Related papers: Disentangling co-occurrence patterns in n-partite …

Presence-absence data is defined by vectors or matrices of zeroes and ones, where the ones usually indicate a "presence" in a certain place. Presence-absence data occur for example when investigating geographical species distributions,…

While network science has become an indispensable tool for studying complex systems, the conventional use of pairwise links often shows limitations in describing high-order interactions properly. Hypergraphs, where each edge can connect…

Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…

The representation of complex systems as networks is inappropriate for the study of certain problems. We show several examples of social, biological, ecological and technological systems where the use of complex networks gives very limited…

A central feature of complex systems is the relevance and entanglement of different levels of description. For instance, the dynamics of ecosystems can be alternatively described in terms of large ecological processes and classes of…

Ecological systems have a high level of complexity combined with stability and rich biodiversity. Recently, the analysis of their properties and evolution has been pushed forward on a basis of concept of mutualistic networks that provides a…

Many decision-making algorithms draw inspiration from the inner workings of individual biological systems. However, it remains unclear whether collective behavior among biological species can also lead to solutions for computational tasks.…

Many natural ecosystems harbor large numbers of coexisting species competing for far fewer distinct resources, in apparent defiance of the competitive exclusion principle. Various mechanisms have been proposed to explain this apparent…

Ecology and evolution are inseparable. Motivated by some recent experiments, we have developed models of evolutionary ecology from the perspective of dynamic networks. In these models, in addition to the intra-node dynamics, which…

Spatial ecological networks are widely used to model interactions between georeferenced biological entities (e.g., populations or communities). The analysis of such data often leads to a two-step approach where groups containing similar…

Contemporary Niche Theory is a useful framework for understanding how organisms interact with each other and with their shared environment. Its graphical representation, popularized by Tilman's Resource Ratio Hypothesis, facilitates the…

Community structure is a typical property of many real-world networks, and has become a key to understand the dynamics of the networked systems. In these networks most nodes apparently lie in a community while there often exists a few nodes…

Local coexistence of species in large ecosystems is traditionally explained within the broad framework of niche theory. However, its rationale hardly justifies rich biodiversity observed in nearly homogeneous environments. Here we consider…

In this paper, we use a partition of the links of a network in order to uncover its community structure. This approach allows for communities to overlap at nodes, so that nodes may be in more than one community. We do this by making a node…

Given an undirected graph representing similarities between a set of items and an additive measure evaluating the items, we treat the position of a special subset of items in an ordinal ranking through a collection of combinatorial…

Ecosystems are commonly conceptualized as networks of interacting species. However, partitioning natural diversity of organisms into discrete units is notoriously problematic, and mounting experimental evidence raises the intriguing…

Underpinning the past decades of work on the design, initialization, and optimization of neural networks is a seemingly innocuous assumption: that the network is trained on a \textit{stationary} data distribution. In settings where this…

Mutualistic interactions are vital constituents of ecological and socio-economic systems. Empirical studies have found that the patterns of reciprocal relations among the participants often shows the salient features of being simultaneously…

We review and generalize the recently introduced framework of entropy vectors for detecting and quantifying genuine multipartite entanglement in high dimensional multicomponent quantum systems. We show that these ideas can be extended to…

Compound graphs are networks in which vertices can be grouped into larger subsets, with these subsets capable of further grouping, resulting in a nesting that can be many levels deep. In several applications, including biological workflows,…