Joint estimation of multiple related biological networks

DOI10.1214/14-AOAS761zbMATH Open1304.62136arXiv1302.1969MaRDI QIDQ484069FDOQ484069

Authors: Jim Korkola, Joe W. Gray, Sach Mukherjee, Chris J. Oates 

Publication date: 17 December 2014

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

Abstract: Graphical models are widely used to make inferences concerning interplay in multivariate systems. In many applications, data are collected from multiple related but nonidentical units whose underlying networks may differ but are likely to share features. Here we present a hierarchical Bayesian formulation for joint estimation of multiple networks in this nonidentically distributed setting. The approach is general: given a suitable class of graphical models, it uses an exchangeability assumption on networks to provide a corresponding joint formulation. Motivated by emerging experimental designs in molecular biology, we focus on time-course data with interventions, using dynamic Bayesian networks as the graphical models. We introduce a computationally efficient, deterministic algorithm for exact joint inference in this setting. We provide an upper bound on the gains that joint estimation offers relative to separate estimation for each network and empirical results that support and extend the theory, including an extensive simulation study and an application to proteomic data from human cancer cell lines. Finally, we describe approximations that are still more computationally efficient than the exact algorithm and that also demonstrate good empirical performance.

Full work available at URL: https://arxiv.org/abs/1302.1969

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zbMATH Keywords

Bayesian networkhierarchical modelinformation sharingbelief propagation

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Estimation in multivariate analysis (62H12) Graphical methods in statistics (62A09) Systems biology, networks (92C42) Small world graphs, complex networks (graph-theoretic aspects) (05C82)

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Cited In (11)

• On Joint Estimation of Gaussian Graphical Models for Spatial and Temporal Data
• Inference and characterization of multi-attribute networks with application to computational biology
• Using Complexity for the Estimation of Bayesian Networks
• Quantifying the multi-scale performance of network inference algorithms
• Bayesian Approaches for Large Biological Networks
• Exact estimation of multiple directed acyclic graphs
• Research in Computational Molecular Biology
• Joint estimation of multiple related biological networks
• Title not available (Why is that?)
• Inferring multiple graphical structures
• Bayesian Graphical Regression

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