BIOwulf BIOwulf Radiology Radiology BIOwulf R A D I O L O G Y BIOwulf Technologies Genomics Radiology
Jan 04, 2016
BIOwulf
BIOwulf Radiology
Radiology
BIOwulf
RADIOLOGY
BIOwulf
TechnologiesGenomics
Radiology
BIOwulf
•Company Overview•Analytics•Current Projects•Future Applications
AgendaBIOwulf
RADIOLOGY
Company OverviewBIOwulf
BIOwulf
RADIOLOGY
People
Technology
Applications
Intellectual Property
Company OverviewBIOwulf
BIOwulf
RADIOLOGY
People
•Washington University
•St. Louis University
•Chief of Diagnostic Radiology
•25 years of practice
Garry Carls,M.D., M.B.A.
Garry Carls has Radiology experience in both the academic
and private practice arenas.
Company OverviewBIOwulf
BIOwulf
RADIOLOGY
People
•University of Pittsburgh
•Purdue University
•20+ Medical and Technical journals
•NCI – Ovarian cancer detection
Hong Zhang,Ph.D.
While attending college, Hong Zhang won a national
math competition in China.
Company OverviewBIOwulf
BIOwulf
RADIOLOGY
People
•Academy of Sciences in USSR
•Institute of Electrical Communications
•150+ published papers
•Pattern recognition
Shelia Guberman, Ph.D.
Shelia Guberman authored the first applied pattern
recognition program.
Company OverviewBIOwulf
BIOwulf
RADIOLOGY
People
•Illinois State University
•Merck Pharmaceuticals
•Analytical biochemistry
•Finance and marketing
Tony Barnes,Ph.D., M.B.A.
Tony Barnes holds a Ph.D. in analytical biochemistry from the
University of Illinois.
PHOTO
Company OverviewBIOwulf
BIOwulf
RADIOLOGY
PeoplePeople
Management Team
Peter Farley, M.D., MBA
Tony Barnes, Ph.D., MBA
Garry Carls, M.D., MBA
Russ Clark, JD
Katherine DeYoung, Ph.D.
Isabelle Guyon, Ph.D.
Ramananda Madyastha, M.D., Ph.D
Mary Napier, MS
Tim O’Hayer
Trey Rossiter, MBA
Michael Stern, MBA
Company OverviewBIOwulf
BIOwulf
RADIOLOGY
PeoplePeople
Mathematical Team
Peter Bartlett, Ph.D.
Asa Ben-Hur, Ph.D.
Olivier Bousquet, Ph.D.
Olivier Chappelle, Ph.D.
Nello Christianini, Ph.D.
Rene Doursat, Ph.D.
Andre Elisseeff, Ph.D.
Shelia Guberman, Ph.D.
Isabelle Guyon, Ph.D.
Bernhard Schoelkopf, Ph.D.
Vladimir Vapnik, Ph.D.
Jason Weston, Ph.D.
Hong Zhang, Ph.D.
Company OverviewBIOwulf
BIOwulf
RADIOLOGY
PeoplePeople
Science Advisory BoardVladimir N. Vapnik, Ph.D. (Co-Chairman)
AT&T Labs - Research
Herbert A. Fritsche, Jr., Ph.D. (Co-Chairman) University of Texas M.D. Anderson Cancer Center
Daniel W. Chan, Ph.D.John Hopkins University School of MedicineThe John Hopkins Hospital
Alexey Chervonenkis, Ph.D.Institute of Control Sciences, Russian Academy of
Sciences
Jeffery Cossman, M.D.Georgetown University Medical Center
Alex Gammerman, Ph.D.Royal Holloway College, University of London
Company OverviewBIOwulf
BIOwulf
RADIOLOGY
PeoplePeople
Science Advisory BoardFederico Girosi, PH.D.
Harvard University
Kelvin G. Lynn, Ph.D. Boeing Chair, Washington State University
Tomaso A. Poggio, Ph.D.Massachusetts Institute of Technology
Thomas A. Stamey, M.D.Stanford University School of Medicine
Morton Schwartz, Ph.D.Memorial Sloan-Kettering Cancer Center
John F.R. Robertson, M.D.The University of Nottingham
Company OverviewBIOwulf
BIOwulf
RADIOLOGY
PeoplePeople
Collaborations
Johns Hopkins University
M.D. Anderson Cancer Center
Stanford University
University of Nottingham
University of Cincinnati
Company OverviewBIOwulf
BIOwulf
RADIOLOGY
TechnologyTechnology
Supervised machine learning techniques
including Support Vector Machines.
Company OverviewBIOwulf
BIOwulf
RADIOLOGY
Applications
Life Sciences
Imaging
Financial
Seismic Geological
Telecom Internet
QualityManagement
Military
Company OverviewBIOwulf
BIOwulf
RADIOLOGY
Intellectual Property
Patents Issued & Pending 09/303,386 Pre-Processing and Post Processing for Enhancing Knowledge Discovery
Using Support Vector Machines.
09/303,387 Enhancing Knowledge Discovery Using Multiple Support Vector Machines.
09/303,389 Optimal Categorization of a Continuous Variable.
09/305,345 Enhancing Knowledge Discovery Using Support Vector Machines in a
Distributed Network Environment.
PCT/US99/09666 Pre-processing and Post Processing for Enhancing Knowledge DiscoveryUsing Support Vector Machines.
09/568,301 Enhancing Knowledge Discovery From Multiple Data Sets Using Multiple
Support Vector Machines.
09/578,011 Enhancing Knowledge Discovery from Multiple Datasets using Multiple
Support Vector Machines.
Company OverviewBIOwulf
BIOwulf
RADIOLOGY
Intellectual Property
Patents Issued & Pending60/161,806 Applications of SVMs in Genomics and Cancer Research.
PCT/US00/14326 Enhancing Knowledge Discovery from Multiple Datasets using Multiple Support Vector Machines.
09/633,850 Methods of Identifying Patterns in Biological Systems and Methods of Uses Thereof.
09/633,616 Enhancing Biological Knowledge Discovery Using Multiple Support Vector Machines.
09/633,615 Methods of Identifying Biological Patterns Using Optimal Categorization of a continuous variable.
09/633,627 Methods of Identifying Biological Patterns in a Distributed Network andMultiple Data sets.
60/168,703 Applications of SVMs in Genomics and Cancer Research ALL/AMLLeukemia Classifier.
Company OverviewBIOwulf
BIOwulf
RADIOLOGY
Intellectual Property
Patents Issued & Pending60/184,596 Applications of SVMs in Genomics and Cancer Research (Colon Cancer).
60/191,219 Gene Selection for Cancer Classification Using Support Vector Machines.
60/207,026 Applications of SVMs in Genomics and Cancer Research ALL/AMLLeukemia Classifier.
AnalyticsBIOwulf
BIOwulf
RADIOLOGY
AnalyticsBIOwulf
BIOwulf
RADIOLOGY
Machine Learning
Advantages of Machine Learning
•Data driven, automated learning
•May handle highly complex systems
•Can detect subtle patterns
AnalyticsBIOwulf
BIOwulf
RADIOLOGY
Machine Learning
Inversion of Convoluted Data
AnalyticsBIOwulf
BIOwulf
RADIOLOGY
Machine Learning
Methodologies
Holistic
Analytic
AnalyticsBIOwulf
BIOwulf
RADIOLOGY
Machine Learning
Holistic Methods
AnalyticsBIOwulf
BIOwulf
RADIOLOGY
Machine Learning
Analytic Methods
Preprocessing Learning Machine
AnalyticsBIOwulf
BIOwulf
RADIOLOGY
Machine Learning
Analytic Tools
Radon
WaveletFFT
ANNKernel PCA
PCA LDA
SVM
Perceptron
HMM
Learning Machines
Feature Extraction
RKHS …
…
Hough Splines
AnalyticsBIOwulf
BIOwulf
RADIOLOGY
Machine Learning
Designer Math: An Evolutional Process
•Custom designed mathematical techniques focused on specific
real problems
•Cross-training between mathematicians and
biologists/physicians/other experts
•Applications of cutting edge mathematical theories
•Integration of expert domain knowledge
AnalyticsBIOwulf
BIOwulf
RADIOLOGY
Machine Learning
Domain Specific Solutions
TheoreticalFoundation
BIOwulf will extract pertinent knowledge by using the raw data, incorporating domain specific expertise in biology, applying leading mathematical theory, developing customized algorithms, and including the outcome feedback to fine tune predictive solutions.
Fine TuneTo Problem
AlgorithmDevelopment
DataDomain Expertise
Problem Solving Cycle
AnalyticsBIOwulf
BIOwulf
RADIOLOGY
Imaging
Example: Imaging
•Combination of radiology, machine learning, image processing,
and mathematical analysis
•Effective algorithm based on radiologists’ knowledge
•Customized SVM for “transduction”
AnalyticsBIOwulf
BIOwulf
RADIOLOGY
Imaging
Example: Imaging
•Modified SVM with variable input size and adjustable
regularizations
•Innovative feature extractions (e.g., Radon transform)
•Unparalleled accuracy in initial calcification detection system
AnalyticsBIOwulf
BIOwulf
RADIOLOGY
Imaging
Imaging Related IP
• A holistic method for computer aided automatic detection of micro calcification clusters in mammogram images.• Support vector machine based system for multi-spectra image analyses.• Mammogram feature selection based on Radon transform.• Combining image data with clinical information using kernel techniques for comprehensive diagnostic systems.• An efficient automatic border detection method for mammogram images.• Orientation detection based on orthogonal group representation and support vector machine.• Multi-scale histogram method for preprocessing of image data in support vector based classification systems.• A transduction method for variable point evaluations in image analyses.• Asymmetry detection using graph theoretic models in mammogram images.• Accurate calculations of geometric invariants in parameters from planar and volumetric image data.• •
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
- Calcification detection
- Mass detection
- Structure distortion detection
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Breast Cancer
•700,000 deaths in the world in 2000
•41,000 deaths in USA in 2000
•1 in 8 probability that a woman will develop breast cancer
in her lifetime
•1 in 30 probability she will die as a result
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Scope of the Problem
•False negative rate as high as 25%
•Double reading improves diagnosis by 15%
•70% of lesions are benign at biopsy
•Up to 75% of cancers visible in retrospect
•Sensitivity of current CAD programs 85%,
but specificity is less than 40%
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Computer Aided Diagnosis
•Consistency:Reduce missed interpretations due to fatigue and
distraction
•Improved Confidence:An additional diagnostic tool
•Enhanced Performance:Draws attention to suspicious microcalcifications,
masses, and architectural distortion
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Market
•44.5 million mammograms in USA in 2000
•6% increase compared to 1999
•CAD in its infancy
•10,000 registered mammography sites in US
•9% currently use CAD
•8% indicate intent to purchase CAD in next 3 years
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Local SVM analyzer
Calcification segmentation
Speculation detector
Mass segmentation
Feature extraction
Asymmetry detection
SVM classifier
Overall SVM analyzer
Feature extraction
Global SVM classifier
SVM classifier
Feature extraction
Mammogram Images
Calcification detection subsystem
Structure distortion detection subsystem
Mass detection subsystem
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Mammogram Images
Overall SVM Analyzer
CalcificationDetection
Subsystem
MassDetection
Subsystem
Structure DistortionDetection
Subsystem
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Mammogram Images
Overall SVM Analyzer
CalcificationDetection
Subsystem
MassDetection
Subsystem
Structure DistortionDetection
Subsystem
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Calcification Detection
CalcificationSegmentation
FeatureExtraction
Local SVMAnalyzer
GlobalSVM Classifier
MammogramImages
Overall SVMAnalyzer
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Calcification Detection
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Feature Extraction
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Preliminary Statistics
Negative Positive Total
Normal 106 4 110
Malignant 15 152 167
Total 121 156 277
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Mammogram Images
Overall SVM Analyzer
CalcificationDetection
Subsystem
MassDetection
Subsystem
Structure DistortionDetection
Subsystem
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Mammogram Images
Overall SVM Analyzer
CalcificationDetection
Subsystem
MassDetection
Subsystem
Structure DistortionDetection
Subsystem
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Mass Detection
AsymmetryDetection
FeatureExtraction
MassSegmentation
SVMClassifier
MammogramImages
Overall SVMAnalyzer
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Mammogram Images
Overall SVM Analyzer
CalcificationDetection
Subsystem
MassDetection
Subsystem
Structure DistortionDetection
Subsystem
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Mammogram Images
Overall SVM Analyzer
CalcificationDetection
Subsystem
MassDetection
Subsystem
Structure DistortionDetection
Subsystem
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Structure Distortion Detection
SpiculationDetector
FeatureExtraction
SVMClassifier
MammogramImages
Overall SVMAnalyzer
Current Project(s)BIOwulf
BIOwulf
RADIOLOGY
Mammography
Mammogram Images
Overall SVM Analyzer
CalcificationDetection
Subsystem
MassDetection
Subsystem
Structure DistortionDetection
Subsystem
Future ApplicationsBIOwulf
BIOwulf
RADIOLOGY
Computerized Axial Tomography (CAT)
Magnetic Resonance Imaging (MRI)
•Computer Aided Diagnosis•Tumor Volume Analysis
•Diagnosis/Prognosis•Response to Therapy
•Functional Molecular Imaging
Life Science Imaging Science
Future ApplicationsBIOwulf
BIOwulf
RADIOLOGY
General Radiology
Positron Emission Tomography (PET)
Computer Aided Diagnosis
Ultrasound
Future ApplicationsBIOwulf
BIOwulf
RADIOLOGY
MRI
• Edema (bone)• Joint fluid• Loose bodies• Capsule thickening• Intact meniscus evaluation• Ligament evaluation• Cartilage integrity• Trauma• Clinical