Bayesian model selection for exponential random graph models via adjusted pseudolikelihoods

Models with intractable likelihood functions arise in areas including network analysis and spatial statistics, especially those involving Gibbs random fields. Posterior parameter es timation in these settings is termed a doubly-intractable problem because both the likelihood function and the posterior distribution are intractable. The comparison of Bayesian models is often based on the statistical evidence, the integral of the un-normalised posterior distribution over the model parameters which is rarely available in closed form. For doubly-intractable models, estimating the evidence adds another layer of difficulty. Consequently, the selection of the model that best describes an observed network among a collection of exponential random graph models for network analysis is a daunting task. Pseudolikelihoods offer a tractable approximation to the likelihood but should be treated with caution because they can lead to an unreasonable inference. This paper specifies a method to adjust pseudolikelihoods in order to obtain a reasonable, yet tractable, approximation to the likelihood. This allows implementation of widely used computational methods for evidence estimation and pursuit of Bayesian model selection of exponential random graph models for the analysis of social networks. Empirical comparisons to existing methods show that our procedure yields similar evidence estimates, but at a lower computational cost.Comment: Supplementary material attached. To view attachments, please download and extract the gzzipped source file listed under "Other formats

Statistical Network Analysis with Bergm

Recent advances in computational methods for intractable models have made network data increasingly amenable to statistical analysis. Exponential random graph models (ERGMs) emerged as one of the main families of models capable of capturing the complex dependence structure of network data in a wide range of applied contexts. The Bergm package for R has become a popular package to carry out Bayesian parameter inference, missing data imputation, model selection and goodness-of-fit diagnostics for ERGMs. Over the last few years, the package has been considerably improved in terms of efficiency by adopting some of the state-of-the-art Bayesian computational methods for doubly-intractable distributions. Recently, version 5 of the package has been made available on CRAN having undergone a substantial makeover, which has made it more accessible and easy to use for practitioners. New functions include data augmentation procedures based on the approximate exchange algorithm for dealing with missing data, adjusted pseudo-likelihood and pseudo-posterior procedures, which allow for fast approximate inference of the ERGM parameter posterior and model evidence for networks on several thousands nodes.Comment: 22 pages, 5 figure

Bayesian Model Selection for Exponential Random Graph Models via Adjusted Pseudolikelihoods

Models with intractable likelihood functions arise in areas including network analysisand spatial statistics, especially those involving Gibbs random fields. Posterior parameter estimationin these settings is termed a doubly-intractable problem because both the likelihoodfunction and the posterior distribution are intractable. The comparison of Bayesian models isoften based on the statistical evidence, the integral of the un-normalised posterior distributionover the model parameters which is rarely available in closed form. For doubly-intractablemodels, estimating the evidence adds another layer of difficulty. Consequently, the selectionof the model that best describes an observed network among a collection of exponentialrandom graph models for network analysis is a daunting task. Pseudolikelihoods offer atractable approximation to the likelihood but should be treated with caution because they canlead to an unreasonable inference. This paper specifies a method to adjust pseudolikelihoodsin order to obtain a reasonable, yet tractable, approximation to the likelihood. This allowsimplementation of widely used computational methods for evidence estimation and pursuitof Bayesian model selection of exponential random graph models for the analysis of socialnetworks. Empirical comparisons to existing methods show that our procedure yields similarevidence estimates, but at a lower computational cost.Science Foundation IrelandInsight Centre for Data Analytic

Efficient Bayesian inference for exponential random graph models by correcting the pseudo-posterior distribution

Exponential random graph models are an important tool in the statistical analysis of data. However, Bayesian parameter estimation for these models is extremely challenging, since evaluation of the posterior distribution typically involves the calculation of an intractable normalizing constant. This barrier motivates the consideration of tractable approximations to the likelihood function, such as the pseudolikelihood function, which offers an approach to constructing such an approximation. Naive implementation of what we term a pseudo-posterior resulting from replacing the likelihood function in the posterior distribution by the pseudolikelihood is likely to give misleading inferences. We provide practical guidelines to correct a sample from such a pseudo-posterior distribution so that it is approximately distributed from the target posterior distribution and discuss the computational and statistical efficiency that result from this approach. We illustrate our methodology through the analysis of real-world graphs. Comparisons against the approximate exchange algorithm of Caimo and Friel (2011) are provided, followed by concluding remarks.Science Foundation IrelandInsight Research Centr

Model comparison for Gibbs random fields using noisy reversible jump Markov chain Monte Carlo

The reversible jump Markov chain Monte Carlo (RJMCMC) method offers an across-model simulation approach for Bayesian estimation and model comparison, by exploring the sampling space that consists of several models of possibly varying dimensions. A naive implementation of RJMCMC to models like Gibbs random fields suffers from computational difficulties: the posterior distribution for each model is termed doubly-intractable since computation of the likelihood function is rarely available. Consequently, it is simply impossible to simulate a transition of the Markov chain in the presence of likelihood intractability. A variant of RJMCMC is presented, called noisy RJMCMC, where the underlying transition kernel is replaced with an approximation based on unbiased estimators. Based on previous theoretical developments, convergence guarantees for the noisy RJMCMC algorithm are provided. The experiments show that the noisy RJMCMC algorithm can be much more efficient than other exact methods, provided that an estimator with controlled Monte Carlo variance is used, a fact which is in agreement with the theoretical analysis.Science Foundation IrelandThe Insight Centre for Data Analytics24m embargo-A

Statistical Network Analysis with Bergm

Recent advances in computational methods for intractable models have made network data increasingly amenable to statistical analysis. Exponential random graph models (ERGMs) emerged as one of the main families of models capable of capturing the complex dependence structure of network data in a wide range of applied contexts. The Bergm package for R has become a popular package to carry out Bayesian parameter inference, missing data imputation, model selection and goodness-of-fit diagnostics for ERGMs. Over the last few years, the package has been considerably improved in terms of efficiency by adopting some of the state-of-the-art Bayesian computational methods for doublyintractable distributions. Recently, version 5 of the package has been made available on CRAN having undergone a substantial makeover, which has made it more accessible and easy to use for practitioners. New functions include data augmentation procedures based on the approximate exchange algorithm for dealing with missing data, adjusted pseudolikelihood and pseudo-posterior procedures, which allow for fast approximate inference of the ERGM parameter posterior and model evidence for networks on several thousands nodes