Bayesian Network Constraint-Based Structure Learning Algorithms: Parallel and Optimised Implementations in the bnlearn R Package

TL;DR

This paper compares traditional backtracking optimization with parallel processing approaches for constraint-based Bayesian network structure learning, demonstrating that parallel implementations are more effective on modern hardware.

Contribution

It introduces a parallel architecture for constraint-based structure learning in bnlearn, showing improved performance over backtracking on current multi-core systems.

Findings

Parallel implementations outperform backtracking in speed.

Parallel methods are more stable and scalable.

Performance tested on real-world biological data.

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 optimisation theory, which can be adapted to the task by using the network score as the objective function to maximise. This is not true for approaches based on conditional independence tests, called constraint-based learning algorithms. The only optimisation in widespread use, backtracking, leverages the symmetries implied by the definitions of neighbourhood 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 parallelise 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.