Learning and Inference

Head:
Sayan Mukherjee

Phone:
+49 (0) 341 - 9959 - 50

Fax:
+49 (0) 341 - 9959 - 658

Address:
Inselstr. 22
04103 Leipzig

Publications Sayan Mukherjee

Journal Articles To top of page

S. I. Berchuck ; M. Janko ; F. A. Medeiros ; W. Pan and S. Mukherjee: Bayesian non-parametric factor analysis for longitudinal spatial surfaces. Bayesian analysis, 17 (2022) 2, p. 435-464 Bibtex [DOI] [ARXIV] Journal Open Access

K. McGoff ; S. Mukherjee and A. Nobel: Gibbs posterior convergence and the thermodynamic formalism. The annals of applied probability, 32 (2022) 1, p. 461-496 Bibtex [DOI] [ARXIV] Repository Open Access

J. D. Silverman ; K. Roche ; Z. C. Holmes ; L. A. David and S. Mukherjee: Bayesian multinomial logistic normal models through Marginally Latent Matrix-T processes. Journal of machine learning research, 23 (2022) 7, p. 1-42 Bibtex [ARXIV] [FREELINK] [CODELINK] Journal Open Access

B. St. Thomas ; L. Lin ; L.-H. Lim and S. Mukherjee: Learning subspaces of different dimensions. Journal of computational and graphical statistics, 31 (2022) 2, p. 337-350 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access

J. Bryan ; A. Mandan ; G. Kamat ; W. K. Gottschalk ; A. Badea ; K. J. Adams ; J. W. Thompson ; C. A. Colton ; S. Mukherjee and M. W. Lutz: Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways. Alzheimer's and dementia, 17 (2021) 4, p. 561-573 Bibtex [DOI] [CODELINK]

T. Gao ; J. Brodzki and S. Mukherjee: The geometry of synchronization problems and learning group actions. Discrete and computational geometry, 65 (2021) 1, p. 150-211 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access

R. A. Johnston ; P. Vullioud ; J. Thorley ; H. Kirveslahti ; L. Shen ; S. Mukherjee ; C. M. Karner ; T. Clutton-Brock and J. Tung: Morphological and genomic shifts in mole-rat 'queens' increase fecundity but reduce skeletal integrity. eLife, 10 (2021), e65760 Bibtex [DOI] [ARXIV] Journal Open Access

W. Li ; J. Hannig and S. Mukherjee: Subspace clustering through sub-clusters. Journal of machine learning research, 22 (2021), 53 Bibtex [ARXIV] [FREELINK] Journal Open Access

B. Wang ; T. Sudijono ; H. Kirveslahti ; T. Gao ; D. M. Boyer ; S. Mukherjee and L. Crawford: A statistical pipeline for identifying physical features that differentiate classes of 3D shapes. The annals of applied statistics :, 15 (2021) 2, p. 638-661 Bibtex [DOI] [ARXIV] Journal Open Access

L. Crawford ; A. Monod ; A. X. Chen ; S. Mukherjee and R. Rabadán: Predicting clinical outcomes in glioblastoma : an application of topological and functional data analysis. Journal of the American Statistical Association, 115 (2020) 531, p. 1139-1150 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access

J. D. Silverman ; K. Roche ; S. Mukherjee and L. A. David: Naught all zeros in sequence count data are the same. Computational and structural biotechnology journal, 18 (2020), p. 2789-2798 Bibtex [DOI] [ARXIV] Journal Open Access

S. I. Berchuck ; S. Mukherjee and F. A. Medeiros: Estimating rates of progression and predicting future visual fields in glaucoma using a deep variational autoencoder. Scientific reports, 9 (2019), 18113 Bibtex [DOI] [ARXIV] Journal Open Access

M. Cakir ; S. Mukherjee and K. C. Wood: Label propagation defines signaling networks associated with recurrently mutated cancer genes. Scientific reports, 9 (2019), 9401 Bibtex [DOI] [ARXIV] Journal Open Access

T. Vilgalys ; J. Rogers ; C. J. Jolly ; S. Mukherjee and J. Tung: Evolution of DNA methylation in Papio baboons. Molecular biology and evolution, 36 (2019) 3, p. 527-540 Bibtex [DOI] [ARXIV] Journal Open Access

A. D. Washburne ; J. D. Silverman ; J. T. Morton ; D. Becker ; D. Crowley ; S. Mukherjee ; L. A. David and R. K. Plowright: Phylofactorization : a graph partitioning algorithm to identify phylogenetic scales of ecological data. Ecological monographs, 89 (2019) 2, e01353 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access

F. Wu ; A. J. Lopatkin ; D. A. Needs ; C. T. Lee ; S. Mukherjee and L. You: A unifying framework for interpreting and predicting mutualistic systems. Nature communications, 10 (2019), 242 Bibtex [DOI] Journal Open Access

S. Barish ; S. Nuss ; I. Strunilin ; S. Bao ; S. Mukherjee ; C. D. Jones and P. C. Volkan: Combinations of DIPs and Dprs control organization of olfactory receptor neuron terminals in Drosophila. PloS genetics, 14 (2018) 8, e1007560 Bibtex [DOI] [ARXIV] Journal Open Access

L. Crawford ; K. C. Wood ; X. Zhou and S. Mukherjee: Bayesian approximate kernel regression with variable selection. Journal of the American Statistical Association, 113 (2018) 524, p. 1710-1721 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access

T. Gao ; G. S. Yapuncich ; I. Daubechies ; S. Mukherjee and D. M. Boyer: Development and assessment of fully automated and globally transitive geometric morphometric methods, with application to a biological comparative dataset with high interspecific variation. The anatomical record : advances in integrative anatomy and evolutionary biology, 301 (2018) 4, p. 636-658 Bibtex [DOI] [ARXIV] Repository Open Access

J. D. Silverman ; H. K. Durand ; R. J. Bloom ; S. Mukherjee and L. A. David: Dynamic linear models guide design and analysis of microbiota studies within artificial human guts. Microbiome, 6 (2018), 202 Bibtex [DOI] [ARXIV] [CODELINK] Journal Open Access

S. Zhao ; B. E. Engelhardt ; S. Mukherjee and D. B. Dunson: Fast moment estimation for generalized latent Dirichlet models. Journal of the American Statistical Association, 113 (2018) 524, p. 1528-1540 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access

O. Bobrowski ; S. Mukherjee and J. E. Taylor: Topological consistency via kernel estimation. Bernoulli, 23 (2017) 1, p. 288-328 Bibtex [DOI] [ARXIV] Repository Open Access

L. Crawford ; S. Mukherjee ; S. Mukherjee and X. Zhou: Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits. PloS genetics, 13 (2017) 7, e1006869 Bibtex [DOI] [ARXIV] [CODELINK] Journal Open Access

G. Darnell ; S. Georgiew ; S. Mukherjee and B. E. Engelhardt: Adaptive randomized dimension reduction on massive data. Journal of machine learning research, 18 (2017), 140 Bibtex [ARXIV] [FREELINK] [CODELINK] Journal Open Access

S. Lunagómez ; S. Mukherjee ; R. L. Wolpert and E. M. Airoldi: Geometric representations of random hypergraphs. Journal of the American Statistical Association, 112 (2017) 517, p. 363-383 Bibtex [DOI] [ARXIV] Repository Open Access

J. Lynch ; K. Tang ; S. Priya ; J. Sands ; M. Sands ; E. Tang ; S. Mukherjee ; D. Knights and R. Blekhaman: HOMINID : a framework for identifying associations between host genetic variation and microbiome composition. GigaScience, 6 (2017) 12, gix107 Bibtex [DOI] [ARXIV] [CODELINK] Journal Open Access

J. D. Silverman ; A. D. Washburne ; S. Mukherjee and L. A. David: A phylogenetic transform enhances analysis of compositional microbiota data. eLife, 6 (2017), e21887 Bibtex [DOI] [ARXIV] [FREELINK] [CODELINK] Journal Open Access

K. R. Singleton ; L. Crawford ; E. Tsui ; H. E. Manchester ; O. Maertens ; X. Liu ; M. Liberti ; A. N. Magpusao ; D. J. Adams ; J. W. Locasale ; K. Cichowski ; S. Mukherjee and K. C. Wood: Melanoma therapeutic strategies that select against resistance by exploiting MYC-driven evolutionary convergence. Cell reports, 21 (2017) 10, p. 2796-2812 Bibtex [DOI] Journal Open Access

S. Sun ; M. Hood ; L. Scott ; Q. Peng ; S. Mukherjee ; J. Tung and X. Zhou: Differential expression analysis for RNAseq using Poisson mixed models. Nucleic acids research, 45 (2017) 11, e106 Bibtex [DOI] [ARXIV] Journal Open Access

A. D. Washburne ; J. D. Silverman ; J. W. Leff ; D. J. Bennett ; J. L. Darcy ; S. Mukherjee ; N. Fierer and L. A. David: Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets. PeerJ, 5 (2017), e2969 Bibtex [DOI] [ARXIV] [CODELINK] Journal Open Access

K. J. Galinsky ; G. Bhatia ; P.-R. Loh ; S. Georgiew ; S. Mukherjee ; N. J. Patterson and A. L. Price: Fast principal-component analysis reveals convergent evolution of ADH1B in Europe and East Asia. American journal of human genetics : AJHG, 93 (2016) 3, p. 456-472 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access

S. Mukherjee and J. Steenbergen: Random walks on simplicial complexes and harmonics. Random structures and algorithms, 49 (2016) 2, p. 379-405 Bibtex [DOI] [ARXIV] Journal Open Access

N. Snyder-Mackler ; W. H. Majoros ; M. L. Yuan ; A. O. Shaver ; J. B. Gordon ; G. H. Kopp ; S. A. Schlebusch ; J. D. Wall ; S. C. Alberts ; S. Mukherjee ; X. Zhou and J. Tung: Efficient genome-wide sequencing and low-coverage pedigree analysis from noninvasively collected samples. Genetics, 203 (2016) 2, p. 699-714 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access

S. Zhao ; C. Gao ; S. Mukherjee and B. E. Engelhardt: Bayesian group factor analysis with structured sparsity. Journal of machine learning research, 17 (2016), 196 Bibtex [ARXIV] [FREELINK] [CODELINK] Journal Open Access

O. Bobrowski and S. Mukherjee: The topology of probability distributions on manifolds. Probability theory and related fields, 161 (2015) 3/4, p. 651-686 Bibtex [DOI] [ARXIV] Repository Open Access

D. M. Boyer ; J. Puente ; J. T. Gladman ; C. Glynn ; S. Mukherjee ; G. S. Yapuncich and I. Daubechies: A new fully automated approach for aligning and comparing shapes. The anatomical record : advances in integrative anatomy and evolutionary biology, 298 (2015) 1, p. 249-276 Bibtex [DOI] [FREELINK] [CODELINK] Repository Open Access

K. McGoff ; S. Mukherjee ; A. Nobel and N. Pillai: Consistency of maximum likelihood estimation for some dynamical systems. The annals of statistics, 43 (2015) 1, p. 1-29 Bibtex [DOI] [ARXIV] Repository Open Access

K. McGoff ; S. Mukherjee and N. Pillai: Statistical inference for dynamical systems : a review. Statistics surveys, 9 (2015), p. 209-252 Bibtex [DOI] [ARXIV] Journal Open Access

E. Munch ; K. Turner ; P. Bendich ; S. Mukherjee ; J. C. Mattingly and J. Harer: Probabilistic Fréchet means for time varying persistence diagrams. Electronic journal of statistics, 9 (2015) 1, p. 1173-1204 Bibtex [DOI] [ARXIV] Journal Open Access

G. Raskutti and S. Mukherjee: The information geometry of mirror descent. IEEE transactions on information theory, 61 (2015) 3, p. 1451-1457 Bibtex [DOI] [ARXIV] Repository Open Access

L. Stewart ; E. L. MacLean ; D. Ivy ; V. Woods ; E. Cohen ; K. Rodriguez ; M. McIntyre ; S. Mukherjee ; J. Call ; J. Kaminski ; M. Adáms ; R. W. Wrangham and B. Hare: Citizen science as a new tool in dog cognition research. PLOS ONE, 10 (2015) 9, e0135176 Bibtex [DOI] Journal Open Access

D. Fusco ; T. J. Barnum ; A. E. Bruno ; J. R. Luft ; E. H. Snell ; S. Mukherjee and P. Charbonneau: Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanism. PLOS ONE, 9 (2014) 7, e101123 Bibtex [DOI] Journal Open Access

B. Huang ; N. W. D. Jarrett ; S. Babu ; S. Mukherjee and J. Yang: Cumulon : cloud-based statistical analysis from users perspective. Bulletin of the Technical Committee on Data Engineering, 37 (2014) 3, p. 77-89 Bibtex [FREELINK] Journal Open Access

A. Kapur ; J. A. Schneider ; D. Heard ; S. Mukherjee ; P. Schumm ; G. Oruganti and E. O. Laumann: A digital network approach to infer sex behavior in emerging HIV epidemics. PLOS ONE, 9 (2014) 7, e101416 Bibtex [DOI] Journal Open Access

J. Steenbergen ; C. Klivans and S. Mukherjee: A Cheeger-type inequality on simplicial complexes. Advances in applied mathematics, 56 (2014), p. 56-77 Bibtex [DOI] [ARXIV] Repository Open Access

K. Turner ; Y. Mileyko ; S. Mukherjee and J. Harer: Fréchet means for distributions of persistence diagrams. Discrete and computational geometry, 52 (2014) 1, p. 44-70 Bibtex [DOI] [ARXIV] Repository Open Access

K. Turner ; S. Mukherjee and D. M. Boyer: Persistent homology transform for modeling shapes and surfaces. Information and inference, 3 (2014) 4, p. 310-344 Bibtex [DOI] [ARXIV] Repository Open Access

M. Weiser ; S. Mukherjee and T. S. Furey: Novel distal eQTL analysis demonstrates effect of population genetic architecture on detecting and interpreting associations. Genetics, 198 (2014) 3, p. 879-893 Bibtex [DOI] [CODELINK] Repository Open Access

O. Whitney ; A. R. Pfenning ; J. T. Howard ; C. A. Blatti ; F. Liu ; J. M. Ward ; R. Wang ; J.-N. Audet ; M. Kellis ; S. Mukherjee ; S. Sinha ; A. J. Hartemink ; A. E. West and E. D. Jarvis: Core and region-enriched networks of behaviorally regulated genes and the singing genome. Science, 346 (2014) 6215, 1256780 Bibtex [DOI]

Q. Xiong ; S. Mukherjee and T. S. Furey: GSAASeqSP : a toolset for gene set association analysis of RNA-seq data. Scientific reports, 4 (2014), 6347 Bibtex [DOI] Journal Open Access

B. D. Bennett ; Q. Xiong ; S. Mukherjee and T. S. Furey: Correction [update acknowledgement]: 'A predictive framework for integrating disparate genomic data types using sample-specific gene set enrichment analysis and multi-task learning' [In: PLOS ONE, 7 (2012) 9 , e44635]. PLOS ONE, 8 (2013) 9, p. 1-1 Bibtex [DOI] Journal Open Access

J. M. Blum ; L. Ano ; Z. Li ; D. Van Mater ; B. D. Bennett ; M. Sachdeva ; I. Lagutina ; M. Zhang ; J. K. Mito ; C. Lepper ; C. M. Linardic ; S. Mukherjee ; G. C. Grosveld ; C.-M. Fan and D. G. Kirsch: Distinct and overlapping sarcoma subtypes initiated from muscle stem and progenitor cells. Cell reports, 5 (2013) 4, p. 933-940 Bibtex [DOI] Journal Open Access

D. Hafez ; T. Ni ; S. Mukherjee ; J. Zhu and U. Ohler: Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation. Bioinformatics, 29 (2013) 13, p. i108-i116 Bibtex [DOI] Journal Open Access

P. R. Hahn ; C. M. Carvalho and S. Mukherjee: Partial factor modeling : predictor-dependent shrinkage for linear regression. Journal of the American Statistical Association, 108 (2013) 503, p. 999-1008 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access

M. Megraw ; S. Mukherjee and U. Ohler: Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. Genome biology, 14 (2013), R85 Bibtex [DOI] Journal Open Access

B. A. Perez ; A. P. Ghafoori ; C.-L. Lee ; S. M. Johnston ; Y. Li ; J. G. Moroshek ; Y. Ma ; S. Mukherjee ; Y. Kim ; C. T. Badea and D. G. Kirsch: Assessing the radiation response of lung cancer with different gene mutations using genetically engineered mice. Frontiers in oncology, 3 (2013), 72 Bibtex [DOI] Journal Open Access

D. E. Runcie and S. Mukherjee: Dissecting high-dimensional phenotypes with Bayesian sparse factor analysis of genetic covariance matrices. Genetics, 194 (2013) 3, p. 753-767 Bibtex [DOI] [ARXIV] [CODELINK] Repository Open Access

L. A. Simmons Kovacs ; M. B. Mayhew ; D. A. Orlando ; Y. Jin ; Q. Li ; C. Huang ; S. I. Reed ; S. Mukherjee and S. B. Haase: Erratum: 'Cyclin-dependent kinases are regulators and effectors of oscillations driven by a transcription factor network' [In: Molecular cell, 45 (2012) 5, p. 669-679]. Molecular cell, 49 (2013) 6, p. 1177-1179 Bibtex [DOI]

P. Stifanelli ; T. M. Creanza ; R. Anglani ; V. C. Liuzzi ; S. Mukherjee ; F. P. Schena and N. Ancona: A comparative study of covariance selection models for the inference of gene regulatory networks. Journal of biomedical informatics, 46 (2013) 5, p. 894-904 Bibtex [DOI] Journal Open Access

D. R. Winter ; L. Song ; S. Mukherjee ; T. S. Furey and G. E. Crawford: DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types. Genome research, 23 (2013) 7, p. 1118-1129 Bibtex [DOI] [FREELINK] Repository Open Access

Q. Wu ; F. Liang and S. Mukherjee: Kernel sliced inverse regression : regularization and consistency. Abstract and applied analysis, 2013 (2013), 540725 Bibtex [DOI] [CODELINK] Journal Open Access

B. D. Bennett ; Q. Xiong ; S. Mukherjee and T. S. Furey: A predictive framework for integrating disparate genomic data types using sample-specific gene set enrichment analysis and multi-task learning. PLOS ONE, 7 (2012) 9, e44635 Bibtex [DOI] Journal Open Access

D. E. Runcie ; D. A. Garfield ; C. C. Babbitt ; J. A. Wygoda ; S. Mukherjee and G. A. Wray: Genetics of gene expression responses to temperature stress in a sea urchin gene network. Molecular ecology, 21 (2012) 18, p. 4547-4562 Bibtex [DOI]

L. A. Simmons Kovacs ; M. B. Mayhew ; D. A. Orlando ; Y. Jin ; Q. Li ; C. Huang ; S. I. Reed ; S. Mukherjee and S. B. Haase: Cyclin-dependent kinases are regulators and effectors of oscillations driven by a transcription factor network. Molecular cell, 45 (2012) 5, p. 669-679 Bibtex [DOI]

J. Tung ; M. J. E. Charpentier ; S. Mukherjee ; J. Altmann and S. C. Alberts: Genetic effects on mating success and partner choice in a social mammal. The American naturalist, 180 (2012) 1, p. 113-129 Bibtex [DOI] [FREELINK] Repository Open Access

Q. Xiong ; N. Ancona ; E. R. Hauser ; S. Mukherjee and T. S. Furey: Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets. Genome research, 22 (2012) 2, p. 386-397 Bibtex [DOI] [FREELINK] Journal Open Access

A. D'Addabbo ; O. Palmieri ; A. Latiano ; V. Annese ; S. Mukherjee and N. Ancona: RS-SNP : a random-set method for genome-wide association studies. BMC genomics, 12 (2011), 166 Bibtex [DOI] Journal Open Access

A. D'Addabbo ; O. Palmieri ; R. Maglietta ; A. Latiano ; S. Mukherjee ; V. Annese and N. Ancona: Discovering genetic variants in Crohn's disease by exploring genomic regions enriched of weak association signals. Digestive and liver disease, 43 (2011) 8, p. 623-631 Bibtex [DOI]

J. Guinney ; Q. Wu and S. Mukherjee: Estimating variable structure and dependence in multitask learning via gradients. Machine learning, 83 (2011) 3, p. 265-287 Bibtex [DOI] Journal Open Access

Y. Mileyko ; S. Mukherjee and J. Harer: Probability measures on the space of persistence diagrams. Inverse problems, 27 (2011) 12, 124007 Bibtex [DOI] [FREELINK] Repository Open Access

S. Mukherjee: Book reviw: 'Inference and prediction in large dimensions' by Dennis Bosq and Delphine Blanke, Wiley, 2007. Journal of the American Statistical Association, 106 (2011) 496, p. 1642-1643 Bibtex [DOI]

S. Georgiew ; A. P. Boyle ; K. Jayasurya ; X. Ding ; S. Mukherjee and U. Ohler: Evidence-ranked motif identification. Genome biology, 11 (2010), R19 Bibtex [DOI] [CODELINK] Journal Open Access

R. Maglietta ; A. Distaso ; A. Piepoli ; O. Palumbo ; M. Carella ; A. D'Addabbo ; S. Mukherjee and N. Ancona: On the reproducibility of results of pathway analysis in genome-wide expression studies of colorectal cancers. Journal of biomedical informatics, 43 (2010) 3, p. 397-406 Bibtex [DOI]

S. Mukherjee: Book reviw: 'Computational intelligence and feature selection: rough and fuzzy approaches' by Richard Jensen and Qiang Shen, Wiley, 2008. Journal of the American Statistical Association, 105 (2010) 489, p. 438-438 Bibtex [DOI]

S. Mukherjee ; Q. Wu and D.-X. Zhou: Learning gradients on manifolds. Bernoulli, 16 (2010) 1, p. 181-207 Bibtex [DOI] [ARXIV] Repository Open Access

Q. Wu ; J. Guinney ; M. Maggioni and S. Mukherjee: Learning gradients : predictive models that infer geometry and dependence. Journal of machine learning research, 11 (2010), p. 2175-2198 Bibtex [FREELINK] Journal Open Access

Q. Wu ; F. Liang and S. Mukherjee: Localized sliced inverse regression. Journal of computational and graphical statistics, 19 (2010) 4, p. 843-860 Bibtex [DOI] [FREELINK] [CODELINK] Repository Open Access

L. Abatangelo ; R. Maglietta ; A. Distaso ; A. D'Addabbo ; T. M. Creanza ; S. Mukherjee and N. Ancona: Comparative study of gene set enrichment methods. BMC bioinformatics, 10 (2009), 275 Bibtex [DOI] Journal Open Access

D. S. Hsu ; C. R. Acharya ; B. S. Balakumaran ; R. F. Riedel ; M. K. Kim ; M. Stevenson ; S. Tuchman ; S. Mukherjee ; W. Barry ; H. K. Dressman ; J. R. Nevins ; S. Powers ; D. Mu and A. Potti: Characterizing the developmental pathways TTF-1, NKX2-8, and PAX9 in lung cancer. Proceedings of the National Academy of Sciences of the United States of America, 106 (2009) 13, p. 5312-5317 Bibtex [DOI] [FREELINK] Repository Open Access

J. Lesneck ; S. Mukherjee ; Z. Yurkovetsky ; M. Clyde ; J. R. Marks ; A. E. Lokshin and J. Y. Lo: Do serum biomarkers really measure breast cancer?. BMC cancer, 9 (2009), 164 Bibtex [DOI] Journal Open Access

J. K. Mito ; R. F. Riedel ; L. Dodd ; G. Lahat ; A. J. Lazar ; R. D. Dodd ; L. Stangenberg ; W. C. Eward ; F. J. Hornicek ; S. S. Yoon ; B. E. Brigman ; T. Jacks ; D. Lev ; S. Mukherjee and D. G. Kirsch: Cross species genomic analysis identifies a mouse model as undifferentiated Pleomorphic Sarcoma/Malignant Fibrous Histiocytoma. PLOS ONE, 4 (2009) 11, e8075 Bibtex [DOI] Journal Open Access

S. Mukherjee: Book reviw: 'The probabilistic method' by Noga Alon and Joel H. Spencer, Wiley, 3rd ed., 2008. Journal of the American Statistical Association, 104 (2009) 488, p. 1723-1723 Bibtex [DOI]

J. Tung ; O. Fédrigo ; R. Haygood ; S. Mukherjee and G. A. Wray: Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation. Molecular biology and evolution, 26 (2009) 9, p. 2047-2059 Bibtex [DOI] Journal Open Access

E. J. Edelman ; J. Guinney ; J.-T. Chi ; P. G. Febbo and S. Mukherjee: Modeling cancer progression via pathway dependencies. PLoS computational biology, 4 (2008) 2, e28 Bibtex [DOI] Journal Open Access

K. H. Salter ; C. R. Acharya ; K. S. Walters ; R. Redman ; A. Anguiano ; K. S. Garman ; C. K. Anders ; S. Mukherjee ; H. K. Dressman ; W. T. Barry ; K. P. Marcom ; J. Olson ; J. R. Nevins and A. Potti: An integrated approach to the prediction of chemotherapeutic response in patients with breast cancer. PLOS ONE, 3 (2008) 4, e1908 Bibtex [DOI] Journal Open Access

Z. Wang ; H. F. Willard ; S. Mukherjee and T. S. Furey: Evidence of influence of genomic DNA sequence on human X chromosome inactivation. PLoS computational biology, 2 (2008) 9, e113 Bibtex [DOI] Journal Open Access

J.-T. Chi ; E. H. Rodriguez ; Z. Wang ; D. S. A. Nuyten ; S. Mukherjee ; M. Van de Rijn ; M. J. Van de Vijver ; T. Hastie and P. O. Brown: Gene expression programs of human smooth muscle cells : tissue-specific differentiation and prognostic significance in breast cancers. PloS genetics, 9 (2007) 3, e164 Bibtex [DOI] Journal Open Access

E. Edelman ; A. Porrello ; J. Guinney ; B. Balakumaran ; A. Bild ; P. G. Febbo and S. Mukherjee: Analysis of sample set enrichment scores : assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles. Bioinformatics, 22 (2007) 14, p. e108-e116 Bibtex [DOI] [FREELINK] Journal Open Access

L. Goh ; S. K. Murphy ; S. Mukherjee and T. S. Furey: Genomic sweeping for hypermethylated genes. Bioinformatics, 23 (2007) 3, p. 281-288 Bibtex [DOI] [FREELINK] Repository Open Access

F. Liang ; S. Mukherjee and M. West: The use of unlabeled data in predictive modeling. Statistical science, 22 (2007) 2, p. 189-205 Bibtex [DOI] [ARXIV] Repository Open Access

N. S. Pillai ; Q. Wu ; F. Liang ; S. Mukherjee and R. L. Wolpert: Characterizing the function space for Bayesian kernel models. Journal of machine learning research, 8 (2007), p. 1769-1797 Bibtex [FREELINK] Journal Open Access

S. Mukherjee ; P. Niyogi ; T. Poggio and R. Rifkin: Learning theory : stability is sufficient for generalization and necessary and sufficient for consistency of empirical risk minimization. Advances in computational mathematics, 25 (2006) 1-3, p. 161-193 Bibtex [DOI] [FREELINK] Repository Open Access

S. Mukherjee and Q. Wu: Estimation of gradients and coordinate covariation in classification. Journal of machine learning research, 7 (2006), p. 2481-2514 Bibtex [FREELINK] Journal Open Access

S. Mukherjee and D.-X. Zhou: Learning coordinate covariances via gradients. Journal of machine learning research, 7 (2006), p. 519-549 Bibtex [FREELINK] Journal Open Access

D. Tropea ; G. Kreiman ; A. Lyckman ; S. Mukherjee ; H. Yu ; S. Horng and M. Sur: Gene expression changes and molecular pathways mediating activity-dependent plasticity in visual cortex. Nature neuroscience, 9 (2006) 5, p. 660-668 Bibtex [DOI] [FREELINK] Repository Open Access

A. Rahkhlin ; D. Panchenko and S. Mukherjee: Risk bounds for mixture density estimation. ESAIM : Probability and statistics, 9 (2005), p. 220-229 Bibtex [DOI] Journal Open Access

A. Rakhlin ; S. Mukherjee and T. Poggio: Stability results in learning theory. Analysis and applications, 3 (2005) 4, p. 397-417 Bibtex [DOI]

A. Subramanian ; P. Tomayo ; V. K. Mootha ; S. Mukherjee ; B. L. Ebert ; M. A. Gillette ; A. Paulovich ; S. L. Pomeroy ; T. R. Golub ; E. S. Lander and J. P. Mesirov: Gene set enrichment analysis : a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America, 102 (2005) 43, p. 15545-15550 Bibtex [DOI] [CODELINK]

A. Sweet-Cordero ; S. Mukherjee ; A. Subramanian ; H. You ; J. J. Roix ; C. Ladd-Acosta ; J. Mesirov ; T. R. Golub and T. Jacks: An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nature genetics, 37 (2005) 1, p. 48-55 Bibtex [DOI] [FREELINK] Repository Open Access

R. Berger ; P. G. Febbo ; P. K. Majumder ; J. J. Zhao ; S. Mukherjee ; S. Signoretti ; K. T. Campbell ; W. R. Sellers ; T. M. Roberts ; M. Loda ; T. R. Golub and W. C. Hahn: Androgen-induced differentiation and tumorigenicity of human prostate epithelial cells. Cancer research, 64 (2004) 24, p. 8867-8875 Bibtex [DOI]

S. Mukherjee ; P. Tamayo ; S. Rogers ; R. Rifkin ; A. Engle ; C. Campbell ; T. R. Golub and J. P. Mesirov: Estimating dataset size requirements for classifying DNA microarray data. Journal of computational biology, 10 (2004) 2, p. 119-142 Bibtex [DOI] [FREELINK] Repository Open Access

T. Poggio ; R. Rifkin ; S. Mukherjee and P. Niyogi: General conditions for predictivity in learning theory. Nature, 428 (2004), p. 419-422 Bibtex [DOI] Repository Open Access

R. Rinfkin ; S. Mukherjee ; P. Tamayo ; S. Ramaswamy ; C.-H. Yeang ; M. Angelo ; M. Reich ; T. Poggio ; E. S. Lander ; T. R. Golub and J. P. Mesirov: An analytical method for multiclass molecular cancer classification. SIAM review, 45 (2003) 4, p. 706-723 Bibtex [DOI] [FREELINK] Repository Open Access

O. Chapelle ; V. Vapnik ; O. Bousquet and S. Mukherjee: Choosing multiple parameters for support vector machines. Machine learning, 46 (2002) 1-3, p. 131-159 Bibtex [DOI] [FREELINK] Repository Open Access

L. D. Miller ; P. M. Long ; L. Wong ; S. Mukherjee ; L. M. McShane and E. T. Liu: Optimal gene expression analysis by microarrays. Cancer cell, 2 (2002) 5, p. 353-361 Bibtex [DOI]

S. Pomeroy ; P. Tamayo ; M. Gaasenbeek ; L. M. Sturla ; M. Angelo ; M. E. McLaughlin ; J. Y. H. Kim ; L. C. Goumnerova ; P. M. Black ; C. Lau ; J. Allen ; D. Zagzag ; J. M. Olson ; T. Curran ; D. Wetmore ; J. A. Biegel ; T. Poggio ; S. Mukherjee ; R. Rifkin ; A. Califano ; G. Stolovitzky ; D. N. Louis ; J. P. Mesirov ; E. S. Lander and T. R. Golub: Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature, 415 (2002) 6870, p. 436-442 Bibtex [DOI] [FREELINK] Repository Open Access

S. Ramaswamy ; P. Tomayo ; R. Rifkin ; S. Mukherjee ; C.-H. Yeang ; M. Angelo ; C. Ladd ; M. Reich ; E. Latulippe ; J. P. Mesirov ; T. Poggio ; W. Gerald ; M. Loda ; E. S. Lander and T. R. Golub: Multiclass cancer diagnosis using tumor gene expression signatures. Proceedings of the National Academy of Sciences of the United States of America, 98 (2001) 26, p. 15149-15154 Bibtex [DOI]

C.-H. Yeang ; S. Ramaswamy ; P. Tamayo ; S. Mukherjee ; R. Rifkin ; M. Angelo ; M. Reich ; E. Lander ; J. Mesirov and T. Golub: Molecular classification of multiple tumor types. Bioinformatics, 17 (2001) Suppl. 1, p. S316-S322 Bibtex [DOI] [FREELINK] Repository Open Access

Publications in Books and Conference Proceedings To top of page

X. Zhang ; R. Bashizade ; Y. Wang ; S. Mukherjee and A. R. Lebeck: Statistical robustness of Markov chain Monte Carlo accelerators. ASPLOS 2021 : Proceedings of the 26th ACM international conference on architectural support for programming languages and operating systems ; virtual ; April 19 - 23, 2021 / T. Sherwood (ed.). Association for Computing Machinery, 2021. - P. 959-974 Bibtex [DOI] [FREELINK] Repository Open Access

Z. Tan ; K. Roche ; X. Zhou and S. Mukherjee: Scalable algorithms for learning high-dimensional linear mixed model. Proceedings of the Thirty-Fourth Conference on Uncertainty in Artificial Intelligence, {UAI} 2018, Monterey, California, USA, August 6-10, 2018 / A. Globerson... (eds.). AUAI Press, 2018. - P. 259-268 Bibtex [ARXIV] [FREELINK] [CODELINK] Repository Open Access

Z. Tan and S. Mukherjee: Partitioned tensor factorizations for learning mixed membership models. Proceedings of the 34th international conference on machine learning : 6-11 August 2017, International Convention Centre, Sydney, Australia / D. Precup... (eds.). PMLR, 2017. - P. 3358-3367 (Proceedings of machine learning research ; 70) Bibtex [ARXIV] [FREELINK] [CODELINK] Repository Open Access

S. Lunagómez ; S. Mukherjee and R. L. Wolpert: Priors on hypergraphical models via simplicial complexes. Current trends in Bayesian methodology with applications / S. Upadhyay... (eds.). CRC Press, 2015. - P. 391-413 Bibtex [FREELINK]

G. Raskutti and S. Mukherjee: The information geometry of mirror descent. Geometric science of information : second international conference, GSI 2015, Palaiseau, France, October 28-30, 2015, proceedings / F. Nielsen... (eds.). Springer, 2015. - P. 359-368 (Lecture notes in computer science ; 9389) Bibtex [DOI] [ARXIV] Repository Open Access

W. Zhang ; P. K. Agarwal and S. Mukherjee: Contour trees of uncertain terrains. SIGSPATIAL '15 : Proceedings of the 23rd SIGSPATIAL international conference on advances in geographic information systems ; November 3 - 6, 2015 ; Washington, Seattle / M. Ali... (eds.). ACM, 2015 Bibtex [DOI] Journal Open Access

P. Bendich ; B. Wang and S. Mukherjee: Local homology transfer and stratification learning. Proceedings of the 23rd annual ACM-SIAM symposium on discrete algorithms, SODA 2012, Kyoto, Japan, January 17-19, 2012 Society for Industrial and Applied Mathematics, 2012. - P. 1355-1370 Bibtex [DOI] Journal Open Access

E. Edelman ; K. Garman ; A. Potti and S. Mukherjee: Making mountains out of molehills : moving from single gene to pathway based models of colon cancer progression. Medical biostatistics for complex diseases / F. Emmert-Streib... (eds.). Wiley-VCH, 2010. - P. 75-87 Bibtex [DOI]

J. Guinney ; P. Febbo ; M. Maggioni and S. Mukherjee: Multiscale factor models for molecular networks. JSM proceedings of the American Statistical Association : papers presented at the joint statistical meetings 2010 ASA, 2010. - P. 4887-4901 Bibtex [FREELINK] Repository Open Access

K. Mao ; F. Liang and S. Mukherjee: Supervised dimension reduction using Bayesian mixture modeling. Proceedings of the thirteenth international conference on artificial intelligence and statistics PMLR, 2010. - P. 501-508 (Proceedings of machine learning research ; 9) Bibtex [FREELINK] [CODELINK] Repository Open Access

Q. Wu ; S. Mukherjee and F. Liang: Localized sliced inverse regression. Advances in neural information processing systems 21 : NIPS 2008 Neural Information Processing Systems, 2008. - P. 1785-1792 Bibtex [FREELINK] [CODELINK] Repository Open Access

P. Golland ; F. Liang ; S. Mukherjee and D. Panchenko: Permutation tests for classification. Learning theory.: 18th annual conference on learning theory, COLT 2005, Bertinoro, Italy, June 27-30, 2005 ; proceedings / P. Auer... (eds.). Springer, 2005. - P. 501-515 (Lecture notes in computer science ; 3559) Bibtex [DOI] [FREELINK]

S. Mukherjee: Classifying microarray data using support vector machines. A practical approach to microarray data analysis / D. P. Berrar... (eds.). Kluwer Academic, 2003. - P. 166-185 Bibtex [DOI]

S. Mukherjee ; R. Rifkin and P. Tomaso: Regression and classification with regularization. Nonlinear estimation and classification / D. D. Denison... (eds.). Springer, 2003. - P. 111-128 (Lecture notes in statistics ; 171) Bibtex [DOI] [FREELINK] Repository Open Access

T. Poggio ; S. Mukherjee ; R. Rifkin ; A. Rakhlin and A. Verri: B. Uncertainty in geometric computations / J. Winkler... (eds.). Springer, 2002. - P. 131-141 (The Springer international series in engineering and computer science ; 704) Bibtex [DOI]

J. Sadr ; S. Mukherjee ; K. Thoresz and P. Sinha: The fidelity of local ordinal encoding. Advances in neural information processing systems 14 : NIPS 2001 ; proceedings of the 2001 neural information processing systems conference / T. G. Dietterich... (eds.). MIT Press, 2002. - P. 1279-1286 Bibtex [FREELINK] Repository Open Access

B. Heisele ; T. Serre ; S. Mukherjee and T. Poggio: Feature reduction and hierarchy of classifiers for fast object detection in video images. Proceedings of the 2001 IEEE computer society conference on computer vision and pattern recognition : CVPR 2001 ; Dec. 8 2001 to Dec. 14 2001 ; Kauai, Hawaii ; Volume 2 IEEE, 2001. - P. 18-24 Bibtex [DOI] [FREELINK] Repository Open Access

L. Peshkin and S. Mukherjee: Bounds on sample size for policy evaluation in Markov environments. Computational learning theory : 14th annual conference, COLT 2001, and 5th European conference, EuroCOLT 2001, Amsterdam, Netherlands, July 16-19, 2001 ; proceedings / D. Helmbold... (eds.). Springer, 2001. - P. 616-629 (Lecture notes in computer science ; 2111) Bibtex [DOI] [ARXIV] Repository Open Access

J. Weston ; S. Mukherjee ; O. Chapelle ; M. Pontil ; T. Poggio and V. Vapnik: Feature selection for SVMs. Advances in neural information processing systems 13 : NIPS 2000 ; proceedings of the 2000 neural information processing systems conference / T. K. Leen... (eds.). MIT Press, 2001. - P. 668-674 Bibtex [FREELINK] Repository Open Access

M. Pontil ; S. Mukherjee and F. Girosi: On the noise model of support vector machines regression. Algorithmic learning theory : 11th international conference, ALT 2000, Sydney, Australia, December 11-13, 2000 ; proceedings / H. Arimura... (eds.). Springer, 2000. - P. 316-324 (Lecture notes in computer science ; 1968) Bibtex [DOI] [FREELINK] Repository Open Access

V. Vapnik and S. Mukherjee: Support vector method for multivariate density estimation. Advances in neural information processing systems 12 : NIPS 1999 ; proceedings of 1999 neural information processing systems conference / S. A. Solla... (eds.). MIT Press, 2000. - P. 659-665 Bibtex [FREELINK] Repository Open Access

Preprints To top of page

S. Arya ; J. Curry and S. Mukherjee: A sheaf-theoretic construction of shape space. Bibtex [ARXIV] Repository Open Access

J. R. Björk ; M. R. Dasari ; K. Roche ; L. Grieneisen ; T. J. Gould ; J.-C. Grenier ; V. Yotova ; N. Gottel ; D. Jansen ; L. R. Gesquiere ; J. B. Gordon ; N. H. Learn ; T. L. Wango ; R. S. Mututua ; J. K. Warutere ; L. Siodi ; S. Mukherjee ; L. B. Barreiro ; S. C. Alberts ; J. A. Gilbert ; J. Tung ; R. Blekhman and E. A. Archie: Synchrony and idiosyncrasy in the gut microbiome of wild baboons. Bibtex [ARXIV] Repository Open Access

M. Pistner Nixon ; J. Letourneau ; L. David ; S. Mukherjee and J. D. Silverman: A statistical analysis of compositional surveys. Bibtex [ARXIV] Repository Open Access

R. Bashizade ; X. Zhang ; S. Mukherjee and A. R. Lebeck: Accelerating markov random field inference with uncertainty quantification. Bibtex [ARXIV] Repository Open Access

M. Caprio ; A. Aveni and S. Mukherjee: Concerning three classes of non-Diophantine arithmetics. Bibtex [ARXIV] Repository Open Access

M. Caprio and S. Mukherjee: Extended probabilities and their application to statistical inference. Bibtex [ARXIV] Repository Open Access

H. Kirveslahti and S. Mukherjee: Representing fields without correspondences : the lifted Euler characteristic transform. Bibtex [ARXIV] Repository Open Access

K. E. Roche and S. Mukherjee: The accuracy of absolute differential abundance analysis from relative count data. Bibtex [ARXIV] Repository Open Access

L. Su and S. Mukherjee: A large deviation approach to posterior consistency in dynamical systems. Bibtex [ARXIV] Repository Open Access

W. S. Tang ; G. Monteiro da Silva ; H. Kirveslahti ; E. Skeens ; B. Feng ; T. Sudijono ; K. K. Yang ; S. Mukherjee ; B. Rubenstein and L. Crawford: A topological data analytic approach for discovering biophysical signatures in protein dynamics. Bibtex [ARXIV] Repository Open Access

A. K. Yanchenko ; M. Soltani ; R. J. Ravier ; S. Mukherjee and V. Tarokh: A methodology for exploring deep convolutional features in relation to hand-crafted features with an application to music audio modeling. Bibtex [ARXIV] [CODELINK] Repository Open Access

M. Caprio and S. Mukherjee: Ergodic theorems in dynamic imprecise probability kinematics. Bibtex [ARXIV] Repository Open Access

M. Caprio and S. Mukherjee: Finite mixture models : a bridge with stochastic geometry and Choquet theory. Bibtex [ARXIV] Repository Open Access

Z. Ding and S. Mukherjee: At the intersection of deep sequential model framework and state-space model framework : study on option pricing. Bibtex [ARXIV] Repository Open Access

N. Fraiman ; S. Mukherjee and G. Thoppe: The bulk and the extremes of minimal spanning acycles and persistence diagrams of random complexes. Bibtex [ARXIV] Repository Open Access

D. Li and S. Mukherjee: Random Lie brackets that induce torsion : a model for noisy vector fields. Bibtex [ARXIV] Repository Open Access

A. K. Yanchenko and S. Mukherjee: Stanza : a nonlinear state space model for probabilistic inference in non-stationary time series. Bibtex [ARXIV] Repository Open Access

X. Zhang ; R. Bashizade ; Y. Wang ; C. Lyu ; S. Mukherjee and A. R. Lebeck: Beyond application end-point results : quantifying statistical robustness of MCMC accelerators. Bibtex [ARXIV] Repository Open Access

S. I. Berchuck ; F. A. Medeiros and S. Mukherjee: Scalable modeling of spatiotemporal data using the variational autoencoder : an application in glaucoma. (The annals of applied statistics :) Bibtex [ARXIV] Repository Open Access

J. D. Silverman ; R. J. Bloom ; S. Jiang ; H. K. Durand ; S. Mukherjee and L. A. David: Measuring and mitigating PCR bias in microbiome data. Bibtex [ARXIV] Repository Open Access

Z. Zou ; S. Mukherjee ; H. Antil and W. Aquino: Adaptive particle-based approximations of the Gibbs posterior for inverse problems. Bibtex [ARXIV] Repository Open Access

J. Curry ; S. Mukherjee and K. Turner: How many directions determine a shape and other sufficiency results for two topological transforms. (Transactions of the American Mathematical Society) Bibtex [ARXIV] Repository Open Access

J. D. Silverman ; L. Shenhav ; E. Halperin ; S. Mukherjee and L. A. David: Statistical considerations in the design and analysis of longitudinal microbiome studies. Bibtex [ARXIV] Repository Open Access

Z. Tan and S. Mukherjee: Learning integral representations of Gaussian processes. Bibtex [ARXIV] [CODELINK] Repository Open Access

M. Vejdemo-Johansson and S. Mukherjee: Multiple testing with persistent homology. Bibtex [ARXIV] Repository Open Access

A. Zaidi and S. Mukherjee: Gaussian process mixtures for estimating heterogeneous treatment effects. Bibtex [ARXIV] Repository Open Access

A. K. Yanchenko and S. Mukherjee: Classical music composition using state space models. Bibtex [ARXIV] [CODELINK] Repository Open Access

J. E. Johndrow ; J. C. Mattingly ; S. Mukherjee and D. B. Dunson: Optimal approximating Markov chains for Bayesian inference. Bibtex [ARXIV] Repository Open Access

P. Bendich ; S. Mukherjee and B. Wang: Towards stratification learning through homology inference. Bibtex [ARXIV] Repository Open Access
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