##### Preprints

Maximum likelihood estimation for Brownian motion tree models based on one sample

Truell, M., Huetter, J.-C., Squires, C., Zwiernik, P. and Uhler, C.

submitted

Keywords: graphical models, total positivity

A mechanism for producing aligned latent spaces with autoencoders

Jain, S., Radhakrishnan, A. and Uhler, C.

submitted

Keywords: autoencoders

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

Efficient permutation discovery in causal DAGs

Squires, C., Amaniampong, J. and Uhler, C.

submitted

Keywords: causal inference

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

2022

Simple, fast, and flexible framework for matrix completion with infinite width neural networks

Radhakrishnan, A., Stefanakis, G., Belkin, M. and Uhler, C.

to appear in Proceedings of the National Academy of Sciences, U.S.A.

Keywords: theory of neural networks, applications to biology

Identifying 3D genome organization in diploid organisms via Euclidean distance geometry

Belyaeva, A., Kubjas, K., Sun, L.J. and Uhler, C.

to appear in SIAM Journal on Mathematics of Data Science

Keywords: optimization, applications to biology

Causal structure discovery between clusters of nodes induced by latent factors

Squires, C., Yun, A., Nichani, E. and Uhler, C.

to appear in Causal Learning and Reasoning (CLearR 2022).

Keywords: causal inference, applications to biology

Causal imputation via synthetic interventions

Squires, C., Shen, D., Agarwal, A., Shah, D. and Uhler, C.

to appear in Causal Learning and Reasoning (CLearR 2022).

Keywords: causal inference, applications to biology

Learning the effective dynamics of complex multiscale systems

Vlachas, P. R., Arampatzis, G., Uhler, C. and Koumoutsakos, P.

to appear in Nature Machine Intelligence

Keywords: autoencoders, applications to physics

##### 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.

Proceedings of the Conference on Computer Vision and Pattern Recognition (CVPR2021)

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

Annals of Statistics 49 (2021), pp. 1436-1459

[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

Matching a desired causal state via shift interventions

Zhang, J., Squires, C. and Uhler, C.

Advances in Neural Information Processing Systems 34 (NeurIPS 2021)

Keywords: causal inference, applications to biology

Near-optimal multi-perturbation experimental design for causal structure learning

Scott, S., Krause, A. and Uhler, C.

Advances in Neural Information Processing Systems 34 (NeurIPS 2021)

Keywords: causal inference, applications to biology

Causality in digital medicine

Glocker, B., Musolesi, M., Richens, J. and C. Uhler

Nature Communications 12 (2021), pp. 5471

[arXiv]

Keywords: causality, applications to biology

Maximum likelihood estimation for totally positive log-concave densities

E. Robeva, B. Sturmfels, N. Tran and C. Uhler

Scandinavian Journal of Statistics 48 (2021), pp. 817-844

[arXiv]

Keywords: shape-constrained density estimation, total positivity

Do deeper convolutional networks perform better?

Nichani, E., Radhakrishnan, A. and Uhler, C.

ICML Workshop on "Over-Parameterization: Pitfalls and Opportunities" (ICML 2021)

Keywords: theory of neural networks

On alignment in deep linear neural networks

Radhakrishnan, A., Nichani, E., Bernstein, D. and Uhler, C.

ICML Workshop on "Over-Parameterization: Pitfalls and Opportunities" (ICML 2021)

Keywords: theory of neural networks

Local quadratic convergence of stochastic gradient descent with adaptive step size

Radhakrishnan, A., Belkin, M. and Uhler, C.

ICML Workshop on "Over-Parameterization: Pitfalls and Opportunities" (ICML 2021)

Keywords: theory of neural networks

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