeny on November 6-7, 13-15 and 20-24, 2006, are available as streaming video on http://videocollege.tue.nl/, select course 8D010.


28 July 2006: Ir. Frans Kanters has received one of the STW Valorisation Grants, which is a grant to help young companies to get started, for his project on an automatic crack detection system for natural stone slabs. See for more details: www.stw.nl/Nieuws/20060713.htm. 27 June 2006: The STW grant application, titled “Robust detection of line structures and texture on anomalies using multi-scale context filters” has been awarded a 3-year postdoc position. 13 June 2006: The Biomedical Image Analysis Group has been selected as the organizer of the 9th International Mathematica Symposium: 20-24 June 2008 in Maastricht. See: http://www.internationalmathematicasymposium.org/.

2.3.7 Contribution of EUR-RMI-bigr Cardiovascular image analysis Vascular imaging has gone beyond the traditional depiction of vascular luminal morphology. State-of-the art imaging techniques have the potential to provide detailed information on the vessel wall, such as plaque composition, elastic wall properties, and even biochemical processes that take place in the plaque. In addition, dynamic and perfusion imaging can provide functional information, e.g. for determining the perfusion or motion of the heart. Owing to the growing complexity and sheer size of cardiovascular data, in combination with the large increase in the number of studies in clinical practice and biomedical research, there is a strong and increasing interest in robust, automated processing tools to aid in the analysis of these data. This research line aims to develop and evaluate novel image processing techniques for visualization, quantification and integrated analysis of multimodal anatomical and functional cardiovascular imaging data. Cellular and molecular image analysis Advances in imaging technology have revolutionized medicine and biology and have opened the door to studying structure and function of cells and even single molecules. Accurate and reproducible methods for automated processing and analysis of the image data acquired for such studies are still lacking however. Since manual image analysis is very time-consuming and thus costly, as well as potentially inaccurate and poorly reproducible, many biologically and clinically relevant questions are either left unaddressed, or answered with great uncertainty. The goal of this theme group is to develop automated image processing and analysis technology for accurate and reproducible quantification of dynamical processes at the cellular and molecular levels. Neuro image analysis The mountains of MR brain data generated in large-scale neurological studies and population-based epidemiological studies have prompted the development of automated analysis techniques. Neuro research in the Biomedical Imaging Group Rotterdam (BIGR) aims at developing and evaluating state-of-the-art classification tools for accurate and reproducible quantification of brain changes in healthy elderly subjects. Research is carried out within the scope of the Rotterdam Scan Study (see also Highlights and Implementation sections). This longitudinal population-based study, initiated by the department of Epidemiology & Biostatistics, investigates effects of aging. In August 2005, the study was extended by installing a dedicated MR scanner at a remote site (the Rotterdam district of Ommoord) and by including more subjects. About 6000 elderly people will be scanned every two or three years (about 1700 MR images per subject per examination). Recent work has focused on the automated segmentation of gray matter, white matter and cerebrospinal fluid , as well as on the detection and analysis of white matter lesions. Notably the combination of statistical voxel classification with non-rigid brain registration gave very promising results. The non-rigid registration techniques are also used for brain extraction and the automated detection of brain structures such as the ventricles, hippocampus, entorhinal cortex, basal ganglia, and corpus callosum. 2005 also saw the start of another major BIGR research topic, i.e. the processing of functional brain image data and of images obtained with Diffusion Tensor Imaging. Image analysis in oncology In cancer imaging, advances in MR hardware and software have resulted in the ability to visualize biochemical processes superimposed on anatomic images. For example, the oxygenation status, the acidity, the Brownian motion of water molecules and the blood perfusion can be imaged. Currently, there is a strong interest in determining the value of these functional characteristics as non-invasive biomarkers to evaluate treatment response and outcome. In order to sensitively and reproducibly measure, changes in, these functional parameters, robust and automated


processing tools are needed. This research line aims to develop and evaluate image processing techniques for visualization, quantification and integrated analysis of anatomical and functional cancer imaging data. Image guided interventions Image guided interventions are generally performed using interventional imaging modalities such as fluoroscopy and ultrasound. These modalities allow for instantaneous visualization of the interventional instruments in relation to the patient anatomy, but are limited in their visualization capabilities: X-ray imaging yields 2D projection images and ultrasound probes allow sweeping a 2D slice through the patient. Diagnostic imaging modalities such as MRI and CT, on the other hand, allow for accurate 3D imaging of the anatomy, but such imaging modalities are generally not suitable for or available in interventional settings. The primary goal of our research is to improve visual guidance and feedback for the interventionalist by introducing (the pre-operative diagnostic) 3D images into the interventional suite. Whereas such navigation approaches are becoming state-of-the art in applications such as brain surgery and orthopedics, application of this type of technology in interventions in soft tissue anatomy has been hampered by issues such as tissue motion and deformation. Our focus is to address these challenges related to image guidance and navigation in soft tissue applications. External projects Quantification of tumor vessel morphology: a tool to monitor treatment, 2005-2009, NWO-MOZAIEK 2005. Project number 017.002.019, EUR 180.000. This project aims to develop and validate methods for microvascular morphology quantification from Contrast Enhanced MR Angiography in order to monitor cancer treatment in vivo. The resulting microvascular morphology features will be evaluated for their suitability to monitor treatment effects in an animal tumor model and in a clinical study. MMOSAA: Multiscale modeling of object shape and appearance for analyzing 3D image content, 2005-2009, NWO Open Competition 2004. Project number 612.065.412. EUR 440.058. This project aims to develop methods for the simultaneous segmentation of multiple structures. Model-Driven Spatiotemporal Tracking for Quantitative Analysis of Subcellular Dynamics, 2005-2009, NWO-VIDI 2004. Project number EW 639.022.401. EUR 600.000. To develop and evaluate automated image analysis techniques for the accurate and reproducible quantification of the motion of subcellular structures from time-lapse fluorescence microscopy image data. Advance, 2005-2009, SenterNovem. Project number: ISO044070. EUR 987.000. To develop techniques towards a computer-aided diagnosis system of vascular disease from CT angiography data. Collaboration with other ASCI-groups: LKEB, LUMC. Aneurist. Integrated biomedical informatics for the management of cerebral aneurysms, 2006-2009. European Commission 6th Framework programme. Project number 027703. EUR 419.074. This research project is part of a large European grant to improve the management of cerebral aneurysms by vertical integration of data from the genetic up to the population level. Our taks in the project is to analyze aneurysm morphodynamics from CTA data. 3D Multimodel vascular image analysis for improved diagnosis and therapy, 2006-2011, NWO-VICI 2005. Project number RPG.7191, EUR 1.250.000. This research aims to develop and evaluate novel image processing techniques for visualization, quantification and integrated analysis of multimodal anatomical and functional cardiovascular imaging data. Neuroweb. Integration and sharing of information and knowledge in neurology and neurosciences. 2006-2008. European Commission 6th Framework programme. Project number 518513, EUR 71.677. The project aims at designing and developing a software tool, neuroweb, to allow:

A. to integrate clinical and genetic databases of the participating centres, different from structure, language, territorial area and pathologies of interest, into a single virtual database;


B. to be able to query the databanks present on the web containing human polymorphism profiles in normal and pathological populations.

Doctoral degrees Manniesing, R.; October 19 2006; Image analysis in CT angiography. UMC Utrecht, Utrecht 2006, xiii+104 pp., ISBN 90-393-4315-2, Funding: UMC Utrecht Promotors: Niessen, prof.dr. W.J. en Viergever, prof.dr.ir. M.A.

Papers in international journals Alderliesten T, Konings MK, Niessen WJ. Robustness and complexity of a minimally invasive vascular intervention simulation system. Med Phys. 2006;33:4758-69. De Weert TT, Ouhlous M, Meijering E, Zondervan PE, Hendriks JM, van Sambeek MR, Dippel DW, van der Lugt A. In vivo characterization and quantification of atherosclerotic carotid plaque components with multidetector computed tomography and histopathological correlation. Arteriosclerosis Thrombosis, and Vascular Biology 2006;26:2366-72. Gratama van Andel HA, Meijering E, van der Lugt A, Vrooman HA, de Monye C, Stokking R. Evaluation of an improved technique for automated center lumen line definition in cardiovascular image data. European Radiology 2006;16:391-8. Koning OHJ, Oudegeest OR, Valstar ER, Garling EH, van der Linden E, Hinnen J.W., Hamming J.F., Vossepoel AM, van Bockel JH. Roentgen Stereophotogrammetric Analysis: An Accurate Tool to Assess Stent-Graft Migration. Journal of Endovascular Therapy 2006:13;468-475. Manniesing R, Velthuis BK, van Leeuwen MS, van der Schaaf IC, van Laar PJ, Niessen WJ. Level set based cerebral vasculature segmentation and diameter quantification in CT angiography. Mededical Image Analysis 2006;10:200-14. Manniesing R, Viergever MA, Niessen WJ. Vessel enhancing diffusion. A scale space representation of vessel structures. Medical Image Analysis 2006;10:815-25. Meijering E, Smal I, Danuser G. Tracking in Molecular Bioimaging. IEEE Signal Processing Magazine 2006;23:46-53. Rollano-Hijarrubia E, Stokking R, Niessen WJ. Accuracy comparison of a 16 and 64 multidetector-row computed tomography scanner to image small high-density structures. Investigative Radiology 2006;41:781-92. Rollano-Hijarrubia E, Stokking R, van der Meer F, Niessen WJ. Imaging of small high-density structures in CT A phantom study. Academic Radiology 2006;13:893-908. Rousseau F, Hellier P, Letteboer MM, Niessen WJ, Barillot C. Quantitative evaluation of three calibration methods for 3-D freehand ultrasound. IEEE Transactions on Medical Imaging 2006;25:1492-501. Van de Kraats EB, van Walsum T, Kendrick L, Noordhoek NJ, Niessen WJ. Accuracy evaluation of direct navigation with an isocentric 3D rotational X-ray system. Medical Image Analysis 2006;10:113-24. Van de Kraats EB, van Walsum T, Verlaan JJ, Voormolen MH, Mali WP, Niessen WJ. Three-dimensional rotational X-ray navigation for needle guidance in percutaneous vertebroplasty: an accuracy study. Spine 2006; 31:1359-64. Van Velsen EF, Niessen WJ, de Weert TT, de Monye C, van der Lugt A, Meijering E, Stokking R. Evaluation of an improved technique for lumen path definition and lumen segmentation of atherosclerotic vessels in CT angiography. European Radiology 2006. Epub November 1. Van Walsum T, van de Kraats EB, Voormolen MH, Verlaan JJ, Mali WP, Niessen WJ. Navigation with three-dimensional rotational radiographic data for transpedicular percutaneous needle introduction: feasibility and comparison with fluoroscopic guidance. Journal of Vascular Interventional Radiology 2006;17:1511-8.


Vermeer KA, Reus NJ, Vos F, Vossepoel AM, Lemij HG. Automated detection of wedge shaped defects in polarimetric images of the retinal nerve fiber layer. Eye 2006; 20: 776-784. Vermeer KA, Vos F, Lo B, Zhou Q, Lemij HG, Vossepoel AM, van Vliet LJ. Modeling of Scanning Laser Polarimetry Images of the Human Retina for Progression Detection of Glaucoma, IEEE Transactions on Medical Imaging, 2006;25:517-528. Contributions to international conference proceedings Alic L, Veenland JF, van Vliet LJ, van Dijke CF, Eggermont AMM, Niessen WJ. Quantification of Heterogeneity in Dynamic Contrast Enhanced MRI Data for Tumor Treatment Assessment. In: Proceedings of the Third IEEE International Symposium on Biomedical Imaging - ISBI 2006. IEEE, Piscataway, NJ, 2006:944-947. Manniesing R, Niessen WJ. Shape Constrained vessel centerline extraction by integrating surface evolution and topology analysis. In: Proceedings of the Third IEEE International Symposium on Biomedical Imaging:- ISBI 2006. IEEE, Piscataway, NJ, 2006:165-168. Vrooman HA, Cocosco CA, Stokking R, Ikram MA, Vernooij MW, Breteler MM, Niessen WJ. kNN-based multi-spectral MRI brain tissue classification: manual training versus automated atlas-based training. In: Reinhardt JM, Pluim JP, eds. Proc. SPIE Vol. 6144, 61443L, Medical Imaging 2006: Image Processing, 2006. Smal I, Niessen WJ, Meijering E. Particle filtering for multiple object tracking in molecular cell biology. In: Proceedings of the 2006 Nonlinear Statistical Signal Processing Workshop (Cambridge, UK September 13-15, 2006). Piscataway, NJ, 2006:44.1-44.4. Smal I, Niessen WJ, Meijering E.. Bayesian tracking for fluorescence microscopic imaging. In: Proceedings of the Third IEEE International Symposium on Biomedical Imaging – ISBI 2006. IEEE, Piscataway, NJ, 2006:550-3. Smal I, Niessen WJ, Meijering E.. Bayesian tracking for fluorescence microscopic imaging. In: Proceedings of the Third IEEE International Symposium on Biomedical Imaging – ISBI 2006. IEEE, Piscataway, NJ, 2006:550-3.

Products of scientific research as result of cooperation within ASCI In cardiovascular image analysis, we cowork with LKEB in the Advance project. In neuro image analysis, we cowork with Delft, Image Science & Technology, on the analysis of diffusion tensor MRI data.

2.3.8 Contribution of UvA-FdNWI-ias Perception for autonomous systems We develop methodologies for accurate motion estimation and interpretation from image sequences. Mobile vision platforms have their applications in traffic and driving in unstructured terrain. Applications of static platforms are in public safety and intelligent care homes for the elderly. We cooperate with TNO Defense, Security and Safety on a number of projects, which are related to autonomous systems, such as the RoboJeep autonomous robot vehicle. For safe operation in off-road terrain, autonomous robot vehicles should avoid obstacle hazards such as steep inclines and trees. Stereo vision based approaches to obstacle detection are prone to errors due to inaccuracies in the distance measurements and often perform poorly in situations with unfavorable illumination conditions (e.g. night-time). To improve detection during night-time, we have developed a new stereo disparity estimation method that able to extract dense 3-D terrain points from dimly illuminated images. In order to improve the detection quality, a method was developed that clusters reconstructed terrain points obtained from stereo vision into obstacles. Because it considers the distance uncertainty, which is inherent to stereo ranging, our method detects significantly more obstacle surface pixels at larger distances and suffers less from false detections.


Also in cooperation with TNO D&V methodologies for public safety are developed. Many surveillance algorithms consist of different parts, such as object detection, segmentation, tracking, and recognition. These algorithms are applied onto radar and vision. Literature focuses on algorithms for one of these individual tasks. Integration of and communication between these tasks is often rather ad-hoc. In this project we worked on a statistical framework for visual tracking applications. It allows easy adaptation of the tracking application by substitution of one of the algorithms for part of the problem, without altering the remainder of the application. Furthermore, the framework uses minimum cost classification and feedback for updating the models using knowledge available elsewhere in the application. This research resulted in a PD thesis in 2006. Visual perception of humans and their activities The ability to recognize humans and their activities by vision is key for a machine to interact intelligently and effortlessly with a human-inhabited environment. There are numerous important applications ranging from public safety, elderly care and intelligent vehicles to human motion capture/analysis. Two projects are ongoing in the area of Looking-at-People and public safety. In the MultimediaN – Professional Dashboard project (07/05-06/09) the focus is on 3-D human pose estimation from multi-view images. We are looking into approaches that use a template hierarchy to match hundred of thousands of possible poses in near real-time. In particular, we are investigating appropriate matching metrics for hierarchical detection and subsequent verification stage, and ways to incorporate prior scene knowledge. The CASSANDRA (Context-Aware SenSing for AggressioN Detection and Risk Assessment, 09/05-08/09) project, funded by NWO and in collaboration with the University of Groningen, aims to detect aggression in dynamic environments. Because events, associated with the build-up or enactment of aggression, are difficult to detect by a single sensor modality (e.g. shouting versus hitting someone) we investigate the fusion of video- and audio- sensing. For this purpose, we currently pursue Dynamic Bayes Networks. Learning, probabilistic, and neural computing This year we focussed on algorithms and systems for intelligent environments, which observe the persons moving in it, and have a ‘context awareness’. The multi-camera surveillance application which was patented in 2005 was further developed in the context of a STW ‘Valorization grant’ and tested extensively in a real world setting, in collaboration with a company (Eagle Vision) licensing the patent. In the ‘Cogniron’ project, a 9 MEuro European FP-6 Integrated Project in which a ‘cognitive robot servant’ is developed, we tested novel methods for spatial cognition and space learning. Integration was accomplished with other European partners in the project and several international workshops were organized. A robotic interface (the ‘iCat’) was also used in a project on the acceptance of robots in our daily life, a collaboration between Philips and the Hogeschool van Amsterdam. Dynamic Bayesian Networks for data fusion between audio and video were studied in our multimodal interaction project, funded by MultimediaN. Apart from collaboration with ILSE media we have started a collaboration with NIST on the processing of ‘meeting videos’. Dynamic Bayesian networks are also used in the project CARE (Context Awareness in Residences for Elderly), in which we infer ‘Activities of Daily Life’ (ADL’s) from a system of distributed simple sensors in an elderly home. This project is a collaboration between the Centre for Intelligent Observation Systems (CIOS), the Hogeschool van Amsterdam and an elderly care institute. In collaboration with these partners we also started the project ‘Audiogids’, in which a mobile system is developed for navigation assistance for people with early dementia, using auditory feedback and spatial knowledge. . Considerable effort was spent on finishing a tutorial book for the computer science audience (including a website with downloadable software and interactive figures), to help disseminate the techniques to the field. In an NWO project “Discovery of Articulated Structures in Image Sequences”, we have started to develop geometric algebra data processing techniques. Decision making in single- and multi-agent systems Decision making in teams of agents is a complex task: in order to function optimally with regards to some objective function, the agents must have a good level of situation awareness and adequately perform coordination and planning, the complexity of which increases with the number of agents, their correlations and the planning horizon. In real life, this task is particularly difficult. Still, for most multi-agent systems (MAS) the simplifying assumption is made that the world can be observed and that effects of actions are deterministic. In the real world, however, the environment in which a team of agents is situated is usually stochastic and only partially observable, for example because of sensor noise or perceptual aliasing. In this case the decision making task becomes much harder. In this setting each agent will have to form a belief about the state of the world as well as over the beliefs of other agents, in order to predict their actions. As part of the Interactive Collaborative Information Systems (ICIS) project, we investigate formal models for representing decision problems faced by teams of agents in an uncertain, stochastic world. In particular, we focus on


the decentralized partially observable Markov decision process (Dec-POMDP), a framework for fully cooperative planning by a team of agents in such world. We have furthered our research in the field of agent decision making under uncertainty by extending Perseus, our efficient point-based POMDP solver, to the multi-agent domain. In particular, we are using the ideas developed in Perseus (piecewise linearity and convexity of the value function, point-based approximation, etc.) for tackling the much harder (NEXP-complete) problem of decentralized planning under motion and sensor uncertainty for teams of collaborating agents (known as DEC-POMDP model). The current state of the art in DEC-POMDPs involves very rough approximations (Qmdp-based), which can only address relatively small problems. We have provided the necessary theory as well as an algorithm for computing tighter bounds to the exact solution of the NEXP-complete problem, thus obtaining more accurate results than state-of-the-art methods. We are currently studying extensions to the case of large numbers of agents, where graph-based and message passings techniques are the key to scalability. This was a successful year in the 4-Legged Soccer League. The 4-Legged League defines a standard hardware platform, which allows benchmark the algorithms of different research institutes. To facilitate the demonstration of scientific progress, the soccer-games are accompanied by Technical Challenges. This year we demonstrated our localization algorithm in the Open Challenge. This algorithm allows a robot to orient itself on a field without the use of any landmarks (which is the standard approach in the RoboCup). Instead, a probabilistic model of the frequency of color-transitions in the surroundings is learned. The result is that the robot can orient itself not only an artificial RoboCup soccer-field, but in principle in every wide space. This was for instance demonstrated outside, on a real soccer-field (see next figure). The Dutch Aibo Team received the 3rd price in the Technical Challenges with this achievement. Another successful contribution to the RoboCup was the participation in the Virtual Rescue League. Here our effort was concentrated on simultaneous localization and mapping (SLAM). Many successful SLAM methods impose a-priori detail constraints on the resulting maps, for example by using an occupancy grid. Such data representations are also not straightforward to use in a multi-agent setting. Instead, a successful SLAM method was developed, inspired by the Manifold data structure by Howard et al. This method maintains a graph with sensor observations stored in vertices and pose differences including uncertainty information stored in edges. Through its graph structure, updates are local and can be efficiently communicated to peers. Since sensor observations are stored in the graph, map detail is a question of rendering the graph to an occupancy grid of arbitrary resolution. This method has been tested both in virtual and real world. Also with real measurements accurate occupancy grid maps can be generated (see next figure). With this method the UvA won the Mapping Award in the Rescue Virtual Robots competition in 2006. Distributed perception and sensor fusion Intelligent process control and decision making in complex systems require adequate situation assessment, which in turn requires processing of large amounts of heterogeneous information originating from different, spatially dispersed sources, such as, sensory systems, human observers, databases, etc. However, such "sensor fusion" is not trivial, since it requires adequate mapping between very heterogeneous concepts, we are confronted with noisy information sources and, due to large amounts of information, significant processing resources might be required (i.e. computational bottlenecks). Another characteristic of the domains we are focusing on is that constellations of information sources can change frequently and, prior to the operation, we never know which information sources will be available. In addition, such fusion systems often provide results which have a critical impact on the decision making process and, consequently, further course of events. Therefore, high quality of fusion results and prevention of misleading results is indispensable. In order to be able to deal with the mentioned challenges, we have introduced Distributed Perception Networks (DPN), multi-agent systems which support fusion based on distributed Bayesian Networks (BN). This work was carried out within two projects at the Decis research institute, namely Combined Systems and Interactive Collaborative Information Systems. In this context, our research is focused primarily on the following problems: (i) Task driven self-configuration of DPN agents at runtime, which allows adaptation to dynamic information source constellations and supports reuse of partial fusion results. (ii) Efficient and robust information fusion with distributed BNs, which provide adequate mapping between observable events and beliefs in hypotheses about hidden events. (iii) Resource allocation in distributed fusion systems based on information theoretic criteria. (iv) approaches to


improved fusion accuracy, such as fail-safe design of fusion systems as well as localization of faulty model components and information sources. We find applications of our research in the field of crisis management. Decentralized information sources can fuse information and extract the relevant events in the environment. During 2006, we also emphasized on the automated gathering of information from humans, rather than only from sensors, to be used in the DPN reasoning system. External projects.

Geometric Algebra: a New Foundation for Geometric Programming, 2000-2006, 637kf This projects makes geometric algebra into a practical tool for geometric programming applications within computer science, notably robotics, vision and computer graphics. New techniques for specification of geometric programs are being developed, and a freely available fast implementation constructed. This is an NWO-sponsored project.

Distributed User Modeling for Personalized Exploring Recommender Systems (DUMPERS), 2002-2006, NWO(ToKen2000), 225k€ In the project DUMPERS we will develop methods for adding adaptive navigation support for users of web sites. Goal of this project is to extend existing methods with extra components like exploration of the effect of recommendation by using techniques from the field of reinforcement learning. We will use locally stored user models to provide the information about the individual users needed for personal recommendation without violating the privacy of the users. COMBINED systems, 2002-2006, 800k€ In this project we study innovative methods for disaster management. In particular aspects concerning distributed observation systems are investigated. An important property of distributed observation systems is that they autonomously extract information from the monitored area. This information is shared with other services in the disaster management platform. The project is conducted in cooperation with TUDelft, Thales en TNO within the DECIS laboratory. A structure for maintaining a shared world model in a dynamic environment between differentiated embedded systems and their interaction with human supervisors, 2001-2006, 490 kf We study embedded autonomous systems in distributed environments, for applications in public safety; monitoring and control of traffic and environmental conditions; assistance and clean-up work in disaster areas. Collaboration between systems requires a collective world model, and we develop methods for its consistency maintenance, in time-critical situations. We use robot soccer (RoboCup) as a case study. This project is a collaboration with the VU and is sponsored by Progress. COGNIRON: Cognitive Robot Companion, 2004-2008, 600k€ In this 6th framework project within IST we develop a cognitive robot which interacts with humans and has conceptual representations. Our group works on human activity analysis and on cognitive representations of objects and space. Interactive Collaborative Information Systems, 2004-2009, 736 k€ The ICIS project is an attempt to bridge the gap between traditional information capture, transmission and transaction processing to full-blown intelligent information systems techniques. This is a road starting with traditional information management techniques such as better structuring and managing of information (including data mining and data warehousing) and the development of self-generating software through to artificial intelligence and agent based systems and complete integration of technologies with human and social systems. We are working on flexible situation assessment.

The CASSANDRA (Context-Aware SenSing for AggressioN Detection and Risk Assessment, 2005-09 Funded by NWO and in collaboration with the University of Groningen, this project aims to detect aggression in dynamic environments. Because events, associated with the build-up or enactment of aggression, are difficult to detect by a single sensor modality (e.g. shouting versus hitting someone) we investigate the fusion of video- and audio- sensing. For this purpose, we currently pursue Dynamic Bayes Networks.


Discovery of Articulated Structures in Image Sequences, 2006-2011, 353 k€ This NWO project uses geometric algebra to determine the motion of articulated structures (such as moving humans) in image. It aims at developing the data processing capabilities of geometric algebra.

Audiogids: adaptieve audiotours voor ondersteuning van beginnend dementerenden, 2006-2008, 65 kEuro In this project funded by SenterNovem IOP-MMI we develop a mobile GPS-based device for giving auditory information for wayfinding to elderly with a beginning dementia. We study the man-machine interface, in particular the conceptual representation of space.

Doctoral degrees J.R. Kok, J.R; November 2006; Cooperation and learning in cooperative multiagent systems. University of Amsterdam, Amsterdam 2006, 154 pp, ISBN-13: 978-90-9021073-5, 1st money. M.T.J Spaan; Oktober 2006; Approximate planning under uncertainty in partially observable environments. University of Amsterdam, Amsterdam 2006, 128 pp, ISBN-13, 978-90-74840-79-8, External project STW. P.J. Withagen; February 2006; Object detection and segmentation for visual surveillance. University of Amsterdam Amsterdam 2006, 168 pp, ISBN-13: 978-90-9020282-2, External project: TNO. W.P. Zajdel; January 2006; Bayesian visual surveillance: from object detection to distributed cameras. University of Amsterdam, Amsterdam 2006, 130 pp, ISBN 909020252-8, External project COGNIRON Scientific publications over 2006. Papers in international journals T. Cemgil, A.T., Kappen, H.J., & Barber, D.; A Generative Model for Music Transcription. IEEE Transactions on Speech and Audio Processing, 14(2), 679-694. T. Djekic, Z. Zivkovic and J.J. van der Ham; Determination of the stability constants for cobalt, nickel and palladium. Applied Catalysis A: General, 308, 144-152, 2006. M. Heerink, B.J.A. Kröse, B.J. Wielinga and V. Evers; Studying the acceptance of a robotic agent by elderly users. International Journal of Assistive Robotics and Mechatronics, 7(3), 25-35, 2006. J.R. Kok and N. Vlassis; Collaborative Multiagent Reinforcement Learning by Payoff Propagation. Journal of Machine Learning Research, 7, 1789-1828, 2006. S. Munder and D.M. Gavrila; An Experimental Study on Pedestrian Classification. IEEE Transactions on Pattern Analysis and Machine Intelligence, 28(11), 1863-1868, 2006. J.M. Porta Pleite, N. Vlassis, M.T.J. Spaan and P. Poupart; Point-Based Value Iteration for Continuous POMDPs. Journal of Machine Learning Research, 7, 2329-2367, 2006. J.J. Verbeek, J.R.J. Nunnink and N. Vlassis; Accelerated EM-based clustering of large data sets. Data Mining and Knowledge Discovery, 13(3), 291-307, 2006. J.J. Verbeek and N. Vlassis; Gaussian fields for semi-supervised regression and correspondence learning. Pattern Recognition, 39(10), 1864-1875, 2006. J.J. Verbeek. Learning non-linear image manifolds by combining local linear models. IEEE Transactions on Pattern Analysis and Machine Intelligence, 28(8), 1236-1250, 2006.


W.P. Zajdel, A.T. Cemgil and B.J.A. Kröse; Dynamic Bayesian Networks for Visual Surveillance with Distributed Cameras. Smart Sensing and Context, 4272, 240-243, 2006. Z. Zivkovic and F. van der Heijden; Efficient adaptive density estimation per image pixel for the task of background subtraction. Pattern recognition letters, 27, 773-780, 2006. Contributions to international conference proceedings O. Booij, Z. Zivkovic and B.J.A. Kröse; From sensors to rooms. In Proc. IROS Workshop From Sensors to Human Spatial Concepts. IEEE. 53-58, 2006. O. Booij, Z. Zivkovic and B.J.A. Kröse; Sparse appearance based modeling for robot localization. In Proc. IEEE/RSJ Int. Conf. on Intelligent Robots and Systems. IEEE. 1510-1515, 2006. D.H.F. Fontijne; Gaigen 2: a Geometric Algebra Implementation Generator. In ACM GPCE 2006 Proceedings. 141-151, 2006. A. Frans, F.A. Oliehoek, E.D. de Jong and N. Vlassis; The parallel Nash memory for asymmetric games. In Proc. of the Genetic and Evolutionary Computation Conference. 337-344, 2006. M. Heerink, B.J.A. Kröse, B.J. Wielinga and V. Evers; Human-Robot User Studies in Eldercare: Lessons Learned. In Proceedings ICOST. Belfast. 31-38, 2006. M. Heerink, B.J.A. Kröse, B.J. Wielinga and V. Evers. The Influence of a Robot’s Social Abilities on Acceptance by Elderly Users. In In Proceedings RO-MAN. Hertfordshire. 521-526, 2006. D. Hildenbrand, D.H.F. Fontijne, Y. Wang and L. Dorst; Competitive runtime performance for inverse kinematics algorithms using conformal geometric algebra. In W. Dieter (Ed.), European Association for Computer Graphics (Eurographics) Aire-la_ville: Fellner. 5-9, 2006. J.A. van Kleef and L.J.H.M. Kester; Adaptive State Multiple-Hypothesis Tracking. In Proceedings of Informatik . Dresden. 339-343, 2006. J.A. van Kleef, J. Bergmans and F.C.A. Groen; Multiple-hypothesis trilateration and tracking with distributed radars. In International Conference on Information Fusion 2006. Florence, Italy. 1-7, 2006. K.L. Koay, Z. Zivkovic, B.J.A. Kröse, K. Dautenhahn, M.L. Walters, N.R. Otero and A. Alissandrakis; Methodological issues of annotating vision sensor data using subjects' own judgement of comfort in a robot human following experiment. In Proceedings of IEEE RO-MAN. Hertfordshire UK. 66-73, 2006. A. Noulas and B.J.A. Kröse; E.M. detection of Common Origin of Multi-Modal Cues. In Proceedings of the 8th international conference on Multimodal interfaces. Banff, Alberta, Canada. 201-208, 2006. A. Noulas and B.J.A. Kröse; Unsupervised Visual Object Class Recognition. In Advanced School of Computing & Imaging Conference. 356-361, 2006. J.R.J. Nunnink and G. Pavlin; Towards robust state estimation with bayesian networks: A new perspective on belief propagation. In Proc. 9th Conf. on Intelligent Autonomous Systems. Tokyo, Japan. 722-731, 2006. F.A. Oliehoek and A.Visser; A hierarchical model for decentralized fighting of large scale urban fires. In AAMAS'06 Workshop on Hierarchical Autonomous Agents and Multi-Agent Systems.14-21, 2006.


G. Pavlin, P. de Oude, M.G. Maris and T. Hood; Distributed perception networks: An architecture for information fusion systems based on causal probabilistic models. In Proc. Int. Conf. on Multisensor Fusion and Integration for Intelligent Systems. Heidelberg, Germany. 303-310, 2006 (no page numbers, electronic proceedings). G. Pavlin and J.R.J. Nunnink; Inference meta models: Towards robust information fusion with bayesian networks. In Proc. Fusion 2006. 2006. P. Poupart, N. Vlassis, J. Hoey and K. Regan; An analytic solution to discrete Bayesian reinforcement learning. In Proc. Int. Conf. on Machine Learning. Pittsburgh, USA. 697-704, 2006. D.A. van Soest, M. de Greef, J. Sturm and A. Visser; Autonomous color learning in an artificial environment. In Proc. 18th Dutch-Belgian Artificial Intelligence Conference, BNAIC'06. Namur, Belgium. 299-306, 2006. M.T.J. Spaan, G.J. Gordon and N. Vlassis; Decentralized planning under uncertainty for teams of communicating agents. In Proc. Int. Joint Conference on Autonomous Agents and Multiagent Systems. Hakodate, Japan. 249-256, 2006. T. Spexard, S. Li, B. Wrede, J. Fritsch, G. Sagerer, O. Booij, Z. Zivkovic, B. Terwijn and B.J.A. Kröse; BIRON, where are you? - Enabling a robot to learn new places in a real home environment by integrating spoken dialog and visual localization. In Proc. IEEE/RSJ Int. Conf. on Intelligent Robots and Systems. IEEE. 934-940, 2006. A. Visser, J. Sturm and F.C.A.; Groen. Robot companion localization at home and in the office. In Proc. 18th Dutch-Belgian Artificial Intelligence Conference, BNAIC'06. 347-354, 2006. Z. Zivkovic, B. Bakker, B.J.A. Kröse; Hierarchical map building and planning based on graph partitioning. In Proc. IEEE Int. Conf. on Robotics and Automation. 803-809, 2006. Z. Zivkovic and J.J. Verbeek; Transformation invariant component analysis for binary images. In Proceedings IEEE Conference on Computer Vision and Pattern Recognition. 254-259, 2006. Experimental software The Dutch AIBO Team – Bremen 2006 Source Code, C++, 2006. http://www.dutchaiboteam.nl/robocup/robocup2006/DT2006-diff-DT2005.zip. Source code for the Dutch robot dog team; quarter-finalist in the world championships. The UvA Rescue Team – Bremen 2006 Source Code, C++, 2006. http://www.science.uva.nl/~arnoud/research/roboresc/UvAvirtualResq2006.tg. Source code for the Rescue team of the UvA; 3rd at the world championships.

Datasets Multimodal dataset (laser range data, odometry, sonar and omnidirectional vision) of a robot moving in two realistic environments http://www2.science.uva.nl/sites/cogniron/ Products of scientific research as results of cooperation within ASCI. RoboCup/Progress: with TUD -TN en VU, also UU (Siks) and TUD- ET (DISC).


2.3.9 Contribution of LUMC-lkeb The main goal of the Division of Image Processing is the research, implementation and validation of image processing approaches, which allow the objective and reproducible assessment of objects in medical images. LKEB activities belong to one of the seven main research fields of the LUMC under the headings “Vascular Medicine”, “Neuro-science” and “Molecular Imaging”. Part of the research involves computer vision research and algorithm development, whereas clinical applications also play an important role. Applications focus on Neuro-imaging, Pulmonology, Orthopaedics, Cardiology and molecular and cellular imaging. In 2006, important research directions were: Statistical shape modeling Statistical shape models are widely used to integrate a-priori knowledge about shape and image appearance into segmentation algorithms. Research at LKEB is directed towards dimensional extension of statistical shape models. A 3D Active Shape Model has been developed, along with 3D and multi-view Active Appearance Models; these models have been applied to segmentation of cardiac MR, CT, echo and X-angiographic data. Apart from segmentation, we are developing statistical shape models for computer-aided diagnosis to detect cardiac shape- and motion abnormalities in MR images for patients with a cardiac infarction, and for quantifying local shape changes caused by brain diseases. We recently investigated shape differences of the brain ventricles in the aging population and Alzheimer disease. Because of the challenging shape of the ventricles, we developed a new method based on growing neural networks to fully automatically model complexly shaped objects.

Multi-agent image processing The major objective of this research is to develop a general and adaptive learning multi-agent image interpretation system, which automatically learns how to interpret (medical) images from examples and user-interactions. The system should be flexible and easy to adapt to changes in patient context, expert preferences, or imaging devices, by the use of both low-level training / optimization and high-level rules. The system will be applied to very difficult segmentation problems in images that cannot be solved with only traditional and/or model-based segmentation methods alone. To this end we are investigating how probabilistic models, reinforcement learning techniques, evolutionary algorithms, high-level (explicit) knowledge and low-level image processing may be integrated into our current multi-agent image interpretation system. The system will first be used for the interpretation of IntraVascular UltraSound (IVUS) and Computed Tomography Angiography (CTA) images. Molecular image integration In this project, we are investigating novel algorithms to combine complementary information in molecular, structural and functional imaging. We address novel image processing challenges brought on by new molecular imaging modalities such as bioluminenscence imaging and fluorescence imaging. We focus on whole body registration between optical and structural data in follow-up studies, detection of changes and abnormalities and on integrating information sources over the scale range from molecule to organism. Development of a virtual mobile exploration robot In this project, we address the problem of virtual central navigation in 3D tubular structures. A virtual mobile robot, equipped with a neuro-fuzzy controller, is trained to navigate inside image datasets of tubular structures, keeping a central position; virtual range sensors are used to sense the surrounding walls and to provide input to the controller. Aim of this research is: first the identification of smooth and continuous central paths which are useful in several medical applications: virtual endoscopy, virtual colonoscopy, virtual angioscopy, virtual bronchoscopy, etc. We fully validated the algorithm on synthetic datasets, and performed successful experiments on a colon dataset. Second to train the virtual robot to detect novelties (pathologies) along the path, just like a security agent would do. It will highlight any significant deviation from the normal environment (training using images acquired from healthy subjects), Clinical Image Analysis Applications Much of the research at LKEB is driven by questions from clinical partners. To this end, we are developing algorithms and software for:

Detection and quantification of pulmonary emphysema in CT Images Early detection of micro motion of prosthetic implants in bi-plane X-ray images Automatic analysis of coronary vessels in CT and intravascular ultrasound images Automatic analysis of coronary and left-ventricular angiograms


Automatic analysis of cardiac function in MR and CT patient studies Automatic analysis of changes in brain structure with ageing and disease Automatic analysis of vascular MR data Automatic white matter lesion detection in MR images of the brain

External projects

2004-2008 CYTTRON, BSIK, with UL-WI-I and TUD-TNW-tn-qi: Development of a comprehensive, integrated infrastructure for bio-imaging and modeling cells down to atomic detail.

2004-2008 SAVAGE, NWO-E, with UL-WI-I: Development of self-learning image processing agents in a multi-agent framework for medical image interpretation. 2004-2008 LAISA, STW: Application of multi-agent image processing platform in IVUS and CTA image data. 2004-2007 Automated evaluation of vascular MR image data, STW. 2003-2007 Autonomous virtual robots for medical image exploration, SNN. 2003-2007 Software Development for the Detection and Assessment of Small Airways Disease in COPD with Multi Slice Computed Tomography, Netherlands Asthma Foundation. 2002-2007 Data fusion of different components of MR patient studies, STW. 2002-2007 Computer-aided diagnosis for cardiac MR data, NWO VIDI. Doctoral degrees Van Assen, H.C.;10-5-2006; 3D Active Shape Modeling for Cardiac MR and CT Image Segmentation. Leiden University; Leiden 2006;147 paginas; ISBN 90-8559-163-5, internally funded. Bosch, J.G.; 12-6-2006; Automated contour detection in echocardiographic images. Leiden University; Leiden 2006; 227 paginas; ISBN 90-810712-1-1, funded from external projects. Scientific publications Books or Contributions to books Proc. Of the 12th annual conference of the Advanced School for Computing and Imaging, eds B.P.F. Lelieveldt (Chair), B. Haverkort, C.T.A.M. de Laat, J.W.J. Heijnsdijk, ISBN 90-810847-1-7, 2006.

B.P.F. Lelieveldt, A.F. Frangi, S.C. Mitchell, H.C. van Assen, S. Ordas, J.H.C. Reiber, M. Sonka, “3D active shape and appearance models in cardiac image analysis”, in “Handbook of Mathematical Models of Computer Vision” (eds N. Paragios, O. Faugeras), pp 471-484, Springer Verlag, ISBN-10: 0-387-26371-3, 2006. Papers in international journals Üzümcü M, Geest RJ van der, Swingen C, Reiber JHC, Lelieveldt BPF. Time continuous tracking and segmentation of cardiovascular magnetic resonance images using multidimensional dynamic programming. Invest Radiol 2006; 41: 52-62.


Assen HC van, Danilouchkine MG, Frangi AF, Orda’s S, Westenberg JJM, Reiber JHC, Lelieveldt BPF. SPASM: a 3-D-ASM for segmentation of sparse and arbitrarily oriented cardiac MRI data. Medical Image Analysis 2006; 10: 286-303. Adame IM, Koning PJH de, Lelieveldt BPF, Wasserman BA, Reiber JHC, Geest R van der. An integrated automated analysis method for quantifying vessel stenosis and plaque burden from carotid MRI images: combined postprocessing of MRA and vessel wall MR. Stroke 2006; 37: 2162-4. I.M. Adame, R.J. van der Geest, D. A. Bluemke, J.A.C. Lima, J.H.C. Reiber, B.P.F.Lelieveldt, “Automatic Vessel Wall Contour Detection and Quantification of Wall Thickness in in-vivo MR Images of the Human Aorta”, Journal of Magnetic Resonance Imaging, vol. 24(3), pp 595-602, 2006. Oost E, Koning G, Sonka M, Oemrawsingh PV, Reiber JHC, Lelieveldt BPF. Automated contour detection in X-ray left ventricular angiograms using multi-view Active Appearance Models and Dynamic Programming. IEEE Trans Medical Imaging 2006; 25: 1158-71. Westenberg JJM, Lamb HJ, Geest RJ van der, Bleeker GB, Holman ER, Schalij MJ, Roos A de, Wall EE van der, Reiber JHC, Bax JJ.Assessment of left ventricular dyssynchrony in patients with conduction delay and idiopathic dilated cardiomyopathy. J Am Coll Cardiol 2006; 47: 2042-8. Hoeven BL van der, Liem S-S, Oemrawsingh PV, Dijkstra J, Jukema JW, Putter H, Atsma DE, Wall EE van der, Bax JJ, Reiber JHC, Schalij MJ. Role of calcified spots detected by intravascular ultrasound in patients with ST-segment elevation acute myocardial infarction. Am J Cardiol 2006; 98: 309-13. Tuinenburg JC, Koning G, Seppenwoolde Y, Reiber JHC. Is there an effect of flat-panel-based imaging systems on quantitative coronary and vascular angiography? Cath Cardiovasc interventions 2006; 68: 561-6. Chun C, Hendriks EA, Duin RPW, Reiber JHC, Hiemstra PS, de Weger LA, Stoel BC, Feasibility study on automated recognition of allergenic pollen: grass, birch and mugwort, Aerobiologia 22:275–284, 2006. Nieber N, Putter H, Stolk J, Reiber JHC, Stoel BC: Prediction of Pulmonary Function in COPD on the Basis of CT Measurements of Bronchial Wall Thickness, Letter to the Editor, Radiology, 238:374-375, 2006. Parr DG, Stoel BC, Stolk J, Stockley RA: Validation of computed tomographic lung densitometry for monitoring emphysema in alpha1-antitrypsin deficiency. Thorax 61: 485-90, 2006. Stavngaard T, Shaker SB, Bach KS, Stoel BC, Dirksen A. Quantitative assessment of regional emphysema distribution in patients with chronic obstructive pulmonary disease (COPD). Acta Radiol. 47(9):914-21, 2006. Kaptein BL, Valstar ER, Spoor CW, Stoel BC, Rozing PM. Model-based RSA of a femoral hip stem using surface and geometrical shape models. Clin Orthop Relat Res. 448:92-7, 2006. van de Sande MA, Stoel BC, Rozing PM. Subacromial space measurement: a reliable method indicating fatty infiltration in patients with rheumatoid arthritis. Clin Orthop Relat Res. 451:73-9, 2006. Do an H, Kroft LJ, Bax JJ, Schuijf JD, van der Geest RJ, Doornbos J, de Roos A. MDCT assessment of right ventricular systolic function. Am J Roentgenol. 2006;186(6 Suppl 2): S366-370. Schoonman GG, Bakker D, Schmitz N, van der Geest RJ, van der Grond J, Ferrari MD, van Buchem MA. Magnetic resonance angiography of the human middle meningeal artery: implications for migraine. J Magn Reson Imaging. 2006;24(4):918-921. Aortic root dysfunctioning and its effect on left ventricular function in Ross procedure patients assessed with magnetic resonance imaging. Grotenhuis HB, Westenberg JJM, Doornbos J, Kroft LJM, Schoof PH, Hazekamp MG, Vliegen HW, Ottenkamp J, de Roos A. Am Heart J. 2006 Nov;152(5):975.e1-8.


Tofts, P. S., Steens, S. C., Cercignani, M., Admiraal-Behloul, F., Hofman, P. A., van Osch, M. J., Teeuwisse, W. M., Tozer, D. J., van Waesberghe, J. H., Yeung, R., Barker, G. J., and van Buchem, M. A., "Sources of variation in multi-centre brain MTR histogram studies: body-coil transmission eliminates inter-centre differences," MAGMA., vol. 19, no. 4, pp. 209-222, Sept.2006. Emmer, B. J., Steens, S. C., Steup-Beekman, G. M., van der, Grond. J., Admiraal-Behloul, F., Olofsen, H., Bosma, G. P., Ouwendijk, W. J., Huizinga, T. W., and van Buchem, M. A., "Detection of change in CNS involvement in neuropsychiatric SLE: a magnetization transfer study," J.Magn Reson.Imaging, vol. 24, no. 4, pp. 812-816, Oct.2006. Ferrarini, L., Palm, W. M., Olofsen, H., van Buchem, M. A., Reiber, J. H., and Admiraal-Behloul, F., "Shape differences of the brain ventricles in Alzheimer's disease," Neuroimage., vol. 32, no. 3, pp. 1060-1069, Sept.2006. Van den Heuvel, D. M., ten Dam, V. H., de Craen, A. J., Admiraal-Behloul, F., van Es, A. C., Palm, W. M., Spilt, A., Bollen, E. L., Blauw, G. J., Launer, L., Westendorp, R. G., and van Buchem, M. A., "Measuring longitudinal white matter changes: comparison of a visual rating scale with a volumetric measurement," AJNR Am.J.Neuroradiol., vol. 27, no. 4, pp. 875-878, Apr.2006. Van den Heuvel, D. M., ten Dam, V. H., de Craen, A. J., Admiraal-Behloul, F., Olofsen, H., Bollen, E. L., Jolles, J., Murray, H. M., Blauw, G. J., Westendorp, R. G., and van Buchem, M. A., "Increase in periventricular white matter hyperintensities parallels decline in mental processing speed in a non-demented elderly population," J.Neurol.Neurosurg.Psychiatry, vol. 77, no. 2, pp. 149-153, Feb.2006. Palm, W. M., Walchenbach, R., Bruinsma, B., Admiraal-Behloul, F., Middelkoop, H. A., Launer, L. J., van der, G. J., and van Buchem, M. A., "Intracranial compartment volumes in normal pressure hydrocephalus: volumetric assessment versus outcome," AJNR Am.J.Neuroradiol., vol. 27, no. 1, pp. 76-79, Jan.2006. Van Es, A. C., van der Flier, W. M., Admiraal-Behloul, F., Olofsen, H., Bollen, E. L., Middelkoop, H. A., Weverling-Rijnsburger, A. W., Westendorp, R. G., and van Buchem, M. A., "Magnetization transfer imaging of gray and white matter in mild cognitive impairment and Alzheimer's disease," Neurobiol.Aging, vol. 27, no. 12, pp. 1757-1762, Dec.2006. Contributions to international conference proceedings H.C. van Assen, A.F. Frangi, M.G. Danilouchkine, S. Ordas, J.J.M. Westenberg, J.H.C. Reiber, B.P.F. Lelieveldt, “Efficient reconstruction of cardiac LV surfaces using a 3D sparse ASM”, proc. ISBI 2006, 117-120. J.R. Milles, R.J. van der Geest, M. Jerosch-Herold, Johan H.C. Reiber, B.P.F.Lelieveldt, “Analysis of First Pass Myocardial Perfusion MRI using Independent Component Analysis”, proc. SPIE medical imaging 2006, paper 1R. A.E.H. Scheenstra, J. Dijkstra, R.C.G. van de Ven, L. van der Weerd, J.H.C. Reiber Semi-Automated Registration of Single Histology Sections with ex-Vivo MRM Volumes, in Proceedings of thelfth annual conference of the Advanced School for Computing and Imaging, pp 400-405. L. Ferrarini, H. Olofsen, W.M. Palm, M.A. van Buchem, J.H.C. Reiber, F. Admiraal-Behloul, ”Growing Cell Neural Networks for Fully Automatic Shape Modeling”, proc. Medical Image Understanding and Analysis (MIUA), 2006. Li R, Emmerich MTM, Bovenkamp EGP, Eggermont J, Bäck Th, Dijkstra J, Reiber JHC. Mixed-integer evolution strategies and their application to intravascular ultrasound image analysis. In: EvoWorkshops 2006. F. Rothlauf et al. (Eds.) Lecture Notes Computer Sicence, Springer-Verlag, Berlin, 2006; 3907: 415-26. Eggermont J, Bovenkamp EGP, Li R, Emmerich MTM, Bäck Th, Dijkstra J, Reiber JHC. Extending NK Landscapes to the mixed-integer domain. Proceedings 18th Belgium-Netherlands Conference on Artificial Intelligence, Namur, Oct 5-6, 2006: 373-4. Emmerich MTM, Li R, Eggermont J, Bovenkamp EGP, Bäck Th, Dijkstra J, Reiber JHC. Optimizing parameters of


coronary vessel image analysis using evolution strategies. Proceedings 18th Belgium-Netherlands Conference on Artificial Intelligence, Namur, Oct 5-6, 2006: 375-6. Bovenkamp EGP, Eggermont J, Li R, Emmerich MTM, Bäck Th, Dijkstra J, Reiber JHC. Optimizing IVUS lumen segmentations using evolutionary algorithms. 1st Int. Workshop on Computer Vision for Intra-vascular and Intracardiac Imaging, MICCAI, Copenhagen, Oct. 1, 2006: 74-81. Leung KYE, Stralen M van, Burken G van, Voormolen MM, Nemes A, Cate FJ ten, Jong N de, Steen AFW van der, Reiber JHC, Bosch JG. Sparse Appearance Model Based Registration of 3D ultrasound images. In MIAR 2006. G-Z Yang et al (Eds.). Lectures Notes in Computer Science 2006; 4091: 236-43. Leung KYE, Stralen M van, Voormolen MM, Burken G van, Nemes A, Cate FJ ten, Geleijnse ML, Jong N de, Steen AFW van der, Reiber JHC, Bosch JG. Registration of 2D cardiac images to real-time 3D ultrasound volumes for 3D stress echocardiography. In: Medical Imaging 2006: Image Processing, JM Reinhardt, JPW Pluim (Eds.). Proc of SPIE 2006; Vol. 6144: 18-1-18-12. Experimental software Vessel wall MASS: segmentation and analysis of vessel wall MR images. INTEGRIM: analysis software for fusion of molecular, functional and structural imaging. Segmentation component for MRA-CMS: segmentation and analysis of MRA datasets. Segmentation component for Qangio CT: segmentation and analysis of CT angiography datasets. SNIPER: quantification and segmentation software for brain MR studies.

2.3.10 Contribution of Tue-WI-vis Information visualization We have studied and developed a variety of new methods for the visualization of abstract data, with a focus on the visualization of software systems. These include a new way to visualize software evolution, hierarchical data with a superimposed network, extensions of treemap visualization, multiple views on state spaces, finding skeletons in volume data, and highlighting areas of interest in software diagrams. Besides publications, this work has led to two best paper awards, at IEEE InfoVis and at ACM SoftVis. Scientific visualization Robert van Liere and his PhD students have developed novel ways to visualize a variety of different types of data sets, coming from confocal microscopy, chemistry, and life sciences. External projects VOLTS, 2004-2008, NWO, 315 KE The aim is to develop new methods to gain insight in large state transition graphs, such as produced when formal methods, i.e. process algebra, is applied to model dynamic systems. The project is a collaboration with the group Design and Analysis of Systems at TU/e. SMARTER, 2002-2007, NWO, 572 KE The aim of the project is to develop new methods and techniques for the simulation of anisotropic turbulent transport. These new methods are based on Local Defect Correction (LDC). This project is a collaboration between four research groups at TU/e. Our contribution concerns the development of new visualization methods.


MULTISKEL, 2005-2008, NWO, 110KE The aim is to develop new methods for the skeletonization of high-dimensional data-sets. RECONSTRUCTOR, 2005-2008, NWO, 1,290 KE Development of new methods for the analysis and understanding of large software systems. Collaboration with the Software Engineering group of prof. dr. A. van Deursen, TU Delft. EXPRESSION OF INTEREST, 2006-2009, NWO, 480 KE Development of generic models and guidelines to enable users of visualization to specify and capture their interest easily and effectively, and to show interesting data in a clear way. Contributions to Books Frasincar, F., Telea, A.C., Houben, G.J.P.M.; Adapting graph visualization techniques for the visualization of RDF data. Geroimenko, V., Chen, C. (Eds.); Visualizing the Semantic Web: XML-based Internet and Information Visualization (Second Edition). New York, 2006, Springer, pp. 154-171. Papers in international journals Burakiewicz, W., Liere, R. van; Analyzing complex FTMS simulations : a case study in high-level visualization of ion motions. IEEE Transactions on Visualization and Computer Graphics, 12, 2006, 5, pp. 1037-1044. Fiers, M.W.E.J., Wetering, H.M.M. van de, Peeters, T.H.J.M, Wijk, J.J. van, Nap, J.P.; DNAVis : interactive visualization of comparative genome annotations. Bioinformatics, 22, 2006, 3, pp. 354-355. Groote, J.F., Ham, F.J.J. van; Interactive visualization of large state spaces. International Journal on Software Tools for Technology Transfer, 8, 2006, 1, pp. 77-91. Holten, D.H.R., Wijk, J.J. van, Martens, J.-B.O.S. ; A perceptually based spectral model for isotropic textures. ACM Transactions on Applied Perception, 3, 2006, 4, pp. 376-398. Holten, D.H.R.; Hierarchical edge bundles: visualization of adjacency relations in hierarchical data. IEEE Transactions on Visualization and Computer Graphics, 12, 2006, 5, pp. 741-748. Keim, D.A., Robertson, G.G., Thomas, J.J., Wijk, J.J. van; Guest editorial (Special section on visual analytics). IEEE Transactions on Visualization and Computer Graphics, 12, 2006, 6, pp. 1361-1362. Leeuw, W.C. de, Verschure, P., Liere, R. van; Visualization and analysis of large data collections: a case study applied to confocal microscopy data. IEEE Transactions on Visualization and Computer Graphics, 12, 2006, 5, pp. 1251-1258. Mei, K., Zheng, N., Wetering, H.M.M. van de; High-speed and memory-efficient VLSI design of 2D DWT for JPEG2000. Electronics Letters, 42, 2006, 16, pp. 907-908. Parsons, D., Rashid, A., Telea, A.C., Speck, A.; An architectural pattern for designing component-based application frameworks. Software : Practice and Experience, 36, 2006, 2, pp.157-190. Pretorius, A.J., Wijk, J.J. van; Visual analysis of multivariate transition systems. IEEE Transactions on Visualization and Computer Graphics, 12, 2006, 5, pp. 685-692. Vliegen, R., Wijk, J.J. van, Linden, E.J. van der; Visualizing business data with generalized treemaps. IEEE Transactions on Visualization and Computer Graphics, 12, 2006, 5, pp. 789-796. Wijk, J.J. van Wijk, Cohen, A.M.; Visualization of Seifert Surfaces. IEEE Transactions on Visualization and Computer Graphics, 12, 2006, 4, pp. 485-496.


Wijk, J.J. van; Views on visualization. IEEE Transactions on Visualization and Computer Graphics, 12, 2006, 4, pp. 421-433. Wijk, J.J. van; Bridging the gaps. IEEE Computer Graphics and Applications, 26, 2006, 6, pp. 6-9. Contributions to international conference proceedings Byelas, H., Telea, A.C.; Visualization of areas of interest in software architecture diagrams. SoftVis’06, Brighton, UK, September 4-5, 2006, Proceedings 2006 ACM Symposium on Software Visualization, 2006, ACM Press, pp. 105-114. Byelas, H., Bondarev, E., Telea, A.C.; Visualization of areas of interest in component-based system architectures. Euromicro-SEAA'06, Dubrovnik, Croatia, August 29-September 1, 2006, Proceedings 32nd Euromicro Conference on Software Engineering and Advanced Applications, Los Alamitos CA, 2006, IEEE Computer Society, pp. 160-169. Cheng, H., Zheng, N., Sun, C., Wetering, H.M.M. van de; Vanishing point and Gabor feature based multi-resolution on-road vehicle detection. Third International Symposium on Neural Networks, Chengdu, China, May 28-June 1, 2006,J. Wang et al. (Eds.), Advances in Neural Networks - ISNN 2006, Part III Vol. 3973. Lecture Notes in Computer Science, Berlin, 2006, Springer, pp. 46-51. Cheng, H., Zheng, N., Sun, Chong, Wetering, H.M.M. van de. Boosted crucial Gabor features applied to vehicle detection. ICPR'06, Hong Kong, August 20-24, 2006, Proceedings 18th International Conference on Pattern Recognition, volume 2, IEEE Press, pp. 662-666. Dortmont, M.A.M.M. van, Wetering, H.M. 13th International Conference Discrete Geometry for Computer Imagery, Szeged, Hungary, October 25-27, 2006, A. Kuba, L.G. Nyúl, & K. Palágyi (Eds.), Discrete Geometry for Computer Imagery, Vol. 4245. Lecture Notes in Computer Science, Berlin, 2006, Springer, pp. 617-629. Eede, M. van, Macrini, D., Telea, A.C., Sminchisescu, C., Dickinson, S. Canonical skeletons for shape matching. ICPR'06, Hong Kong, August 20-24, 2006, Proceedings 18th International Conference on Pattern Recognition, volume 2, IEEE Press, pp. 64-69. Kruszynski, K.J., Liere, R. van, Kaandorp, J.A. An interactive visualization system for quantifying coral structures. EuroVis 2006, Lisbon, Portugal, May 8-10, 2006, Proceedings Eurographics/IEEE VGTC Symposium on Visualization, Aire-la-Ville, Switzerland, 2006, Eurographics Association, pp. 283-290. Middelkoop, R., Huizing, C., Kuiper, R., Luit, E.J.; Cooperation-based invariants for OO languages. FACS'05, Macao, October 24-25, 2005, Z. Liu & L. Barbosa (Eds.), Proceedings of the 2nd International Workshop on Formal Aspects of Component Software, Vol. 160, August 2006, Electronic Notes in Theoretical Computer Science, pp. 225-237. Reniers, D., Telea, A.C. ; Quantitative comparison of tolerance-based feature transforms. VISAPP'06, Setúbal, Portugal, February 26-28, 2006, Proceedings First International Conference on Computer Vision Theory and Applications, 2006, INSTICC Press, pp. 107-114. Smit, F., Rhijn, A.J. van, & Liere, R. van (2006). GraphTracker : a topology projection invariant optical tracker. EGVE'06, Lisbon, Portugal, May 8-10, 2006, Proceedings 12th Eurographics Symposium on Virtual Environments, 2006, pp. 63-70. Telea, A.C.; Combining extended table lens and treemap techniques for visualizing tabular data. EuroVis 2006, Lisbon, Portugal, May 8-10, 2006, Proceedings Eurographics/IEEE VGTC Symposium on Visualization, Aire-la-Ville, Switzerland, 2006, Eurographics Association, pp. 51-58. Telea, A.C., Preusser, T., Garbe, C., Droske, M., Rumpf, M.; A variational approach to joint denoising, edge detection and motion estimation. DAGM'06, Berlin, Germany, September 12-14, 2006, K. Franke, K.R. Müller, B. Nickolay, R. Schäfer (Eds.), Pattern Recognition (Proceedings 28th Annual Symposium of the German Association for Pattern Recognition), Vol. 4174. Lecture Notes in Computer Science, Berlin, 2006, Springer, pp. 525-535.


Telea, A.C., Strzodka, R.; Multiscale image based flow visualization. VDA'06, San Jose CA, USA, January 15-19, 2006, R.F. Erbacher et al. (Eds.), Visualization and Data Analysis 2006, Article 606001 Vol. 6060. SPIE Proceedings. SPIE Press, pp. 1-11. Telea, A.C., Voinea, S.L.; An open framework for CVS repository querying: analysis and visualization. MSR 2006, Shanghai, China, May 22-23, 2006, Proceedings of the 2006 International Workshop on Mining Software Repositories, ACM Press, pp. 33-39. Telea, A.C., & Voinea, S.L.; Mining software repositories with CVSgrab. MSR 2006, Shanghai, China, May 22-23, 2006, Proceedings of the 2006 International Workshop on Mining Software Repositories, ACM Press, pp. 167-168. Termeer, M., Oliván Bescos, J., Telea, A.C. (2006). Preserving sharp edges with volume clipping. VMV'06, Aachen, Germany, November 22-24, 2006, L. Kobbelt et al. (Eds.), Proceedings 11th International Fall Workshop on Vision, Modeling and Visualization, Amsterdam, 2006, IOS Press. Voinea, S.L., Telea, A.C.; Multiscale and multivariate visualizations of software evolution. SoftVis'06, Brighton, UK, September 4-5, 2006, Proceedings 2006 ACM Symposium on Software Visualization, ACM Press., pp. 115-124. Voinea, S.L., Telea, A.C.; How do changes in Buggy Mozilla files propagate?. SoftVis'06, Brighton, UK, September 4-5, 2006, Proceedings 2006 ACM Symposium on Software Visualization, ACM Press, pp. 147-148. Voinea, S.L., Telea, A.C.; CVSgrab : mining the history of large software projects. EuroVis 2006, Lisbon, Portugal, May 8-10, 2006, Proceedings Eurographics/IEEE VGTC Symposium on Visualization, Aire-la-Ville, Switzerland, 2006, Eurographics Association, pp. 187-194. Experimental software Pretorius, A.J; Diagraphica.2005-2007 C++, Windows, LinuxDiagraphica provides a variety of views on large state spaces, including user definable diagrams, attribute based clusterings of states, and transitions between states. Holten, D.H.R.; ExtraVis – Execution Trace Visualizer2006-2007 Delphi, Windows ExtraVis is a tool for the visualization of execution traces of software. Views on the static structure as well as the dynamics are given. High-light Hierarchical edge bundles We developed hierarchical edge bundling as a flexible and generic technique for the visualization of compound (directed) graphs. A compound (di)graph is a frequently encountered type of data set; relations are given between items, and a hierarchy is defined on the items as well. Software systems are a typical example, consisting of for instance a hierarchy of subsystems, modules, classes, with calls between classes. Many visualization methods for hierarchical data have been developed, extra relations between elements can be shown by just drawing edges as straight lines, connecting these elements. However, this gives a messy result, and a better result can be obtained when these edges are bundled. We do this in a hierarchical way. Each adjacency edge, modeled as a B-spline curve,


is moved toward the polyline defined by the path via the inclusion edges from one node to another. This hierarchical bundling reduces visual clutter, and can be used in combination with existing tree visualization techniques. Also, they visualize implicit adjacency edges between parent nodes that are the result of explicit adjacency edges between their respective child nodes. Furthermore, the bundling strength can be used to provide a continuous trade-off between a low-level and a high-level view of the adjacency relations. The use of more advanced blending modes than standard alpha blending can provide a valuable addition to the rendering of hierarchical edge bundles, for instance to show outliers more clearly. Finally, they lend themselves well to easy interaction, such as selecting all edges between two parent elements. The image shows a software system and its associated call graph, using a balloon layout, a radial layout and a squarified treemap layout respectively to show the hierarchy. Bundling reduces clutter, making both major connections between subsystems more visible as well as sparse connections (encircled regions).

2.3.11 Contribution of TUD-mm-ict Pattern Recognition A typical human ability is the recognition of patterns in the world around us. It constitutes the basis of each natural science: the laws of physics, the description of species in biology or the analysis of human behavior; they are all based on seeing patterns. Also in daily life pattern recognition plays an import role: reading texts, identifying people, retrieving objects or finding the way in a city. Once patterns are established, learned from some examples or from a teacher, we are able to classify new objects or phenomena into a class of known patterns. The study of automatic pattern recognition has two sides, one purely fundamentally scientific and one applied. By trying to build a system with pattern recognition capabilities more will become clear about the human ability to learn, recognize and classify. At the same time, systems are constructed that may be applied in various areas of science as well as in many places in society to assist human decision making. In our research, both aspects are treated. There are two projects focusing on the foundations of pattern recognition: representation and generalization, in which new ways of describing objects and learning from examples are studied. In addition, there are several applied projects focusing on the recognition of spectra. Like images and time signals, spectra constitute a pattern domain with an unsolved problem: how to represent patterns in their entirety, when only a set of samples (pixels or bins) is available. The research makes clear that automatic pattern recognition systems may successfully be applied in several places but that an understanding of the human ability of recognizing patterns is still in its early days. Bioinformatics Knowledge discovery and machine learning play an increasingly important role in biomolecular science, now that micro-array technology reaches maturity and genomes of different organisms are being published with increasing frequency. As a consequence, massive amounts of data are being (and will be) produced that contain important facts about the "Book of Life" of living organisms. These measurements have opened new avenues to discover novel functionalities within cells (e.g. function of genes and gene pathways). Although molecular biologists are extremely enthusiastic about these developments, they are confronted with the availability of enormous amounts of data about a very complex (many genes, hence many parameters) and heterogeneous (many elements such as genes, proteins metabolites etc.) system. Traditional ways to study biological phenomena in a gene-by-gene approach (reductionism) are no longer adequate. Instead, the cell should be studied as a network of complex interactions. This systems view, coupled with the integration of already available knowledge, defines the core of our approach to biomolecular knowledge discovery. External projects ALL-AGE ("Analysis of gene expression profiles of children with acute lymphomatic leukaemia by bioinformatics"), 2004-2008, EUR, 280 k€. The ALL-AGE project is a co-operation with the Department of Immunology of the Erasmus University Medical Center in Rotterdam. Jointly, we apply, evaluate and develop techniques for the analysis of microarray data and other molecular measurements. Applications include: basis molecular biology, molecular diagnosis and gene therapy.


The analysis of spatial structures in hyperspectral images, 2003-2007, STW, 470 k€. The construction of an initial toolbox for hyperspectral image recognition was finalized. We are now focusing on applications in various areas like agriculture, mining, paper production and infra-red imaging for microscopic particle analysis. On a more fundamental level we study procedures fo the selection of subbands, good for classification. Proximity-based representations for pattern learning, 2004-2008, NWO, 370 k€. The essential difference between proximity representations and kernel approached has been studied and resulted in understanding of the possible advantage of non-Euclidean object representations. Further the construction of augmented representation spaces and the application for invariant representations has been studied. Computer-aided detection and characterization of interstitial lung disease, 2004-2008, STW, 200 k€. This project started as a cooperation with the Image Science Institute in Utrecht. We intend to make use of the one-class classifier technique and study the use of spatial data-connectivity for improved recognition. Mineral spectral analysis, 2003-2005, DeBeers, 90 k€. This project aims at a robust spectral recognition of multi-class minerals for changing class distributions. Extensive experiments have been performed in which many classification techniques have been evaluated. Unknown priors, novelty detection and changing class distributions are the challenges for this real world application. ITB, "Innovative therapies for bone recovery", 2004-2007, Senter/Organon, 290 k€. Due to the continuous increase of people's life expectancy, there is an urgent need for effective therapies for the recovery and prevention of bone loss due to osteoporosis. In this project, the newest developments in genomics are integrated with the latest techniques in pathway discovery and pattern recognition. This will lead to a faster and novel approach to discover and functionally characterize genes involved in bone development. REGNET, "Unravelling the hierarchy of transcriptional regulation in chemostat cultures of Saccharomyces cerevisiae: a bioinformatics approach", 2004-2008, NGI/Kluyver Centre for Genomics of Industrial Fermentation, 230 k€. The Kluyver Center generates large transcriptome datasets of Saccharomyces cerevisiae grown under a wide range of carefully defined, industrially relevant, cultivation conditions in steady-state chemostat cultures. These different environmental conditions lead to widely differing physiological responses. The general objective of this project is to implement and develop bioinformatics approaches to unravel the underlying transcriptional regulation networks. Special emphasis will be placed on the hierarchy of transcriptional regulation, i.e., the quantitative analysis of how the (simultaneous) action of different transcription factors acting at the same promoter region determine the transcriptional response of a promoter. Analysis of regulatory networks in Saccharomyces Cerevisiae, 2004-2008, NGI/Kluyver Centre for Genomics of Industrial Fermentation, 150k€. The overall aim of this project is to investigate genome-wide regulatory circuitry (transcription and signal transduction), by concurrently developing and performing bioinformatic analyses of various genome-scale data sets: expression microarray data; chromosome localization microarray data; protein-protein interaction data; high throughout phenotype data; sequence data as well as data currently stored in databases. METNET, " Data-driven discovery of metabolic and regulatory network structure", 2004-2008, Delft Research Center Life Science and Technology, 210 k€. This project is collaboration with the Bioprocess Technology Group at the TUDelft that studies mathematical techniques to accurately model metabolic reactions using metabolic control analysis when the structure of networks of such reactions is assumed to be known. In this project, tools developed for genetic network discovery will be adapted and extended to allow ab initio metabolic network structure discovery, facilitating detailed modeling by the Bioprocess Technology Group. These models will subsequently be extended to incorporate regulatory mechanisms at the genomic and proteomic level. Such models will allow targeted interference at the genomic level to obtain certain desired metabolic behaviour. BioRange-SP121, “Unifying framework for data-driven pathway discovery”, 2004-2009, NBIC-BioRange, 350 k€. Together with the Radboud University Nijmegen, the University Medical Center Utrecht and the Dutch Cancer institute we study the integration of various genomic sources to arrive at novel pathways. In particular we look at the


development of a unifying framework to integrate this data and at the analysis of insertion sites in retroviral insertional mutagenesis screens and relate them to onco-genetic events. BioRange-SP132, “Developing clinical predictors based on high-dimensional genomics data, pathway information and directed experimentation”, NBIC-BioRange, 350 k€. Together with the Leiden University Medical Center and the Dutch Cancer institute this project studies data-driven approaches based on genomics data to construct predictors for diagnosis and prognosis in human disease. We will develop statistical techniques which regulate the gene selection strategy such that it takes particular known relationships between genes, defining e.g. a particular pathway, into account. In addition, we explore how predictors based on gene expression data can be augmented with prognostic predictors derived from proteomics data originating from the same patient series. BioRange-SPHGL, Bioinformatics, NBIC-BioRange, 450 k€. This project concerns funding by NBIC-BioRange for the chair of Prof. Reinders in Bioinformatics. CANCER, "Molecular Classification of Cancer", 2002-2007, NKI, 300 k€. This project is conducted in close collaboration with the Dutch Cancer Institute (NKI). Central to the program lies the prediction of prognosis and optimal treatment choice for cancer patients, which is dependent on correct disease classification. Our goal within this program is to perform computational analysis of all information sources to construct a taxonomy of breast cancer (sub-)types, such that the classes correlate strongly with survival and response to radio- or chemotherapy Doctoral Degrees Juszczak, P (2006, juni 08). Learning to recognise. TUD Technische Universiteit Delft (143 pag.) (Delft: P. Juszczak) (ISBN 90-9020684-1). Prom./coprom.: Prof.dr.ir. MJT Reinders & Dr.ir. RPW Duin (ISBN 90-9020684-1). 2e geldstroom. Books Duin, RPW & Pekalska, EM (2006). Object representation, sample size, and data set complexity. In M Basu & TK Ho (Eds.), Data Complexity in Pattern Recognition (pp. 25-47). London: Springer-Verlag London Ltd (ISBN 1-84628-171-7). Papers in international journals Bard, MPL, Amelink, A , Skurichina, M , Noordhoek Hegt, V , Duin, RPW , Sterenborg, HJCM , Hoogsteden, HC & Aerts, JGJV (2006). Optical spectroscopy for the classification of malignant lesions of the bronchial tree. Chest, (ISSN 0012-3692), 129(4), 995-1001. Chen, C , Hendriks, EA , Duin, RPW , Reiber, JHC , Hiemstra, PS , Weger, LA de & Stoel, BC (2006). Feasability study on automated recognition of allergenic pollen: grass, birch and mugwort. Aerobiologia, (ISSN 0393-5965), 1-10. Fan, C , Oh, DS , Wessels, LFA , Weigelt, B , Nuyten, DSA , Nobel, AB , Veer, LJ van 't & Perou, CM (2006). Concordance among gene-expression-based predictors for breast cancer. New england journal of medicine, (ISSN 0028-4793), 355(6), 560-569. Houwelingen, HC van , Bruinsma, T , Hart, AAM , Veer, LJ van 't & Wessels, LFA (2006). Cross-validated Cox regression on microarray gene expression data. Statistics in medicine, (ISSN 0277-6715), 25(18), 3201-3216. Knijnenburg, TA , Reinders, MJT & Wessels, LFA (2006). Artifacts of Markov blanket filtering based on discretized features in small sample size applications. Pattern recognition letters, (ISSN 0167-8655), 27(7), 709-714.


Kresnowati, MTAP (sect Bioprocess Technology (BT/BPT)), Winden, WA van (sect Bioprocess Technology (BT/BPT)), Almering, MJH (sect Industrial Microbiology (BT/IMB)), Pierick, A ten , Ras, C (sect Bioprocess Technology (BT/BPT)), Knijnenburg, TA , Daran-Lapujade, PAS (sect Industrial Microbiology (BT/IMB)), Pronk, JT (sect Industrial Microbiology (BT/IMB)), Heijnen, JJ (sect Bioprocess Technology (BT/BPT)) & Daran, JM (sect Industrial Microbiology (BT/IMB)) (2006). When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation. Molecular Systems Biology, (ISSN 1744-4292), 2(49), 1-16. Lai, C , Reinders, MJT , Veer, LJ van 't & Wessels, LFA (2006). A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets. Bmc bioinformatics, (ISSN 1471-2105), 7(235). Lai, C , Reinders, MJT & Wessels, LFA (2006). Random subspace method for multivariate feature selection. Pattern recognition letters, (ISSN 0167-8655), 27(10), 1067-1076. Landgrebe, TCW & Duin, RPW (2007). Approximating the multiclass ROC by pairwise analysis. Pattern recognition letters, (ISSN 0167-8655), 28, 1747-1758. Landgrebe, TCW , Tax, DMJ , Paclik, P & Duin, RPW (2006). The interaction between classification and rejection performance for distance-based reject-option classifiers. Pattern recognition letters, (ISSN 0167-8655), 27(8), 908-917. Lozano, M , Sotoca, JM , Sánchez, JS , Pla, F , Pekalska, EM & Duin, RPW (2006). Experimental study on prototype optimisation algorithms for prototype-based classification in vector spaces. Pattern recognition, (ISSN 0031-3203), 39(10), 1827-1838. Orozco Alzate, M , Garcia Ocampo, ME , Duin, RPW & Castellanos Dominguez, CG (2006). Dissimilarity-based classification of seismic signals at Nevado del Ruiz volcano. Earth Sciences Research Journal, (ISSN 1794-6190), 10(2), 57-65. Paclik, P , Leitner, R & Duin, RPW (2006). A study on design of object sorting algorithms in the industrial application using hyperspectral imaging. Journal of Real-Time Image Processing, (ISSN 1861-8219), 1-10. Paclik, P , Novovicova, J & Duin, RPW (2006). Building road-sign classifiers using a trainable similarity measure. Ieee transactions on intelligent transportation systems, (ISSN 1524-9050), 7(3), 309-321. Paclik, P, Novovicova, J & Duin, RPW (2006). Building road-sign classifiers using a trainable similarity measure. Ieee transactions on intelligent transportation systems, (ISSN 1524-9050), 7(3), 309-321. Pekalska, EM , Duin, RPW & Paclik, P (2006). Prototype selection for dissimilarity-based classifiers. Pattern recognition, (ISSN 0031-3203), 39(2), 189-208. Pike-Overzet, K , Ridder, D de , Weerkamp, F , Baert, MRM , Verstegen, MM , Brugman, MH , Howes, SJ , Reinders, MJT , Thrashers, AJ , Wagemaker, G , Dongen, JJM van & Staal, FJT (2006). Is IL2RG oncogenic in T-cell development? Nature, (ISSN 0028-0836), 443(7109). Ridder, D de , Staal, FJT , Dongen, JJM van & Reinders, MJT (2006). Maximum significance clustering of oligonucleotide microarrays. Bioinformatics, (ISSN 1367-4803), 22(3), 326-331. Ridder, J de , Uren, A , Kool, J , Reinders, MJT & Wessels, LFA (2006). Detecting statistically significant common insertion sites in retroviral insertional mutagenesis screens. PLoS Computational Biology, (ISSN 1553-7358), 2(12), 0001-0013. Roepman, P , Kemmeren, P , Wessels, LFA , Slootweg, PJ & Holstege, FCP (2006). Multiple robust signatures for detecting lymph node metastasis in head and neck cancer. Cancer research, (ISSN 0008-5472), 66(4), 2361-2366. Someren, EP van , Vaes, BLT , Steegenga, WT , Sijbers, AM , Dechering, KJ & Reinders, MJT (2006). Least absolute regression network analysis of the murine osteoblast differentiation network. Bioinformatics, (ISSN 1367-4803), 22(4), 477-484.


Vaes, BLT , Ducy, P , Sijbers, AM , Hendriks, JMA , Someren, EP van , Jong, NG de , Heuvel, ER van den , Olijve, W , Zoelen, EJJ van & Dechering, KJ (2006). Microarray analysis on Runx2-deficient mouse embryos reveals novel Runx2 functions and target genes during intramembranous and endochondral bone formation. Bone, (ISSN 8756-3282), 39(4), 724-738. Verhaak, RGW , Staal, FJT , Valk, PJM , Lowenberg, B , Reinders, MJT & Ridder, D de (2006). The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies. Bmc bioinformatics, (ISSN 1471-2105), 7(105), 1-15. Contributions to international conference proceedings Arzhaeva, Y, Ginneken, B van & Tax, DMJ (2006). Image classification from generalized image distance features: application to detection of interstitial disease in chest radiographs. In s.n. (Ed.), Proceedings of the 18th international conference on pattern recognition (pp. 1-4). USA: IEEE (ISBN 0-7695-2521-0). Arzhaeva, Y , Tax, DMJ & Ginneken, B van (2006). Improving computer-aided diagnosis of interstitial disease in chest radiographs by combining one-class and two-class classifiers. In JM Reinhardt & JPW Pluim (Eds.), Proceedings of SPIE Medical Imaging 2006: Image Processing Vol. 6144. Proceedings SPIE, (ISSN 0277-786X) (pp. 1-8). Clevers, JGPW , Heijden, GWAM van der , Verzakov, S & Schaepman, M (2005). Estimating spatial patterns of biomass and nitrogen status in grasslands through imaging spectrometry. In S Liang, J Liu, X Li & R Liu (Eds.), ISPRS WG VII/1 Vol. XXXVI. International archives of photogrammetry, remote sensing and spatial information sciences, (ISSN 1682-1750) (pp. 56-59). ISPRS. Duin, RPW & Pekalska, EM (2006). Structural inference of sensor-based measurements. In DY Yeung, JT Kwok, A Fred, F Roli & D de Ridder (Eds.), Structural, syntactic and statistical pattern recognition Vol. 4109. Lecture notes in computer science, (ISSN 0302-9743) (pp. 41-55). Berlin-Heidelberg: Springer (ISBN 3-540-37236-9). Gangeh, MJ , Duin, RPW , Eswaran, C & Haar Romeny, B.M. ter (2006). Scale space texture classification using combined classifiers with application to ultrasound tissue characterization. In F Ibrahim, NA Abu Osman, J Usman & NA Kadri (Eds.), Proceedings of the International Conference on Biomedical Engineering (pp. 303-306). s.l. (ISBN 3540680160). Harol, A , Pekalska, EM , Verzakov, S & Duin, RPW (2006). Augmented embedding of dissimilarity data into (pseudo-) Euclidean spaces. In BPF Lelieveldt, B Haverkort, CTAM de Laat & JWJ Heijnsdijk (Eds.), Proceedings of the twelfth annual conference of the Advanced School for Computing and Imaging (pp. 307-312). Delft: ASCI (ISBN 90-810849-1-7). Juszczak, P , Tax, DMJ , Verzakov, S & Duin, RPW (2006). Domain based LDA and QDA. In s.n. (Ed.), Proceedings of the 18th international conference on pattern recognition (pp. 1-4). USA: IEEE (ISBN 0-7695-2521-0). Knijnenburg, TA , Wessels, LFA & Reinders, MJT (2006). Condition transition analysis reveals TF activity to nutrient-limitation-specific effects of oxygen presence in yeast. In C Priami (Ed.), Computational Methods in Systems Biology (pp. 271-284). Berlin,Heidelberg: Springer (ISBN 3-540-46166-3). Landgrebe, TCW & Duin, RPW (2006). A simplified extension of the area under the ROC to the multiclass domain. In A Louw, N Kleynhans & N Zulu (Eds.), Proceedings of the Seventeenth Annual Symposium of the Pattern Recognition Association of South Africa (pp. 241-245). USA: The International Association for Pattern Recognition (ISBN 0-620-37384-9). Landgrebe, TCW & Duin, RPW (2006). Combining accuracy and prior sensitivity for classifier design under prior uncertainty. In DY Yeung, JT Kwok, A Fred, F Roli & D de Ridder (Eds.), Structural, syntactic and statistical pattern recognition Vol. 4109. Lecture notes in computer science, (ISSN 0302-9743) (pp. 512-521). Berlin-Heidelberg: Springer (ISBN 3-540-37236-9).


Landgrebe, TCW , Paclik, P & Duin, RPW (2006). Precision-recall operating characteristic (P-ROC) curves in imprecise environments. In s.n. (Ed.), Proceedings of the 18th international conference on pattern recognition (pp. 1-4). USA: IEEE (ISBN 0-7695-2521-0). Loog, M & Ridder, D de (2006). Local discriminant analysis. In s.n. (Ed.), Proceedings of the 18th international conference on pattern recognition (pp. 1-4). USA: IEEE (ISBN 0-7695-2521-0). Meuleman, W , Welten, MCM & Verbeek, FJ (2006). Construction of correlation networks with explicit time-slices using time-lagged, variable interval standard and partial correlation coefficients. In MR Berthold, R. Glen & I. Fischer (Eds.), Computational Life Sciences II (pp. 236-246). Berlin-Heidelberg: Springer (ISBN 3-540-45767-4). Orozco-Alzate, M , Garcia-Ocampo, ME , Duin, RPW & Castellanos-Dominguez, CG (2006). Dissimilarity-based classification of seismic signals at Nevado del Ruiz volcano. In CA Vargas, A Caneva, H Monsalve, ML Bermudez & SM Bahamon (Eds.), Proceedings of the II Latin American Congress of seismology, III Colombian Congress of seismology, Latin American and Caribbean symposium of geophysics (pp. 1-16). Colombia: Geoslac (ISBN 958-33-9649-4). Paclik, P , Novovicova, J & Duin, RPW (2006). A trainable similarity measure for image classification. In s.n. (Ed.), Proceedings of the 18th international conference on pattern recognition (pp. 1-4). USA: IEEE (ISBN 0-7695-2521-0). Pekalska, EM & Duin, RPW (2006). Dissimilarity-based classification for vectorial representations. In s.n. (Ed.), Proceedings of the 18th international conference on pattern recognition (pp. 1-4). USA: IEEE (ISBN 0-7695-2521-0). Pekalska, EM & Duin, RPW (2006). Learning with general proximity measures. In A Fred & A Lourenco (Eds.), Proceedings of the 6th International Workshop on Pattern Recognition in Information Systems (PRIS2006) (pp. IS-15-IS-24). Portugal: INSTICC PRESS (ISBN 978-972-8865559). Pekalska, EM , Harol, A , Duin, RPW , Spillmann, B & Bunke, H (2006). Non-Euclidean or non-metric measures can be informative. In DY Yeung, JT Kwok, A Fred, F Roli & D de Ridder (Eds.), Structural, syntactic and statistical pattern recognition Vol. 4109. Lecture notes in computer science, (ISSN 0302-9743) (pp. 871-880). Berlin-Heidelberg: Springer (ISBN 3-540-37236-9). Shao, L , Saikalis, G , McCune, DJ & Ridder, J de (2006). An electronic throttle simulation model with automatic parameter tuning. In s.n. (Ed.), Systems engineering, electronics simulation, advanced electronics packaging and electromagnetic compatibility (SAE internation) Vol. 2005. SAE Technical Paper Series, (ISSN 0148-7191). USA: SAE. Skurichina, M , Verzakov, S , Paclik, P & Duin, RPW (2006). Effectiveness of spectral band selection/extraction techniques for spectral data. In DY Yeung, JT Kwok, A Fred, F Roli & D de Ridder (Eds.), Structural, syntactic and statistical pattern recognition Vol. 4109. Lecture notes in computer science, (ISSN 0302-9743) (pp. 541-550). Berlin-Heidelberg: Springer (ISBN 3-540-37236-9). Spillmann, B , Neuhaus, M , Bunke, H , Pekalska, EM & Duin, RPW (2006). Transforming strings to vector spaces using prototype selection. In DY Yeung, JT Kwok, A Fred, F Roli & D de Ridder (Eds.), Structural, syntactic and statistical pattern recognition Vol. 4109. Lecture notes in computer science, (ISSN 0302-9743) (pp. 287-296). Berlin-Heidelberg: Springer (ISBN 3-540-37236-9). Tax, DMJ , Duin, RPW & Arzhaeva, Y (2006). Linear model combining by optimizing the area under the ROC curve. In s.n. (Ed.), Proceedings of the 18th international conference on pattern recognition (pp. 1-4). USA: IEEE (ISBN 0-7695-2521-0). Tax, DMJ , Juszczak, P , Pekalska, EM & Duin, RPW (2006). Outlier detection using ball descriptions with adjustable metric. In DY Yeung, JT Kwok, A Fred, F Roli & D de Ridder (Eds.), Structural, syntactic and statistical pattern recognition Vol. 4109. Lecture notes in computer science, (ISSN 0302-9743) (pp. 587-595). Berlin-Heidelberg: Springer (ISBN 3-540-37236-9).


Verzakov, S , Paclik, P & Duin, RPW (2006). Edge detection in hyperspectral imaging: multivariate statistical approaches. In DY Yeung, JT Kwok, A Fred, F Roli & D de Ridder (Eds.), Structural, syntactic and statistical pattern recognition Vol. 4109. Lecture notes in computer science, (ISSN 0302-9743) (pp. 551-559). Berlin-Heidelberg: Springer (ISBN 3-540-37236-9). Experimental software Duin, R.P.W., Ridder, D. de, Juszczak, P., Pavel, P., Pekalska, E.M., Tax, D.M.J. PR Tools is a Matlab based toolbox for pattern recognition. It can freely be used for academic research. here you find the software itself, documentation, some datasets and other related items. http://www.prtools.org. Products of scientific research as results of cooperation within ASCI. Chen, C , Hendriks, EA , Duin, RPW , Reiber, JHC , Hiemstra, PS , Weger, LA de & Stoel, BC (2006). Feasability study on automated recognition of allergenic pollen: grass, birch and mugwort. Aerobiologia, (ISSN 0393-5965), 1-10. Group: UL-LUMC-LKEB. Products of research as a result of cooperatin within ASCI. Haratcherev, IJ (2006, maart 14). Application-oriented link adaptation for IEEE 802.11. TUD Technische Universiteit Delft (110 pag.) (ISBN 90-9020513-6). Prom./coprom.: Prof.dr.ir. HJ Sips & Prof.dr.ir. RL Lagendijk (ISBN 90-9020513-6). Group: TUD-EWI-isa-pds Persa, SF (2006, juni 06). Sensor fusion in head pose tracking for augmented reality. TUD Technische Universiteit Delft (169 pag.) (ISBN 90-9020777-5). Prom./coprom.: Prof.dr. IT Young & Prof.dr.ir. RL Lagendijk (ISBN 90-9020777-5). 2e geldstroom Group: TUD-TNW-tn-qi Haratcherev, IJ , Taal, JR , Langendoen, KG , Lagendijk, RL & Sips, HJ (2006). Optimized video streaming over 802.11 by cross-layer signaling. Ieee communications magazine, (ISSN 0163-6804), 44(1), 115-121. Group: TUD-EWI-isa-pds Reinders, MJT , Sips, HJ Steen, MR van , Epema, DHJ, Wang, J , Garbacki, P. , Pouwelse, JA, Bakker, A , Iosup, A & wang, J. (2007). Tribler: a sicial-based peer-to-peer system. Concurrency-practice and experience, (ISSN 1040-3108). Group: TUD-EWI-isa-pds Ruijsscher, B de, Gaydadjiev, GN , Lichtenauer, JF & Hendriks, EA (2006). FPGA accelerator for real-time skin segmentation. In S. Ha & S Chakraborty (Eds.), Proceedings of the 2006 IEEE/ACM/IFIP Workshop on Embedded Systems for Real Time Multimedia (pp. 93-97). US: IEEE (ISBN 0-7803-9783-5). Group: TUD-EWI-me-ce Wang, J , Pouwelse, JA, Fokker, JE & Reinders, MJT (2006). Personalization of a peer-to-peer television system. In G Doukidis, K Chorianopoulos & G Lekakos (Eds.), Proceedings of the 4th European conference on interactive television (pp. 147-155). Athens, Greece: Athens University of Economics and Business. Group: TUD-EWI-isa-pds High-light Signal Processing in the Encrypted Domain1 Recent advances in technological development have created many new application fields where new business models emerged. These new applications range from multimedia content production and distribution, to advanced healthcare

1 Signal Processing in the Encrypted Domain, SPEED, is a project supported by EU. www.speedproject.eu.


systems for continuous health monitoring. However, this rapid transformation of services has raised several important concerns regarding the security of the digital contents themselves, including intellectual property rights management, authenticity, privacy, and conditional access to digital contents. A simple example would be the privacy concerns of patients in a healthcare monitoring system. In the near future, it is projected that people would like to get service from the medical authorities with the help of small sensors connected to their body. Such devices will then collect measures such as blood pressure and compare them to reference data stored in a remote location. Automated systems will interpret that data for the patients and detect anomalies. Yet, it is evident that digital data such as medical records can easily be abused, raising privacy concerns for the patients. Currently concerns regarding security and privacy are solved by simply applying cryptographic precautions on top of applications. For example, the medical record data in question is protected by encryption. Data is stored encrypted and decrypted prior to later processing. The key required for the decryption is necessarily kept by the service provider and hence, trust to the service provider is essential. Signal processing in the encrypted domain aims to combine signal processing modules and cryptographic primitives in such a way that the same diagnosis can be made without decrypting the data first. In other words, data collected from the patients are all encrypted and in the remote location, this encrypted data is processed; the resulting diagnosis, which is also encrypted, can only be accessed by the owner patient who has the proper decryption key. As in this example, processing encrypted data is possible thanks to the homomorphism property of cryptosystems that enables us either add or multiply plaintext values by simply multiplying their encrypted forms. Unfortunately, this homomorphism property is only known for asymmetric cryptosystems which depend on certain difficult problems like factorization of large numbers, solving discrete logarithm or finding nth root of a composite number in modular arithmetic. Another related example to the idea of combining signal processing and cryptography is protecting intellectual property. Fingerprinting represent one particular approach for solving the problem of duplicating content by embedding the buyer identification into the digital data. Conventional fingerprinting schemes, called symmetric, require the merchant to prepare a slightly different copy of the digital content for each buyer. If the merchant finds a redistributed copy, he can easily determine the corresponding buyer. However, in such systems the merchant can not convince any third party about the identity of the malicious buyer since the information found in the redistributed copy is not necessarily linked to the buyer because it can be easily made up by the merchant. In contrast, an interactive protocol between the buyer and the merchant takes place to hide the buyer’s identity from the merchant in asymmetric fingerprinting while forcing the buyer to commit to the embedded identity. Only when a copy of the fingerprinted data is found out, can the merchant extract the buyer’s identity. A related work by Kuribayashi and Tanaka [1] introduced a relatively efficient solution to protect the privacy of the buyer while embedding his identity to the digital content. The proposed solution is dependent on an additively homomorphic cryptosystem and embeds the encrypted identity bits to the digital content using quantization index modulation (QIM) as the watermarking technique. While the security of the scheme is proved, the robustness of the underlying watermarking technique is a big concern as the QIM is a basic watermarking technique that does not even robust to simple noise attacks. Therefore, we adapted [2] more robust watermarking schemes, namely Distortion Compensated QIM (DC-QIM) and Rational Dither Modulation (RDM) to the framework of Kuribayashi and Tanaka.

Figure 1 Rational Dither Modulation (RDM)


The figure 1 illustrates the RDM scheme where signal samples are dithered and quantized and, a single bit is added or subtracted depending on the value of the watermark bit. The robustness of the RDM against fixed gain attacks is due to the normalization of signal samples with a function of previous watermarked signal values. Considering that the input signal is encrypted, implementing the consequent steps with an only additively homomorphic cryptosystems is challenging. To begin with, in this scheme normalized signal values are not integers as it is required by the encryption scheme thus, introducing a scaling problem. What is more, as mentioned before, the encryption scheme only allows for addition of the plaintext signal values while division is necessary for the quantizer. Despite such challenges, we achieved to adapt more robust watermarking schemes to the anonymous fingerprinting scheme of Kuribayashi and Tanaka. This showed us that combining signal processing and cryptography is promising and it has many application areas where the privacy is a concern. [1] M. Kuribayashi and H. Tanaka. Fingerprinting protocol for images based on additive homomorphic property. IEEE

Transactions on Image Processing, 14(12):2129-2139, 2005. [2] J.P. Prins, Z. Erkin and R. L. Lagendijk, Anonymous Fingerprinting with Robust QIM Watermarking Techniques,

Eurasip Journal on Information Society, (accepted).

2.3.12 Contribution of UL-LIACS Multimedia Information Retrieval We completed the first stage of research and experiments on the new paradigm of Artificial Imagination in multimedia information retrieval in the area of texture retrieval. The latest survey of the state of the art and grand challenges in the field was completed and published in the leading ACM Multimedia journal, and we served as advisers on the leading video analysis research evaluation project, TRECVID. Human Computer Interaction In this research theme we have explored interactive tracking of humans in real time video, and also completed a beta-version of the first 3D-structure integrated audio-video massive multiplayer virtual world over the Internet. In addition, we completed the first stage of a research survey on HCI through organizing the primary European scientific meeting on human-computer interaction. Bioinformatics Developed new algorithms for genotype/phenotype data mining. The development of an Hidden Markov Model based classifier for biological imagery was completed and tested under a wide variety of different tissue samples. A new method for viewing the development of micro-tubules was completed. External projects VIRSI, 2006-2009, NWO, BSIK/BRICKS/FOCUS, 400 KEuro, This project aims at developing a new paradigm called artificial imagination within the scope of multimedia information retrieval. In this new paradigm, we investigate how the computer can actively synthesize imagery to improve relevance feedback based retrieval. CYTTRON, 2004-2008, BSIK, 8.8MEuro, TUD, UU In this project, we are developing the first super microscope based on the implementation of the various forms of bio-imaging techniques toward creating a virtual window on the machinery of life and a comprehensive, integrated infrastructure for bio-imaging and modeling cells down to atomic detail. CMSB DIAL, 2004-2007, Dutch Government, 16MEuro, VUA DIAL investigates the integration and analysis of phenotype and genotype data sets from different CMSB research groups.


Books Huang, T., Sebe, N., Lew, M., Pavlovic, V., Kolsch, M., Galata, A., Kisacanin, B.; Computer Vision in Human-Computer Interaction. 2006, Springer, Lecture Notes in Computer Science (LNCS) Vol. 3979, ISBN 978 3 540 34202 1,first edition. Papers in international journals Lew, M. , Sebe, N., Djeraba, C., Jain R.; Content-based Multimedia Information Retrieval: State of the Art and Challenges. ACM Transactions on Multimedia Computing, Communications, and Applications (ISSN 1551-6857) volume 2, 2006, 1, pp. 1-19. Ghafoor, A., Zhang, Z., Lew, M., Zhou, Z.; Introduction to machine learning approaches to multimedia information retrieval. ACM Multimedia Systems Journal (ISSN 0942-4962). Vol. 12, No. 1, 2006, pp. 1-2. Contributions to international conference proceedings (only international congresses). Yu, F. and Ip, H.; Automatic Semantic Annotation of Images Using Spatial Hidden Markov Model. Proceedings of International Conference on Multimedia and Expo (ICME 2006), Hong Kong, 2006, IEEE Computer Society, pp. 305-308. Yu, F. and Ip, H.; Spatial-HMM: A new approach for Semantic Annotations of Histological Images. Proceedings of International Conference on Pattern Recognition (ICPR 2006), 2006, IEEE Publications, pp. 663-666. Experimental software Sicking, F.J., Bakker, E.M.; CGH Database 2003-2006 PHP, SQL, UNIX This software consolidates the micro array CGH experimental data of micro array facilities at different university medical centres. Thomee, B., Lew, M.; The Matrix 2005-2006 C++, Windows XP This software was designed to allow thousands of people over the Internet to share their ideas, culture, and knowledge in a realistic 3D virtual world using both audio and visual communication. Cooperation within ASCI Both publications below were the result of collaboration between UL-LIACS and Uva-Isla. Huang, T., Sebe, N., Lew, M., Pavlovic, V., Kolsch, M., Galata, A., Kisacanin, B.; Computer Vision in Human-Computer Interaction. 2006, Springer, Lecture Notes in Computer Science (LNCS) Vol. 3979, ISBN 978 3 540 34202 1, first edition. Lew, M. , Sebe, N., Djeraba, C., Jain R.; Content-based Multimedia Information Retrieval: State of the Art and Challenges. ACM Transactions on Multimedia Computing, Communications, and Applications (ISSN 1551-6857) volume 2, 2006, 1, pp. 1-19.

2.3.13 Contribution of TUE-EE-dmes Video processing: algorithms and architectures The focus of our video processing research is targeted on high-end consumer applications. The current activities fall into two categories, format conversion and video enhancement. The format conversion activities have focused on performance enhancement of the motion estimation unit. (Patent) literature research was carried out to determine state of the art motion compensation/estimation knowledge in industry


and academia. Selected subcomponents of algorithms found in literature were tested; of particular interest were (I) candidate generation and selection methods, (II) motion estimator (discontinuity preserving) smoothness constraints and related convergence performance, and (III) occlusion detection and correction methods. A new hierarchical motion estimator has been designed where the candidates from the first hierarchical level are generated in the radon transform domain (topic I). We plan to put together the results of our format conversion activities in a software package. The focus of the video enhancement activities shifts from resolution up-conversion, necessary since modern displays have more pixels than the video signal contains, to the enhancement of compressed video. A new classification method for image processing using Gaussian mixture models has been developed. Furthermore, a new blur estimation algorithm has been designed, patented and published. External projects Design of systems on silicon for video enhancement and format conversion 2002-2006, Philips Research, 180 k€ The goal of this research project is the design of a system on silicon for video enhancement and format conversion, aiming at the joint optimisation of algorithms and architecture for a single chip video converter/enhancer. Fields of interest are motion estimation and compensation, picture rate conversion, de-interlacing, resolution enhancement, noise reduction, power optimisation, VLSI design. Video coding artefact reduction 2005-2009, Philips research, 180 k€ The aim of this project is to gather and evaluate what has been achieved (benchmarking) in the area of coding artifact reduction and to propose (synthesize) some optimal techniques for coding artifact reduction, taking into account constraints of implementation in current technologies and keeping in mind the developments in the area of digitally transmitted video. Motion estimation 2006-2010, Philips research, 200 k€ The aim of the PhD-study is to gather and evaluate what is available (benchmarking) in the area of motion estimation/compensation algorithms and to propose (synthesize) new algorithms attractive for Philips CE Connected Displays. Doctoral Degrees Zhao, M.; 15 June 2006; Video Enhancement using Content-Adaptive Least Mean Square Filters. Technische Universiteit Eindhoven, Eindhoven, 2006. pp. 1-129. ISBN 90-386-0774-1, External project funded by Philips research. Contributions to international conference proceedings Beric, A.; Sethuraman, R.; Alba Pinto, C.A.; Peters, H.; Veldman, G.; Haar, P. van de; Duranton, M.: Heterogeneous multiprocessor for high definition video. Proceedings of the IEEE International Conference on Consumer Electronics, 7-11 January 2006, pp. 401-402. Haan, G. de; Zhao, M.: Making the best of legacy video on modern displays. Digest of the SID'06. 37, 9-9 June 2006, pp. 1888-1891. Heesch, F.; Klompenhouwer, M.A.; Haan, G. de: Masking coding artifacts on large displays. Proceedings of the International Conference on Consumer Electronics, 2006, 7-11 January 2006, pp. 207-208. Hu, Hao; Haan, G. de: Classification-based hybrid filters for image processing. Proceedings of SPIE, Visual Communications and Image Processing; onbekend, 2006.


Hu, Hao; Haan, G. de: Low cost blur estimator. Proceedings of IEEE International Conference On Image Processing ICIP 2006, 8-11 October 2006; IEEE Society Press, Los Alamitos, USA, 2006, pp. 617-620. Visser, M.; Muiswinkel, A. van; Ciuhu, C.; Haan, G. de: Enhanced MRI resolution for clinical applications. Proceedings of the ISMRM 14th Scientific meeting & exhibition., 6-12 May 2006. Patent Cordes, C.N.; Haan, G. de: Luminance and colour separation. Philips, EP1639835 A1, 29 March 2006. Haan, G. de; Bellers, E.B.: Biased motion vector interpolation for reduced video artifacts. Philips, EP1627533 A2, 22 February 2006. Haan, G. de: Estimating an edge orientation. Philips, EP1629435 A1, 1 March 2006. Haan, G. de: Estimating an edge orientation. Philips, EP1627533 A2, 1 March 2006. Haan, G. de; Cordes, C.N.: Luminance and colour separation. Philips, EP1639836 A1, 29 March 2006. Haan, G. de; Hofman, M.: Method and apparatus for rendering smooth teletext graphics. Philips, EP1683353 A1, 26 July 2006. Haan, G. de; Ciuhu, C.: Motion compensated de-interlacing with film mode adaptation. Philips, EP1714482 A1, 25 October 2006. Haan, G. de; Pelagotti, A.: Motion estimator for reduced halos in MC up-conversion. Philips, US7,058,227, 6 June 2006. Haan, G. de; Mertens, M.: Motion estimator for reduced halos in MC up-conversion. Philips, US7,010,039, 7 March 2006. Haan, G. de: Motion-compensated image signal interpolation. Philips, EP1647143 A1, 19 April 2006. Haan, G. de; Bellers, E.B.: Post-processing of interpolated images. Philips, US7,136,107, 14 November 2006. Haan, G. de; Bellers, E.B.: Post-processing of interpolated images. Philips, EP1654872 A1, 10 May 2006. Haan, G. de; Ciuhu, C.: Robust de-interlacing of video signals. Philips, EP1665780 A1, 7 June 2006. Haan, G. de: Robust de-interlacing of video signals. Philips, EP1665781 A1, 7 June 2006. Haan, G. de: Spatial image conversion. Philips, EP1616301 A2, 18 January 2006. Haan, G. de: Spatial image conversion. Philips, EP1616300 A1, 18 February 2006. Haan, G. de: Spatial signal conversion. Philips, EP1636987 A1, 22 March 2006. Ojo, O.A.; Kwaaitaal-Spassova, T.G.; Haan, G. de: Electronic circuit and method for enhancing an image. Philips, US7,009,662, 7 March 2006. Tegenbosch, J.A.P.; Haan, G. de: Image enhancement. Philips, EP1661087 A1, 31 May 2006. Wittebrood, R.B; Haan, G. de: Motion vector field re-timing. Philips, EP1661087 A1, 7 June 2006.


2.3.14 Contribution of TUD-LR-frs Reconstruction of building models from aerial photographs and 2D GIS databases The research on the interpretation of the aerial images focuses on knowledge-based 3D reconstruction of buildings. Three-dimensional building models are increasingly required for urban planning, tourism, telecommunication, etc. Since manual 3D processing of aerial images is very time consuming, speeding up the reconstruction by automatic procedures has become a necessity. Our approach relies on combining pairs of stereo images with 2D GIS (Geographic Information System) data and domain knowledge. The domain knowledge includes a building library describing primitive building models (flat roof, gable roof, and hip roof building) since most buildings can be described as an aggregation of these building primitives. In 2002, the performance of the building reconstruction system was evaluated. About 75% of buildings in a suburban environment were successfully reconstructed. This result implies that a significant cost reduction is possible in the production of 3D city models that are currently based on manual measurements. Reconstruction of industrial sites from terrestrial laser scanner data and photographs We present a method for 3D reconstruction of industrial sites using a combination of images and point clouds with a motivation of achieving higher levels of automation, precision, and reliability. Recent advances in 3D scanning technologies have made possible rapid and cost-effective acquisition of dense point clouds for 3D reconstructions. As the point clouds provide explicit 3D information they have a much higher potential for the automation of reconstruction. The modelling pipeline in our algorithm starts from point clouds as the main data source for automation. First of all we segment the point cloud using surface smoothness and detect simple objects like planes and cylinders using Hough Transform. This is followed by fitting of CSG objects to a combination of segments. The fitted CAD models are used as registration targets for adding more scans to the project. Additionally, by fitting the projected edges to image gradients we register images to point clouds. (STAR project) Reconstruction of natural sites from terrestrial laser scanner data and photographs The purpose of the research is 3D modelling and reconstruction of (real world) trees on the basis of terrestrial laser scans. To identify the structure of a tree in terms of stem and branches, an algorithm has been designed in 3D voxel space, based on a selection of basic and advanced 2D raster (image) processing algorithms, transferred into the 3D domain. The selection includes filtering, mathematical morphology, skeletonization, connected component labelling and shortest route computation. (Natscan project) Traffic monitoring and modelling using helicopter video sequences Traffic congestion is an important problem in modern society. Better understanding of its causes is needed to be able to more effectively reduce its effects. Congestion appears under a variety of circumstances. Beside the size and amount of roads and the number of vehicles on those roads, the occurrence of traffic congestion is highly dependent upon the behaviour of the individual vehicle drivers. Important factors are reaction speeds, the gap-acceptance and the lane-changing behaviour of the drivers. Due to the lack of detailed data on driver behaviour, contemporary traffic flow theories and models cannot be rigorously calibrated and validated, although there are very strong indications that these models are not able to correctly capture complex driving dynamics during congested or near-congested traffic flow.

External Projects Tracing Congestion Dynamics STW/CITG, Dec. 2004 – Dec. 2008, k€ 178,4 The goal of the proposed research project is to develop a traffic data collection system based on image sequences taken from a helicopter as well as to use this traffic data to calibrate and improve driver behaviour models.

2.3.15 Contribution of UvA- FdNWI-isis The main research themes are In the area of computer vision our efforts concentrate on semantic access to images by providing a description of objects regardless the accidental effects that illumination and viewpoint have on the appearance of the objects. As a


next type we do similar research in the description of object classes regardless the accidental recording conditions. Specifically, we employ color as an important source of information, as well as texture and local shape. Content-based access of visual data has been a topic of study for some time now. Based on the invariant colour, texture, and shape features, described above, successful methods have been designed to achieve image description at a semantic level. Recently, we have included the recognition of emotion, motion patterns, scenes, and individuals, in addition to objects and object types as important means to access visual data. Computer vision Colour is an important cue in image analysis. Image processing of color images requires special attention as well as new possibilities to see detail where grey value methods cannot. In previous years, local color, geometric and spatial frequency invariants were developed at ISIS. These local features aim at the robust measurement of the color, shape and texture of an object, under the most common accidental viewing conditions. These accidental conditions can be largely characterized by direction of view, the incident light, the color of the light and the other accidents such as the presence of foreground or background cluttering. An invariant representation of the object implies that the various conditions under which the same view of the object may be perceived do not have to be learned. To test the discriminative power of color, geometric and spatial frequency invariants, the ALOI collection was recorded, containing color images of 1000 real-world objects recorded under various illumination directions, and different illumination colors. Another important topic is feature detection by color saliency boosting. There exists a broad agreement that local features (such as depicted in Figure 2) are an efficient tool for object recognition due to their robustness with respect to occlusion and geometrical transformations. The success of local features is greatly dependent on the information content of the selected features. From information theory it is known that the information content of a feature is related to its frequency of occurrence. Features with high information content, so called salient features, are characterized by a low frequency of occurrence. They represent rare events in the world. Another important research result is on color invariance. We proposed invariants which increase discriminative power for object recognition when compared to the visual measurements of which the invariants were composed. More specifically, the illumination intensity invariant W and the color constant shadow and shading invariant N proof to be discriminative when recognizing objects from a data set containing much photometric variation. However, the invariants are shown to be only marginally color constant. The invariant sets outperform SIFT-features extracted from distinctive key points when the object is recorded under various illumination directions or when the object is rotated in 3 dimensions. Combining local invariant features and the incorporation of color are known to be nontrivial problems in computer vision, for which we have provided solutions. From the general theory, methods are derived for industrial colour vision, analysis of colour in documents, colour in microscopy, general images as appearing on the worldwide web. The topic on colour has led a Ph.D. thesis by J. van de Weijer entitled "Color Features and Local Structure in Images" and many publications in journals (International Journal on Computer Vision and IEEE Trans. on Pattern Analysis and Machine Intelligence). IEEE Trans. on PAMI is the most prominent journal in the area of pattern recognition and is among the top three journals in computer science in the world. We aim at expanding the analysis to take on the same invariant representation of texture next, learning to fuse various color invariant models as well as the semantic meaning of colour. Another important aspect in computer vision is Segmentation and Learning and Tracking. Image segmentation is the task of delineating the image of an object from the real world in the digital data array. It is one of the fundamental difficulties of computer vision, easily surpassed by man's superior capabilities. The difficulty resides in the fact that even man cannot rarely give a formal pictorial description why a boundary is positioned at a certain location and that is what a computer needs to perform the job. We contribute a variety of solutions.

First, we found proper solutions to combine derivatives of the different color channels to compute locale image structures such as edges, corners, circles etc. Further, learning methods have been used to select and weight color (invariant) models for discriminatory and robust image feature detection. Finally, we proposed a classification scheme to classify the physical nature of image structures such as shadow, highlight and material edges/corners.


Content-based access of visual data Color plays an indispensable role in the attribution of saliency. Postboxes are painted red to facilitate locating them, flowers take on bright colors to attract birds, and traffic signs use highly saturated colors to attract attention of traffic participants. An evaluation of existing features detectors, including both color and luminance-based methods reveals that these methods fail to detect salient features. We have developed powerful methods to improve the saliency, and thereby the information content, of existing feature detectors. To assess the information content of color features, we investigated their frequency of occurrence. To this end, the probability distribution of color-derivatives, which are the most commonly used building blocks for feature detectors, is computed on a dataset of 40.000 images (the Corel dataset). The distribution is given in Figure 2. The axes are in the opponent color space, where the xy-plane indicates the variation in color values, and the z-axis the variation in intensity. Here an interesting phenomena is revealed, which clarifies the failure of classical feature detectors. Variations in the real world are dominated by luminance changes. Classical feature detectors which equally value changes in the color and in the luminance direction are therefore dominated by luminance variations. To improve the saliency of the detected features, we developed a proper method to correct the inhomogeneous distribution of color derivatives. The function which attains this result, called the color saliency boosting function, regulates the amplification of the color variations. The amount of amplification is derived from information theory applied to the distribution of color derivatives. Results of saliency boosting are depicted in Figure 2. After saliency boosting the detectors focus on the regions with higher information content: the commercial panes in the shopping street, and the yellow-jersey and the American flag in the sport picture.

Figure 2. a) Distribution of color derivatives in opponent color space. The ellipsoid-like surfaces indicate derivatives with equal probability. Variations in the luminance direction (z-axis) occur more frequent than in the variations in the color-plane (xy-plane). b) Kalverstraat-image, with in red a Harris detector and in yellow the Harris detector with color saliency boosting. c) Lance-image, with in yellow the affine invariant features Harris-Laplace detector, and in red the same detector after color boosting. In the context of object recognition, proper methods to recognize object classes have been proposed. The first solution is to formulate the recognition task as a graph problem searching for the characteristic geographical arrangements of (possibly missing) parts. The objective function is Bayesian maximum a posteriori estimation, integrating the image likelihood as a posteriori probability of the part detectors. The variability in the arrangement of object parts is captured by a Gaussian distribution after translation normalization. Further, a sparse representation has been proposed for coarse and fine object recognition The topic on learning for object recognition has led a Ph.D. thesis by Pham Viet Thang entitled "Learning Spatial Relations for Object Recognition" and one publication will appear in IEEE Trans. on PAMIi. Further, the topic on learning and image segmentation has lead to several papers in Conference on Computer Vision and Pattern Recognition, the most prestigious conference on the field of compute vision.


Figure 1. The MediaMill Semantic Video Search Engine, showing various advanced interfaces for effective video retrieval. External Projects ImIK 2002-2005, IOP, 400 Keuro, Uva-Science-ISIS and VU. The project considers the interactive exploration of multimedia information and knowledge. A computational theory for visual cognition (NWO Veni) 2003-2007, NWO, Uva-Science-ISIS, 200 KEuro. The project aims at developing a computational theory of vision based on invariant representations. MultimediaN 2004-2008, BSIK, 32 MEuro, UvA-Science-ISIS, UU-CS, UT-CS, TUD-CS, CTIT-CS, VU-CS, TNO, NFI, Telematica Inst., V2, Philips, Ilse, LogicaCMG, Waag Society, DBNL, eMAXX, NOS*NSF, Thales, SPSS, Compano, Paradiso, Verenigd Digitaal Erfgoed. The project aims at various forms of multi-media access including e-documents and video. Image retrieval 2001-2005, IOP, Markgraaf, UvA-Science-ISIS. The project aims at analyzing logos, signs to classify them on perceptual similarity. Tracking Sport Video 2002-2005, IOP, Philips CFT, UvA-Science-ISIS. The project aims at tracking of objects in sport video. AMIS NWO, UvA-Science-ISIS, UU-CS, UT-CS, TUD-CS. The project studies multi-media information analysis.


Parallel library tools for image processing NWO, TUD-CS, TUD-PH, UvA-ISIS. The project aims at analyzing parallel processes, processing for image processing. MuNCH a NWO-CATCH project for the semantic access to video archives, with Guus Schreiber, VU and Maarten de Rijke, ISLA-ILPS, Beeld&Geluid. Jade a NWO-Glance project for parallel processing of multimedia data with Henri Bal, VU, and CWI. TODS A project with NFI, the forensic lab and ISIS, for forensic data processing, among others on surveillance and crime scene reconstruction. CIOS, ISIS participates in the TNO-center. The Intelligent Sensory Information Systems group was supported by: bsik, IOP-BV, IOP-MMI, EU, NWO, STW, Netherlands Forensic Institute, TNO, Philips, Beeld en Geluid.

2.4 D: MULTIMEDIA INFORMATION SYSTEMS

2.4.1 Contribution of TUD-mm-ict Image and Video Processing The research on image and video processing in the ICT Group encompasses four topics: Video compression. Compression techniques are essential in variety of Internet applications, television broadcasting, digital cameras, music distribution and consumer digital video applications, such as DVD's and DV-cam cording. Research concentrates on novel compression techniques for applications where the communication medium is error-prone and cases where the device on which the compression algorithm runs is complexity constrained. Computer vision. Focus is on 3D reconstruction of objects from multiple cameras or moving camera(s) for e.g. face recognition, remote handling, 3D editing for 3D teleconferencing. Recent research also considers the problem of gesture recognition. Cultural heritage informatics. Research concerns the application and development of image processing, pattern recognition and artificial intelligence techniques for the benefit of our cultural heritage. The focus is on virtual restoration of paintings as well as on the dating and authenticity of painting and etchings. Restoration. In the area of post-processing the emphasis is on the quality improvement of degraded digital image sequences. An important application is the restoration of historically important (analogue) film and video recordings. Multimedia Retrieval The research efforts in the ICT Group in the field of multimedia content management address the following challenges: - Automating multimedia content indexing and retrieval processes; - Enabling quick, easy and personalized access to multimedia content. We combine our expertise in multimedia signal processing and machine intelligence with state-of-the-art achievements in the fields of "traditional" information retrieval and human perception and aim at bridging the gap between the measurable properties (features) of one hand, by optimizing the way multimedia content is stored, organized, abstracted and represented and, on the other hand, by developing methods for reliably learning user preferences and for filtering, pruning, adapting and delivering multimedia content accordingly. External projects NON OBTRUSIVE GESTURE RECOGNITION, 2003-2007, Delft Research Center ICT, 180 k€. In this gesture recognition project we will focus on problems involved in tracking and interpretation of hand movements (gestures) with cameras without using additional obtrusive sensors or markers and how this can be used optimally in different


applications. Gestures that can be indicated as conventionalized symbols are predominantly studied in an application where a sign language recognition system will be developed and integrated in an e-learning system to assist the learning process for deaf and hearing-impaired children of Dutch sign language vocabulary. The focus is on detection and tracking of the hand/arm movements and the extraction of relevant features for recognition. CACTUS, 2002-2004, EZ/Freeband K.I., 1.350 M€, TUD-EWI-mm-cgcc, TUD-EWI-st-pds. In this project we concentrate on the interaction between a user and his mobile device and between the mobile device and the network. Specific research questions concern the discovery of available foreign "resources" and the willingness of users and devices to share their own resources. AUTHENTICITY, 2004-2007, NOW/TOKEN2000, 300 k€. Authenticity determination and dating of works of art play an important role in the field of art history. In the AUTHENTIC-project it is investigated how existing and new techniques from digital image processing and knowledge discovery (data mining) can be developed and applied in order to support the process of determination of authenticity, dating and the assessment of other characteristics of both graphic art and paintings. REMBRANDT PROJECT, 2004-2007, NTWO/TOKEN2000, 300 k€. In this project methods for automatic extraction of watermarks and features concerning the paper structure are developed. On the basis of these features, etchings printed on similar papers can be recognized by means of automatic matching procedures. With this questions concerning authenticity and dating can be answered. Since the aim is to construct a database of all the papers used by Dutch artists, specific attention is paid to how to make this database self-organizing and self-learning. This requires the application of advanced techniques from computational intelligence. I-SHARE, 2004-2008, EZ BSIK/Freeband, 8 M€, TUD-EWI-st-pds. Sharing resources in virtual communities for storage, communications and processing of multimedia data. The FREEBAND I-SHARE-project investigates the sharing resources in virtual communities, which are (dynamic) groups of nodes that are willing to collaborate for the better of the whole. In particular, I-SHARE considers the sharing of resources for processing, transmitting and storing multimedia streams: - Funtionality sharing. Specific capabilities of terminals embodied in algorithms – or, more abstractly, in services – are shared to support applications and to form new ones. - Content sharing. This pertains to particular assets related to local hardware. We think of processing power and storage to start with, but specific processing hardware (co-processors) and special purpose hardware are possible as well. VIDEO-AT-YOUR-FINGERTIPS, 2004-2008, EZ/OC&W BSIK/Multimedian, 2,5 M€. The goal of this project is video content extraction technology suited for practical use in selectec application contexts. The basis of this technology consists of video content analysis algorithms, which include the modeling of the semantic content in terms of signal processing and analysis routines, and the methods of implementing the content models in software or hardware. In particular, Video-at-your-fingertips considers the following research topics: 1. Robust, unconstrained face detection and recognition with applications in security (smart camera's) and media (consumer home video). 2. Human body motion analysis with applications in surveillance (suspicious behavior and aggression detection) and personal health care (revalidation at home). 3. Video content management: The parsing, pruning, abstracting, summarization and classification of video content with a Video Concert Browser as media application. Papers in international journals Cai, R , Lu, L , Hanjalic, A & Cai, LH (2006). A flexible framework for key audio effects detection and auditory context inference. Ieee transactions on speech and audio processing, (ISSN 1063-6676), 14(3), 1026-1039. Hanjalic, A (2006). Extracting moods from pictures and sounds. Ieee signal processing magazine, (ISSN 1053-5888), 23(2), 90-100.


Haratcherev, IJ , Taal, JR , Langendoen, KG , Lagendijk, RL & Sips, HJ (2006). Optimized video streaming over 802.11 by cross-layer signaling. Ieee communications magazine, (ISSN 0163-6804), 44(1), 115-121. Holt, GA ten , Hendriks, P & Andringa, T.C. (2006). Why don't you see what I mean? Prospects and limitations of current automatic sign recognition research. Sign Language Studies, (ISSN 0302-1475), 6(4), 416-437. Kankanhalli, MS , Wang, J & Jain, R (2006). Experiental sampling in multimedia systems. Ieee transactions on multimedia, (ISSN 1520-9210), 8(5), 937-946. Shterev, ID & Lagendijk, RL (2006). Amplitude scale estimation for quantization-based watermarking. Ieee transactions on signal processing, (ISSN 1053-587X), 54(11), 4146-4155. Visser, M de , Schwering, PBW , Groot, JF de & Hendriks, EA (2006). Passive ranging using an infrared search and track sensor. Optical engineering, (ISSN 0091-3286), 45(2), 026402-1-026402-14. Doctoral Degrees Haratcherev, IJ (2006, maart 14). Application-oriented link adaptation for IEEE 802.11. TUD Technische Universiteit Delft (110 pag.) (ISBN 90-9020513-6). Prom./coprom.: Prof.dr.ir. HJ Sips & Prof.dr.ir. RL Lagendijk (ISBN 90-9020513-6). 2e geldstroom. Persa, SF (2006, juni 06). Sensor fusion in head pose tracking for augmented reality. TUD Technische Universiteit Delft (169 pag.) (ISBN 90-9020777-5). Prom./coprom.: Prof.dr. IT Young & Prof.dr.ir. RL Lagendijk (ISBN 90-9020777-5). 2e geldstroom. Contributions to international conference proceedings Celik, H , Hanjalic, A & Hendriks, EA (2006). Towards a robust solution to people counting. In s.n. (Ed.), Proceeding 2006 IEEE International Conference on Image Processing (pp. 2403-2406). USA: IEEE (ISBN 1-4244-0481-9). Deac, AI , Lubbe, JCA van der & Backer, E (2006). Feature selection for paintings classification by optimal tree pruning. In B Gunsel, AK Jain, AM Tekalp & B Sankur (Eds.), Multimedia content representation, classification and security Vol. 4105. Lecture notes in computer science, (ISSN 0302-9743) (pp. 354-361). Berlin/Heidelberg, Germany: Springer (ISBN 3-540-39392-7). Doets, PJO & Lagendijk, RL (2006). Extension of a stochastic model for the Philips audio fingerprint. In JH Weber & RL Lagendijk (Eds.), Proceedings of the twenty-seventh symposium on information theory in the Benelux (pp. 189-196). Delft: Werkgemeenschap Informatie- en Communicatietheorie (WIC) (ISBN 90-71048-22-5). Doets, PJO, Menor Gisbert, M. & Lagendijk, RL (2006). Comparing audio fingerprints for extracting quality parameters of compressed audio. In BPF Lelieveldt, B Haverkort, CTAM de Laat & JWJ Heijnsdijk (Eds.), Proceedings of the twelfth annual conference of the Advanced School for Computing and Imaging (pp. 284-291). Delft: ASCI (ISBN 90-810849-1-7). Gedrojc, B , Cartrysse, K & Lubbe, JCA van der (2006). Private bidding for mobile agents. In M Malek, E Fernández-Medina & J Hernando (Eds.), Proceedings of the international conference on security and cryptography (SECRYPT 2006) (pp. 277-282). Portugal: INSTICC. Gedrojc, B & Lubbe, JCA van der (2006). Private matching of noisy data. In JH Weber & RL Lagendijk (Eds.), Proceedings of the twenty-seventh symposium on information theory in the Benelux (pp. 275-282). Delft: Werkgemeenschap Informatie- en Communicatietheorie (WIC) (ISBN 90-71048-22-5). Hanjalic, A , Sebe, N & Chang, E (2006). Multimedia content analysis, management and retrieval: trends and challenges. In EY Chang, A Hanjalic & N Sebe (Eds.), Proceedings Electronic Imaging Sicence and Technology


"Multimedia Content Analysis, Management and Retrieval 2006 (pp. 607301-1-607301-5). USA: IS&T / SPIE (ISBN 0-8194-6113-X). Kohlweiss, M & Gedrojc, B (2006). Privacy friendly location based service protocols using efficient oblivious transfer. In F Armknecht & D Stegemann (Eds.), Book of abstracts of the Kryptowochenende Juli 2006 (pp. 29-32). s.l.. Lichtenauer, JF , Hendriks, EA & Reinders, MJT (2006). 3D versus 2D pose information for recognition of NGT signs. In JH Weber & RL Lagendijk (Eds.), Proceedings of the twenty-seventh symposium on information theory in the Benelux (pp. 291-298). Delft: Werkgemeenschap Informatie- en Communicatietheorie (WIC) (ISBN 90-71048-22-5). Lu, L , Cai, R & Hanjalic, A (2006). Audio elements based auditory scene segmentation. In s.n. (Ed.), Proceedings of the 2006 IEEE international conference on acoustics, speech and signal processing (ICASSP) (pp. V-17-V-20). USA: IEEE Signal Processing Society (ISBN 1-4244-0469-X). Lu, L & Hanjalic, A (2006). Towards optimal audio "keywords" detection for audio content analysis and discovery. In K Nahrstedt & M Turk (Eds.), Proceedings ACM Multimedia 2006 (pp. 825-834). NY, USA: ACM (ISBN 1-59593-447-2). Naci, SU & Hanjalic, A (2006). Low level analysis of video using spatiotemporal pixel blocks. In B Gunsel, AK Jain, AM Tekalp & B Sankur (Eds.), Multimedia Content Representation, Classification and Security Vol. 4105. Lecture notes in computer science, (ISSN 0302-9743) (pp. 777-784). Berlin-Heidelberg: Springer (ISBN 9783540393924). Pérez-González, F , Mosquera, C , Alvarez, M & Lagendijk, RL (2006). High-rate quantization data hiding robust to arbitrary linear filtering attacks. In EJ Delp & PW Wong (Eds.), Proceedings Electronic Imaging Science and Technology "Security, Steganography, and Watermarking of Multimedia Contents VIII" (pp. 60720C-1-60720C-12). USA: IS&T / SPIE (ISBN 0-8194-6112-1). Pogalin, E , Redert, PA Patras, I & Hendriks, EA (2006). Gaze tracking by using factorized likelihoods particle filtering and stereo vision. In M Pollefeys & K Daniilidis (Eds.), Proceedings 2006 Third International Symposium on 3D Data Processing, Visualization and Transmission 3DPVT 2006 (pp. 1-8). USA: IEEE. Ruijsscher, B de, Gaydadjiev, GN , Lichtenauer, JF & Hendriks, EA (2006). FPGA accelerator for real-time skin segmentation. In S. Ha & S Chakraborty (Eds.), Proceedings of the 2006 IEEE/ACM/IFIP Workshop on Embedded Systems for Real Time Multimedia (pp. 93-97). US: IEEE (ISBN 0-7803-9783-5). Staalduinen, M van , Backer, E & Lubbe, JCA van der (2006). Adaptive scale selection for robust mode seeking. In JH Weber & RL Lagendijk (Eds.), Proceedings of the twenty-seventh symposium on information theory in the Benelux (pp. 125-132). Delft: Werkgemeenschap Informatie- en Communicatietheorie (ISBN 90-71048-22-5). Staalduinen, M van , Lubbe, JCA van der , Dietz, G , Laurentius, F & Laurentius, T (2006). Comparing X-ray and backlight imaging for paper structure visualization. In V Cappellini & J Hemsley (Eds.), Proceedings of the Electronic imaging & The visual arts conference (pp. 108-113). Florence, Italy: Università di Firenze (ISBN 88-371-1610-1). Staalduinen, M van , Lubbe, JCA van der , Backer, E & Paclik, P (2006). Paper retrieval based on specific paper features: chain and laid lines. In B Gunsel, AK Jain, AM Tekalp & B Sankur (Eds.), Multimedia Content Representation, Classification and Security Vol. 4105. Lecture notes in computer science, (ISSN 0302-9743) (pp. 346-353). Berlin, Heidelberg: Springer (ISBN 9783540393924). Taal, JR & Lagendijk, RL (2006). Asymmetric multiple description coding using layered coding and lateral error correction. In JH Weber & RL Lagendijk (Eds.), Proceedings of the twenty-seventh symposium on information theory in the Benelux (pp. 39-44). Delft: Werkgemeenschap Informatie- en Communicatietheorie (ISBN 90-71048-22-5). Taal, JR & Lagendijk, RL (2006). Hybrid temporal-SNR multiple description coding for peer-to-peer television. In s.n. (Ed.), Proceedings of the Picture coding symposium (pp. 1-5). China: Tsinghua Univ./Microsoft Research (ISBN 3-00-018726-X).


Wang, J , Vries, AP de & Reinders, MJT (2006). A user-item relevance model for log-based collaborative filtering. In M Lalmas, A MacFarlane, S Rüger, A Tombros, T Tsikrika & A Yavlinsky (Eds.), Advances in information retrieval Vol. 3936. Lecture notes in computer science, (ISSN 0302-9743) (pp. 37-48). Heidelberg: Springer. Wang, J , Vries, AP de & Reinders, MJT (2006). On combining user-based and item-based collaborative filtering. In JH Weber & RL Lagendijk (Eds.), Proceedings of the twenty-seventh symposium on information theory in the Benelux (pp. 307-315). Delft: Werkgemeenschap Informatie- en Communicatietheorie (WIC) (ISBN 90-71048-22-5). Wang, J , Pouwelse, JA, Fokker, JE & Reinders, MJT (2006). Personalization of a peer-to-peer television system. In G Doukidis, K Chorianopoulos & G Lekakos (Eds.), Proceedings of the 4th European conference on interactive television (pp. 147-155). Athens, Greece: Athens University of Economics and Business. Wang, J , Vries, AP de & Reinders, MJT (2006). Unifying user-based and item-based collaborative filtering approaches by similarity fusion. In S Dumais, EN Efthimiadis, D Hawking & K Järvelin (Eds.), Proceedings of the twenty-ninth annual international ACM SIGIR conference on research and development in information retrieval (pp. 501-508). New York, USA: The Association for Computing Machinery (ISBN 1-59593-369-7). Wang, Jinshen , Shterev, ID & Lagendijk, RL (2006). Scale estimation in two-band filter attacks on QIM watermarks. In EJ Delp & PW Wong (Eds.), Proceedings Electronic Imaging Science and Technology "Security, Steganography, and Watermarking of Multimedia Contents VIII" (pp. 60720B-1-60720B-10). USA: IS&T / SPIE (ISBN 0-8194-6112-1). Westerlaken, RP , Borchert, S , Klein Gunnewiek, R & Lagendijk, RL (2006). Dependency channel modeling for a LDPC-based Wyner-Ziv video compression scheme. In s.n. (Ed.), Proceedings 2006 IEEE International Conference on Image Processing (pp. 277-280). USA: IEEE (ISBN 1-4244-0481-9).

2.4.2 Contribution of UL-LIACS Multimedia Information Retrieval We completed the first stage of research and experiments on the new paradigm of Artificial Imagination in multimedia information retrieval in the area of texture retrieval. The latest survey of the state of the art and grand challenges in the field was completed and published in the leading ACM Multimedia journal, and we served as advisers on the leading video analysis research evaluation project, TRECVID. Human Computer Interaction In this research theme we have explored interactive tracking of humans in real time video, and also completed a beta-version of the first 3D-structure integrated audio-video massive multiplayer virtual world over the Internet. In addition, we completed the first stage of a research survey on HCI through organizing the primary European scientific meeting on human-computer interaction. Bioinformatics Developed new algorithms for genotype/phenotype data mining. The development of an Hidden Markov Model based classifier for biological imagery was completed and tested under a wide variety of different tissue samples. A new method for viewing the development of micro-tubules was completed. External projects VIRSI, 2006-2009, NWO, BSIK/BRICKS/FOCUS, 400 KEuro This project aims at developing a new paradigm called artificial imagination within the scope of multimedia information retrieval. In this new paradigm, we investigate how the computer can actively synthesize imagery to improve relevance feedback based retrieval.


CYTTRON, 2004-2008, BSIK, 8.8MEuro, TUD, UU In this project, we are developing the first super microscope based on the implementation of the various forms of bio-imaging techniques toward creating a virtual window on the machinery of life and a comprehensive, integrated infrastructure for bio-imaging and modeling cells down to atomic detail. CMSB DIAL, 2004-2007, Dutch Government, 16MEuro, VUA DIAL investigates the integration and analysis of phenotype and genotype data sets from different CMSB research groups. Books Huang, T., Sebe, N., Lew, M., Pavlovic, V., Kolsch, M., Galata, A., Kisacanin, B.; Computer Vision in Human-Computer Interaction. 2006, Springer, Lecture Notes in Computer Science (LNCS) Vol. 3979, ISBN 978 3 540 34202 1,first edition. Papers in international journals (only international journals) Lew, M. , Sebe, N., Djeraba, C., Jain R.; Content-based Multimedia Information Retrieval: State of the Art and Challenges. ACM Transactions on Multimedia Computing, Communications, and Applications (ISSN 1551-6857) volume 2, 2006, 1, pp. 1-19. Ghafoor, A., Zhang, Z., Lew, M., Zhou, Z.; Introduction to machine learning approaches to multimedia information retrieval. ACM Multimedia Systems Journal (ISSN 0942-4962) Vol. 12, No. 1, 2006, pp. 1-2. Contributions to international conference proceedings (only international congresses) Yu, F. and Ip, H.; Automatic Semantic Annotation of Images Using Spatial Hidden Markov Model. Proceedings of International Conference on Multimedia and Expo (ICME 2006), Hong Kong, 2006, IEEE Computer Society, pp. 305-308. Yu, F. and Ip, H.; Spatial-HMM: A new approach for Semantic Annotations of Histological Images. Proceedings of International Conference on Pattern Recognition (ICPR 2006), 2006, IEEE Publications, pp. 663-666. Experimental software Sicking, F.J., Bakker, E.M.; CGH Database 2003-2006 PHP, SQL, UNIX This software consolidates the micro array CGH experimental data of micro array facilities at different university medical centres. Thomee, B., Lew, M.; The Matrix 2005-2006 C++, Windows XP This software was designed to allow thousands of people over the Internet to share their ideas, culture, and knowledge in a realistic 3D virtual world using both audio and visual communication. Cooperation within ASCI With Uva-ISLA (Intelligent Systems Laboratory Amsterdam): Huang, T., Sebe, N., Lew, M., Pavlovic, V., Kolsch, M., Galata, A., Kisacanin, B.; Computer Vision in Human-Computer Interaction. 2006, Springer, Lecture Notes in Computer Science (LNCS) Vol. 3979, ISBN 978 3 540 34202 1, first edition. Lew, M. , Sebe, N., Djeraba, C., Jain R.; Content-based Multimedia Information Retrieval: State of the Art and Challenges. ACM Transactions on Multimedia Computing, Communications, and Applications (ISSN 1551-6857) volume 2, 2006, 1, pp. 1-19.


2.4.3 Contribution of UVA-FdNWI-isis Systems for retrieval of video In the theme systems for retrieval of video, we aim to make multimedia archives accessible. To that end, our research efforts concentrate on automatic semantic indexing and interactive retrieval of multimedia sources. To value the merit of our efforts on high international standards, all research is and will be evaluated within the TRECVID benchmark for multimedia retrieval. To this end, we have developed the MediaMill semantic video search engine which uses a lexicon of detectable concepts in combination with several advanced user interfaces. The MediaMill system obtained the highest score for the interactive video retrieval task of TRECVID 2005. The topic on retrieval of video has led a Ph.D. thesis by C. Snoek entitled "The Authoring Metaphor to Machine Understanding of Multimedia" and many publications in journals (e.g. IEEE Trans. on Multimedia). We will continue this line of research with a further integration of multi-media sources, a further understanding of the structure of video documents and interactive access to the semantic content of large collections of multi-media information using advanced interfaces. The year 2005 has been a period of change for software engineering from the large complex and abstract Horus system which is now completed to smaller targets systems solving one computer vision task at the time but completely. The Monet database kernel and its modules for image and geo-spatial reasoning are realized in close co-operation with the CWI-database group. In the area of database kernels, an innovative experimental analysis uncovered the lack of performance improvement in database technology over the last decade. The underlying reason is the relative progress in CPU- and RAM-technology, which shows an increasing performance bottleneck. As a result, traditional database solutions use less then a few percent of the available resources. This observation has led to novel techniques to measure the resource waste and new database algorithms to avoid resource stales. A separate topic is the study of parallelism in multimedia processing tasks. The purpose of the research is to anticipate on future generation computer systems while constructing a parallel processing library compatible with Horus. The developed parallel software has been applied in the 2005 TRECVID competition. 2006 and beyond With first priority we will increase the effectiveness of our solutions in image retrieval and image search engines by expanding on our experience with learning from image databases. Computational efficiency of image search engines will be increased by the joint development with spatial and extensible databases. This is important as it will open up domains of hundreds of thousands of images, a significant step towards data-mining the content. At the same time, we aim to expand to create full access to multimedia documents. The integration of information from text and pictures is a very interesting topic both scientifically, as it reveals a lot about the nature of information, as well as practically as multimedia documents will be ubiquitous as is the need for their access. The MultimediaN project provides the opportunity to reach this goal with the intended delivery of a large-scale experimentation platform for multimedia information analysis. Concerning color research, we aim at the extraction of invariants from interesting regions of the image. Regions improve on the robustness when compared to strictly local interest point based object recognition. For instance, from color distributions we may derive appearance properties. Further, we aim at exploiting distributions of color edges to derive texture properties. We will concentrate on regions that are interesting from an information theoretical point of view. To increase the specifity of regions, we will incorporate the statistics of regions throughout the ALOI collection. We consider this collection to be a natural starting point for visual cognition. Over the years we have invested in a new, object-oriented software platform for vision. By the end of the year we hope to deliver a first complete system for internal use with an expected life time of 10 years. Further, the available parallel functionality to heterogeneous wide-area Grid systems is projected to be extended in 2005. The main focus is on the development of an efficient and easy-to-use execution model based on so-called Multimedia Grid Services, i.e. high-performance multimedia functionality that can be invoked from within sequential applications running on a standard desktop machine. A key example is our Aibo robot dog, whose video data is being processed at multiple cluster systems all over the globe. This research direction is prioritized with the arrival of the new Distributed ASCI Supercomputer 3 (DAS-3), which is co-financed by the MultimediaN consortium.


3 ASCI-wide Events

3.1 Cooperation within ASCI Distributed ASCI Supercomputer DAS 2 and DAS 3 The DAS 2 will be succeeded by DAS 3: 2005-2009, NWO-EW, 900 KEuro, cooperation with all partners of the ASCI graduate school and SURFnet. A Computer Science Grid with revolutionairy Optical interconnect. DAS-3 (Distributed ASCI Supercomputer) is a wide-area distributed system designed by the Advanced School for Computing and Imaging (ASCI). As one of its distinguishing features, DAS-3 employs a very novel internal wide area interconnect based on light paths. The DAS-3 system is used for research on parallel and distributed computing and imaging. DAS-3 consists of 272 compute nodes, spread out over five clusters, located at the four universities: Vrije Universiteit, Amsterdam (VU), Leiden University (LU), University of Amsterdam (UvA), Delft University of Technology (TUD), The MultimediaN project (UvA-MN). The system is currently being built by ClusterVision. Unlike its predecessor, DAS-2, DAS-3 is rather heterogeneous in design. “ADVAnCE: Automatic Diagnostic Vascular Analysis of CTA Examinations”. Senter grant, 600 kEuro: 2005-2009. In this project, computer aided diagnosis techniques will be developed to support the analysis of CTA data in clinical practice, to improve the workflow of cardiovascular diagnosis. EUR-RMI-bigr collaboration with LKEB-Leiden AMIS NWO, UvA-Science-ISIS, UU-CS, UT-CS, TUD-CS. The project studies multi-media information analysis.

Architectures for scientific and medical visualization, Bsik VL-e (Virtual Laboratory for e-science) 2004 - 2007, postdoc, dr. C.P. Botha. The aim of this project is to extend the DeVIDE visualization architecture with more general facilities for grid-based computing (resource and data management) and intelligent techniques for semi-automatic network configuration and prototyping for component development. TUD-EWI-cgcc cooperation with LUMC (Reiber, Lelieveldt) and UvA (Belleman, Olabarriaga). Artemis STW/Progress,2005-2009, Euro 500K is a cooperation between the University of Amsterdam, Leiden University, Delft University of Technology and Philips Research, studies the design of Network-on-Chip (NoC) based MP-SoCs. Our role in this project constitutes of developing a high-level modeling and simulation framework for system-level design space exploration of these NoC-based MP-SoCs. ARTEMISIA 2004-2009, Progress/STW, 930 K Eur. Leiden University, Delft University of Technology, University of Amsterdam, Philips Research Value: 1 Ph.D. student, 1 Post-Doc Sponsor: PROGRESS, Philips Research The project includes the following: Firstly, translate given applications input-output equivalent process networks (an automated translator does exist for a restricted class of applications and is called Compaan. Secondly, model the platform, the architecture templates derived from it as well as the instantiation of these to architectures. Also on a high level of abstraction.Thirdly, provide low-level performance/cost numbers for the processing units on the architecture so that high-level performance/cost numbers are well calibrated and, hence, sufficiently accurate (a calibration tool/platform does exist for a restricted class processing units and is called Laura. A more advanced calibration tool/platform is to be developed/designed within Artemisia. A structure for maintaining a shared world model in a dynamic environment between differentiated Embedded Systems and their interaction with human supervisors 2001-2006, 490 kf We study embedded autonomous systems in distributed environments, for applications in public safety; monitoring and control of traffic and environmental conditions; assistance and clean-up work in disaster areas. Collaboration between systems requires a collective world model, and we develop methods for its consistency


maintenance, in time-critical situations. We use robot soccer (RoboCup) as a case study. This project is a collaboration between UvA and the VU and is sponsored by Progress. Beyond the Ordinary: Design of Embedded Real-time Control (BODERC) 2003-2007. Senter, 2.5 M€, Océ Technologies, Philips CFT, AAS, Imtech ICT, Chess iT, Katholieke Universiteit Nijmegen, Universiteit Twente, TU/e The Boderc project focuses on distributed embedded real-time controllers of complex systems. An Océ printer is taken as a case-study and acts as a driver for the project. The target is an integral approach for a systematic architectural design, modeling, analysis, and validation methodology for such heterogeneous systems. BRICKS, Bsik 2004-2008, subproject Modelling, Simulation and Visualization, 320 KEuro Our subproject concentrates on interaction with virtual environments. In particular we work on navigation through virtual environments and manipulation of objects in virtual environments. UU and other ASCI groups in Delft and CWI are involved in this project as well. A computational theory for visual cognition (NWO Veni) 2003-2007, NWO, TUD-EWI- cgcc, Uva-Science-ISIS, 200 KEuro. The project aims at developing a computational theory of vision based on invariant representations. CoreGRID 2004-2008, EU (Network of Excellence), EURO 38.000, ASCI partners TUD, VU. This network integrates the grid research of 42 universities in Europe. CIM 2003-2007, Senter, 300k€. TUD-EWI, VU, CWI, Almende, This project aims at the development and specification of distributed incident management techniques. COMBINED systems 2002-2006, 800kE In this project innovative methods for disaster management are being studied. In particular aspects concerning distributed observation systems are investigated. An important property of distributed observation systems is that they autonomously extract information from the monitored area. This information is shared with other services in the disaster management platform. The project is conducted in cooperation with UvA, TUDelft, Thales en TNO within the DECIS laboratory.

CSI The CSI project is a close collaboration between LIACS of Leiden University and the CE Laboratory of TU Delft. CSI Media Architecture. The Complex Streamed Instruction Set Architecture (CSI) is a memory-to-memory vector architecture targeted at multimedia applications. A single CSI instruction can process data streams of arbitrary length and, in addition to traditional arithmetic and logical operations, performs data accesses, conversion between storage and computation formats (packing and unpacking), and complex arithmetic hardwired computation. The main new features of the CSI are elimination of the vector sectioning instructions, elimination of the packing/unpacking instructions, and introduction of new complex media related arithmetic instructions.

CYTTRON Bio-Computing Search Project 2004-2008 BSIK, Bsik, 8.8 MEuro with UL-LUMC, UL-WI-I and TUD-TNW-tn-qi: Development of a comprehensive, integrated infrastructure for bio-imaging and modeling cells down to atomic detail. The Cyttron consortium wants to implement a comprehensive, integrated infrastructure for bio-imaging and modeling cells down to atomic detail. We would like to provide a generic tool for identifying the molecular causes of disease, essential for the prevention of disease and the development of new drug and therapies, and to establish a platform for advanced diagnosis and tuning of individualized therapy, increasing effectiveness in health care.


“3D Multimodal vascular image analysis for improved diagnosis and therapy” NWO STW VICI grant, 1,25 MEuro: 2006-2010 In this project, methods for the integrated analysis of vascular imaging data obtained with various imaging techniques will be developed and evaluated. The focus is on the analysis of the diseased vessel wall, so as to improve diagnosis of cardiovascular diseases, and to monitor and guide their treatment. EUR-RMI-bigr collaboration with Applied Physics, Delft. Fexible Application Mapping Environment (FAME) 2002-2006, NOW-EW, Leiden University, Delft University of Technology, TUE The FAME project aims at developing a novel approach to program optimization, namely, iterative compilation in which the transformation space is searched and profiling is used to measure the impact of transformations. One of the most important goals of this project is to develop heuristics to control the complexity of the search by using analytical models and domain specific knowledge. Freeband/PNP2008 SIK, 500 kEuro (DACS) . Cooperation project between UT and TUDelft, Philips, KPN, WMC,and TNO, to research and develop a Personal Network, focussing on the prototyping of a Personal Mobile Gateway. Gigaport NG Research on Networks, 2005-2007, BSIK, 150KE, UvA & TUD. Within this project the UT investigates self-management of hybrid IP/ Optical networks, and the measurement of traffic flows within such networks. The project is managed by SURFnet, and supports the introduction of SURFnet6. Globule 2003-2007, KEURO 147,(a.o.Proactive Construction of Semantic Overlay Networks) The work on Globule and other peer-to-peer related research is done a cooperation between the VU-WI-i and TUD-EWI-st-pds, TUD-ti-ki. There has been a joint NWO proposal (granted). I-SHARE (part of Freeband) 2004-2008, EZ BSIK/Freeband, 8 M€, TUD-EWI-st-pds. Sharing resources in virtual communities for storage, communications and processing of multimedia data. The FREEBAND I-SHARE-project investigates the sharing resources in virtual communities, which are (dynamic) groups of nodes that are willing to collaborate for the better of the whole. In particular, I-SHARE considers the sharing of resources for processing, transmitting and storing multimedia streams: - Funtionality sharing. Specific capabilities of terminals embodied in algorithms or, more abstractly, in services are shared to support applications and to form new ones. - Content sharing. This pertains to particular assets related to local hardware. We think of processing power and storage to start with, but specific processing hardware (co-processors) and special purpose hardware are possible as well. “Model-driven spatiotemporal tracking for quantitative analysis of subcellular dynamics” NWO EW VIDI grant, 600 kEuro: 2005-2009 In this project, automated image analysis techniques for the accurate and reproducible quantification of the motion of subcellular structures from time-lapse fluorescence microscopy image data are developed and evaluated. EUR- RMI-bigr Collaboration with Applied Physics, Delft.

Multifield Medical Visualization NWO-VIEW, 2005-2010, 2 OIO, ir. J. Blaas and S. Busking, MSc. An increasing number of medical acquisition and processing techniques are generating large amounts of multi-field data, such as data from different imaging modalities. Many of these datasets are also time-varying, for example in heart motion studies. In this project, we want to transfer knowledge and techniques from closely related fields such as vector and tensor field visualization in scientific visualization, to medical visualization applications. Joint project TUD-ewi-cgcc with TUE-BME (ter Haar-Romeny, Vilanova). MultimediaN 2004-2008, BSIK, 35 MEuro, UvA-Science-ISIS, CWI, TUD-Mediamatica, UT-CTIT-CS, VU-CS, UU-CS, TNO, Nederlands Forensisch Instituut, Telematica Instituut, IBM, V2_, Philips, Ilse Media, LogicaCMG, Waag Society, DBNL, eMAXX, NOC*NSF, SPSS, Compano, Beeld en Geluid, FabChannel, ZiuZ, DBNL, de Politie Amstellanden, Vereniging


Digitaal Erfgoed, Roessingh. The project aims at various forms of multi-media, multi-modal analysis, interaction, system design and knowledge engineering for several scientific and applied science goals. RoboCup/Progress UvA, TUD -TN en VU, also UU (Siks) and TUD- ET (DISC). SCALPE 2004-2008, STW, EURO 220.000, ASCI partners VU and TUD This project deals with high-productivity methods for programming parallel systems on a chip. SmartCam 2002-2006. STW/PROGRESS, TUE-EE-dmes, Philips Natlab, Philips CFT, TNO-FEL, In3D, HP Bristol labs, 1.4 M€, TUD-TNW-tn-ph The SmartCam project investigates low-cost one-chip Smart Camera solutions, contributing to a quantitatively guided design trajectory. In particular, we investigate the impact of current applications, and we try to define relevant architectural parameters and to develop an architectural template. Other aims are to enhance and integrate existing application mapping environments for SIMD and ILP processors.

Surface and volume geometry processing for lesion detection and segmentation in virtual colonoscopy Philips Medical Systems, 2004-2008, 1 AIO, Lingxiao Zhao MSc.Research on the determination and use of geometric properties of the inner surface of the human colon for automatic pre-detection of colonic polyps. Invertigation of higher-order geometric properties (curvature) for claculation of distinctive features for polyp detection. TUD-EWI-cgcc Cooperation with TUD-TNW-QI (van Vliet).

Techniques for Collaborative Visualization in Virtual Environments, Bsik VL-e 2004-2007, post-doc, dr. M. Koutek. Techniques for distributed and collaborative visualization in virtual environments, and 3D interaction; design of software architectures for multi-platform collaborative VR support. TUD-EWI-cgcc cooperation with CWI (van Liere), VU (Bal) and TUD-PGS (Epema). Token2000 People: A.G. Hoekstra, P.M.A. Sloot, E.V. Zudilova, M. Scarpa, L. Abrahamyan ASCI partner: LKEB/LUMC (P.I.: Reiber). Token2000 is a nationally funded project (NWO), where we collaborate closely with the Universities of Leiden and Twente on the development of an interactive medical application, somewhat similar to the work in CrossGrid. This application is intended for training of surgeons. In collaboration with Leiden University Medical Centre we have created Hemosolve, a problem-solving environment for image based computational Haemodynamics. Hemosolve includes our L-BGK solver, but also a FEM Navier-Stokes solver. Moreover, it contains a 3D editing tool and powerful visualization modules. Project Trader 2004-2008, ESI, 1 AIO, TUD EWI/ UL-LERC/LIACS Modern systems such as household appliances, DVD players, PCs, medical X-ray imaging systems, printers, advanced vehicles, and airplanes rely increasingly on software, in particular for system integration. Embedded software monitors the whole system taking care that the system accomplishes more than its parts would. In such software intensive systems, reliability is of prime importance. Two-level Peer-to-Peer Systems 2003-2007, NWO, KEURO 147, ASCI partners TUD-EWI-pds, VU-group Large-Scale Distributed Systems. This project aims at exploring the notion of superpeers in p2p systems in order to improve the performance of such systems. The work on Globule and other peer-to-peer related research is done a cooperation between the VU-WI-I and TUD-ti-ki. Efforts continue in the Bsik IShare project, in which the TUD and VU jointly work on the Tribler.


Virtual Laboratory for e-Science (VL-e) 2004-2009, EZ (BSIK program), EURO 1.000.000 (TUD-EWI-st-pds part), ASCI partners TUD-EWI-mm-cgcc, VU-EW-cs-I, UvA-FdNWI-caps, UvA-FdNWI-scs. Amolf, Nikhef, CWI, SARA, IBM, LigicaCMG, Philips, FEI This projects aims at designing and implementing grid technology (schedulers, communication libraries, problem-solving and visualization environments, etc) for virtual laboratories (e.g., for simulations in the sciences) on top of the basic grid fabric.

3.2 ASCI 2006 Conference ASCI 2006 was the twelfth annual conference organized by ASCI. Apart from keynotes, and paper and poster presentations, the program consisted of theme presentations by senior ASCI researchers. Keynotes Bart de Moor from University of Leuven, Belgium. Bill St. Arnaud from CANARIE Inc, Canada. Tim Cootes from the University of Manchester.

About the conference Number of theme presentations 3 Number of poster presentations 28 Numer of paper presentations 32 Date: June 14-16, 2006 Location: Conference Center De Vossemeren, Lommel, Belgium Number of participants 120 Proceedings Lelieveldt, BPF; Haverkort, B; Laat, CTAM de; Heijnsdijk JWJ. Proceedings of the twelfth annual conference of the Advanced School for Computing and Imaging, De Vossemeren, Lommel, Belgium, June 14-16, 2006. ISBN 978-90-810849-1-8, Delft, 2006.

annual report 2006 versie4 - asci.tudelft.nl report 2006.pdf · asci annual report 2006 5 preface...

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