Goodness of fit for log-linear ERGMs

TL;DR

This paper introduces a new log-linear ERGM model called the $p_1$-SBM, along with an efficient exact conditional test for model fit, demonstrated on biological network data.

Contribution

It proposes the $p_1$-SBM model combining node and group effects and develops scalable testing methods for log-linear ERGMs.

Findings

Effective model fit testing on biological networks

Scalable sampling methods using Markov bases

Demonstrated on C. elegans connectome and Arabidopsis interactome

Abstract

Many popular models from the networks literature can be viewed through a common lens of contingency tables on network dyads, resulting in \emph{log-linear ERGMs}: exponential family models for random graphs whose sufficient statistics are linear on the dyads. We propose a new model in this family, the \emph{$p_1$-SBM}, which combines node and group effects common in network formation mechanisms. In particular, it is a generalization of several well-known ERGMs including the stochastic blockmodel for undirected graphs with known block assignment, the degree-corrected version of it, and the directed $p_1$ model without group structure. We frame the problem of testing model fit for the log-linear ERGM class through an exact conditional test whose $p$-value can be approximated efficiently in networks of both small and moderately large sizes. The sampling methods we build rely on a dynamic adaptation of Markov bases. We use quick estimation algorithms adapted from the contingency table literature and effective sampling methods rooted in graph theory and algebraic statistics. The performance and scalability of the method is demonstrated on two data sets from biology: the connectome of \emph{C. elegans} and the interactome of \emph{Arabidopsis thaliana}. These two networks -- a network and a protein-protein interaction network -- have been popular examples in the network science literature. Our work provides a model-based approach to studying them.