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The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
Does an ecological community allow stable coexistence? Identifying the general principles that determine the answer to this question is a central problem of theoretical ecology. Random matrix theory approaches have uncovered the general…
The dynamical evolution of complex networks underpins the structure-function relationships in natural and artificial systems. Yet, restoring a network's formation from a single static snapshot remains challenging. Here, we present a…
Information networks are ubiquitous and are ideal for modeling relational data. Networks being sparse and irregular, network embedding algorithms have caught the attention of many researchers, who came up with numerous embeddings algorithms…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
As a model of temporally evolving networks, we consider a globally coupled logistic map with variable connection weights. The model exhibits self-organization of network structure, reflected by the collective behavior of units. Structural…
Disordered systems theory provides powerful tools to analyze the generic behaviors of highdimensional systems, such as species-rich ecological communities or neural networks. By assuming randomness in their interactions, universality…
Identifying and explaining the structure of complex networks at different scales has become an important problem across disciplines. At the mesoscale, modular architecture has attracted most of the attention. At the macroscale, other…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…
The robustness of an ecological network quantifies the resilience of the ecosystem it represents to species loss. It corresponds to the proportion of species that are disconnected from the rest of the network when extinctions occur…
The co-evolution of network topology and dynamics is studied in an evolutionary Boolean network model that is a simple model of gene regulatory network. We find that a critical state emerges spontaneously resulting from interplay between…
We study here the social network generated by the asynchronous visits, to a fixed set of sites, of mobile agents modelled as independent random walks on the plane lattice. The social network is constructed by assuming that a group of agents…
In the last years, a remarkable theoretical effort has been made in order to understand stability and complexity in ecological communities. The non-random structures of real ecological interaction networks has been recognized as one key…
We explore a systematic approach to studying the dynamics of evolving networks at a coarse-grained, system level. We emphasize the importance of finding good observables (network properties) in terms of which coarse grained models can be…
Networks in nature are often formed within a spatial domain in a dynamical manner, gaining links and nodes as they develop over time. We propose a class of spatially-based growing network models and investigate the relationship between the…
We introduce Network Automata, a framework which couples the topological evolution of a network to its structure. It is useful for dealing with networks in which the topology evolves according to some specified microscopic rules and,…
The evolutionary balance between innate and learned behaviors is highly intricate, and different organisms have found different solutions to this problem. We hypothesize that the emergence and exact form of learning behaviors is naturally…
Control of the living cell functions with remarkable reliability despite the stochastic nature of the underlying molecular networks -- a property presumably optimized by biological evolution. We here ask to what extent the property of a…
Species sampling processes have long served as the fundamental framework for modeling random discrete distributions and exchangeable sequences. However, data arising from distinct but related sources require a broader notion of…
Several mechanisms have been proposed to explain the spontaneous generation of self-organized patterns, hypothesised to play a role in the formation of many of the magnificent patterns observed in Nature. In several cases of interest, the…