We present a scalable nonparametric Bayesian method to perform network reconstruction from observed functional behavior, that at the same time infers the communities present in the network. We show that the joint reconstruction with community detection has a synergistic effect, where the edge correlations used to inform the existence of communities are inherently also used to improve the accuracy of the reconstruction, which in turn can better inform the uncovering of communities. We illustrate the use of our method with observations arising from epidemic models and the Ising model, both on synthetic and empirical networks, as well as on data containing only functional information.
Empirical networks are often globally sparse, with a small average number of connections per node, when compared to the total size of the network. However this sparsity tends not to be homogeneous, and networks can also be locally dense, for example with a few nodes connecting to a large fraction of the rest of the network, or with small groups of nodes with a large probability of connections between them. Here we show how latent Poisson models which generate hidden multigraphs can be effective at capturing this density heterogeneity, while being more tractable mathematically than some of the alternatives that model simple graphs directly. We show how these latent multigraphs can be reconstructed from data on simple graphs, and how this allows us to disentangle dissortative degree-degree correlations from the constraints of imposed degree sequences, and to improve the identification of community structure in empirically relevant scenarios.
This chapter provides a self-contained introduction to the use of Bayesian inference to extract large-scale modular structures from network data, based on the stochastic block model (SBM), as well as its degree-corrected and overlapping generalizations. We focus on nonparametric formulations that allow their inference in a manner that prevents overfitting, and enables model selection. We discuss aspects of the choice of priors, in particular how to avoid underfitting via increased Bayesian hierarchies, and we contrast the task of sampling network partitions from the posterior distribution with finding the single point estimate that maximizes it, while describing efficient algorithms to perform either one. We also show how inferring the SBM can be used to predict missing and spurious links, and shed light on the fundamental limitations of the detectability of modular structures in networks.
A principled approach to understand network structures is to formulate generative models. Given a collection of models, however, an outstanding key task is to determine which one provides a more accurate description of the network at hand, discounting statistical fluctuations. This problem can be approached using two principled criteria that at first may seem equivalent: selecting the most plausible model in terms of its posterior probability; or selecting the model with the highest predictive performance in terms of identifying missing links. Here we show that while these two approaches yield consistent results in most of cases, there are also notable instances where they do not, that is, where the most plausible model is not the most predictive. We show that in the latter case the improvement of predictive performance can in fact lead to overfitting both in artificial and empirical settings. Furthermore, we show that, in general, the predictive performance is higher when we average over collections of models that are individually less plausible, than when we consider only the single most plausible model.
A principled approach to characterize the hidden structure of networks is to formulate generative models, and then infer their parameters from data. When the desired structure is composed of modules or "communities", a suitable choice for this task is the stochastic block model (SBM), where nodes are divided into groups, and the placement of edges is conditioned on the group memberships. Here, we present a nonparametric Bayesian method to infer the modular structure of empirical networks, including the number of modules and their hierarchical organization. We focus on a microcanonical variant of the SBM, where the structure is imposed via hard constraints, i.e. the generated networks are not allowed to violate the patterns imposed by the model. We show how this simple model variation allows simultaneously for two important improvements over more traditional inference approaches: 1. Deeper Bayesian hierarchies, with noninformative priors replaced by sequences of priors and hyperpriors, that not only remove limitations that seriously degrade the inference on large networks, but also reveal structures at multiple scales; 2. A very efficient inference algorithm that scales well not only for networks with a large number of nodes and edges, but also with an unlimited number of modules. We show also how this approach can be used to sample modular hierarchies from the posterior distribution, as well as to perform model selection. We discuss and analyze the differences between sampling from the posterior and simply finding the single parameter estimate that maximizes it. Furthermore, we expose a direct equivalence between our microcanonical approach and alternative derivations based on the canonical SBM.