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Interaction nets are a form of restricted graph rewrite system that can serve as a graphical or textual programming language. As such, benefits include one-step confluence, ease of parallelism and explicit garbage collection. However, some…
We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate…
We discuss a model for evolutionary game dynamics in a growing, network-structured population. In our model, new players can either make connections to random preexisting players or preferentially attach to those that have been successful…
In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated…
Social network structures play an important role in the lives of animals by affecting individual fitness and the spread of disease and information. Nevertheless, we still lack a good understanding of how these structures emerge from the…
An important feature of many complex systems, both natural and artificial, is the structure and organization of their interaction networks with interesting properties. Here we present a theory of self-organization by evolutionary adaptation…
Recent technological advances and long-term data studies provide interaction data that can be modelled through dynamic networks, i.e a sequence of different snapshots of an evolving ecological network. Most often time is the parameter along…
Evolutionary and ecosystem dynamics are often treated as different processes --operating at separate timescales-- even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field…
The interplay between topology and dynamics in complex networks is a fundamental but widely unexplored problem. Here, we study this phenomenon on a prototype model in which the network is shaped by a dynamical variable. We couple the…
Despite their claimed biological plausibility, most self organizing networks have strict topological constraints and consequently they cannot take into account a wide range of external stimuli. Furthermore their evolution is conditioned by…
Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations…
Several methods have recently been developed for joint structure learning of multiple (related) graphical models or networks. These methods treat individual networks as exchangeable, such that each pair of networks are equally encouraged to…
Plasticity-led evolution is a form of evolution where a change in the environment induces novel traits via phenotypic plasticity, after which the novel traits are genetically accommodated over generations under the novel environment. This…
We explore the interplay between the topological relevance of a neuron and its dynamical traces in experimental cultured neuronal networks. We monitor the growth and development of these networks to characterise the evolution of their…
We study aggregation as a mechanism for the creation of complex networks. In this evolution process vertices merge together, which increases the number of highly connected hubs. We study a range of complex network architectures produced by…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
Natural selection and random drift are competing phenomena for explaining the evolution of populations. Combining a highly fit mutant with a population structure that improves the odds that the mutant spreads through the whole population…
Many scientific collaboration networks exhibit clear community and small world structures. However, the studies on the underlying mechanisms for the formation and evolution of community and small world structures are still insufficient. The…
Cooperation is observed widely in nature and is thought an essential component of many evolutionary processes, yet the mechanisms by which it arises and persists are still unclear. Among several theories, network reciprocity -- a model of…
In distributed systems, knowledge of the network structure of the connections among the unitary components is often a requirement for an accurate prediction of the emerging collective dynamics. However, in many real-world situations, one…