Estimating Bayesian networks for high-dimensional data with complex mean structure and random effects

DOI10.1111/J.1467-842X.2012.00662.XzbMATH Open1334.62011arXiv1002.2168MaRDI QIDQ2802789FDOQ2802789

Authors: Jessica Kasza, Gary Glonek, Patty Solomon 

Publication date: 27 April 2016

Published in: Australian \& New Zealand Journal of Statistics (Search for Journal in Brave)

Abstract: The estimation of Bayesian networks given high-dimensional data, in particular gene expression data, has been the focus of much recent research. Whilst there are several methods available for the estimation of such networks, these typically assume that the data consist of independent and identically distributed samples. However, it is often the case that the available data have a more complex mean structure plus additional components of variance, which must then be accounted for in the estimation of a Bayesian network. In this paper, score metrics that take account of such complexities are proposed for use in conjunction with score-based methods for the estimation of Bayesian networks. We propose firstly, a fully Bayesian score metric, and secondly, a metric inspired by the notion of restricted maximum likelihood. We demonstrate the performance of these new metrics for the estimation of Bayesian networks using simulated data with known complex mean structures. We then present the analysis of expression levels of grape berry genes adjusting for exogenous variables believed to affect the expression levels of the genes. Demonstrable biological effects can be inferred from the estimated conditional independence relationships and correlations amongst the grape-berry genes.

Full work available at URL: https://arxiv.org/abs/1002.2168

Recommendations

• Using Complexity for the Estimation of Bayesian Networks
• Bayesian approaches for large biological networks
• A hybrid Bayesian network learning method for constructing gene networks
• Comparing score-based methods for estimating Bayesian networks using the Kullback-Leibler divergence
• Using Bayesian networks to analyze gene expression data

zbMATH Keywords

Bayesian networkvariance componentsregulatory networkexogenous variablegrape-berry gene expressionscore-based metric

Mathematics Subject Classification ID

Bayesian inference (62F15) Factor analysis and principal components; correspondence analysis (62H25) Applications of statistics to biology and medical sciences; meta analysis (62P10) Applications of graph theory (05C90) Genetics and epigenetics (92D10) Graphical methods in statistics (62A09) Theory of languages and software systems (knowledge-based systems, expert systems, etc.) for artificial intelligence (68T35)

Cites Work

• Sparse graphical models for exploring gene expression data
• Parameter priors for directed acyclic graphical models and the characterization of several probability distributions
• Large-sample learning of Bayesian networks is NP-hard
• Title not available (Why is that?)
• Probabilistic graphical models.
• Linear Recursive Equations, Covariance Selection, and Path Analysis
• Exploration, normalization, and summaries of high density oligonucleotide array probe level data
• Establishing the Positive Definiteness of the Sample Covariance Matrix
• Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

Cited In (4)

• Comparing Score-Based Methods for Estimating Bayesian Networks Using the Kullback–Leibler Divergence
• Joint Bayesian Variable and DAG Selection Consistency for High-dimensional Regression Models with Network-structured Covariates
• Using Complexity for the Estimation of Bayesian Networks
• Complex networks identification using Bayesian model with independent Laplace prior

Uses Software

• R
• Graphviz

This page was built for publication: Estimating Bayesian networks for high-dimensional data with complex mean structure and random effects

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2802789)