Published by the Foundation for Open Access Statistics
Editors-in-chief: Bettina Grün, Torsten Hothorn, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
Bayesian Network Constraint-Based Structure Learning Algorithms: Parallel and Optimized Implementations in the bnlearn R Package | Scutari | Journal of Statistical Software
Authors: Marco Scutari
Title: Bayesian Network Constraint-Based Structure Learning Algorithms: Parallel and Optimized Implementations in the bnlearn R Package
Abstract: It is well known in the literature that the problem of learning the structure of Bayesian networks is very hard to tackle: Its computational complexity is super-exponential in the number of nodes in the worst case and polynomial in most real-world scenarios. Efficient implementations of score-based structure learning benefit from past and current research in optimization theory, which can be adapted to the task by using the network score as the objective function to maximize. This is not true for approaches based on conditional independence tests, called constraint-based learning algorithms. The only optimization in widespread use, backtracking, leverages the symmetries implied by the definitions of neighborhood and Markov blanket. In this paper we illustrate how backtracking is implemented in recent versions of the bnlearn R package, and how it degrades the stability of Bayesian network structure learning for little gain in terms of speed. As an alternative, we describe a software architecture and framework that can be used to parallelize constraint-based structure learning algorithms (also implemented in bnlearn) and we demonstrate its performance using four reference networks and two real-world data sets from genetics and systems biology. We show that on modern multi-core or multiprocessor hardware parallel implementations are preferable over backtracking, which was developed when single-processor machines were the norm.

Page views:: 548. Submitted: 2014-06-30. Published: 2017-03-31.
Paper: Bayesian Network Constraint-Based Structure Learning Algorithms: Parallel and Optimized Implementations in the bnlearn R Package     Download PDF (Downloads: 192)
Supplements:
bnlearn_4.1.1.tar.gz: R source package Download (Downloads: 7; 1MB)
v77i02-replication.zip: Replication materials Download (Downloads: 16; 2MB)

DOI: 10.18637/jss.v077.i02

by
This work is licensed under the licenses
Paper: Creative Commons Attribution 3.0 Unported License
Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license.