july 2012 update july 12, 2012 andrew j. buckler, ms principal investigator, qi-bench
DESCRIPTION
July 2012 Update July 12, 2012 Andrew J. Buckler, MS Principal Investigator, QI-Bench. With Funding Support provided by National Institute of Standards and Technology. Agenda for Today. Approach, plans , and progress on Testing Analysis Modules Overview Bias- Linearity Demo - PowerPoint PPT PresentationTRANSCRIPT
July 2012 UpdateJuly 12, 2012
Andrew J. Buckler, MSPrincipal Investigator,
QI-Bench
WITH FUNDING SUPPORT
PROVIDED BY NATIONAL
INSTITUTE OF STANDARDS AND
TECHNOLOGY
Agenda for Today• Approach, plans, and progress on Testing• Analysis Modules
– Overview– Bias-Linearity Demo
• Second development iteration
22222222
Testing: System Under Test• Funtionality perspective:
– Specify, Formulate, Execute, Analyze, Package• Range of supported information:
– _loc, _dcm, _seg, _chg, and _cov data types
33333333
44444444
55555555
66666666
77777777
88888888
SUBJID ARM DOSE REGION AGE COUNTRY RACE SEX
99999999
1010101010101010
Testing: Risk-based, Multiple Scopes• Risk analysis (RA) specifies what level of
unit/module, integration, verification, and validation is needed based on application
• Validation itself: – Installation Qualification (IQ)– Operational Qualification (OQ)– Performance Qualification (PQ):
• capacity• speed• correctness (including curation and computation) • usability• utility
1111111111111111
TEST PLANS, PROTOCOLS, AND REPORTS
1212121212121212
Analysis ModulesModule Specification Status
Method Comparison
Radar plots and related methodology based on readings from multiple methods on data set with ground truth
Currently have 3A pilot in R, not yet generalized but straightforward to do so.Plan to refine based on Metrology Workshop results and include case of comparison without truth also.
Bias and Linearity
According to Metrology Workshop specifications
Demonstrate version today that works from summary statistics, e.g., to support meta-analysis. Plan to add analysis of individual reads.
Test-retest Reliability
According to Metrology Workshop specifications
Prototype demonstrated last month.Plan to build real module in next month.
Reproducibility (including detailed factor analysis)
Accepts as input fractional factorial data of cross-sectional biomarker estimates with range of fixed and random factors, produces mixed effects model
Module under development that will support both meta-analysis as well as direct data.
Variance Components Assessment
Accepts as input longitudinal change data, estimates variance due to various non-treatment factors
Module under development to support direct data.
1313131313131313
1414141414141414
1515151515151515
1616161616161616
Second development iteration: content and priorities
FunctionalityTheoretical Base Test Beds
Domain Specific Language
Executable Specifications
Computational Model
Enterprise vocabulary / data service registry
End-to-end Specify-> Package workflows
Curation pipeline workflows
DICOM:• Segmentation objects• Query/retrieve• Structured Reporting
Worklist for scripted reader studies
Improved query / search tools (including link of Formulate and Execute)
Continued expansion of Analyze tool box
Further analysis of 1187/4140, 1C, and other data sets using LSTK and/or use API to other algorithms
Support more 3A-like challenges
Integration of detection into pipeline
Meta-analysis of reported results using Analyze
False-positive reduction in lung cancer screening
Other biomarkers
1717171717171717
1818
Value proposition of QI-Bench• Efficiently collect and exploit evidence establishing
standards for optimized quantitative imaging:– Users want confidence in the read-outs– Pharma wants to use them as endpoints– Device/SW companies want to market products that produce them
without huge costs– Public wants to trust the decisions that they contribute to
• By providing a verification framework to develop precompetitive specifications and support test harnesses to curate and utilize reference data
• Doing so as an accessible and open resource facilitates collaboration among diverse stakeholders
1919
Summary:QI-Bench Contributions• We make it practical to increase the magnitude of data for increased
statistical significance. • We provide practical means to grapple with massive data sets.• We address the problem of efficient use of resources to assess limits of
generalizability. • We make formal specification accessible to diverse groups of experts that are
not skilled or interested in knowledge engineering. • We map both medical as well as technical domain expertise into
representations well suited to emerging capabilities of the semantic web. • We enable a mechanism to assess compliance with standards or
requirements within specific contexts for use.• We take a “toolbox” approach to statistical analysis. • We provide the capability in a manner which is accessible to varying levels of
collaborative models, from individual companies or institutions to larger consortia or public-private partnerships to fully open public access.
2020
QI-BenchStructure / Acknowledgements• Prime: BBMSC (Andrew Buckler, Gary Wernsing, Mike Sperling, Matt Ouellette, Kjell Johnson, Jovanna
Danagoulian)
• Co-Investigators– Kitware (Rick Avila, Patrick Reynolds, Julien Jomier, Mike Grauer)– Stanford (David Paik)
• Financial support as well as technical content: NIST (Mary Brady, Alden Dima, John Lu)
• Collaborators / Colleagues / Idea Contributors– Georgetown (Baris Suzek)– FDA (Nick Petrick, Marios Gavrielides) – UMD (Eliot Siegel, Joe Chen, Ganesh Saiprasad, Yelena Yesha)– Northwestern (Pat Mongkolwat)– UCLA (Grace Kim)– VUmc (Otto Hoekstra)
• Industry– Pharma: Novartis (Stefan Baumann), Merck (Richard Baumgartner)– Device/Software: Definiens, Median, Intio, GE, Siemens, Mevis, Claron Technologies, …
• Coordinating Programs– RSNA QIBA (e.g., Dan Sullivan, Binsheng Zhao)– Under consideration: CTMM TraIT (Andre Dekker, Jeroen Belien)
2121