Untangling the roles of parasites in food webs with generative network models

Food webs represent the set of consumer-resource interactions among a set of species that co-occur in a habitat, but most food web studies have omitted parasites and their interactions. Recent studies have provided conflicting evidence on whether including parasites changes food web structure, with some suggesting that parasitic interactions are structurally distinct from those among free-living species while others claim the opposite. Here, we describe a principled method for understanding food web structure that combines an efficient optimization algorithm from statistical physics called parallel tempering with a probabilistic generalization of the empirically well-supported food web niche model. This generative model approach allows us to rigorously estimate the degree to which interactions that involve parasites are statistically distinguishable from interactions among free-living species, whether parasite niches behave similarly to free-living niches, and the degree to which existing hypotheses about food web structure are naturally recovered. We apply this method to the well-studied Flensburg Fjord food web and show that while predation on parasites, concomitant predation of parasites, and parasitic intraguild trophic interactions are largely indistinguishable from free-living predation interactions, parasite-host interactions are different. These results provide a powerful new tool for evaluating the impact of classes of species and interactions on food web structure to shed new light on the roles of parasites in food webs

Assembling thefacebook: Using heterogeneity to understand online social network assembly

Online social networks represent a popular and diverse class of social media systems. Despite this variety, each of these systems undergoes a general process of online social network assembly, which represents the complicated and heterogeneous changes that transform newly born systems into mature platforms. However, little is known about this process. For example, how much of a networks assembly is driven by simple growth? How does a networks structure change as it matures? How does network structure vary with adoption rates and user heterogeneity, and do these properties play different roles at different points in the assembly? We investigate these and other questions using a unique dataset of online connections among the roughly one million users at the first 100 colleges admitted to Facebook, captured just 20 months after its launch. We first show that different vintages and adoption rates across this population of networks reveal temporal dynamics of the assembly process, and that assembly is only loosely related to network growth. We then exploit natural experiments embedded in this dataset and complementary data obtained via Internet archaeology to show that different subnetworks matured at different rates toward similar end states. These results shed light on the processes and patterns of online social network assembly, and may facilitate more effective design for online social systems.

A unified view of generative models for networks: models, methods, opportunities, and challenges

Research on probabilistic models of networks now spans a wide variety of fields, including physics, sociology, biology, statistics, and machine learning. These efforts have produced a diverse ecology of models and methods. Despite this diversity, many of these models share a common underlying structure: pairwise interactions (edges) are generated with probability conditional on latent vertex attributes. Differences between models generally stem from different philosophical choices about how to learn from data or different empirically-motivated goals. The highly interdisciplinary nature of work on these generative models, however, has inhibited the development of a unified view of their similarities and differences. For instance, novel theoretical models and optimization techniques developed in machine learning are largely unknown within the social and biological sciences, which have instead emphasized model interpretability. Here, we describe a unified view of generative models for networks that draws together many of these disparate threads and highlights the fundamental similarities and differences that span these fields. We then describe a number of opportunities and challenges for future work that are revealed by this view.