相关论文: Local search on protein residue networks

Paths are important structural elements in complex networks because they are finite (unlike walks), related to effective node coverage (minimum spanning trees), and can be understood as being dual to star connectivity. This article…

Predicting links in complex networks has been one of the essential topics within the realm of data mining and science discovery over the past few years. This problem remains an attempt to identify future, deleted, and redundant links using…

Random walks have been proposed as a simple method of efficiently searching, or disseminating information throughout, communication and sensor networks. In nature, animals (such as ants) tend to follow correlated random walks, i.e., random…

Consider the following routing problem in the context of a large scale network $G$, with particular interest paid to power law networks, although our results do not assume a particular degree distribution. A small number of nodes want to…

In the present work, we study random walks on complex networks subject to stochastic resetting when the resetting probability is node-dependent. Using a renewal approach, we derive the exact expressions of the stationary occupation…

We study random walks with stochastic resetting to the initial position on arbitrary networks. We obtain the stationary probability distribution as well as the mean and global first passage times, which allow us to characterize the effect…

It is not merely the position of residues that are of utmost importance in protein function and stability, but the interactions between them. We illustrate, by using a network construction on a set of 595 non-homologous proteins, that…

Predicting the occurrence of links is a fundamental problem in networks. In the link prediction problem we are given a snapshot of a network and would like to infer which interactions among existing members are likely to occur in the near…

We consider a minimal model of persistent random searcher with short range memory. We calculate exactly for such searcher the mean first-passage time to a target in a bounded domain and find that it admits a non trivial minimum as function…

The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the…

A protein structure is represented as a network of residues whereby edges are determined by intra-molecular contacts. We introduce inhomogeneity into these networks by assigning each edge a weight that is determined by amino-acid pair…

We study the biased random walk process in random uncorrelated networks with arbitrary degree distributions. In our model, the bias is defined by the preferential transition probability, which, in recent years, has been commonly used to…

We investigate simplified models of computer data networks and examine how the introduction of additional random links influences the performance of these net works. In general, the impact of additional random links on the performance of…

We study a model for a random walk of two classes of particles (A and B). Where both species are present in the same site, the motion of A's takes precedence over that of B's. The model was originally proposed and analyzed in Maragakis et…

Dynamic processes on networks, be it information transfer in the Internet, contagious spreading in a social network, or neural signaling, take place along shortest or nearly shortest paths. Unfortunately, our maps of most large networks are…

Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…

Link prediction is an open problem in the complex network, which attracts much research interest currently. However, little attention has been paid to the relation between network structure and the performance of prediction methods. In…

In this Letter, we proposed a mixing navigation mechanism, which interpolates between random-walk and shortest-path protocol. The navigation efficiency can be remarkably enhanced via a few routers. Some advanced strategies are also…

Random walks are the simplest way to explore or search a graph, and have revealed a very useful tool to investigate and characterize the structural properties of complex networks from the real world, e.g. they have been used to identify the…

Random walks process on networks plays a fundamental role in understanding the importance of nodes and the similarity of them, which has been widely applied in PageRank, information retrieval, and community detection, etc. Individual's…