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One of the most interesting scientific challenges nowadays deals with the analysis and the understanding of complex networks' dynamics. A major issue is the definition of new frameworks for the exploration of the dynamics at play in real…
The increasing volume of ecologically and biologically relevant data has revealed a wide collection of emergent patterns in living systems. Analyzing different datasets, ranging from metabolic gene-regulatory to species interaction…
Understanding the structural complexity and predictability of complex networks is a central challenge in network science. Although recent studies have revealed a relationship between compression-based entropy and link prediction…
Recently, one paper in Nature(Papadopoulos, 2012) raised an old debate on the origin of the scale-free property of complex networks, which focuses on whether the scale-free property origins from the optimization or not. Because the…
Ecological communities with many species can be classified into dynamical phases. In systems with all-to-all interactions, a phase where a fixed point is always reached and a dynamically-fluctuating phase have been found. The dynamics when…
It is known that individuals in social networks tend to exhibit homophily (a.k.a. assortative mixing) in their social ties, which implies that they prefer bonding with others of their own kind. But what are the reasons for this phenomenon?…
Ecosystems are among the most interesting and well-studied examples of self-organized complex systems. Community ecology, the study of how species interact with each other and the environment, has a rich tradition. Over the last few years,…
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…
A recent problem in community ecology lies in defining structures behind matrices of species interactions. The interest in this area is to quantify the nestedness degree of the matrix after its maximal packing. In this work we evaluate…
The ecological principle of limiting similarity dictates that species similar in resource requirements will compete, with the superior eventually excluding the inferior competitor from the community. The observation that nonetheless…
Interactions are ubiquitous across biological systems. These interactions can be abstracted as patterns of connections among distinct units such as genes, proteins, individual organisms, or species which form a hierarchy of biological…
An analytic theory of species abundance patterns (SAPs) in biological networks is presented. The theory is based on multispecies replicator dynamics equivalent to the Lotka-Volterra equation, with diverse interspecies interactions. Various…
Species interaction networks are a powerful tool for describing ecological communities; they typically contain nodes representing species, and edges representing interactions between those species. For the purposes of drawing abstract…
Community detection is an important tool for exploring and classifying the properties of large complex networks and should be of great help for spatial networks. Indeed, in addition to their location, nodes in spatial networks can have…
Many complex systems can be described in terms of networks of interacting units. Recent studies have shown that a wide class of both natural and artificial nets display a surprisingly widespread feature: the presence of highly heterogeneous…
We present novel analytical results about ecosystem species diversity that stem from a proposed coarse grained neutral model based on birth-death processes. The relevance of the problem lies in the urgency for understanding and synthesizing…
Over the last decade, significant progress has been made in understanding complex biological systems, however there have been few attempts at incorporating this knowledge into nature inspired optimization algorithms. In this paper, we…
We study the statistics of ecosystems with a variable number of co-evolving species. The species interact in two ways: by prey-predator relationships and by direct competition with similar kinds. The interaction coefficients change slowly…
In natural ecosystems, species can be characterized by the nonlinear density-dependent self-regulation of their growth profile. Species of many taxa show a substantial density-dependent reduction for low population size. Nevertheless, many…
Neutral models for the dynamics of a system of competing species are used, nowadays, to describe a wide variety of empirical communities. These models are used in many situations, ranging from population genetics and ecological biodiversity…