An empirical Bayes approach to network recovery using external knowledge

DOI10.1002/BIMJ.201600090MaRDI QIDQ5364032zbMATH OpenOpenAlexWikidataFDO

Authors

Publication date 2 October 2017

Published in Biometrical Journal (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1605.07514, http://europepmc.org/articles/pmc5510725

zbMATH Keywords

empirical Bayesprior informationGibbs samplingvariational approximationundirected networkhigh-dimensional Bayesian inference

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Estimation in multivariate analysis (62H12)

Abstract: Reconstruction of a high-dimensional network may benefit substantially from the inclusion of prior knowledge on the network topology. In the case of gene interaction networks such knowledge may come for instance from pathway repositories like KEGG, or be inferred from data of a pilot study. The Bayesian framework provides a natural means of including such prior knowledge. Based on a Bayesian Simultaneous Equation Model, we develop an appealing empirical Bayes procedure which automatically assesses the relevance of the used prior knowledge. We use variational Bayes method for posterior densities approximation and compare its accuracy with that of Gibbs sampling strategy. Our method is computationally fast, and can outperform known competitors. In a simulation study we show that accurate prior data can greatly improve the reconstruction of the network, but need not harm the reconstruction if wrong. We demonstrate the benefits of the method in an analysis of gene expression data from GEO. In particular, the edges of the recovered network have superior reproducibility (compared to that of competitors) over resampled versions of the data.

Recommendations

• Reconstructing Gene Regulatory Networks with Bayesian Networks by Combining Expression Data with Multiple Sources of Prior Knowledge
• Gene network reconstruction using global-local shrinkage priors
• Bayesian approaches for large biological networks
• Priors on network structures. Biasing the search for Bayesian networks
• Reconstructing consensus Bayesian network structures with application to learning molecular interaction networks

Cited in

(5)

• Reconstructing consensus Bayesian network structures with application to learning molecular interaction networks
• Bayesian community detection
• Reconstructing Gene Regulatory Networks with Bayesian Networks by Combining Expression Data with Multiple Sources of Prior Knowledge
• Drug sensitivity prediction with normal inverse Gaussian shrinkage informed by external data
• Gene network reconstruction using global-local shrinkage priors

This page was built for publication: An empirical Bayes approach to network recovery using external knowledge

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q5364032)