Variable selection for BART: an application to gene regulation

DOI10.1214/14-AOAS755zbMATH Open1304.62132arXiv1310.4887MaRDI QIDQ484051FDOQ484051

Authors: Justin Bleich, Adam Kapelner, Shane T. Jensen, Edward I. George 

Publication date: 17 December 2014

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: We consider the task of discovering gene regulatory networks, which are defined as sets of genes and the corresponding transcription factors which regulate their expression levels. This can be viewed as a variable selection problem, potentially with high dimensionality. Variable selection is especially challenging in high-dimensional settings, where it is difficult to detect subtle individual effects and interactions between predictors. Bayesian Additive Regression Trees [BART, Ann. Appl. Stat. 4 (2010) 266-298] provides a novel nonparametric alternative to parametric regression approaches, such as the lasso or stepwise regression, especially when the number of relevant predictors is sparse relative to the total number of available predictors and the fundamental relationships are nonlinear. We develop a principled permutation-based inferential approach for determining when the effect of a selected predictor is likely to be real. Going further, we adapt the BART procedure to incorporate informed prior information about variable importance. We present simulations demonstrating that our method compares favorably to existing parametric and nonparametric procedures in a variety of data settings. To demonstrate the potential of our approach in a biological context, we apply it to the task of inferring the gene regulatory network in yeast (Saccharomyces cerevisiae). We find that our BART-based procedure is best able to recover the subset of covariates with the largest signal compared to other variable selection methods. The methods developed in this work are readily available in the R package bartMachine.

Full work available at URL: https://arxiv.org/abs/1310.4887

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zbMATH Keywords

variable selectionmachine learningnonparametric regressiondecision treesBayesian learninggene regulatory networkpermutation testing

Mathematics Subject Classification ID

Bayesian inference (62F15) Nonparametric regression and quantile regression (62G08) Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10)

Cites Work

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Cited In (28)

• Group variable selection via group sparse neural network
• Operator-induced structural variable selection for identifying materials genes
• Nowcasting in a pandemic using non-parametric mixed frequency VARs
• Bayesian regression trees for high-dimensional prediction and variable selection
• Variable selection using Bayesian additive regression trees
• Bayesian CART models for insurance claims frequency
• Bayesian neural networks for selection of drug sensitive genes
• Nonparametric failure time: time-to-event machine learning with heteroskedastic Bayesian additive regression trees and low information omnibus Dirichlet process mixtures
• BART-based inference for Poisson processes
• Posterior concentration for Bayesian regression trees and forests
• Gibbs Priors for Bayesian Nonparametric Variable Selection with Weak Learners
• Bayesian neural tree models for nonparametric regression
• A new method for clustered survival data: estimation of treatment effect heterogeneity and variable selection
• CR-Lasso: robust cellwise regularized sparse regression
• An integrated Bayesian framework for multi-omics prediction and classification
• bartMachine
• BART: Bayesian additive regression trees
• Bayesian phase II clinical trial design with noncompliance
• Performance of variable and function selection methods for estimating the nonlinear health effects of correlated chemical mixtures: a simulation study
• mBART: multidimensional monotone BART
• Variable selection for BART: an application to gene regulation
• Log-linear Bayesian additive regression trees for multinomial logistic and count regression models
• Uncertainty quantification for Bayesian CART
• Nonlinear Variable Selection via Deep Neural Networks
• Variable Selection Via Thompson Sampling
• Bayesian additive regression trees using Bayesian model averaging
• Prediction with missing data via Bayesian additive regression trees
• Nonparametric machine learning for precision medicine with longitudinal clinical trials and Bayesian additive regression trees with mixed models

Uses Software

• R
• glmnet
• SSS
• BayesTree
• GeneSrF
• spikeslab
• EMVS
• BartPy

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