Related papers: Tree-based Inference of Species Interaction Networ…

We define the concept of dependence among multiple variables using maximum entropy techniques and introduce a graphical notation to denote the dependencies. Direct inference of information theoretic quantities from data uncovers…

Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and…

Ecologists have long suspected that species are more likely to interact if their traits match in a particular way. For example, a pollination interaction may be more likely if the proportions of a bee's tongue fit a plant's flower shape.…

With the internet, a massive amount of information on species abundance can be collected under citizen science programs. However, these data are often difficult to use directly in statistical inference, as their collection is generally…

Can evolving networks be inferred and modeled without directly observing their nodes and edges? In many applications, the edges of a dynamic network might not be observed, but one can observe the dynamics of stochastic cascading processes…

Microbes can affect processes from food production to human health. Such microbes are not isolated, but rather interact with each other and establish connections with their living environments. Understanding these interactions is essential…

Mutualistic networks are formed when the interactions between two classes of species are mutually beneficial. They are important examples of cooperation shaped by evolution. Mutualism between animals and plants plays a key role in the…

Network inference approaches are now widely used in biological applications to probe regulatory relationships between molecular components such as genes or proteins. Many methods have been proposed for this setting, but the connections and…

Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A…

Over the past decade network theory has been applied successfully to the study of a variety of complex adaptive systems. However, the application of these techniques to non-human social networks has several shortfalls. Firstly, in most…

Networks provide a skeleton for the spread of contagions, like, information, ideas, behaviors and diseases. Many times networks over which contagions diffuse are unobserved and need to be inferred. Here we apply survival theory to develop…

One can often make inferences about a growing network from its current state alone. For example, it is generally possible to determine how a network changed over time or pick among plausible mechanisms explaining its growth. In practice,…

A critical task in systems biology is the identification of genes that interact to control cellular processes by transcriptional activation of a set of target genes. Many methods have been developed to use statistical correlations in…

The decline in ecological connections signifies the potential extinction of species, which can be attributed to disruptions and alterations. The decrease in interconnections among species reflects their susceptibility to changes. For…

Networks are often characterized by node heterogeneity for which nodes exhibit different degrees of interaction and link homophily for which nodes sharing common features tend to associate with each other. In this paper, we propose a new…

Genetic data are often used to infer demographic history and changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed…

Inference of species networks from genomic data under the Network Multispecies Coalescent Model is currently severely limited by heavy computational demands. It also remains unclear how complicated networks can be for consistent inference…

Understanding the behaviors of ecological systems is challenging given their multi-faceted complexity. To proceed, theoretical models such as Lotka-Volterra dynamics with random interactions have been investigated by the dynamical…

Inferring topological characteristics of complex networks from observed data is critical to understand the dynamical behavior of networked systems, ranging from the Internet and the World Wide Web to biological networks and social networks.…

As impacts of introduced species cascade through trophic levels, they can cause indirect and counter-intuitive effects. To investigate the impact of invasive species at the network scale, we use a generalized food web model, capable of…