designing interactive visualisations to solve analytical problems in biology
TRANSCRIPT
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(Designing)
Interactive
Visualisations to
Solve Analytical
Problems (in biology) CAGATAY TURKAY,
giCentre, City University London
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Who?
• Lecturer in Applied Data Science @ the giCentre, CUL
• PhD @ VisGroup at Univ. of Bergen, Norway
• Research interests:– Integrating Computational Tools in Interactive Visual Analysis
Methods
– Perceptually Optimized Visualization
• Methods for several domains:– Biology, transport, intelligence, neuroscience
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giCentre (www.giCentre.net)
• 6 academics
• 2 researchers
• 5 PhDs
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Data supported science
• Data analysis in almost all scientific fields
–Biology, medicine, astronomy, psychology,…
• Data driven science
• Research in several fields
–Visualization
–Data Mining
–Machine Learning
–Statistics
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Visualization ?
“Computer-based visualization systems
provide visual representations of datasets
designed to help people carry out tasks more
effectively.” [Tamara Munzner, 2014]
“The use of computer-generated, interactive, visual
representations of data to amplify cognition”[Card,
Mackinlay, & Shneiderman 1999]
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VIS -- a mature field already
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Biological data + VIS:
A good synergy
.. but why?
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Why biology is interesting for VIS?
Datasets are large & heterogeneous
Yeast Protein interaction network, Barabási & Oltvai, 2004
Clustering miR expressions
http://gdac.broadinstitute.org/
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Why biology is interesting for VIS?
Things happen at multiple scales
[ by O’Donoghue et al., 2010]
[Nye, 2008]
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Why biology is interesting for VIS?
Processes are dynamic (spatio-temporal complexity)
Neutrophil chasing a bacteria by David Rogers
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Why biology is interesting for VIS?
• Computational methods are central in analysis
–Uncertainties hinder reliability
– Interpretation is a problem (black-box alg., little
context)
Comprehensive molecular portraits of human breast tumours, TCGA Network, Nature, 2012
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How can visualisation help?
• Ease of cognition & communication
• Relating multiple aspects
• Compare multiple computational outputs
• Investigate uncertainties
• Seamless integration of computation
and …
• Enable & foster hypothesis generation
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Forms of visualisation support
VIS as a presentation medium
+
VIS with interaction
+
VIS with integrated computations
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Visualisation as a
presentation medium
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Cross-section of Escherichia coli cell, Illustration by David S. Goodsell, the Scripps Research Institute
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106 diffusing and reacting molecules in real-time, Muzic et al., 2014
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NATURE METHODS: POINTS OF VIEW, by Wong et al.
http://blogs.nature.nom/methagora/2013/07/data-visualization-points-of-view.html
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Why is VIS good here?
• Analysts’ perceptual & cognitive capabilities
• Better interpretation
• Communication
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Visualisation
with interaction
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Example: MizBee - Synteny Browser
Meyer et al., MizBee: A Multiscale Synteny Browser, 2009
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Why is VIS good here?
• Linking multiple aspects
• Interactively varying the focus
• Display multiple-scales concurrently
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Visualisation with
integrated computations
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Combine the best of two worlds: human capabilities and
power
Facilitate the informed use of
computation through interactive visual methods
(a.k.a. Visual Analytics)
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Example: StratomeX, Caleydo
http://caleydo.org
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Pat
ien
ts (
sam
ple
s)
Genes
Candidate Subtype /Heat Map
Header /Summary of whole Stratification
Cancers have subtypes• different histology• different molecular alterations
Subtypes are identified by stratifying datasets, e.g.,
• based on an expression pattern• a mutation status• a copy number alteration• a combination of these
Case: Cancer Subtype Analysis
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Multiple Stratifications
Many shared Patients
Clustering 1 Clustering 2
Sample Overlaps
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Dependent PathwaysSlide by Alex Lex
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Slide by Alex Lex
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Multiple Stratifications (again)
Many shared Patients
Clustering 1 Clustering 2
Sample OverlapsG
en
e O
verl
ap
s ??
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Finding distinctive genes
Characterizing cancer subtypes using dual analysis in Caleydo StratomeX, Turkay et al., IEEE CG&A, 2014
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Finding distinctive genes (ex. BRCA types)
[*] Cancer Genome Atlas Network. (2012). Comprehensive molecular portraits of human breast tumours. Nature, 490(7418), 61-70.
Luminal-A
underexpressed genes
Luminal-A
overexpressed genes
Basal-like
overexpressed
Basal-like
underexpressed
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Ex: Cavity analysis in molecular simulations
Cavities on molecular surfaces
• Important in ligand binding
• Drug design, etc.
Long molecular simulations
Cavities are dynamic, hard to track
Amino-acids to characterize the
cavity
• hydrophobicity (grey)
• polarity (green)
• positively charged (blue)
• negatively charged (red) Visual Cavity Analysis in Molecular Simulations
J. Parulek, C. Turkay, N. Reuter, I. Viola. BMC Bioinformatics, 2013.
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1. Run the simulation
2. Fit graphs cavities
3. Compute measures
4. Find touching amino-acids
5. Perform visual analysis
Analysis of Proteinase 3
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A hydrophobic cavity
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Why is VIS good here?
• Multiple linked data sets – improve interpretation
• Multiple computational results – deal with
uncertainty
• Integrate computation outputs, i.e., clusters, derived
data
• Allows a fast-paced iterative process
• Quick idea prototyping
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Wrap up !
VIS as a presentation medium
+
VIS with interaction
+
VIS with integrated computations
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Visualisation is very good to answer
HOW & WHY?questions ..
- How do these genomes overlap?
- Why is this a cluster?
....
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Outlook
• Interaction and explorative analysis is key!
• Seamless support from integrated computation, i.e., t-tests
• Visual analysis as an everyday tool for analysts
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Thanks ! (& more biovis ?)
http://www.biovis.net
#biovis
Paper deadline: February 15, 2015
Data & Design Contests: May 1, 2015
• VisGroup (Helwig Hauser, Julius Parulek & Ivan Viola) and
Nathalie Reuter from University of Bergen
• Caleydo team (Alex Lex, Hanspeter Pfister, Nils Gehlenborg, Marc Streit)