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Many growing networks possess accelerating statistics where the number of links added with each new node is an increasing function of network size so the total number of links increases faster than linearly with network size. In particular,…
Networks are widely used to model the interaction between individual dynamical systems. In many instances, the total number of units as well as the interaction coupling are not fixed in time, but rather constantly evolve. In terms of…
The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological…
Imitation is a basic updating mechanism for strategy evolution in structured populations, determining how individuals sample social information and translate it into behavioral changes. Higher-order networks, such as hypergraphs, generalize…
We describe systems using Kauffman and similar networks. They are directed funct ioning networks consisting of finite number of nodes with finite number of discr ete states evaluated in synchronous mode of discrete time. In this paper we…
Self-organization and pattern formation in network-organized systems emerges from the collective activation and interaction of many interconnected units. A striking feature of these non-equilibrium structures is that they are often…
A common feature of biological networks is the geometric property of self-similarity. Molecular regulatory networks through to circulatory systems, nervous systems, social systems and ecological trophic networks, show self-similar…
Living organisms produce metabolites of many types via their metabolisms. Especially, flavonoids, a kind of secondary metabolites, of plant species are interesting examples. Since plant species are believed to have specific flavonoids with…
We introduce a growing network model---the copying model---in which a new node attaches to a randomly selected target node and, in addition, independently to each of the neighbors of the target with copying probability $p$. When…
Networks play a prominent role in the study of complex systems of interacting entities in biology, sociology, and economics. Despite this diversity, we demonstrate here that a statistical model decomposing networks into matching and…
The host immune response can often efficiently suppress a virus infection, which may lead to selection for immune-resistant viral variants within the host. For example, during HIV infection, an array of CTL immune response populations…
Bow-tie or hourglass structure is a common architectural feature found in biological and technological networks. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output…
We introduce a new class of latent process models for dynamic relational network data with the goal of detecting time-dependent structure. Network data are often observed over time, and static network models for such data may fail to…
Living systems are often described utilizing informational analogies. An important open question is whether information is merely a useful conceptual metaphor, or intrinsic to the operation of biological systems. To address this question,…
can evolve simultaneously. For the information-driven adaptive process, susceptible (infected) individuals who have abilities to recognize the disease would break the links of their infected (susceptible) neighbors to prevent the epidemic…
Topological features of gene regulatory networks can be successfully reproduced by a model population evolving under selection for short dynamical attractors. The evolved population of networks exhibit motif statistics, summarized by…
Many complex systems--from social and communication networks to biological networks and the Internet--are thought to exhibit scale-free structure. However, prevailing explanations rely on the constant addition of new nodes, an assumption…
Systems of dynamical interactions between competing species can be used to model many complex systems, and can be mathematically described by {\em random} networks. Understanding how patterns of activity arise in such systems is important…
We introduce a population dynamics model, where individual genomes are represented by bit-strings. Selection is described by death probabilities which depend on these genomes, and new individuals continuously replace the ones that die,…
A stochastic reaction-diffusion model is studied on a networked support. In each patch of the network two species are assumed to interact following a non-normal reaction scheme. When the interaction unit is replicated on a directed linear…