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Research Output 1993 2019

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Article
2019
Microscopy
Proteins
Learning
Computational Biology
Datasets
2 Citations (Scopus)

A simple convolutional neural network for prediction of enhancer-promoter interactions with DNA sequence data

Zhuang, Z., Shen, X. & Pan, W., Sep 1 2019, In : Bioinformatics. 35, 17, p. 2899-2906 8 p.

Research output: Contribution to journalArticle

DNA sequences
Promoter
DNA Sequence
Cells
Neural Networks
1 Citation (Scopus)

Constrained likelihood for reconstructing a directed acyclic Gaussian graph

Yuan, Y., Shen, X., Pan, W. & Wang, Z., Mar 1 2019, In : Biometrika. 106, 1, p. 109-125 17 p.

Research output: Contribution to journalArticle

Parameter estimation
Error analysis
Maximum likelihood
Computational complexity
Likelihood

Likelihood Ratio Tests for a Large Directed Acyclic Graph

Li, C., Shen, X. & Pan, W., Jan 1 2019, In : Journal of the American Statistical Association.

Research output: Contribution to journalArticle

Directed Acyclic Graph
Likelihood Ratio Test
Asymptotic distribution
Pathway
Chi-squared

On High-Dimensional Constrained Maximum Likelihood Inference

Zhu, Y., Shen, X. & Pan, W., Jan 1 2019, In : Journal of the American Statistical Association.

Research output: Contribution to journalArticle

Likelihood Inference
Maximum Likelihood
High-dimensional
Regularization
Nuisance Parameter

Scalable Collaborative Ranking for Personalized Prediction

Dai, B., Shen, X., Wang, J. & Qu, A., Jan 1 2019, (Accepted/In press) In : Journal of the American Statistical Association.

Research output: Contribution to journalArticle

Ranking
Prediction
Pairwise
Query
Ranking Function
1 Citation (Scopus)

Smooth neighborhood recommender systems

Dai, B., Wang, J., Shen, X. & Qu, A., Feb 1 2019, In : Journal of Machine Learning Research. 20

Research output: Contribution to journalArticle

Recommender Systems
Recommender systems
Covariates
Alternating Least Squares
Pooling
2018
2 Citations (Scopus)

Multilayer tensor factorization with applications to recommender systems

Bi, X., Qu, A. & Shen, X., Jan 1 2018, In : Annals of Statistics. 46, 6B, p. 3308-3333 26 p.

Research output: Contribution to journalArticle

Recommender Systems
Multilayer
Factorization
Tensor
Recommendations
2017
6 Citations (Scopus)

A Group-Specific Recommender System

Bi, X., Qu, A., Wang, J. & Shen, X., Jul 3 2017, In : Journal of the American Statistical Association. 112, 519, p. 1344-1353 10 p.

Research output: Contribution to journalArticle

Recommender Systems
Backfitting Algorithm
Alternating Least Squares
Competitive System
User Preferences

A novel and efficient algorithm for de novo discovery of mutated driver pathways in cancer

Liu, B., Wu, C., Shen, X. T. & Pan, W., Sep 2017, In : Annals of Applied Statistics. 11, 3, p. 1481-1512 32 p.

Research output: Contribution to journalArticle

Open Access
Driver
Pathway
Cancer
Mutation
Efficient Algorithms

Automatic tagging with existing and novel tags

Wang, J., Shen, X., Sun, Y. & Qu, A., Jun 1 2017, In : Biometrika. 104, 2, p. 273-290 18 p.

Research output: Contribution to journalArticle

Tagging
Linguistics
Labels
Margin
Pairwise
4 Citations (Scopus)

Word segmentation in Chinese language processing

Shu, X., Wang, J., Shen, X. & Qu, A., Jan 1 2017, In : Statistics and its Interface. 10, 2, p. 165-173 9 p.

Research output: Contribution to journalArticle

Labels
Segmentation
Processing
Internet
Statistical Learning
2016
6 Citations (Scopus)

A new algorithm and theory for penalized regression-based clustering

Wu, C., Kwon, S., Shen, X. & Pan, W., Oct 1 2016, In : Journal of Machine Learning Research. 17

Research output: Contribution to journalArticle

Penalized Regression
Method of multipliers
Alternating Direction Method
Clustering
Grouping
4 Citations (Scopus)

Classification With Unstructured Predictors and an Application to Sentiment Analysis

Wang, J., Shen, X., Sun, Y. & Qu, A., Jul 2 2016, In : Journal of the American Statistical Association. 111, 515, p. 1242-1253 12 p.

Research output: Contribution to journalArticle

Sentiment Analysis
Predictors
Classifier
Linear Constraints
Vertex of a graph
6 Citations (Scopus)

Estimation of multiple networks in Gaussian mixture models

Gao, C., Zhu, Y., Shen, X. T. & Pan, W., Jan 1 2016, In : Electronic Journal of Statistics. 10, 1, p. 1133-1154 22 p.

Research output: Contribution to journalArticle

Gaussian Mixture Model
Functional Genomics
Unknown
Gene Networks
Gene Regulation
8 Citations (Scopus)

Integrative and regularized principal component analysis of multiple sources of data

Liu, B., Shen, X. & Pan, W., Jun 15 2016, In : Statistics in Medicine. 35, 13, p. 2235-2250 16 p.

Research output: Contribution to journalArticle

Information Storage and Retrieval
Principal Component Analysis
DNA Methylation
Neoplasms
DNA
1 Citation (Scopus)

Nonlinear joint latent variable models and integrative tumor subtype discovery

Liu, B., Shen, X. T. & Pan, W., Apr 1 2016, In : Statistical Analysis and Data Mining. 9, 2, p. 106-116 11 p.

Research output: Contribution to journalArticle

Latent Variable Models
Joint Model
Tumors
Tumor
Feature extraction
7 Citations (Scopus)

Personalized Prediction and Sparsity Pursuit in Latent Factor Models

Zhu, Y., Shen, X. T. & Ye, C., Jan 2 2016, In : Journal of the American Statistical Association. 111, 513, p. 241-252 12 p.

Research output: Contribution to journalArticle

Factor Models
Pursuit
Sparsity
Prediction
Factorization
2015

Adaptive Modeling Procedure Selection by Data Perturbation

Zhang, Y. & Shen, X., Oct 2 2015, In : Journal of Business and Economic Statistics. 33, 4, p. 541-551 11 p.

Research output: Contribution to journalArticle

Data Perturbation
selection procedure
Selection Procedures
Model Selection
Uncertainty Modeling
1 Citation (Scopus)

A Novel Statistic for Global Association Testing Based on Penalized Regression

Austin, E., Shen, X. T. & Pan, W., Sep 1 2015, In : Genetic epidemiology. 39, 6, p. 415-426 12 p.

Research output: Contribution to journalArticle

Linkage Disequilibrium
Public Opinion
Genetic Structures
Logistic Models
Hypertension
9 Citations (Scopus)

Efficient nonconvex sparse group feature selection via continuous and discrete optimization

Xiang, S., Shen, X. T. & Ye, J., Jul 2015, In : Artificial Intelligence. 224, p. 28-50 23 p., 2829.

Research output: Contribution to journalArticle

Feature extraction
Group
Parameter estimation
projection
Feature Selection
32 Citations (Scopus)

Fused multiple graphical lasso

Yang, S., Lu, Z., Shen, X., Wonka, P. & Ye, J., Jan 1 2015, In : SIAM Journal on Optimization. 25, 2, p. 916-943 28 p.

Research output: Contribution to journalArticle

Lasso
Brain
Subgraph
Graph in graph theory
Neuroimaging
4 Citations (Scopus)

Simultaneous pursuit of sparseness and rank structures for matrix decomposition

Yan, Q., Jieping, Y. & Shen, X. T., 2015, In : Journal of Machine Learning Research. 16, p. 47-55 9 p.

Research output: Contribution to journalArticle

Matrix Decomposition
Pursuit
Decomposition
Time series analysis
Convex optimization
2014
83 Citations (Scopus)

A powerful and adaptive association test for rare variants

Pan, W., Kim, J., Zhang, Y., Shen, X. T. & Wei, P., 2014, In : Genetics. 197, 4, p. 1081-1095 15 p.

Research output: Contribution to journalArticle

Exome
Genotype
Population
Genes
28 Citations (Scopus)

Comparison of statistical tests for group differences in brain functional networks

Kim, J., Wozniak, J. R., Mueller, B. A., Shen, X. T. & Pan, W., Nov 1 2014, In : NeuroImage. 101, p. 681-694 14 p.

Research output: Contribution to journalArticle

Brain
Ecology
Neuroimaging
Magnetic Resonance Imaging
1 Citation (Scopus)

Does the inclusion of rare variants improve risk prediction?

Austin, E., Pan, W. & Shen, X. T., Jun 17 2014, In : BMC Proceedings. 8, S94.

Research output: Contribution to journalArticle

Blood pressure
Blood Pressure
Genes
Maximum likelihood estimation
Polymorphism
22 Citations (Scopus)
Neuroimaging
Polymorphism
cross-sectional studies
single nucleotide polymorphism
Single Nucleotide Polymorphism
3 Citations (Scopus)

Penalized regression approaches to testing for quantitative trait-rare variant association

Kim, S., Pan, W. & Shen, X. T., Jan 1 2014, In : Frontiers in Genetics. 5, MAY, p. 1 1 p., 121.

Research output: Contribution to journalArticle

Statistical Data Interpretation
Genetic Testing
Education
27 Citations (Scopus)

Structural Pursuit Over Multiple Undirected Graphs

Zhu, Y., Shen, X. & Pan, W., Oct 2 2014, In : Journal of the American Statistical Association. 109, 508, p. 1683-1696 14 p.

Research output: Contribution to journalArticle

Pursuit
Undirected Graph
Vertex of a graph
Clustering
Penalized Maximum Likelihood
38 Citations (Scopus)

Testing for association with multiple traits in generalized estimation equations, with application to neuroimaging data

Zhang, Y., Xu, Z., Shen, X. T. & Pan, W., Aug 1 2014, In : NeuroImage. 96, p. 309-325 17 p.

Research output: Contribution to journalArticle

Neuroimaging
Alzheimer Disease
Phenotype
Single Nucleotide Polymorphism
Genome
2013
13 Citations (Scopus)

Adjusting for population stratification in a fine scale with principal components and sequencing data

Zhang, Y., Shen, X. T. & Pan, W., Dec 1 2013, In : Genetic epidemiology. 37, 8, p. 787-801 15 p.

Research output: Contribution to journalArticle

Population
Principal Component Analysis
Genome-Wide Association Study
Economic Inflation
Gene Frequency
28 Citations (Scopus)

Cluster analysis: Unsupervised learning via supervised learning with a non-convex penalty

Pan, W., Shen, X. & Liu, B., Jun 1 2013, In : Journal of Machine Learning Research. 14, p. 1865-1889 25 p.

Research output: Contribution to journalArticle

Clustering Analysis
Unsupervised learning
Unsupervised Learning
Supervised learning
Cluster analysis
18 Citations (Scopus)

Network-Based Penalized Regression With Application to Genomic Data

Kim, S., Pan, W. & Shen, X., Sep 2013, In : Biometrics. 69, 3, p. 582-593 12 p.

Research output: Contribution to journalArticle

Penalized Regression
Convex optimization
Gene expression
Parameter estimation
Genomics
9 Citations (Scopus)

On constrained and regularized high-dimensional regression

Shen, X. T., Pan, W., Zhu, Y. & Zhou, H., Oct 1 2013, In : Annals of the Institute of Statistical Mathematics. 65, 5, p. 807-832 26 p.

Research output: Contribution to journalArticle

High-dimensional
Regression
Feature Selection
Parameter Estimation
Regularization
12 Citations (Scopus)

Penalized regression and risk prediction in genome-wide association studies

Austin, E., Pan, W. & Shen, X. T., Aug 1 2013, In : Statistical Analysis and Data Mining. 6, 4, p. 315-328 14 p.

Research output: Contribution to journalArticle

Penalized Regression
Shrinkage
Single nucleotide Polymorphism
Genome
Nucleotides
22 Citations (Scopus)

Simultaneous grouping pursuit and feature selection over an undirected graph

Zhu, Y., Shen, X. & Pan, W., Dec 16 2013, In : Journal of the American Statistical Association. 108, 502, p. 713-725 13 p.

Research output: Contribution to journalArticle

Pursuit
Undirected Graph
Grouping
Feature Selection
Optimal Estimation
2012
2 Citations (Scopus)

A Two-Step Penalized Regression Method with Networked Predictors

Luo, C., Pan, W. & Shen, X. T., May 1 2012, In : Statistics in Biosciences. 4, 1, p. 27-46 20 p.

Research output: Contribution to journalArticle

Penalized Regression
Predictors
Variable Selection
Convex optimization
Biometrics
8 Citations (Scopus)

Generalized degrees of freedom and adaptive model selection in linear mixed-effects models

Zhang, B., Shen, X. & Mumford, S. L., Mar 1 2012, In : Computational Statistics and Data Analysis. 56, 3, p. 574-586 13 p.

Research output: Contribution to journalArticle

Linear Mixed Effects Model
Fixed Effects
Covariance Structure
Hormones
Random Effects
95 Citations (Scopus)

Likelihood-based selection and sharp parameter estimation

Shen, X. T., Pan, W. & Zhu, Y., Jul 2 2012, In : Journal of the American Statistical Association. 107, 497, p. 223-232 10 p.

Research output: Contribution to journalArticle

Feature Selection
Parameter Estimation
Likelihood
Gene Expression Profile
Metastasis
3 Citations (Scopus)

Maximum likelihood estimation over directed acyclic gaussian graphs

Yuan, Y., Shen, X. & Pan, W., Dec 1 2012, In : Statistical Analysis and Data Mining. 5, 6, p. 523-530 8 p.

Research output: Contribution to journalArticle

Maximum likelihood estimation
Directed Acyclic Graph
Adjacency Matrix
Maximum Likelihood Estimation
Convex Relaxation
14 Citations (Scopus)

Simultaneous supervised clustering and feature selection over a graph

Shen, X. T., Huang, H. C. & Pan, W., Dec 1 2012, In : Biometrika. 99, 4, p. 899-914 16 p.

Research output: Contribution to journalArticle

Feature Selection
Cluster Analysis
Feature extraction
Homogeneous Groups
Genes
2011
36 Citations (Scopus)

Adaptive tests for association analysis of rare variants

Pan, W. & Shen, X., Jul 2011, In : Genetic Epidemiology. 35, 5, p. 381-388 8 p.

Research output: Contribution to journalArticle

Viverridae
Weights and Measures
Direction compound
9 Citations (Scopus)

Adaptive tests for detecting gene-gene and gene-environment interactions

Pan, W., Basu, S. & Shen, X., Oct 2011, In : Human Heredity. 72, 2, p. 98-109 12 p.

Research output: Contribution to journalArticle

Gene-Environment Interaction
Single Nucleotide Polymorphism
Genetic Association Studies
Genes
Regression Analysis

Generalized degrees of freedom and adaptive model selection in linear mixed-eects models

Shen, X. & Zhang, B., 2011, In : Statistical Analysis and Data Mining. 56, p. 574-586

Research output: Contribution to journalArticle

Large margin hierarchical classication with exclusive membership

Shen, X., Wang, H. & Pan, W., 2011, In : Journal of Machine Learning Research. 12, p. 2721-2748

Research output: Contribution to journalArticle

7 Citations (Scopus)

Large margin hierarchical classification with mutually exclusive class membership

Wang, H., Shen, X. T. & Pan, W., Sep 1 2011, In : Journal of Machine Learning Research. 12, p. 2721-2748 28 p.

Research output: Contribution to journalArticle

Hierarchical Classification
Mutually exclusive
Margin
Path
Labels
11 Citations (Scopus)

Multilocus association testing with penalized regression

Basu, S., Pan, W., Shen, X. T. & Oetting, W. S., Dec 1 2011, In : Genetic epidemiology. 35, 8, p. 755-765 11 p.

Research output: Contribution to journalArticle

Logistic Models
Kidney
alachlor
Transplant Recipients
2010

Bayesian variable selection in regression with networked predictors

Shen, X., Tai, F. & Pan, W., 2010, In : Frontiers in Statistics.

Research output: Contribution to journalArticle

61 Citations (Scopus)

Grouping pursuit through a regularization solution surface

Shen, X. & Huang, H. C., Jun 1 2010, In : Journal of the American Statistical Association. 105, 490, p. 727-739 13 p.

Research output: Contribution to journalArticle

Pursuit
Grouping
Regularization
Penalty
Predictors

Grouping pursuit through a regularization surface

Shen, X. & Huang, H. S., 2010, In : Journal of the American Statistical Association. 105

Research output: Contribution to journalArticle