Abstract:
Exponential Random Graph models are an important tool in network analysis for describing complicated dependency structures. 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 pseudolikelihoods, which offer a principled approach to constructing such an approximation. Naive implementation of a posterior from a misspecified model is likely to give misleading inferences. We provide practical guidelines to calibrate in a quick and efficient manner samples coming from an approximated posterior and discuss the efficiency of this approach. The exposition of the methodology is accompanied by the analysis of real-world graphs. Comparisons against the Approximate Exchange algorithm of Caimo and Friel (2011) are provided, followed by concluding remarks.

Abstract:
Exponential random graph models are a class of widely used exponential family models for social networks. The topological structure of an observed network is modelled by the relative prevalence of a set of local sub-graph configurations termed network statistics. One of the key tasks in the application of these models is which network statistics to include in the model. This can be thought of as statistical model selection problem. This is a very challenging problem---the posterior distribution for each model is often termed "doubly intractable" since computation of the likelihood is rarely available, but also, the evidence of the posterior is, as usual, intractable. The contribution of this paper is the development of a fully Bayesian model selection method based on a reversible jump Markov chain Monte Carlo algorithm extension of Caimo and Friel (2011) which estimates the posterior probability for each competing model.

Abstract:
We extend the well-known and widely used Exponential Random Graph Model (ERGM) by including nodal random effects to compensate for heterogeneity in the nodes of a network. The Bayesian framework for ERGMs proposed by Caimo and Friel (2011) yields the basis of our modelling algorithm. A central question in network models is the question of model selection and following the Bayesian paradigm we focus on estimating Bayes factors. To do so we develop an approximate but feasible calculation of the Bayes factor which allows one to pursue model selection. Two data examples and a small simulation study illustrate our mixed model approach and the corresponding model selection.

Abstract:
Across the sciences, the statistical analysis of networks is central to the production of knowledge on relational phenomena. Because of their ability to model the structural generation of networks based on both endogenous and exogenous factors, exponential random graph models are a ubiquitous means of analysis. However, they are limited by an inability to model networks with valued edges. We address this problem by introducing a class of generalized exponential random graph models capable of modeling networks whose edges have continuous values (bounded or unbounded), thus greatly expanding the scope of networks applied researchers can subject to statistical analysis.

Abstract:
In this paper we describe the main featuress of the Bergm package for the open-source R software which provides a comprehensive framework for Bayesian analysis for exponential random graph models: tools for parameter estimation, model selection and goodness-of-fit diagnostics. We illustrate the capabilities of this package describing the algorithms through a tutorial analysis of two well-known network datasets.

Abstract:
In this paper, a Bayesian inference technique based on Taylor series approximation of the logarithm of the likelihood function is presented. The proposed approximation is devised for the case, where the prior distribution belongs to the exponential family of distributions. The logarithm of the likelihood function is linearized with respect to the sufficient statistic of the prior distribution in exponential family such that the posterior obtains the same exponential family form as the prior. Similarities between the proposed method and the extended Kalman filter for nonlinear filtering are illustrated. Furthermore, an extended target measurement update for target models where the target extent is represented by a random matrix having an inverse Wishart distribution is derived. The approximate update covers the important case where the spread of measurement is due to the target extent as well as the measurement noise in the sensor.

Abstract:
In structural brain networks the connections of interest consist of white-matter fibre bundles between spatially segregated brain regions. The presence, location and orientation of these white matter tracts can be derived using diffusion MRI in combination with probabilistic tractography. Unfortunately, as of yet no approaches have been suggested that provide an undisputed way of inferring brain networks from tractography. In this paper, we provide a computational framework which we refer to as Bayesian connectomics. Rather than applying an arbitrary threshold to obtain a single network, we consider the posterior distribution of networks that are supported by the data, combined with an exponential random graph (ERGM) prior that captures a priori knowledge concerning the graph-theoretical properties of whole-brain networks. We show that, on simulated probabilistic tractography data, our approach is able to reconstruct whole-brain networks. In addition, our approach directly supports multi-model data fusion and group-level network inference.

Abstract:
Nowadays, exponential random graphs (ERGs) are among the most widely-studied network models. Different analytical and numerical techniques for ERG have been developed that resulted in the well-established theory with true predictive power. An excellent basic discussion of exponential random graphs addressed to social science students and researchers is given in [Anderson et al., 1999][Robins et al., 2007]. This essay is intentionally designed to be more theoretical in comparison with the well-known primers just mentioned. Given the interdisciplinary character of the new emerging science of complex networks, the essay aims to give a contribution upon which network scientists and practitioners, who represent different research areas, could build a common area of understanding.

Abstract:
We study the asymptotics for sparse exponential random graph models where the parameters may depend on the number of vertices of the graph. We obtain a variational principle for the limiting free energy, an associated concentration of measure, the asymptotics for the mean and variance of the limiting probability distribution, and phase transitions in the edge-(single)-star and edge-triangle models. Similar analysis is done for directed sparse exponential random graph models parametrized by edges and multiple outward stars.

Abstract:
We introduce priors and algorithms to perform Bayesian inference in Gaussian models defined by acyclic directed mixed graphs. Such a class of graphs, composed of directed and bi-directed edges, is a representation of conditional independencies that is closed under marginalization and arises naturally from causal models which allow for unmeasured confounding. Monte Carlo methods and a variational approximation for such models are presented. Our algorithms for Bayesian inference allow the evaluation of posterior distributions for several quantities of interest, including causal effects that are not identifiable from data alone but could otherwise be inferred where informative prior knowledge about confounding is available.