Abstract Exponential random graph models, or ERGMs, are a flexible and general class of models for modeling dependent data. While the early literature has shown them to be powerful in capturing many network features of interest, recent work highlights difficulties related to the models’ ill behavior, such as most of the probability mass being concentrated on a very small subset of the parameter space. This behavior limits both the applicability of an ERGM as a model for real data and inference and parameter estimation via the usual Markov chain Monte Carlo algorithms. To address this problem, we propose a new exponential family of models for random graphs that build on the standard ERGM framework. Specifically, we solve the problem of computational intractability and “degenerate” model behavior by an interpretable support restriction. We introduce a new parameter based on the graph-theoretic notion of degeneracy, a measure of sparsity whose value is commonly low in real-world networks. The new model family is supported on the sample space of graphs with bounded degeneracy and is called degeneracy-restricted ERGMs, or DERGMs for short. Since DERGMs generalize ERGMs—the latter is obtained from the former by setting the degeneracy parameter to be maximal—they inherit good theoretical properties, while at the same time place their mass more uniformly over realistic graphs. The support restriction allows the use of new (and fast) Monte Carlo methods for inference, thus making the models scalable and computationally tractable. We study various theoretical properties of DERGMs and illustrate how the support restriction improves the model behavior. We also present a fast Monte Carlo algorithm for parameter estimation that avoids many issues faced by Markov Chain Monte Carlo algorithms used for inference in ERGMs.
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Highly scalable maximum likelihood and conjugate Bayesian inference for ERGMs on graph sets with equivalent vertices
The exponential family random graph modeling (ERGM) framework provides a highly flexible approach for the statistical analysis of networks (i.e., graphs). As ERGMs with dyadic dependence involve normalizing factors that are extremely costly to compute, practical strategies for ERGMs inference generally employ a variety of approximations or other workarounds. Markov Chain Monte Carlo maximum likelihood (MCMC MLE) provides a powerful tool to approximate the maximum likelihood estimator (MLE) of ERGM parameters, and is generally feasible for typical models on single networks with as many as a few thousand nodes. MCMC-based algorithms for Bayesian analysis are more expensive, and high-quality answers are challenging to obtain on large graphs. For both strategies, extension to the pooled case—in which we observe multiple networks from a common generative process—adds further computational cost, with both time and memory scaling linearly in the number of graphs. This becomes prohibitive for large networks, or cases in which large numbers of graph observations are available. Here, we exploit some basic properties of the discrete exponential families to develop an approach for ERGM inference in the pooled case that (where applicable) allows an arbitrarily large number of graph observations to be fit at no additional computational cost beyond preprocessing the data itself. Moreover, a variant of our approach can also be used to perform Bayesian inference under conjugate priors, again with no additional computational cost in the estimation phase. The latter can be employed either for single graph observations, or for observations from graph sets. As we show, the conjugate prior is easily specified, and is well-suited to applications such as regularization. Simulation studies show that the pooled method leads to estimates with good frequentist properties, and posterior estimates under the conjugate prior are well-behaved. We demonstrate the usefulness of our approach with applications to pooled analysis of brain functional connectivity networks and to replicated x-ray crystal structures of hen egg-white lysozyme.
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- NSF-PAR ID:
- 10376706
- Editor(s):
- De Vico Fallani, Fabrizio
- Date Published:
- Journal Name:
- PLOS ONE
- Volume:
- 17
- Issue:
- 8
- ISSN:
- 1932-6203
- Page Range / eLocation ID:
- e0273039
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1371/journal.pone.0273039
