A Bayesian nonparametric mixture model for selecting genes and gene subnetworks

DOI10.1214/14-AOAS719zbMATH Open1454.62429arXiv1407.8399OpenAlexW3106134091WikidataQ40710098 ScholiaQ40710098MaRDI QIDQ400643FDOQ400643

Tianwei Yu, Jian Kang, Yize Zhao

Publication date: 22 August 2014

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

Abstract: It is very challenging to select informative features from tens of thousands of measured features in high-throughput data analysis. Recently, several parametric/regression models have been developed utilizing the gene network information to select genes or pathways strongly associated with a clinical/biological outcome. Alternatively, in this paper, we propose a nonparametric Bayesian model for gene selection incorporating network information. In addition to identifying genes that have a strong association with a clinical outcome, our model can select genes with particular expressional behavior, in which case the regression models are not directly applicable. We show that our proposed model is equivalent to an infinity mixture model for which we develop a posterior computation algorithm based on Markov chain Monte Carlo (MCMC) methods. We also propose two fast computing algorithms that approximate the posterior simulation with good accuracy but relatively low computational cost. We illustrate our methods on simulation studies and the analysis of Spellman yeast cell cycle microarray data.

Full work available at URL: https://arxiv.org/abs/1407.8399

zbMATH Keywords

feature selectiondensity estimationmicroarray dataDirichlet process mixtureIsing priors

Mathematics Subject Classification ID

Computational methods for problems pertaining to statistics (62-08) Applications of statistics to biology and medical sciences; meta analysis (62P10)

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Cited In (5)

• A Bayesian nonparametric mixture model for selecting genes and gene subnetworks
• Feature selection and classification over the network with missing node observations
• Molecular multiplex network inference using Gaussian mixture hidden Markov models
• Title not available (Why is that?)
• A spatial Bayesian semiparametric mixture model for positive definite matrices with applications in diffusion tensor imaging

Uses Software

• Pathway Commons

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