Related papers: Reconstructing the evolution history of networked …
Complex interactions between genes or proteins contribute a substantial part to phenotypic evolution. Here we develop an evolutionarily grounded method for the cross-species analysis of interaction networks by {\em alignment}, which maps…
Many animals live in societies where individuals frequently interact socially with each other. The social structures of these systems can be studied in depth by means of network analysis. A large number of studies on animal social networks…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
Taking inspiration from biological evolution, we explore the idea of "Can deep neural networks evolve naturally over successive generations into highly efficient deep neural networks?" by introducing the notion of synthesizing new highly…
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…
It is a significant challenge to predict the network topology from a small amount of dynamical observations. Different from the usual framework of the node-based reconstruction, two optimization approaches (i.e., the global and partitioned…
Adaptive networks are a novel class of dynamical networks whose topologies and states coevolve. Many real-world complex systems can be modeled as adaptive networks, including social networks, transportation networks, neural networks and…
Distinct channels of interaction in a complex networked system define network layers, which co-exist and co-operate for the system's function. Towards realistic modeling and understanding such multiplex systems, we introduce and study a…
Gene and protein networks are very important to model complex large-scale systems in molecular biology. Inferring or reverseengineering such networks can be defined as the process of identifying gene/protein interactions from experimental…
We propose new direction to understanding evolutionary dynamics of complex networks using two different types of collaboration networks: academic collaboration networks; and, disaster collaboration networks. The results show that academic…
The continuous interest in the social network area contributes to the fast development of this field. The new possibilities of obtaining and storing data facilitate deeper analysis of the entire social network, extracted social groups and…
We show that the protein-protein interaction networks can be surprisingly well described by a very simple evolution model of duplication and divergence. The model exhibits a remarkably rich behavior depending on a single parameter, the…
Many social and biological networks consist of communities - groups of nodes within which connections are dense, but between which connections are sparser. Recently, there has been considerable interest in designing algorithms for detecting…
Much of contemporary systems biology owes its success to the abstraction of a network, the idea that diverse kinds of molecular, cellular, and organismal species and interactions can be modeled as relational nodes and edges in a graph of…
We present a general model for the growth of weighted networks in which the structural growth is coupled with the edges' weight dynamical evolution. The model is based on a simple weight-driven dynamics and a weights' reinforcement…
Protein complexes conserved across species indicate processes that are core to cellular machinery (e.g. cell-cycle or DNA damage-repair complexes conserved across human and yeast). While numerous computational methods have been devised to…
Owing to the influence of real-world networks both in science and society, numerous mathematical models have been developed to understand the structure and evolution of these systems, particularly in a temporal context. Recent advancements…
Complex networks have non-trivial characteristics and appear in many real-world systems. Such networks are vitally important, but their full underlying dynamics are not completely understood. Utilizing new data sources, however, can unveil…
We use a generalised version of the individual-based Tangled Nature model of evolutionary ecology to study the relationship between ecosystem structure and evolutionary history. Our evolved model ecosystems typically exhibit interaction…
We present a new model of the evolutionary dynamics and the growth of on-line social networks. The model emulates people's strategies for acquiring information in social networks, emphasising the local subjective view of an individual and…