Winner, 2008 ICMLA Microarray Classification Competition, for the algorithm:
Donald Geman, Bahman Afsari, Aik Choon Tan, Daniel Naiman, "Microarray classification from several two-gene expression comparisons."
Courses
Fall 2008 550:437 Statistical Learning with Applications Expanded the range of applications to include statistical language models, molecular cancer diagnosis and gene network inference. Graduate Students: 16
Fall 2008 550:635 Topics in Bioinformatics Graduate Students: 6
Fall 2006 550.311 Introductory Statistics for the Medical and Biological Sciences Undergraduate Students: 34
Fall 2006 550.635 Topics in Bioinformatics Readings in computational molecular biology Graduate Students: 11
Fall 2004 550.311 Probability and Statistics for the Biological Sciences and Engineering Undergraduate Students: 27
Fall 2004 550.635 Topics in Bioinformatics Newly developed course Undergraduate Students: 1 Graduate Students: 13
Fall 2003 550:437 Information, Statistics and Perception This is an updated version of the course I taught
in 2001, substantially broadening the scope of applications to inlcude sections on neural decoding and functional genomics. Graduate Students: 10
Fall 2002 550:311 Introductory Statistics for the Medical and Biological Sciences Modifcation of 550:311 to illustrate material
with examples from biomedical engineering Undergraduate Students: 30
Fall 2001 550:437 Statistics, Information and Vision Undergraduate Students: 1 Graduate Students: 21
Visiting Position, January - March 2004: Centre de Mathematiques et Leurs Applications, ENS-Cachan, FranceTeaching at Other Institutions
Ph.D. Advisor for Hichem Sahbi, "Support vector machines for hierarchical face detection. Universite de Versailles, France, March 2004Teaching at Other Institutions
Visiting Professor, "Centre de Mathematiques et Leurs
Applications," Ecole Normale Superieure, France.International Collaborations
Experience
Professor, Department of Mathematics and Statistics, University of Massachusetts.
1970 - 2001
Grants and Contracts
Vision Strategies and ATR Performance, Army Research Office $455KStatus: Awarded/ActiveAwarded to University of Massachusetts
September 20, 1996 - March 19, 2002
Coarse-to-Fine Object Detection, Office of Naval Research $240,025Status: Awarded/Active
October 15, 2001 - September 30, 2004
Invariant Detection and Interpretation of Specific Objects in Image Data, National Science Foundation $300,000Status: Awarded/Active
October 01, 2002 - September 30, 2005
Coarse-to-Fine Computational Vision, Army Research Office $182,748Status: Awarded/Active
September 01, 2002 - August 31, 2005
Creative Extension Award, National Science Foundation $143,604Status: Awarded/ActiveFunded uner the NSF ITR program
October 01, 2002 - September 30, 2003
Triage and the Automated Annotation of Large Image Data Sets, NSF $690,925Status: Awarded/ActiveITR
September 01, 2004 - August 31, 2009
Cardiac Vascular Research Grid (Aim 5), NIH $679,196Status: Pending
September 15, 2005 - September 14, 2008
Centers of Research Translation (CORT), NIH $1,387,092Status: Pending
July 01, 2006 - June 30, 2011
Progress in Hierarchical Object Recognition, ARO $469,000Status: Pending
May 01, 2006 - April 30, 2009
Coarse-to-Fine Anomaly Detection in Random Graphs, Naval Surface Warfare Center $421,205Status: Pending
June 01, 2007 - May 31, 2010
Small-Sample Network Inference in Computational Vision and Biology, NSF $479,999Status: Awarded/Active
September 15, 2006 - September 14, 2009
CVRG (Cardiovascular Research Grid), NIH $961,276Status: Awarded/ActiveDirector, Project 5
February 01, 2007 - January 31, 2011
Reproducbible Models for the Statistical Analysis of Biological Systems , NSF $1,595,605Status: Pending
June 01, 2009 - May 31, 2011
Small-Sample Issues in Hierarchical Scene Analysis, ONR $299,610Status: Awarded/Active
May 23, 2007 - December 31, 2009
Multi-Scale Disease Biomarker Discovery, Johns Hopkins School of Medicine $750,000Status: Awarded/ActiveInstitutional funds related to the CTSA
June 01, 2008 - May 31, 2011
Presentations
D. Geman: Stationary Features and Cat Detection NIPS 2007. Whistler, BC. December 08, 2007. (Invited)
D. Geman: Interactive Search for Image Categories by Mental Matching SIAM Meeting. Baltimore, MD. November 14, 2007. Featured Event (Invited)
D. Geman: Image Interpretation: A Critical Overview Distinguished Lecture Series. University of California - San Diego. March 16, 2007. (Invited)
D. Geman: Image Interpretation ONR Workshop. Alexandria, VA. March 02, 2007. (Invited)
D. Geman: Interactive Image Retrieval by Mental Matching Multimedia Image Retrieval (MIR06). Santa Barbara, CA. October 26, 2006. Keynote Address (Invited)
D. Geman: In Search of a Unifying Theory for Image Interpretation Annual Meeting, Norwegian Soceity for Image Processing . Oslo, Norway. September 07, 2006. Keynote Address (Invited)
D. Geman: In Search of a Unifying Theory for Image Interpretation Annual International Symposium on Information Theory. Seattle, WA. July 14, 2006. Plenary Address (Invited)
D. Geman: Coarse-to-fine Hierarchies Visual Learning and Recognition Workshop. IMA, Minneapolis, MN. May 23, 2006. Workshop Organizer (Invited)
D. Geman: Small-sample Learning in Computational Biology and Vision Snowbird Learning Conference. Snowbird, Utah. April 05, 2006.
(Invited)
D. Geman: Efficiency-driven Computational Vision Stochastic Systems Conference. Notre Dame University. March 25, 2006. (Invited)
D. Geman: Efficiency-driven Computational Vision SCI Distinguished Lecture Series. University of Utah. March 17, 2006.
(Invited)
D. Geman: A Statistical Framework for Coarse-to-Fine Classification Caltech. December 13, 2005. (Invited)
D. Geman: Course-to-Fine Classification and Scene Analysis Los Alamos National Laboratory. November 10, 2005. (Invited)
D. Geman: Coarse-to-Fine Classification and Scene Interpretation New York University, Department of Computer Science. November 04, 2005. (Invited)
D. Geman: Interactive Mental Picture Retrieval University of Maryland Baltimore County. October 21, 2005. (Invited)
D. Geman: Image Retrieval from a Mental Picture AMS Seminar. JHU. September 23, 2005. (Invited)
D. Geman: Audio- and Video-Based Biometric Person Authentication AVBPA 2005. Rye, New York. July 21, 2005. (Invited)
D. Geman: Statistical Analysis of Postgenomic Data Institut National Agronomique. Paris, France. April 21, 2005. (Invited)
D. Geman: Workship on Pattern Classification , Learning and Object Recognition MSRI. Berkeley, CA. March 21, 2005. (Invited)
D. Geman: Introductory Workshop: Mathematical, Computational and Statistical Aspects of Image Analysis MSRI. Berkeley, California. January 24, 2005. (Invited)
D. Geman: Workshop on Object Recognition Taromina, Sicily. October, 2004. (Invited)
D. Geman: BME Freshman Lecture JHU. September 23, 2004. (Invited)
D. Geman: Advanced Concepts for Intelligent Vision Systems ACIVS04. Brussels, Belgium. August 31, 2004. Plenary Speaker (Invited)
D. Geman: Bodian Lecture JHU Mind Brain Institute. May 03, 2004. (Invited)
D. Geman: Presentation JHUSPH. April 28, 2004. (Invited)
D. Geman: Presentation on the Center for Imaging Science BME Advisory Council Meeting. JHU SOM. April 27, 2004. Gave presentation in place of Director (Invited)
D. Geman: Rank-Based Classification of Gene Expression Profiles AMS Seminar. JHU. April 22, 2004. (Invited)
D. Geman: Whitaker Site Visit March 18, 2004. (Invited)
D. Geman: Perception in Artificial and Natural Systems Meeting of the Mathematical Association of America. Baltimore, MD. November 07, 2003. (Invited)
D. Geman: Hierarchical Designs for Pattern Recognition Copmutational Sciences Lecture Series: Computational Vision and Image Analysis. University of Wisconsin, Madison, WI. October 30, 2003. (Invited)
D. Geman: Hierarchical Testing Designs for Pattern Recognition Mathematics Day, Institute of Mathematics. Academia Sinica, Taipei, Taiwan. September 03, 2003. (Invited)
D. Geman: Hierarchical Designs for Pattern Recognition DIMACS Workship on Complexity and Inference. Rutgers University, NJ. June 03, 2003. (Invited)
D. Geman: Hierarchical Testing Designs for Pattern Recognition ETH. Zurich, Switzerland. May 23, 2003. (Invited)
D. Geman: Computational Modeling EURANDOM Workshop: "Statistical Learning in Classificaiton and Model Selection". Eindhoven, Netherlands. January 18, 2003. (Invited)
D. Geman: Hierarchical Designs for Object Identification SIAM Minisymposium, Joint Mathematics Meetings. Baltimore, MD. January 16, 2003. (Invited)
D. Geman: Sequential Testing Strategies for Object Identification Statistics Colloquium. University of Michigan. November 15, 2002. (Invited)
D. Geman: Computational Modeling Applied Mathematics Colloquium. Cornell University. October 17, 2002. (Invited)
D. Geman: Computational Modeling A. Rosenfeld Distinguished Lecture Series. University of Maryland. October 16, 2002. (Invited)
D. Geman: Statistical Methods and Learning in Computer Vision SIAM 2002 Annual Meeting. Philadelphia, PA. July 09, 2002. Invited Minitutorial (Invited)
D. Geman: When is Coarse-to-Fine Search Optimal? International Workshop on Energy Minimization Methods in Computer Vision. Sophia Antipolis, France. September, 2001. Plenary Talk (Invited)
D. Geman: Interrogation Bayesienne d'une Base de Donnees 33rd Journees de Statistique. Nantes, France. May, 2001. Keynote address: French Statistical Society (Invited)
D. Geman: Coarse-to-Fine Classification and Visual Recognition Mathematical Sciences Research Institute Workshop. Berkeley, CA. March, 2001. (Invited)
Professional Activities
Reviewer for Inter. J. Comp. Vision
Scientific Committee of Various Conferences
Ph.D. Committee, Vivian Yuan, Department of Applied Mathematics and Statistics
WSE Curriculum Committee
WSE Dean's Search Committee
GBO Committee: Christian D'Avignon, BME
GBO Committee, Kerry Zesker, Astrophysics
Member, Visiting Committee to evaluate the Institute of Mathematics, Academia Sinica, Taipei, Taiwan, September 1-2, 2003
Editor, Exponent, Fall 2003
Editorial Board, Journal of Machine Learning Research
Editorial Board, Applications of Mathematics, Series, Springer-Verlag
Organizing Committee for IMA Concentration Year on Imaging, 2005-2006
Member, Organizing Committee for MSRI Concentration Semester in Imaging, 2005
Member, Department Curriculum Committee
Member, Site Visit Team, NSF SLC Proposal for NE Consortium
GBO Committee, Xiaodong Fan, May 5, 2004
GBO Committee, Iman El-Shehaby, July 7, 2004
GBO Committee, Charles Wright, December 10, 2004
Reviewer for IEEE Transs PAMI
Reviewer for J. Machine Learnjing Research
Reviewer for Pattern Recognition
Organizer, CIS Seminar Series 2003-2004
Introductory Exam Committee, AMS
Academic Affairs Committee, AMS
GBO Exam, Wen Wu, AMS
GBO Exam, Yan Qi, BME
ICM Hiring Committee
Editorial Board, SIAM Journal Imaging Science
Chair, SIAM Activity Group, Imaging Science
Miscellaneous GBO Committees, ECE,BME,AMS
Developed a new BME/AMS course, "Mathematical Methods in Computational Medicine", introducing
mathematical topics arising in proteomics, cardiac modeling, cancer diagnosis and computational anatomy.
Proposal Reviewer, ARO, NSF
Research Interests
Computer Vision
Statistical Learning
Computational Biology
Neural and stochastic modeling
Publications: All Publications
d'Avignon, C. and Geman, D.. "Tree-Structured Neural Decoding".
Fleuret, F., D. Geman. "Coarse-to-Fine Face Detection". International Journal of Computer Vision41 (2001):85-107
Geman, D., B. Jedynak. "Model-Based Classification Trees". IEEE Trans. Information Theory47 (2001):1075-1082
Geman, D.. "Interrogation Bayesienne d'une Base de Donnees". Proceedings 33'rd Journees de Statistique (2001):15-20
Fleuret, F., D. Geman. "Fast Face Detection with Precise Pose Estimation". Proc. ICPR2002. IEEE Computer Society1 (2002):235-238
H. Sahbi, D. Geman and N. Boujemaa. "Coarse-to-Fine support vector networks". Proc. ICIP-023 (2002):925-928
Krempp, S., Geman, D. and Amit, Y.. "Sequential Learning with Reusable Parts for Object Detection". (2002)
Geman, D. "Coarse-to-fine classification and scene labeling." Nonlinear estimation and Classification: Lecture Notes in statistics. Springer Verlag, 2003. 31-48.((pdf))
Geman, D., d'Avignon, C., Naiman, D., Winslow, R., Zeboulon, A.. "Gene expression comparisons for class prediction in cancer studies". Proceedings 36th Symposium on the Interface: Computing Science and Statistics (2004) ((pdf))
Fang, Y., Geman, D.. "Experiments in mental face retrieval". Technical Report, Project IMEDIA. INRIA (2004) ((pdf))
Amit, Y, Geman D., Fan, X.. "A coarse-to-fine strategy for milti-class shape detection". IEEE Trans. PAMI28 (2004):1606-1621
Geman, D., d'Avignon, C., Naiman, D., Winslow, R.. "Classifying gene expression profiles from pairwise mRNA comparisons". Statist Appl in Genetics and MOlecular Biology3 (2004) ((http://www.bepress.com/sagmb/vol3/iss1/art19/))
Blanchard, G., Geman D.. "Sequential testing designs for pattern recognition". Annals of Statistics (2005) ((pdf))
Xu, L., Tan, A-C., Naiman, D., Geman, D., Winslow, R.. "Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data". Bioinformatics21 (2005):3905-3911
Tan, A-C., Naiman, D., Xu, L., Winslow, R., Geman D.. "Simple decision rules for classifying human cancers from gene expression profiles". Bioinformatics21 (2005):3896-3904
Fang, Y., Geman, D.. "Experiments in mental face retrieval". Proceedings AVBPA 2005, Lecture notes in Computer Science (2005):637-646(Best Student Paper Award)
Gangaputra, S., Geman, D.. "A unified stochastic model for detecting and tracking faces". Proceedings Second Canadian Conference on Computer and Robot Vision (CRV'05) (2005):306-315
Blanchard, G., Geman, D.. "Sequential testing designs for pattern recognition". Annals of Statistics33 (2005):1144-1202
Koloydenko, A. and D. Geman . "Ordinal coding of image microstructure". Proc. Inter. Conf. Image Processing, Computer Vision and Pattern Recognition (IPCV'06) (2006)
Gangaputra, S. and D. Geman. "A design principle for coarse-to-fine classification". Proceedings CVPR 2006. IEEE Computer Society (2006):1877-1884
Gangaputra, S., and D. Geman. "The trace model for object detection and tracking". Lecture Notes in Computer Science (2006)
Sahbi, H. and D. Geman. "A hierarchy of support vector machines for pattern detection". Journal of Machine Learning Research7 (2006):2087-2123
Xu, L., D. Geman and R. Winslow . "Large-scale integration of cancer microarray data identifies a robust common cancer signature". BMC Bioinformatics8 (2007):275
Anderson, T. J., I. Tchernyshyov, R. Diez, R.N. Cole, D. Geman, C. V. Dang and R. L. Winslow . "Discovering robust protein biomarkers for disease from relative expression reversals in 2D DIGE data". Proeteomics7 (2007):1197-1207
Fereacatu, M. and D. Geman. "Interactive Search for Image Categories by Mental Matching". Proceedings ICCV 2007 (2007)
Fleuret, F. and D. Geman. "Stationary Features and Cat Detection". Journal of Machine Learning Research (2008)
Xu, L., A-C Tan, R. Winslow and D. Geman . "Merging microarray data from separate breast cancer studies provides a robust prognostic test". BMC Bioinformatics (2008)
Ferecatu, M. and Geman, D.. "A statistical framework for image category search from a mental picture". IEEE Trans PAMI (2008)
Geman, D., Afsari, B., Tan, Aik-Choon, Naiman, Daniel. "Microarray classification from several two-gene expression comparisons". Proceedings ICMLA 2008 (2008)
Lin, X., Afsari, B., Marchionni, L., Parmigiani, G., Cope, L., Naiman, D., Geman, D.. "The ordering among a few genes can provide simple cancer biomarker and signal BRCA1 mutations". PLoS Computational Biology (2008)
Publications: Book Chapters
Geman, D. "Coarse-to-fine classification and scene labeling." Nonlinear estimation and Classification: Lecture Notes in statistics. Springer Verlag, 2003. 31-48.((pdf))
Publications: Journals
Fleuret, F. and D. Geman. "Stationary Features and Cat Detection". Journal of Machine Learning Research (2008)
Xu, L., A-C Tan, R. Winslow and D. Geman . "Merging microarray data from separate breast cancer studies provides a robust prognostic test". BMC Bioinformatics (2008)
Ferecatu, M. and Geman, D.. "A statistical framework for image category search from a mental picture". IEEE Trans PAMI (2008)
Xu, L., D. Geman and R. Winslow . "Large-scale integration of cancer microarray data identifies a robust common cancer signature". BMC Bioinformatics8 (2007):275
Anderson, T. J., I. Tchernyshyov, R. Diez, R.N. Cole, D. Geman, C. V. Dang and R. L. Winslow . "Discovering robust protein biomarkers for disease from relative expression reversals in 2D DIGE data". Proeteomics7 (2007):1197-1207
Koloydenko, A. and D. Geman . "Ordinal coding of image microstructure". Proc. Inter. Conf. Image Processing, Computer Vision and Pattern Recognition (IPCV'06) (2006)
Gangaputra, S., and D. Geman. "The trace model for object detection and tracking". Lecture Notes in Computer Science (2006)
Sahbi, H. and D. Geman. "A hierarchy of support vector machines for pattern detection". Journal of Machine Learning Research7 (2006):2087-2123
Blanchard, G., Geman D.. "Sequential testing designs for pattern recognition". Annals of Statistics (2005) ((pdf))
Xu, L., Tan, A-C., Naiman, D., Geman, D., Winslow, R.. "Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data". Bioinformatics21 (2005):3905-3911
Tan, A-C., Naiman, D., Xu, L., Winslow, R., Geman D.. "Simple decision rules for classifying human cancers from gene expression profiles". Bioinformatics21 (2005):3896-3904
Fang, Y., Geman, D.. "Experiments in mental face retrieval". Proceedings AVBPA 2005, Lecture notes in Computer Science (2005):637-646(Best Student Paper Award)
Gangaputra, S., Geman, D.. "A unified stochastic model for detecting and tracking faces". Proceedings Second Canadian Conference on Computer and Robot Vision (CRV'05) (2005):306-315
Blanchard, G., Geman, D.. "Sequential testing designs for pattern recognition". Annals of Statistics33 (2005):1144-1202
Amit, Y, Geman D., Fan, X.. "A coarse-to-fine strategy for milti-class shape detection". IEEE Trans. PAMI28 (2004):1606-1621
Geman, D., d'Avignon, C., Naiman, D., Winslow, R.. "Classifying gene expression profiles from pairwise mRNA comparisons". Statist Appl in Genetics and MOlecular Biology3 (2004) ((http://www.bepress.com/sagmb/vol3/iss1/art19/))
Fleuret, F., D. Geman. "Coarse-to-Fine Face Detection". International Journal of Computer Vision41 (2001):85-107
Geman, D., B. Jedynak. "Model-Based Classification Trees". IEEE Trans. Information Theory47 (2001):1075-1082
Publications: Conference Proceedings
Geman, D., Afsari, B., Tan, Aik-Choon, Naiman, Daniel. "Microarray classification from several two-gene expression comparisons". Proceedings ICMLA 2008 (2008)
Fereacatu, M. and D. Geman. "Interactive Search for Image Categories by Mental Matching". Proceedings ICCV 2007 (2007)
Gangaputra, S. and D. Geman. "A design principle for coarse-to-fine classification". Proceedings CVPR 2006. IEEE Computer Society (2006):1877-1884
Geman, D., d'Avignon, C., Naiman, D., Winslow, R., Zeboulon, A.. "Gene expression comparisons for class prediction in cancer studies". Proceedings 36th Symposium on the Interface: Computing Science and Statistics (2004) ((pdf))
Fleuret, F., D. Geman. "Fast Face Detection with Precise Pose Estimation". Proc. ICPR2002. IEEE Computer Society1 (2002):235-238
H. Sahbi, D. Geman and N. Boujemaa. "Coarse-to-Fine support vector networks". Proc. ICIP-023 (2002):925-928
Krempp, S., Geman, D. and Amit, Y.. "Sequential Learning with Reusable Parts for Object Detection". (2002)
Geman, D.. "Interrogation Bayesienne d'une Base de Donnees". Proceedings 33'rd Journees de Statistique (2001):15-20
Publications: Reports
Lin, X., Afsari, B., Marchionni, L., Parmigiani, G., Cope, L., Naiman, D., Geman, D.. "The ordering among a few genes can provide simple cancer biomarker and signal BRCA1 mutations". PLoS Computational Biology (2008)
Fang, Y., Geman, D.. "Experiments in mental face retrieval". Technical Report, Project IMEDIA. INRIA (2004) ((pdf))
d'Avignon, C. and Geman, D.. "Tree-Structured Neural Decoding".
Supervised Students
Bahman Afsari
2'nd Year
Graduate
Doctoral student,ECE,in progress
Christian D'Avignon
Graduate
BME, Ph.D., 2004
Xiaodong Fan
4th Year
Graduate
Doctoral Student in ECE, JHU, in progress
Xiaodong Fan
4th Year
Graduate
Doctoral Student in ECE, JHU, in progress
Sachin Gangaputra
4th year
Graduate
Doctoral Student in ECE, JHU, in progress
Kan Jiang
3rd Year
Graduate
Doctoral Student, ECE, in progress
Franck Jung
5th Year
Graduate
Doctoral student at Ecole Polytechnique, France;
Completed dissertation in Fall, 2001
Samuel Krempp
3rd Year
Graduate
Doctoral student at Ecole Normale Superieure, France
Ting Li
4'th Year
Graduate
Doctoral student, BME, in progress
Mary Lin
4'th Year
Graduate
Doctoral Student, AMS, co-supervised with D. Naiman. Graduated 2008.
Francisco Sanchez-Vega
3'rd year
Graduate
Doctoral student, AMS, co-supervised with L.Younes, in progress
David Simcha
2'nd Year
Graduate
Doctoral student, BME, in progress.
Wen Wu
3rd Year
Graduate
Doctoral student, AMS, in progress
Erdem Yoruk
3'rd year
Graduate
Doctoral Student, AMS, in progress; co-supervised with L. Younes