skip to main content


Search for: All records

Award ID contains: 1361425

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. De Vico Fallani, Fabrizio (Ed.)
    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. 
    more » « less
  2. Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a particularly useful way of obtaining highly compressed representations of molecular structures, and simulations operating via such representations can achieve substantial computational savings. A drawback of coarse-graining, however, is the loss of atomistic detail—an effect that is especially acute for topological representations such as protein structure networks (PSNs). Here, we introduce an approach based on a combination of machine learning and physically-guided refinement for inferring atomic coordinates from PSNs. This “neural upscaling” procedure exploits the constraints implied by PSNs on possible configurations, as well as differences in the likelihood of observing different configurations with the same PSN. Using a 1 μs atomistic molecular dynamics trajectory of Aβ1–40, we show that neural upscaling is able to effectively recapitulate detailed structural information for intrinsically disordered proteins, being particularly successful in recovering features such as transient secondary structure. These results suggest that scalable network-based models for protein structure and dynamics may be used in settings where atomistic detail is desired, with upscaling employed to impute atomic coordinates from PSNs. 
    more » « less
  3. null (Ed.)
  4. Many social and other networks exhibit stable size scaling relationships, such that features such as mean degree or reciprocation rates change slowly or are approximately constant as the number of vertices increases. Statistical network models built on top of simple Bernoulli baseline (or reference) measures often behave unrealistically in this respect, leading to the development of sparse reference models that preserve features such as mean degree scaling. In this paper, we generalize recent work on the micro-foundations of such reference models to the case of sparse directed graphs with non-vanishing reciprocity, providing a dynamic process interpretation of the emergence of stable macroscopic behavior. 
    more » « less
  5. Although it is well known that some exponential family random graph model (ERGM) families exhibit phase transitions (in which small parameter changes lead to qualitative changes in graph structure), the behavior of other models is still poorly understood. Recently, Krivitsky and Morris have reported a previously unobserved phase transition in the edge/concurrent vertex family (a simple starting point for models of sexual contact networks). Here, we examine this phase transition, showing it to be a first-order transition with respect to an order parameter associated with the fraction of concurrent vertices. This transition stems from weak cooperativity in the recruitment of vertices to the concurrent phase, which may not be a desirable property in some applications. 
    more » « less