A sparse Ising model with covariates

DOI10.1111/BIOM.12202zbMATH Open1393.62057arXiv1209.6342OpenAlexW2032259302WikidataQ35586841 ScholiaQ35586841MaRDI QIDQ3465372FDOQ3465372

Authors: Jie Cheng, Elizaveta Levina, Pei Wang, Ji Zhu 

Publication date: 21 January 2016

Published in: Biometrics (Search for Journal in Brave)

Abstract: There has been a lot of work fitting Ising models to multivariate binary data in order to understand the conditional dependency relationships between the variables. However, additional covariates are frequently recorded together with the binary data, and may influence the dependence relationships. Motivated by such a dataset on genomic instability collected from tumor samples of several types, we propose a sparse covariate dependent Ising model to study both the conditional dependency within the binary data and its relationship with the additional covariates. This results in subject-specific Ising models, where the subject's covariates influence the strength of association between the genes. As in all exploratory data analysis, interpretability of results is important, and we use L1 penalties to induce sparsity in the fitted graphs and in the number of selected covariates. Two algorithms to fit the model are proposed and compared on a set of simulated data, and asymptotic results are established. The results on the tumor dataset and their biological significance are discussed in detail.

Full work available at URL: https://arxiv.org/abs/1209.6342

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zbMATH Keywords

Lassopseudo-likelihoodgraphical modelIsing modeltumor suppressor genesbinary Markov network

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Estimation in multivariate analysis (62H12) Ridge regression; shrinkage estimators (Lasso) (62J07)

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Cited In (18)

• An Additive Graphical Model for Discrete Data
• Sparse directed acyclic graphs incorporating the covariates
• A stochastic block Ising model for multi-layer networks with inter-layer dependence
• Bayesian graphical models for modern biological applications
• Collaborative Multilabel Classification
• Bayesian graphical regression
• Joint modeling of change-point identification and dependent dynamic community detection
• Bayesian Edge Regression in Undirected Graphical Models to Characterize Interpatient Heterogeneity in Cancer
• Random subspace method for high-dimensional regression with the \texttt{R} package \texttt{regRSM}
• Sufficient dimension reduction and prediction in regression: asymptotic results
• Conditional Gaussian graphical model for estimating personalized disease symptom networks
• Structure estimation of binary graphical models on stratified data: application to the description of injury tables for victims of road accidents
• Covariate-Assisted Bayesian Graph Learning for Heterogeneous Data
• On semiparametric exponential family graphical models
• Community detection with dependent connectivity
• Low-Rank Regression Models for Multiple Binary Responses and their Applications to Cancer Cell-Line Encyclopedia Data
• Consistent Community Detection in Inter-Layer Dependent Multi-Layer Networks
• High-Dimensional Gaussian Graphical Regression Models with Covariates

Uses Software

• glmnet

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