Preprints
Ordering-based causal structure learning in the presence of latent variables
D. I. Bernstein, B. Saeed, C. Squires and C. Uhler
Under review
[arXiv]
Keywords: causal inference, algebraic statistics
Permutation-based causal structure learning with unknown intervention targets
C. Squires, Y. Wang and C. Uhler
Under review
[arXiv]
Keywords: causal inference, applications to biology
Overparameterized neural networks can implement associative memory
A. Radhakrishnan, M. Belkin and C. Uhler
Under review
[arXiv]
Keywords: autoencoders, machine learning
Covariance matrix estimation under total positivity for portfolio selection
R. Agrawal, U. Roy and C. Uhler
Under review
[arXiv]
Keywords: total positivity, applications to finance
Learning high-dimensional Gaussian graphical models under total positivity without tuning parameters
Y. Wang, U. Roy and C. Uhler
Under review
[arXiv]
Keywords: total positivity, applications to finance
Anchored causal inference in the presence of measurement error
B. Saeed, A. Belyaeva, Y. Wang and C. Uhler
Under review
[arXiv]
Keywords: causal inference, applications to biology
Total positivity in structured binary distributions
S. Lauritzen, C. Uhler and P. Zwiernik
Under review
[arXiv]
Keywords: total positivity, algebraic statistics
Brownian motion tree models are toric
B. Sturmfels, C. Uhler and P. Zwiernik
Under review
[arXiv]
Keywords: total positivity, algebraic statistics
Autoencoder and optimal transport to infer single-cell trajectories of biological processes
K.D. Yang, K. Damodaran, S. Venkatchalapathy, A.C. Soylemezoglu, G.V Shivashankar and C. Uhler
Under review
[arXiv]
Keywords: autoencoders, application to biology
Maximum likelihood estimation for totally positive log-concave densities
E. Robeva, B. Sturmfels, N. Tran and C. Uhler
Under review
[arXiv]
Keywords: shape-constrained density estimation, total positivity
High-dimensional joint estimation of multiple directed Gaussian graphical models
Y. Wang, S. Segarra and C. Uhler
Under review
[arXiv]
Keywords: causal inference, high-dimensional statistics
Consistency guarantees for permutation-based causal inference algorithms
L. Solus, Y. Wang, L. Matejovicova and C. Uhler
Under review
[arXiv]
Keywords: causal inference, algebraic statistics
2019
Algebraic statistics in practice: Applications to networks
M. Casanellas, S. Petrovic and C. Uhler
To appear in Annual Review of Statistics and its Applications (invited review)
[arXiv]
Keywords: causal inference, algebraic statistics
Maximum likelihood estimation in Gaussian models under total positivity
S. Lauritzen, C. Uhler and P. Zwiernik
Annals of Statistics 47 (2019), pp. 1835-1863.
[arXiv]
Keywords: total positivity, Gaussian graphical models
Multi-domain translation by learning uncoupled autoencoders
K.D. Yang and C. Uhler
Computational Biology Workshop, International Conference on Machine Learning (ICML 2019)
[arXiv]
Keywords: autoencoders, machine learning
Memorization in overparameterized autoencoders
A. Radhakrishnan, K.D. Yang, M. Belkin and C. Uhler
Deep Phenomena Workshop, International Conference on Machine Learning (ICML 2019)
[arXiv]
Keywords: autoencoders, machine learning
ABCD-Strategy: Budgeted experimental design for targeted causal structure discovery
R. Agrawal, C. Squires, K.D. Yang, K. Shanmugam and C. Uhler
Proceedings of Machine Learning Research 89 (AISTATS 2019), pp. 3400-3409
Keywords: causal inference, experimental design
Size of interventional Markov equivalence classes in random DAG models
D. Katz-Rogozhnikov,K. Shanmugam, C. Squires and C. Uhler
Proceedings of Machine Learning Research 89 (AISTATS 2019), pp. 3234-3243
Keywords: causal inference
Scalable unbalanced optimal transport using generative adversarial networks
K.D. Yang and C. Uhler
International Conference on Learning Representations (ICLR 2019)
[arXiv]
Keywords: optimal transport, applications to biology
Geometry of discrete copulas
E. Perrone, L. Solus and C. Uhler
Journal of Multivariate Analsysis 172 (2019), pp. 162-179
[arXiv]
Keywords: algebraic statistics
Loading monotonicity of weighted premiums, and total positivity properties of weight functions
D. Richards and C. Uhler
Journal of Mathematical Analysis and Applications, 475 (2019), pp. 532-553.
[arXiv]
Keywords: mathematical statistics, total positivity
Generalized Fréchet bounds for cell entries in multidimensional contingency tables
C. Uhler and D. Richards
Journal of Algebraic Statistics 10 (special issue for Stephen E. Fienberg) (2019), pp. 1-12
[arXiv]
Keywords: mathematical statistics, total positivity
Geometry of log-concave density estimation
E. Robeva, B. Sturmfels and C. Uhler
Discrete & Computational Geometry 61 (2019), pp. 136-160
[arXiv]
Keywords: shape-constrained density estimation, algebraic statistics
2018
Direct estimation of differences in causal graphs
Y. Wang, C. Squires, A. Belyaeva and C. Uhler
Advances in Neural Information Processing Systems 31 (2018)
[arXiv]
Keywords: causal inference, applications to biology
PatchNet: Interpretable neural networks for image classification
A. Radhakrishnan, C. Durham, A. Soylemezoglu and C. Uhler
Machine Learning for Health (ML4H) Workshop, Neural Information Processing Systems (2018)
[arXiv]
Keywords: neural nets, applications to biology
Minimal I-MAP MCMC for scalable structure discovery in causal DAG models
R. Agrawal, T. Broderick and C. Uhler
Proceedings of Machine Learning Research 80 (ICML 2018), pp. 89-98
[arXiv]
Keywords: causal inference, Bayesian statistics, applications to biology
Characterizing and learning equivalence classes of causal DAGs under interventions
K. D. Yang, A. Katcoff and C. Uhler
Proceedings of Machine Learning Research 80 (ICML 2018), pp. 5537-5546
[arXiv]
Keywords: causal inference, applications to biology
Learning directed acyclic graphs based on sparsest permutations
G. Raskutti and C. Uhler
Stat 7 (2018), e183
[arXiv]
Keywords: causal inference, algebraic statistics
Counting Markov equivalence classes for DAG models on trees
A. Radhakrishnan, L. Solus and C. Uhler
Discrete Applied Mathematics 244 (2018), pp. 170-185
[arXiv]
Keywords: causal inference, algebraic statistics
Nuclear mechanopathology and cancer diagnosis
C. Uhler and G.V. Shivashankar
Trends in Cancer 4 (2018), pp. 320-331 (invited review)
[journal]
Keywords: applications to biology, chromosome packing
Generalized permutohedra from probabilistic graphical models
F. Mohammadi, C. Uhler, C. Wang and J. Yu
SIAM Journal on Discrete Mathematics 32 (2018), pp. 64-93
[arXiv]
Keywords: causal inference, algebraic statistics
Exact formulas for the normalizing constants of Wishart distributions for graphical models
C. Uhler, A. Lenkoski and D. Richards
Annals of Statistics 46 (2018), pp. 90-118
[arXiv]
Keywords: Gaussian graphical models, Bayesian statistics
Gaussian graphical models: An algebraic and geometric perspective
C. Uhler
Chapter for Handbook on Graphical Models (editors: M. Drton, S. Lauritzen, M. Maathuis and M. Wainwright)
[arXiv]
Keywords: Gaussian graphical models, algebraic statistics
2017
Machine learning for nuclear mechano-morphometric biomarkers in cancer diagnosis
A. Radhakrishnan, D. Damodaran, A. Soylemezoglu, C. Uhler, and G.V. Shivashankar
Scientific Reports 7 (2017), article nr. 17946.
[journal]
Keywords: neural nets, applications to biology
Permutation-based causal inference algorithms with interventions
Y. Wang, L. Solus, K.D. Yang and C. Uhler
Advances in Neural Information Processing (NIPS 2017)
[arXiv]
Keywords: causal inference, algebraic statistics
Network analysis identifies chromosome intermingling regions as regulatory hotspots for transcription
A. Belyaeva, S. Venkatachalapathy, M. Nagarajan, G.V. Shivashankar and C. Uhler
Proceedings of the National Academy of Sciences, U.S.A. 114 (2017), pp. 13714-13719.
[journal]
Keywords: chromosome packing, applications to biology
Regulation of genome organization and gene expression by nuclear mechanotransduction
C. Uhler and G.V. Shivashankar
Nature Reviews Molecular Cell Biology 18 (2017), pp. 717-727 (invited review).
[journal]
Keywords: applications to biology, chromosome packing
Chromosome intermingling: Mechanical hotspots for genome regulation
C. Uhler and G.V. Shivashankar
Trends in Cell Biology 27 (2017), pp. 810-819 (invited review)
[journal]
Keywords: chromosome packing, applications to biology
Orientation and repositioning of chromosomes correlate with cell geometry-dependent gene expression
Y. Wang, M. Nagarajan, C. Uhler and G.V. Shivashankar
Molecular Biology of the Cell 28 (2017), pp. 1997-2009
[journal]
Keywords: chromosome packing, applications to biology
Maximum likelihood estimation for linear Gaussian covariance models
P. Zwiernik, C. Uhler and D. Richards
Journal of the Royal Statistical Society, Series B 79 (2017), pp. 1269-1292
[arXiv]
Keywords: Gaussian models, covariance estimation, optimization
Counting Markov equivalence classes by number of immoralities
A. Radhakrishnan, L. Solus and C. Uhler
Proceedings of the Thirty-Third Conference on Uncertainty in Artificial Intelligence (UAI 2017)
[arXiv]
Keywords: causal inference, algebraic statistics
Total positivity in Markov structures
S. Fallat, L. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth and P. Zwiernik
Annals of Statistics 45 (2017), pp. 1152-1184
[arXiv]
Keywords: total positivity, mathematical statistics
Exact goodness-of-fit testing for the Ising model
A. Martin del Campo, S. Cepeda and C. Uhler
Scandinavian Journal of Statistics 44 (2017), pp. 285-306
[arXiv]
Keywords: hypothesis testing, algebraic statistics
2016
Extremal positive semidefinite matrices for graphs without K5 minors
L. Solus, C. Uhler and R. Yoshida
Linear Algebra and its Applications 509 (2016), pp. 247-275
[arXiv]
Keywords: Gaussian graphical models, algebraic statistics
Geometric control and modeling of genome reprogramming
C. Uhler and G.V. Shivashankar
BioArchitecture 6 (2016), pp. 76-84
[journal]
Keywords: chromosome packing, applications to biology
M. Michalek, B. Sturmfels, C. Uhler and P. Zwiernik
Proceedings of the London Mathematical Society 112 (2016), pp. 27-56
[arXiv]
Keywords: Gaussian graphical models, algebraic statistics
2015
Faithfulness and learning of hypergraphs from discrete distributions
A. Klimova, C. Uhler and T. Rudas
Journal of Computational Statistics and Data Analysis 87 (2015), pp. 57-72.
[arXiv]
Keywords: causal inference, algebraic statistics
2014
Hypersurfaces and their singularities in partial correlation testing
S. Lin, C. Uhler, B. Sturmfels and P. Bühlmann
Foundations of Computational Mathematics 14 (2014), pp. 1079-1116
[arXiv]
Keywords: causal inference, algebraic statistics
Differentially private logistic regression for detecting multiple-SNP association in GWAS databases
F. Yu, M. Rybar, C. Uhler and S.E. Fienberg
Privacy in Statistical Databases 8744 (2014), pp. 170-184
[arXiv]
Keywords: differential privacy, applications to biology
Sphere packing with limited overlap
M. Iglesias-Ham, M. Kerber and C. Uhler
Proceedings of the 26th Canadian Conference on Computational Geometry, Halifax, Nova Scotia (2014), pp. 155-161.
[arXiv]
Keywords: sphere packing, applications to biology
Scalable privacy-preserving data sharing methodology for genome-wide association studies
F. Yu, S.E. Fienberg, A. Slavkovic and C. Uhler
Journal of Biomedical Informatics 50 (2014), pp. 133-141
[arXiv]
Keywords: differential privacy, applications to biology
2013
Packing ellipsoids with overlap
C. Uhler and S.J. Wright
SIAM Review 55 (2013), pp. 671-706 (selected as Research Spotlight)
[arXiv]
Keywords: optimization, sphere packing, chromosome packing
Geometry of faithfulness assumption in causal inference
C. Uhler, G. Raskutti, P. Bühlmann and B. Yu
Annals of Statistics 41 (2013), pp. 436-463
[arXiv]
Keywords: causal inference, algebraic statistics
Privacy-preserving data sharing for genome-wide association studies
C. Uhler, S.E. Fienberg and A. Slavkovic
Journal of Privacy and Confidentiality 5 (2013), pp. 137-166
[arXiv]
Keywords: differential privacy, applications to biology
2012
Geometry of maximum likelihood estimation in Gaussian graphical models
C. Uhler
Annals of Statistics 40 (2012), pp. 238-261
[arXiv]
Keywords: Gaussian graphical models, algebraic statistics
2011
Privacy preserving GWAS data sharing
S.E. Fienberg, A. Slavkovic and C. Uhler
Proceedings of the 11th IEEE International Conference on Data Mining, Vancouver, Canada (2011), pp. 628-635
[pdf]
Keywords: differential privacy, applications to biology
Detecting epistasis via Markov bases
A. Malaspinas and C. Uhler
Journal of Algebraic Statistics 2 (2011), pp. 36-53
[arXiv]
Keywords: algebraic statistics, applications to biology
2010
Multivariate Gaussians, semidefinite matrix completion and convex algebraic geometry
B. Sturmfels and C. Uhler
Annals of the Institute of Statistical Mathematics 62 (2010), pp. 603-638
[arXiv]
Keywords: Gaussian graphical models, algebraic statistics
Commuting birth-and-death processes
S. Evans, B. Sturmfels and C. Uhler
Annals of Applied Probability 20 (2010), pp. 238-266
[arXiv]
Keywords: birth-and-death processes, algebraic statistics
2009
C. Uhler
Journal of Agricaltural, Biological, and Environmental Statistics 14 (2009), pp. 79-98
Keywords: differential privacy, applications to biology
2008
A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing
R.E. Green, A. Malaspinas, J. Krause, A.W. Briggs, P.L. Johnson, C. Uhler, M. Meyer, J.M. Good, T. Maricic, U. Stenzel, K. Prüfer, M. Siebauer, H.A. Burbano, M. Ronan, J.M. Rothberg, M. Egholm, P. Rudan, D. Brajkovic, Z. Kucan, I. Gusic, M. Wikström, L. Laakkonen, J. Kelso, M. Slatkin and S. Pääbo
Cell 134 (2008), pp. 416-426
[journal]
Keywords: applications to biology