Bayesian Structure Learning in Sparse Gaussian Graphical Models

Abstract

Decoding complex relationships among large numbers of variables with relatively few observations is one of the crucial issues in science. One approach to this problem is Gaussian graphical modeling, which describes conditional independence of variables through the presence or absence of edges in the underlying graph. In this paper, we introduce a novel and efficient Bayesian framework for Gaussian graphical model determination which is a trans-dimensional Markov Chain Monte Carlo (MCMC) approach based on a continuous-time birth-death process. We cover the theory and computational details of the method. It is easy to implement and computationally feasible for high-dimensional graphs. We show our method outperforms alternative Bayesian approaches in terms of convergence, mixing in the graph space and computing time. Unlike frequentist approaches, it gives a principled and, in practice, sensible approach for structure learning. We illustrate the efficiency of the method on a broad range of simulated data. We then apply the method on large-scale real applications from human and mammary gland gene expression studies to show its empirical usefulness. In addition, we implemented the method in the R package BDgraph which is freely available at http://CRAN.R-project.org/package=BDgraph

arXiv commentPublished at http://dx.doi.org/10.1214/14-BA889 in the Bayesian Analysis (http://projecteuclid.org/euclid.ba) by the International Society of Bayesian Analysis (http://bayesian.org/)

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• BDgraph: An R Package for Bayesian Structure Learning in Graphical Models
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• Bayesian Inference in Nonparanormal Graphical Models
• Cultures as networks of cultural traits: A unifying framework for measuring culture and cultural distances
• Network reconstruction via the minimum description length principle
• Learning block structured graphs in Gaussian graphical models
• Random graphical model of microbiome interactions in related environments
• Covariate-Assisted Bayesian Graph Learning for Heterogeneous Data