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2023
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Generalized Bayes approach to inverse problems with model misspecification
In: Inverse problems, 39 (2023) 10, p. 105011inJournal
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Ergodic theorems in dynamic imprecise probability kinematics
In: International journal of approximate reasoning, 152 (2023), pp. 325-343Preprint
2023
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Irreducibility of Markov chains on simplicial complexes, the spectrum of the discrete Hodge Laplacian and homology
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The shadow knows : empirical distributions of minimum spanning acycles and persistence diagrams of random complexes
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Universal gut microbial relationships in the gut microbiome of wild baboons
In: eLife, 12 (2023), e8315inJournal
2023
Identifying risk factors for blindness from glaucoma at first presentation to a tertiary clinic
In: American journal of ophthalmology, 250 (2023), pp. 130-137Preprint
2023
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Minimum \(\Phi\)-distance estimators for finite mixing measures
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Bayesian non-parametric factor analysis for longitudinal spatial surfaces
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Synchrony and idiosyncrasy in the gut microbiome of wild baboons
In: Nature ecology and evolution, 6 (2022) 7, pp. 955-964inJournal
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Concerning three classes of non-Diophantine arithmetics
In: Involve : a journal of mathematics, 15 (2022) 5, pp. 763-774inJournal
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How many directions determine a shape and other sufficiency results for two topological transforms
In: Transactions of the American Mathematical Society / B, 9 (2022), pp. 1006-1043inJournal
2022
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Gibbs posterior convergence and the thermodynamic formalism
In: The annals of applied probability, 32 (2022) 1, pp. 461-496Preprint
2022
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A statistical analysis of compositional surveys
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2022
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The accuracy of absolute differential abundance analysis from relative count data
In: PLoS computational biology, 18 (2022) 7, e1010284inJournal
2022
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Bayesian multinomial logistic normal models through Marginally Latent Matrix-T processes
In: Journal of machine learning research, 23 (2022) 7, pp. 1-42inJournal
2022
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Learning subspaces of different dimensions
In: Journal of computational and graphical statistics, 31 (2022) 2, pp. 337-350inJournal
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A topological data analytic approach for discovering biophysical signatures in protein dynamics
In: PLoS computational biology, 18 (2022) 5, e1010045inJournal
2022
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Multiple hypothesis testing with persistent homology
In: Foundations of data science, 4 (2022) 4, pp. 667-705Preprint
2021
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Accelerating markov random field inference with uncertainty quantification
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2021
Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways
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Extended probabilities and their application to statistical inference
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2021
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The geometry of synchronization problems and learning group actions
In: Discrete and computational geometry, 65 (2021) 1, pp. 150-211inJournal
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Morphological and genomic shifts in mole-rat 'queens' increase fecundity but reduce skeletal integrity
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2021
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Representing fields without correspondences : the lifted Euler characteristic transform
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2021
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Subspace clustering through sub-clusters
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A large deviation approach to posterior consistency in dynamical systems
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2021
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A statistical pipeline for identifying physical features that differentiate classes of 3D shapes
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A methodology for exploring deep convolutional features in relation to hand-crafted features with an application to music audio modeling
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2021
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Statistical robustness of Markov chain Monte Carlo accelerators
In: ASPLOS 2021 : Proceedings of the 26th ACM international conference on architectural support for programming languages and operating systems ; virtual ; April 19 - 23, 2021 / Tim Sherwood (ed.)New York, NY : Association for Computing Machinery, 2021. - pp. 959-974
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2020
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Finite mixture models : a bridge with stochastic geometry and Choquet theory
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2020
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Predicting clinical outcomes in glioblastoma : an application of topological and functional data analysis
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2020
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At the intersection of deep sequential model framework and state-space model framework : study on option pricing
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2020
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Random Lie brackets that induce torsion : a model for noisy vector fields
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2020
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Naught all zeros in sequence count data are the same
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2020
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Stanza : a nonlinear state space model for probabilistic inference in non-stationary time series
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2019
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Estimating rates of progression and predicting future visual fields in glaucoma using a deep variational autoencoder
In: Scientific reports, 9 (2019), p. 18113Preprint
2019
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Scalable modeling of spatiotemporal data using the variational autoencoder : an application in glaucoma
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2019
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Label propagation defines signaling networks associated with recurrently mutated cancer genes
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2019
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Measuring and mitigating PCR bias in microbiome data
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2019
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Evolution of DNA methylation in Papio baboons
In: Molecular biology and evolution, 36 (2019) 3, pp. 527-540inJournal
2019
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Phylofactorization : a graph partitioning algorithm to identify phylogenetic scales of ecological data
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A unifying framework for interpreting and predicting mutualistic systems
In: Nature communications, 10 (2019), p. 242Preprint
2019
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Adaptive particle-based approximations of the Gibbs posterior for inverse problems
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2018
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Combinations of DIPs and Dprs control organization of olfactory receptor neuron terminals in Drosophila
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2018
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Bayesian approximate kernel regression with variable selection
In: Journal of the American Statistical Association, 113 (2018) 524, pp. 1710-1721inJournal
2018
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Development and assessment of fully automated and globally transitive geometric morphometric methods, with application to a biological comparative dataset with high interspecific variation
In: The anatomical record : advances in integrative anatomy and evolutionary biology, 301 (2018) 4, pp. 636-658inJournal
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Dynamic linear models guide design and analysis of microbiota studies within artificial human guts
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Statistical considerations in the design and analysis of longitudinal microbiome studies
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Learning integral representations of Gaussian processes
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2018
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Scalable algorithms for learning high-dimensional linear mixed model
In: Proceedings of the Thirty-Fourth Conference on Uncertainty in Artificial Intelligence, {UAI} 2018, Monterey, California, USA, August 6-10, 2018 / Amir Globerson... (eds.)Corvallis, Or. : AUAI Press, 2018. - pp. 259-268
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Gaussian process mixtures for estimating heterogeneous treatment effects
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2018
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Fast moment estimation for generalized latent Dirichlet models
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Topological consistency via kernel estimation
In: Bernoulli, 23 (2017) 1, pp. 288-328inJournal
2017
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Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits
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2017
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Adaptive randomized dimension reduction on massive data
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2017
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Geometric representations of random hypergraphs
In: Journal of the American Statistical Association, 112 (2017) 517, pp. 363-383inJournal
2017
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HOMINID : a framework for identifying associations between host genetic variation and microbiome composition
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2017
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A phylogenetic transform enhances analysis of compositional microbiota data
In: eLife, 6 (2017), e21887inJournal
2017
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Melanoma therapeutic strategies that select against resistance by exploiting MYC-driven evolutionary convergence
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2017
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Differential expression analysis for RNAseq using Poisson mixed models
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2017
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Partitioned tensor factorizations for learning mixed membership models
In: Proceedings of the 34th international conference on machine learning : 6-11 August 2017, International Convention Centre, Sydney, Australia / Doina Precup... (eds.)Long Beach, California : PMLR, 2017. - pp. 3358-3367
(Proceedings of machine learning research ; 70)
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2017
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Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets
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Classical music composition using state space models
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2016
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Fast principal-component analysis reveals convergent evolution of ADH1B in Europe and East Asia
In: American journal of human genetics : AJHG, 93 (2016) 3, pp. 456-472inJournal
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Random walks on simplicial complexes and harmonics
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Efficient genome-wide sequencing and low-coverage pedigree analysis from noninvasively collected samples
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Bayesian group factor analysis with structured sparsity
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The topology of probability distributions on manifolds
In: Probability theory and related fields, 161 (2015) 3/4, pp. 651-686inJournal
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A new fully automated approach for aligning and comparing shapes
In: The anatomical record : advances in integrative anatomy and evolutionary biology, 298 (2015) 1, pp. 249-276Preprint
2015
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Optimal approximating Markov chains for Bayesian inference
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2015
Priors on hypergraphical models via simplicial complexes
In: Current trends in Bayesian methodology with applications / Satyanshu Upadhyay... (eds.)Boca Raton, FL : CRC Press, 2015. - pp. 391-413
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2015
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Consistency of maximum likelihood estimation for some dynamical systems
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Statistical inference for dynamical systems : a review
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Probabilistic Fréchet means for time varying persistence diagrams
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The information geometry of mirror descent
In: Geometric science of information : second international conference, GSI 2015, Palaiseau, France, October 28-30, 2015, proceedings / Frank Nielsen... (eds.)Cham : Springer, 2015. - pp. 359-368
(Lecture notes in computer science ; 9389)
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Contour trees of uncertain terrains
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Cumulon : cloud-based statistical analysis from users perspective
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A digital network approach to infer sex behavior in emerging HIV epidemics
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A Cheeger-type inequality on simplicial complexes
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Fréchet means for distributions of persistence diagrams
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Persistent homology transform for modeling shapes and surfaces
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Novel distal eQTL analysis demonstrates effect of population genetic architecture on detecting and interpreting associations
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Core and region-enriched networks of behaviorally regulated genes and the singing genome
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GSAASeqSP : a toolset for gene set association analysis of RNA-seq data
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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]
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Distinct and overlapping sarcoma subtypes initiated from muscle stem and progenitor cells
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Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation
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2013
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Partial factor modeling : predictor-dependent shrinkage for linear regression
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Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits
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Dissecting high-dimensional phenotypes with Bayesian sparse factor analysis of genetic covariance matrices
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A comparative study of covariance selection models for the inference of gene regulatory networks
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DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types
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Local homology transfer and stratification learning
In: Proceedings of the 23rd annual ACM-SIAM symposium on discrete algorithms, SODA 2012, Kyoto, Japan, January 17-19, 2012Philadelphia, PA : Society for Industrial and Applied Mathematics, 2012. - pp. 1355-1370
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A predictive framework for integrating disparate genomic data types using sample-specific gene set enrichment analysis and multi-task learning
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Genetics of gene expression responses to temperature stress in a sea urchin gene network
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Cyclin-dependent kinases are regulators and effectors of oscillations driven by a transcription factor network
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RS-SNP : a random-set method for genome-wide association studies
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Towards stratification learning through homology inference
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Making mountains out of molehills : moving from single gene to pathway based models of colon cancer progression
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Evidence-ranked motif identification
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Multiscale factor models for molecular networks
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On the reproducibility of results of pathway analysis in genome-wide expression studies of colorectal cancers
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Supervised dimension reduction using Bayesian mixture modeling
In: Proceedings of the thirteenth international conference on artificial intelligence and statisticsLong Beach, California : PMLR, 2010. - pp. 501-508
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Learning gradients on manifolds
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Localized sliced inverse regression
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Comparative study of gene set enrichment methods
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Cross species genomic analysis identifies a mouse model as undifferentiated Pleomorphic Sarcoma/Malignant Fibrous Histiocytoma
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Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation
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Modeling cancer progression via pathway dependencies
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Evidence of influence of genomic DNA sequence on human X chromosome inactivation
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Localized sliced inverse regression
In: Advances in neural information processing systems 21 : NIPS 2008La Jolla, CA : Neural Information Processing Systems, 2008. - pp. 1785-1792
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Gene expression programs of human smooth muscle cells : tissue-specific differentiation and prognostic significance in breast cancers
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Analysis of sample set enrichment scores : assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles
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Characterizing the function space for Bayesian kernel models
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Estimation of gradients and coordinate covariation in classification
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Learning coordinate covariances via gradients
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Learning theory : stability is sufficient for generalization and necessary and sufficient for consistency of empirical risk minimization
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Gene expression changes and molecular pathways mediating activity-dependent plasticity in visual cortex
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Permutation tests for classification
In: Learning theory.: 18th annual conference on learning theory, COLT 2005, Bertinoro, Italy, June 27-30, 2005 ; proceedings / Peter Auer... (eds.)Berlin : Springer, 2005. - pp. 501-515
(Lecture notes in computer science ; 3559)
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Risk bounds for mixture density estimation
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Stability results in learning theory
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Gene set enrichment analysis : a knowledge-based approach for interpreting genome-wide expression profiles
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An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis
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General conditions for predictivity in learning theory
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Classifying microarray data using support vector machines
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Regression and classification with regularization
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An analytical method for multiclass molecular cancer classification
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Optimal gene expression analysis by microarrays
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In: Uncertainty in geometric computations / Joab Winkler... (eds.)New York : Springer, 2002. - pp. 131-141
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Prediction of central nervous system embryonal tumour outcome based on gene expression
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The fidelity of local ordinal encoding
In: Advances in neural information processing systems 14 : NIPS 2001 ; proceedings of the 2001 neural information processing systems conference / Thomas G. Dietterich... (eds.)Cambridge, Mass. : MIT Press, 2002. - pp. 1279-1286
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Feature reduction and hierarchy of classifiers for fast object detection in video images
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Bounds on sample size for policy evaluation in Markov environments
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(Lecture notes in computer science ; 2111)
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Multiclass cancer diagnosis using tumor gene expression signatures
In: Proceedings of the National Academy of Sciences of the United States of America, 98 (2001) 26, pp. 15149-15154inBook
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Feature selection for SVMs
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2001
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Molecular classification of multiple tumor types
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On the noise model of support vector machines regression
In: Algorithmic learning theory : 11th international conference, ALT 2000, Sydney, Australia, December 11-13, 2000 ; proceedings / Hiroki Arimura... (eds.)Berlin : Springer, 2000. - pp. 316-324
(Lecture notes in computer science ; 1968)
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Support vector method for multivariate density estimation
In: Advances in neural information processing systems 12 : NIPS 1999 ; proceedings of 1999 neural information processing systems conference / Sara A. Solla... (eds.)Cambridge, Mass. : MIT Press, 2000. - pp. 659-665
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