A Hypothesis Test for Equality of Bayesian Network Models

Overview

Journal EURASIP J Bioinform Syst Biol

Publisher Springer

Specialty Biology

Date 2010 Oct 29

PMID 20981254

Citations 5

Authors

Anthony Almudevar

Affiliations

Soon will be listed here.

Abstract

Bayesian network models are commonly used to model gene expression data. Some applications require a comparison of the network structure of a set of genes between varying phenotypes. In principle, separately fit models can be directly compared, but it is difficult to assign statistical significance to any observed differences. There would therefore be an advantage to the development of a rigorous hypothesis test for homogeneity of network structure. In this paper, a generalized likelihood ratio test based on Bayesian network models is developed, with significance level estimated using permutation replications. In order to be computationally feasible, a number of algorithms are introduced. First, a method for approximating multivariate distributions due to Chow and Liu (1968) is adapted, permitting the polynomial-time calculation of a maximum likelihood Bayesian network with maximum indegree of one. Second, sequential testing principles are applied to the permutation test, allowing significant reduction of computation time while preserving reported error rates used in multiple testing. The method is applied to gene-set analysis, using two sets of experimental data, and some advantage to a pathway modelling approach to this problem is reported.

Citing Articles

Spectral Bayesian network theory.

Duttweiler L, Thurston S, Almudevar A Linear Algebra Appl. 2023; 674:282-303.

PMID: 37520305 PMC: 10373448. DOI: 10.1016/j.laa.2023.06.003.

Gaussian Bayesian network comparisons with graph ordering unknown.

Zhang H, Huang X, Han S, Rezwan F, Karmaus W, Arshad H Comput Stat Data Anal. 2021; 157.

PMID: 33408431 PMC: 7781289. DOI: 10.1016/j.csda.2020.107156.

Genotypic and Phenotypic Factors Influencing Drug Response in Mexican Patients With Type 2 Diabetes Mellitus.

Sanchez-Ibarra H, Reyes-Cortes L, Jiang X, Luna-Aguirre C, Aguirre-Trevino D, Morales-Alvarado I Front Pharmacol. 2018; 9:320.

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Diversity in Compartmental Dynamics of Gene Regulatory Networks: The Immune Response in Primary Influenza A Infection in Mice.

Qiu X, Wu S, Hilchey S, Thakar J, Liu Z, Welle S PLoS One. 2015; 10(9):e0138110.

PMID: 26413862 PMC: 4586376. DOI: 10.1371/journal.pone.0138110.

Affymetrix GeneChip microarray preprocessing for multivariate analyses.

McCall M, Almudevar A Brief Bioinform. 2012; 13(5):536-46.

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