Network reconstruction via the minimum description length principle

TL;DR

This paper introduces a new network reconstruction method based on the minimum description length principle, which avoids overfitting and is faster than traditional regularization techniques, improving accuracy in both artificial and real-world networks.

Contribution

It proposes a nonparametric Bayesian inference approach using MDL that does not rely on weight shrinkage or cross-validation, enabling efficient and accurate network inference without prior edge count knowledge.

Findings

Systematically increased accuracy in network reconstruction.

Faster inference due to no need for cross-validation.

Effective in reconstructing microbial interaction networks.

Abstract

A fundamental problem associated with the task of network reconstruction from dynamical or behavioral data consists in determining the most appropriate model complexity in a manner that prevents overfitting, and produces an inferred network with a statistically justifiable number of edges. The status quo in this context is based on $L_{1}$ regularization combined with cross-validation. However, besides its high computational cost, this commonplace approach unnecessarily ties the promotion of sparsity with weight "shrinkage". This combination forces a trade-off between the bias introduced by shrinkage and the network sparsity, which often results in substantial overfitting even after cross-validation. In this work, we propose an alternative nonparametric regularization scheme based on hierarchical Bayesian inference and weight quantization, which does not rely on weight shrinkage to promote sparsity. Our approach follows the minimum description length (MDL) principle, and uncovers the weight distribution that allows for the most compression of the data, thus avoiding overfitting without requiring cross-validation. The latter property renders our approach substantially faster to employ, as it requires a single fit to the complete data. As a result, we have a principled and efficient inference scheme that can be used with a large variety of generative models, without requiring the number of edges to be known in advance. We also demonstrate that our scheme yields systematically increased accuracy in the reconstruction of both artificial and empirical networks. We highlight the use of our method with the reconstruction of interaction networks between microbial communities from large-scale abundance samples involving in the order of $10^{4}$ to $10^{5}$ species, and demonstrate how the inferred model can be used to predict the outcome of interventions in the system.