Preprints
The DeCAMFounder: Non-linear causal discovery in the presence of hidden variables
Agrawal, R., Squires, C., Prasad, N. and Uhler, C.
submitted
Keywords: causal inference, applications to biology
Identifying 3D genome organization in diploid organisms via Euclidean distance geometry
Belyaeva, A., Kubjas, K., Sun, L.J. and Uhler, C.
submitted
Keywords: optimization, applications to biology
Causal imputation via synthetic interventions
Squires, C., Shen, D., Agarwal, A., Shah, D. and Uhler, C.
submitted
Keywords: causal inference, applications to biology
Efficient permutation discovery in causal DAGs
Squires, C., Amaniampong, J. and Uhler, C.
submitted
Keywords: causal inference
Do deeper convolutional networks perform better?
Nichani, E., Radhakrishnan, A. and Uhler, C.
submitted
Keywords: deep neural networks
Joint inference of multiple graphs from matrix polynomials
Novarro, M., Wang, Y., Marques, A.G., Uhler, C. and Segarra, S.
submitted
Keywords: causal inference, graphical models
Linear convergence and implicit regularization of generalized mirror descent with time-dependent mirrors
Radhakrishnan, A., Belkin, M. and Uhler, C.
submitted
Keywords: optimization
Learning the effective dynamics of complex multiscale systems
Vlachas, P. R., Arampatzis, G., Uhler, C. and Koumoutsakos, P.
submitted
Keywords: autoencoders, applications to physics
On alignment in deep linear neural networks
Radhakrishnan, A., Nichani, E., Bernstein, D. and Uhler, C.
submitted
Keywords: deep neural networks
2021
Improved conditional flow models for molecule to image synthesis
Yang, K., Goldman, S., Jin, W., Lu, A., Barzilay, R., Jaakkola, T. and Uhler, C.
to appear in Proceedings of the Conference on Computer Vision and Pattern Recognition
Keywords: generative modeling, applications to biology
DCI: Learning causal differences between gene regulatory networks
Belyaeva, A., Squires, C. and Uhler, C.
Bioinformatics, 2021, 1-3, 10.1093/bioinformatics/btab167.
Keywords: causal inference, applications to biology
Total positivity in exponential families with application to binary variables
S. Lauritzen, C. Uhler and P. Zwiernik
to appear in Annals of Statistics
[arXiv]
Keywords: total positivity, algebraic statistics
Causal network models of SARS-CoV-2 expression and aging to identify candidates for drug repurposing
Belyaeva, A., Cammarata, L., Radhakrishnan, A., Squires, C., Yang, K. D., Shivashankar, G. V. and Uhler, C.
Nature Communications, 12 (2021) 1024
Keywords: causal inference, autoencoders, applications to biology
Maximum likelihood estimation for totally positive log-concave densities
E. Robeva, B. Sturmfels, N. Tran and C. Uhler
to appear in Scandinavian Journal of Statistics
[arXiv]
Keywords: shape-constrained density estimation, total positivity
Consistency guarantees for greedy permutation-based causal inference algorithms
L. Solus, Y. Wang, and C. Uhler
Biometrika (2021), asaa104
[arXiv]
Keywords: causal inference, algebraic statistics
Multidomain translation between single-cell imaging and sequencing data using autoencoders
Yang, K. D., Belyaeva, A., Venkatchalapathy, S., Damodaran, K., Radhakrishnan, A., Katcoff, A., Shivashankar, G. V. and Uhler, C.
Nature Communications 12 (2021), article 31
Keywords: autoencoders, applications to biology
Mechanogenomic coupling of lung tissue stiffness, EMT and coronavirus pathogenicity
Uhler, C. and Shivashankar, G. V.
Current Opinion in Solid State and Materials Science 25 (2021), pp. 100874
Keywords: applications to biology
2020
Ordering-based causal structure learning in the presence of latent variables
D. I. Bernstein, B. Saeed, C. Squires and C. Uhler
Proceedings of Machine Learning Research 108 (AISTATS 2020), pp. 4098-4108
[arXiv]
Keywords: causal inference, algebraic statistics
Permutation-based causal structure learning with unknown intervention targets
C. Squires, Y. Wang and C. Uhler
Proceedings of the Thirty-Sixth Conference on Uncertainty in Artificial Intelligence (UAI 2020)
[arXiv]
Keywords: causal inference, applications to biology
Causal structure discovery from distributions arising from mixtures of DAGs
Saeed, B., Panigrahi, S. and Uhler, C.,
Proceedings of Machine Learning Research 119 (ICML 2020)
Keywords: causal inference, applications to biology
Optimal transport using GANs for lineage tracing
Prasad, N., Yang, K.D. and Uhler, C.,
Workshop on Computational Biology, International Conference on Machine Learning (ICML 2020)
Keywords: autoencoders, optimal transport, applications to biology
Overparameterized neural networks can implement associative memory
A. Radhakrishnan, M. Belkin and C. Uhler
Proceedings of the National Academy of Sciences, U.S.A. 117 (2020), pp. 27162-27170
[journal]
Keywords: autoencoders, machine learning
Covariance matrix estimation under total positivity for portfolio selection
R. Agrawal, U. Roy and C. Uhler
Journal of Financial Econometrics (2020), nbaa018
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
Proceedings of Machine Learning Research 108 (AISTATS 2020), pp. 2698-2708
[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
Proceedings of the Thirty-Sixth Conference on Uncertainty in Artificial Intelligence (UAI 2020)
[arXiv]
Keywords: causal inference, applications to biology
Brownian motion tree models are toric
B. Sturmfels, C. Uhler and P. Zwiernik
Kybernetika (special issue for Frantisek Matus) 56 (2020), pp. 1154-1175
Keywords: total positivity, algebraic statistics
Predicting cell lineages using autoencoders and optimal transport
K.D. Yang, K. Damodaran, S. Venkatchalapathy, A.C. Soylemezoglu, G.V Shivashankar and C. Uhler
PLoS Computational Biology 16 (2020), e1007828
Keywords: autoencoders, applications to biology
Mechano-genomic regulation of coronaviruses and its interplay with ageing
Uhler, C. and Shivashankar, G.V.
Nature Reviews Molecular Cell Biology 21 (2020), pp. 247-248
Keywords: applications to biology
High-dimensional joint estimation of multiple directed Gaussian graphical models
Y. Wang, S. Segarra and C. Uhler
Electronic Journal of Statistics 14 (2020), pp. 2439-2483
Keywords: causal inference, high-dimensional statistics
Algebraic statistics in practice: Applications to networks
M. Casanellas, S. Petrovic and C. Uhler
Annual Review of Statistics and its Applications 7 (2020), pp. 227-250 (invited review)
[arXiv]
Keywords: causal inference, algebraic statistics
2019
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
[arXiv]
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
[arXiv]
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 Analysis 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