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Many complex systems in nature and society can be described in terms of networks capturing the intricate web of connections among the units they are made of. A key question is how to interpret the global organization of such networks as the…
Understanding the structure of relationships between objects in a given database is one of the most important problems in the field of data mining. The structure can be defined for a set of single objects (clustering) or a set of groups of…
Landscapes are meaningful ecological units that strongly depend on the environmental conditions. Such dependencies between landscapes and the environment have been noted since the beginning of Earth sciences and cast into conceptual models…
How large ecosystems can create and maintain the remarkable biodiversity we see in nature is probably one of the biggest open questions in science, attracting attention from different fields, from Theoretical Ecology to Mathematics and…
Understanding the dynamics of spatially extended systems represents a challenge in diverse scientific disciplines, ranging from physics and mathematics to the earth and climate sciences or the neurosciences. This challenge has stimulated…
Hypergraphs, describing networks where interactions take place among any number of units, are a natural tool to model many real-world social and biological systems. In this work we propose a principled framework to model the organization of…
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…
Cities can be seen as the epitome of complex systems. They arise from a set of interactions and components so diverse that is almost impossible to describe them exhaustively. Amid this diversity, we chose an object which orchestrates the…
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…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
Ecosystems are commonly organized into trophic levels -- organisms that occupy the same level in a food chain (e.g., plants, herbivores, carnivores). A fundamental question in theoretical ecology is how the interplay between trophic…
An agent-based model of population dynamics is presented. The model has as its expected behaviour the population dynamics of the equation-based Webworld model, within which large communities of species can be grown on evolutionary time…
Systems engineering has developed a mature knowledge on how to design, integrate and manage complex industrial systems, whereas disciplines studying complex systems in nature or society also propose numerous tools for their understanding.…
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…
Modular structure is pervasive in many complex networks of interactions observed in natural, social and technological sciences. Its study sheds light on the relation between the structure and function of complex systems. Generally speaking,…
The analysis of temporal networks heavily depends on the analysis of time-respecting paths. However, before being able to model and analyze the time-respecting paths, we have to infer the timescales at which the temporal edges influence…
Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…
Food-web perturbations stemming from climate change, overexploitation, invasive species, and habitat degradation often cause an initial loss of species that results in a cascade of secondary extinctions, posing considerable challenges to…
The study of temporal networks is motivated by the simple and important observation that just as network structure can affect dynamics, so can structure in time. Just as network topology can teach us about the system in question, so can its…
Living systems operate far from equilibrium, yet few general frameworks provide global bounds on biological transients. In high-dimensional biological networks like ecosystems, long transients arise from the separate timescales of…