Ali Shojaie

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Causal Structure Learning with Reduced Partial Correlation Thresholding

Arjun Sondhi, Ali Shojaie, A. Shojaie, 2016, 2016 IEEE International Conference on Data Science and Advanced Analytics (DSAA).

Link Prediction in Biological Networks using Multi-Mode Exponential Random Graph Models

Ali Shojaie, A. Shojaie, 2013 .

Combining Supervised and Unsupervised Learning for Improved miRNA Target Prediction

Mahmood Fathy, Ali Shojaie, Nafiseh Sedaghat, 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Statistical Inference for Networks of High-Dimensional Point Processes pdf

Mladen Kolar, Ali Shojaie, Xu Wang, 2020, ArXiv.

Adaptive Thresholding for Reconstructing Regulatory Networks from Time-Course Gene Expression Data

Ali Shojaie, George Michailidis, Sumanta Basu, 2012 .

Wavelet regression and additive models for irregularly spaced data

Ali Shojaie, Noah Simon, Asad Haris, 2019, NeurIPS.

Comment: Models as (deliberate) approximations.

David Whitney, Ali Shojaie, Marco Carone, 2019, Statistical science : a review journal of the Institute of Mathematical Statistics.

Gene set analysis methods: a systematic comparison

Ali Shojaie, Ravi Mathur, Alison A. Motsinger-Reif, 2018, BioData Mining.

Generalized Score Matching for Non-Negative Data pdf

Ali Shojaie, Mathias Drton, Shiqing Yu, 2018, J. Mach. Learn. Res..

Using random walks to identify cancer-associated modules in expression data

Ali Shojaie, John H. Gennari, Neil F. Abernethy, 2013, BioData Mining.

A comparative study of topology-based pathway enrichment analysis methods

Ali Shojaie, George Michailidis, Jing Ma, 2019, BMC Bioinformatics.

Penalized likelihood methods for estimation of sparse high-dimensional directed acyclic graphs.

Ali Shojaie, George Michailidis, G. Michailidis, 2009, Biometrika.

Graph Estimation with Joint Additive Models.

Ali Shojaie, Daniela Witten, Arend Voorman, 2013, Biometrika.

Network granger causality with inherent grouping structure

Ali Shojaie, George Michailidis, Sumanta Basu, 2012, J. Mach. Learn. Res..

Consistent Second-Order Conic Integer Programming for Learning Bayesian Networks pdf

Ali Shojaie, Simge Küçükyavuz, Linchuan Wei, 2020, J. Mach. Learn. Res..

Covariate-Adjusted Inference for Differential Analysis of High-Dimensional Networks

Ali Shojaie, Aaron Hudson, 2020 .

Network Reconstruction From High-Dimensional Ordinary Differential Equations

Ali Shojaie, Daniela M Witten, Shizhe Chen, 2016, Journal of the American Statistical Association.

Enrichment Analysis of Metabolic Pathways Using P-value Perturbation

Ali Shojaie, George Michailidis, Moulinath Banerjee, 2012 .

The cluster graphical lasso for improved estimation of Gaussian graphical models

Ali Shojaie, Daniela M. Witten, Kean Ming Tan, 2013, Comput. Stat. Data Anal..

How Different Are Estimated Genetic Networks of Cancer Subtypes

Ali Shojaie, Nafiseh Sedaghat, A. Shojaie, 2017 .

Bayesian hidden Markov models for dependent large-scale multiple testing

Xia Wang, Ali Shojaie, Jian Zou, 2019, Comput. Stat. Data Anal..

Estimation and Inference in High Dimensional Networks, with Applications to Biological Systems.

Ali Shojaie, A. Shojaie, 2010 .

The Cluster Elastic Net for High-Dimensional Regression With Unknown Variable Grouping

Fan Zhang, Ali Shojaie, Daniela M. Witten, 2014, Technometrics.

Directed Graphical Models and Causal Discovery for Zero-Inflated Data

Ali Shojaie, Mathias Drton, Shiqing Yu, 2020, CLeaR.

Bioinformatics in Toxicology: Statistical Methods for Supervised Learning in High-Dimensional Omics Data

Ali Shojaie, N. Sedaghat, I. B. Stanway, 2018 .

Network-based pathway enrichment analysis with incomplete network information

Jing Ma, Ali Shojaie, George Michailidis, 2014, Bioinform..

A significance test for graph‐constrained estimation

Ali Shojaie, Sen Zhao, A. Shojaie, 2015, Biometrics.

Penalized Principal Component Regression on Graphs for Analysis of Subnetworks

Ali Shojaie, George Michailidis, G. Michailidis, 2010, NIPS.

Discovering graphical Granger causality using the truncating lasso penalty

Ali Shojaie, George Michailidis, G. Michailidis, 2010, Bioinform..

Statistical Significance in High-dimensional Linear Mixed Models

Ali Shojaie, Mathias Drton, Lina Lin, 2019, FODS.

Statistical Inference for Qualitative Interactions with Applications to Precision Medicine and Differential Network Analysis

Ali Shojaie, Aaron Hudson, A. Shojaie, 2020, 2010.08703.

Integer Programming for Learning Directed Acyclic Graphs from Continuous Data pdf

Ali Shojaie, Simge Küçükyavuz, Hasan Manzour, 2019, INFORMS J. Optim..

Joint Structural Break Detection and Parameter Estimation in High-Dimensional Nonstationary VAR Models

Ali Shojaie, Abolfazl Safikhani, A. Shojaie, 2017, Journal of the American Statistical Association.

Using Twitter for Demographic and Social Science Research: Tools for Data Collection and Processing

Ali Shojaie, Tyler H McCormick, Emma S. Spiro, 2014, Sociological methods & research.

Graphical Models for Non-Negative Data Using Generalized Score Matching

Ali Shojaie, Mathias Drton, Shiqing Yu, 2018, AISTATS.

The Reduced PC-Algorithm: Improved Causal Structure Learning in Large Random Networks

Arjun Sondhi, Ali Shojaie, A. Shojaie, 2018, J. Mach. Learn. Res..

Differential network analysis: A statistical perspective pdf

Ali Shojaie, A. Shojaie, 2020, Wiley interdisciplinary reviews. Computational statistics.

Analysis of Gene Sets Based on the Underlying Regulatory Network

Ali Shojaie, George Michailidis, G. Michailidis, 2009, J. Comput. Biol..

A comparative study of topology-based pathway enrichment analysis methods

Ali Shojaie, George Michailidis, Jing Ma, 2019, BMC Bioinformatics.

Joint Estimation and Inference for Multi-Experiment Networks of High-Dimensional Point Processes

Ali Shojaie, Xu Wang, A. Shojaie, 2021, 2109.11634.

Interaction Models and Generalized Score Matching for Compositional Data

Ali Shojaie, Mathias Drton, Shiqing Yu, 2021, LoG.

On the Optimality of Nuclear-norm-based Matrix Completion for Problems with Smooth Non-linear Structure

Ali Shojaie, Noah Simon, Xu Wang, 2021, 2105.01874.

Granger Causality: A Review and Recent Advances pdf

Emily B. Fox, Ali Shojaie, E. Fox, 2021, Annual review of statistics and its application.

Definite Non-Ancestral Relations and Structure Learning pdf

Ali Shojaie, Mathias Drton, Wenyu Chen, 2021, ArXiv.

Inference on function-valued parameters using a restricted score test

Ali Shojaie, Marco Carone, Aaron Hudson, 2021, 2105.06646.

Causal Structural Learning Via Local Graphs

Ali Shojaie, Mathias Drton, Wenyu Chen, 2021 .

Direct estimation of differential Granger causality between two high-dimensional time series

Ali Shojaie, Jing Ma, Yue Wang, 2021, 2109.07609.

The Convex Mixture Distribution: Granger Causality for Categorical Time Series

Emily B. Fox, Ali Shojaie, Alex Tank, 2021, SIAM J. Math. Data Sci..

Nonparametric causal structure learning in high dimensions

Ali Shojaie, Shubhadeep Chakraborty, 2021 .

CorDiffViz: an R package for visualizing multi-omics differential correlation networks

Ali Shojaie, Mathias Drton, Daniel E. L. Promislow, 2021, BMC Bioinform..

Convergence Rates of Nonparametric Penalized Regression under Misspecified Smoothness

Ali Shojaie, Noah Simon, N. Simon, 2021 .

Causal Discovery in High-Dimensional Point Process Networks with Hidden Nodes

Ali Shojaie, Xu Wang, A. Shojaie, 2021, Entropy.

Metabolomic profiling reveals potential markers and bioprocesses altered in bladder cancer progression.

Yair Lotan, Ali Shojaie, Huidong Shi, 2011, Cancer research.

Nearly assumptionless screening for the mutually-exciting multivariate Hawkes process.

Ali Shojaie, Shizhe Chen, Daniela Witten, 2017, Electronic journal of statistics.

Comparative Study of Computational Methods for Reconstructing Genetic Networks of Cancer-Related Pathways

Ali Shojaie, Nafiseh Sedaghat, Takumi Saegusa, 2014, Cancer informatics.

High-dimensional inference of graphical models using regularized score matching

Ali Shojaie, Mathias Drton, Lina Lin, 2015 .

In Defense of the Indefensible: A Very Naïve Approach to High-Dimensional Inference.

Ali Shojaie, Daniela Witten, D. Witten, 2017, Statistical science : a review journal of the Institute of Mathematical Statistics.

An Efficient ADMM Algorithm for Structural Break Detection in Multivariate Time Series

Emily B. Fox, Ali Shojaie, Alex Tank, 2017 .

Inhibition of the hexosamine biosynthetic pathway promotes castration-resistant prostate cancer

Ali Shojaie, Katrin Panzitt, Fabio Stossi, 2016, Nature Communications.

Inference in High Dimensions with the Penalized Score Test

Ali Shojaie, Arend Voorman, Daniela Witten, 2014, 1401.2678.

Identifying functional cancer-specific miRNA-mRNA interactions in testicular germ cell tumor.

Mahmood Fathy, Ali Shojaie, Nafiseh Sedaghat, 2016, Journal of theoretical biology.

Selection and estimation for mixed graphical models.

Ali Shojaie, Shizhe Chen, Daniela M Witten, 2013, Biometrika.

An Interpretable and Sparse Neural Network Model for Nonlinear Granger Causality Discovery

Emily B. Fox, Ali Shojaie, Nicholas J. Foti, 2017, 1711.08160.

Inferring Regulatory Networks by Combining Perturbation Screens and Steady State Gene Expression Profiles

Ali Shojaie, George Michailidis, Alexandra Jauhiainen, 2013, PloS one.

Nonparametric regression with adaptive truncation via a convex hierarchical penalty

Ali Shojaie, Noah Simon, Asad Haris, 2016, Biometrika.