2019
- W. Dinalankara, Q. Ke, D. Geman and L. Marchionni, "Divergence: An R
Package for Divergence Analysis of Omics Data," bioRxiv, 2019
- K. Lahouel, D. Geman and L. Younes, "Coarse-to-fine multiple testing
strategies", Electronic Journal of Statistics, 2019 (pdf)
2018
- W. Dinalankara, Q. Ke, Y. Xu, L. Ji, N. Pagane, A. Lien, T. Matam, E.J. Fertig, N. Price, L. Younes, L. Marchionni and D. Geman, "Digitizing omics profiles by divergence from a baseline", PNAS, 2018 (pdf)
- P. Slama, M. R. Hoopmann, R. L. Moritz and D. Geman, "Robust determination of differential abundance in shotgun proteomics using nonparametric statistics", Molecular Omics, 2018 (pdf)
- B. Afsari, T. Guo, M. Considine, L. Florea, L. T. Kagohara, G. L. Stein-O'Brien, D. Kelley, E. Flam, K. D. Zambo, P. K. Ha, D. Geman, M. F. Ochs, J. A. Califano, D. A. Gaykalova, A. V. Favorov and E. J. Fertig, "Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer", Bioinformatics, 2018 (pdf)
2017
- S. Ament, J. Pearl, A. Grindeland, J. St Claire, J. Earls,
M. Kovalenko, T. Gillis, J. Mysore, J. Gusella, et al,
"High resolution time-course mapping of early transcriptomic, molecular
and cellular phenotypes in Huntington's disease CAG knock-in mice
across multiple genetic backgrounds," Human Molecular Genetics, 2017 (pdf)
2016
- D. Geman and S. Geman, "Science in the age of selfies", PNAS, 2016 (pdf)
2015
- L. Chang and D. Geman, "Tracking Cross-Validated Estimates of Prediction Error as Studies Accumulate", Journal of the American Statistical Association, 2015 (pdf)
- D. Geman, S. Geman, N. Hallonquist and L. Younes, "Visual Turing test for computer vision systems", PNAS, 2015 (pdf)
- D. Geman, H. Geman, and N. N. Taleb, "Tail Risk Constraints and Maximum Entropy", Entropy, 2015 (pdf)
- D.Geman, M.Ochs, N.D. Price, C. Tomasetti, and L. Younes, "An argument for mechanism-based statistical inference in cancer", Human Genetics, DOI 10.1007/s00439-014-1501-x, 2014. (pdf)
- A. Rejeb-Sfar, N. Boujemaa and D. Geman, "Confidence sets for fine-grained categorization and plant identification", IJCV, DOI 10.1007/s11263-014-0743-3, 2014. (pdf)
2014
- S. Ma, J. Sung, A. T. Magis, Y. Wang, D. Geman and N.D. Price, "Measuring the effect of inter-study variability on estimating prediction error", PLOS ONE, 9, 2014. (pdf)
- B. Afsari, U. Braga-Neto and D. Geman, "Rank discriminants for predicting phenotypes from RNA expression", Annals of Applied Statistics, 8, 1469-1491, 2014. (pdf)
- B. Afsari, E.J. Fertig, D. Geman and L. Marchionni, "switchBox: An R package for k-Top Scoring Pairs (kTSP) classifier development", Bioinformatics, September, 2014. (pdf)
- B. Afsari, D. Geman and E.J. Fertig, "Learning dysregulated pathways in cancers from differential variability analysis", Cancer Informatics, 13, 62-67, 2014. (pdf)
2013
- A. Rejeb-Sfar, N. Boujemaa, D. Geman, "Vantage feature frames for fine-grained categorization," CVPR 2013 (pdf)
- D. Simcha, L. Younes, M, Aryee and D. Geman, "Identification of direction in gene networks from expression and methylation." BMC Systems Biology 7:118, 2013 (pdf)
- J. Sung, P-J Kim, C. Funk, S. Ma, A. Magis, Y. Wang, L. Hood, D. Geman and N.D. Price, "Multi-study integration of brain cancer transcriptomes reveals organ-level diagnostic signatures," PLOS Computational Biology, Vol 9, Issue 7, e1003148, 2013 (pdf)
- L. Marchionni, B. Afsari, D. Geman and J.T.Leek, "A simple and reproducible breast cancer prognostic test," BMC Genomics 14:336, 2013. (pdf)
- F. Sanchez-Vega, J. Eisner, L. Younes and D. Geman, "Learning multivariate distributions by competitive assembly of marginals," IEEE Transactions on Pattern Analysis and Machine Intelligence 35, 398-410, 2013. (pdf)
2012
- R.L. Winslow, N. Trayanova, D. Geman and M.I. Miller, "Computational medicine: translating models to clinical care," Science Translational Medicine 4, 31 October 2012 (pdf)
- F. Sanchez-Vega, J. Eisner, L. Younes and D. Geman, "Learning multivariate distributions by competitive assembly of marginals,"IEEE Transactions on Pattern Analysis and Machine Intelligence, 2012 (pdf)
- Simcha D, Price ND, Geman D, "The Limits of De Novo DNA Motif Discovery,"PLoS ONE 7(11): e47836 (pdf)
2011
- F. Fleuret, T. Li, C. Dubout, E. K. Wampler, S. Yantis and D. Geman, "Comparing machines and humans on a visual categorization test," PNAS, 108: 17621-17625, 2011. (pdf)
- R. L. Winslow et al., "The CardioVascular Research Grid Project." In: AMIA 2011 Summit on Translational Bioinformatics, March 7-9, San Francisco, CA, 77-81, 2011. (pdf)
- E. Yoruk, M. Ochs, D. Geman and L. Younes, "A comprehensive statistical model for cell signaling," IEEE Trans. Computational Biology and Bioinformatics , 592-606, 2011. (pdf)
2010
- P. Slama and D. Geman, "Identification of family-determining residues in PHD fingers," Nucleic Acids Research , 1-14, 2010. (pdf)
- J.T. Leek, R.B. Scharpf, H.C. Bravo, D. Simcha, B. Langmead, W.E. Johnson, D. Geman, K. Baggerly, R.A. Irisarry, "Tackling the widespread and critical impact of batch effects in high-throughput data," Nature Reviews Genetics , 11, 733-739, 2010. (pdf)
- J.A. Eddy, L. Hood, N.D. Price and D. Geman, "Identifying tightly regulated and variably expressed networks by differential rank conservation," PLoS Computational Biology , 2010. (pdf)
- J.A. Eddy, J. Sung, D. Geman and N.D. Price, "Relative expression analysis for molecular diagnosis and prognosis," Technology in Cancer Research and Treatment 9, 149-159, 2010. (pdf)
2009
- L.B. Edelman, G. Goia, D. Geman,, W. Zhang and N.D. Price, "Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases," BMC Genomics 10:583, 2009. (pdf)
- X. Lin, B. Afsari, L. Marchionni, L. Cope, G. Parmigiani, D. Naiman and D. Geman, "The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations," BMC Bioinformatics 10:256, 2009. (pdf)
- M. Ferecatu and D. Geman, "A statistical framework for image category search from a mental picture," IEEE Trans. PAMI, 31, 1087-1101, 2009. (pdf)
2008
- D. Geman, B. Afsari, A.C. Tan and D. Naiman "Microarray classification from several two-gene experssion comparisons," Proceedings ICMLA, 2008 (Winner, ICMLA Microarray Classification Algorithm Competition). (pdf)
- F. Fleuret and D. Geman, "Stationary features and cat detection," Journal of Machine Learning Research, 9:2549-2578, 2008. (pdf)
- L. Xu, A.C. Tan, R. L. Winslow and D. Geman, "Merging microarray data from separate breast cancer studies provides a robust prognostic signature," BMC Bioinformatics 9:125, 2008. (pdf)
2007
- M. Ferecatu and D. Geman, "Interactive search for image categories by mental matching," Proceedings Inter. Conf. on Computer Vision (ICCV '07) , Rio de Janeiro, October 14-20, 2007. (pdf)
- T.J. Anderson, I. Tchernyshyov, R. Diez, R.N. Cole, D. Geman, C.V. Dang and R. Winslow, "Discovering robust protein biomarkers for disease from relative expression reversals in 2-D DIGE data," Proteomics 7: 1197-1207, 2007. (pdf)
- L. Xu, D. Geman and R. Winslow, "Large-scale integration of cancer microarray data identifies a robust common cancer signature," BMC Bioinformatics 8:275, 2007. (pdf)
2006
- S. Gangaputra and D. Geman, "A design principle for coarse-to-fine classification," Proceedings CVPR 2006, 2, 1877-1884, 2006. (pdf)
- A. Koloydenko and D. Geman, "Ordinal coding of image microstructure," Proceedings Inter. Conf. Image Processing, Computer Vision and Pattern Recognition (IPCV'06), Las Vegas, NV, June, 2006. (pdf)
- S. Gangaputra and D. Geman, "The trace model for object detection and tracking," Toward Category-Level Object Recognition (eds. J. Ponce et al), Lecture Notes in Computer Science, 4170, 401-420, 2006. (pdf)
- H. Sahbi and D. Geman, "A hierarchy of support vector machines for pattern detection," Journal of Machine Learning Research, 7, 2087-2123, 2006. (pdf)
2005
- L. Xu, A-C Tan, D. Naiman, D. Geman and R. Winslow, "Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data," Bioinformatics , 21, 3905-3911, 2005. (pdf)
- A-C Tan, D. Naiman, L. Xu, R. Winslow and D. Geman, "Simple decision rules for classifying human cancers from gene expression profiles," Bioinformatics , 21, 3896-3904, 2005. (pdf)
- Y. Fang and D. Geman, "Experiments in mental face retrieval," Proceedings AVBPA 2005, Lecture Notes in Computer Science, 637-646, July 2005. (Best Student Paper Award) (pdf)
- S. Gangaputra and D. Geman, "A unified stochastic model for detecting and tracking faces," Proceedings Second Canadian Conf. on Computer and Robot Vision (CRV'05), 306-313, 2005. (pdf)
- G. Blanchard and D. Geman, "Sequential testing designs for pattern recognition," Annals of Statistics, 33, 1155-1202, June, 2005. (pdf)
2004
- D. Geman, C. d'Avignon, D. Naiman, R. Winslow and A. Zeboulon, "Gene expression comparisons for class prediction in cancer studies," Proceedings 36'th Symposium on the Interface: Computing Science and Statistics, 2004. (pdf)
- Y. Amit, D. Geman and X. Fan, "A coarse-to-fine strategy for multi-class shape detection," IEEE Trans. PAMI, 28, 1606-1621, 2004. (pdf)
- D. Geman, C. d'Avignon, D. Naiman and R. Winslow, "Classifying gene expression profiles from pairwise mRNA comparisons," Statist. Appl. in Genetics and Molecular Biology, 3, 2004. (pdf)
- S. Gangaputra and D. Geman, "Self-normalized linear tests," Proceedings CVPR 2004, 2, 616-622, 2004 (pdf)
- X. Fan and D. Geman, "Hierarchical object indexing and sequential learning," Proceedings ICPR 2004, 3, 65-68, 2004. (pdf)
2003
- D. Geman, "Coarse-to-fine classification and scene labeling," Nonlinear Estimation and Classification (eds. D. D. Denison et al.), Lecture Notes in Statistics. New York: Springer-Verlag, 31-48, 2003. (pdf)
- C. d'Avignon and D. Geman, "Tree-structured neural decoding ," Journal of Machine Learning Research, 4, 743-754, 2003. (pdf)
2002
- H. Sahbi, D. Geman and N. Boujemaa, "Face detection using coarse-to-fine support vector classifiers," Proceedings ICIP-02, 3, 925-928, 2002. (pdf)
- F. Fleuret and D. Geman, "Fast face detection with precise pose estimation," Proceedings ICPR2002, 1, 235-238, 2002. (pdf)
- S. Krempp, D. Geman and Y. Amit, "Sequential learning with reusable parts for object detection," Technical Report, 2002. (pdf)
2001
- F. Fleuret and D. Geman, "Coarse-to-fine face detection," Inter. Journal of Computer Vision, 41, 85-107, 2001. (pdf)
- D. Geman and B. Jedynak, "Model-based classification trees," IEEE Trans. Info. Theory, 47, 1075-1082, 2001. (pdf)
- D. Geman and R. Moquet, "Q & A models for interactive search," Technical Report, 2001. (pdf)
- D. Geman, "Interrogation Bayesienne d'une base de donnees," Proceedings 33rd Journees de Statistique, Nantes, 15-20, 2001.
Before 2000
- D. Geman and R. Moquet, "A stochastic model for image retrieval," Proc. RFIA 200, Paris, February, 2000. (pdf)
- F. Fleuret and D. Geman, "Graded learning for object detection," Proceedings, IEEE Workshop on Statistical and Computational Theories of Vision, Fort Collins, CO, June, 1999.
- D. Geman and A. Koloydenko, "Invariant statistics and coding of natural microimages," Proceedings, IEEE Workshop on Statistical and Computational Theories of Vision, Fort Collins, CO, June, 1999. (pdf)
- Y. Amit and D. Geman, "A computational model for visual selection," Neural Computation, 11, 1691-1715, 1999. (pdf)
- C. Li and D. Geman, "Active testing at multiple resolutions," Proceedings ASA Conference, Baltimore, 1999.
- Y. Amit, D. Geman and B. Jedynak, "Efficient focusing and face detection," Face Recognition: From Theory to Applications, eds. H. Wechsler et al, NATO ASI Series F, Springer-Verlag, Berlin, 157-173, 1998. (pdf)
- F. Jung, B. Jednyak and D. Geman, "Recognizing buildings in aerial images," Automatic Extraction of Man-Made Objects from Aerial and Space Images, II, Birkhauseer (Basel), Ascona, 173-182, May, 1997.
- Y. Amit, D. Geman and K. Wilder, "Joint induction of shape features and tree classifiers," IEEE Trans. Pattern Anal. Mach. Intell., 19, 1300-1305, 1997. (pdf)
- Y. Amit and D. Geman, "Shape quantization and recognition with randomized trees," Neural Computation., 9, 1545-1588, 1997. (pdf)
- D. Geman and B. Jedynak, "An active testing model for tracking roads from satellite images," IEEE Trans. Pattern Anal. Mach. Intell, 18, 1-14, 1996. (pdf)
- D. Geman and C. Yang, "Nonlinear image recovery with half-quadratic regularization," IEEE Trans. Image Processing, 4, 932-946, 1995. (pdf)
- S. Geman and D. Geman, "Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images," IEEE Trans. Pattern Anal. Mach. Intell, 6, 721-741, 1984. (pdf)