Inspired by empirical studies of networked systems such as the Internet, social networks, and biological networks, researchers have in recent years developed a variety of techniques and models to help us understand or predict the behavior of these systems. Here we review developments in this field, including such concepts as the small-world effect, degree distributions, clustering, network correlations, random graph models, models of network growth and preferential attachment, and dynamical processes taking place on networks.

We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant artificial networks of such a kind came into existence recently. This opens a wide field for the study of their topology, evolution, and complex processes occurring in them. Such networks possess a rich set of scaling properties. A number of them are scale-free and show striking resilience against random breakdowns. In spite of large sizes of these networks, the distances between most their vertices are short — a feature known as the “smallworld” effect. We discuss how growing networks self-organize into scale-free structures and the role of the mechanism of preferential linking. We consider the topological and structural properties of evolving networks, and percolation in these networks. We present a number of models demonstrating the main features of evolving networks and discuss current approaches for their simulation and analytical study. Applications of the general results to particular networks in Nature are discussed. We demonstrate the generic connections of the network growth processes with the general problems

A large body of work has been devoted to identifying community structure in networks. A community is often though of as a set of nodes that has more connections between its members than to the remainder of the network. In this paper, we characterize as a function of size the statistical and structural properties of such sets of nodes. We define the network community profile plot, which characterizes the “best ” possible community—according to the conductance measure—over a wide range of size scales, and we study over 70 large sparse real-world networks taken from a wide range of application domains. Our results suggest a significantly more refined picture of community structure in large real-world networks than has been appreciated previously. Our most striking finding is that in nearly every network dataset we examined, we observe tight but almost trivial communities at very small scales, and at larger size scales, the best possible communities gradually “blend in ” with the rest of the network and thus become less “community-like.” This behavior is not explained, even at a qualitative level, by any of the commonly-used network generation models. Moreover, this behavior is exactly the opposite of what one would expect based on experience with and intuition from expander graphs, from graphs that are well-embeddable in a low-dimensional structure, and from small social networks that have served as testbeds of community detection algorithms. We have found, however, that a generative model, in which new edges are added via an iterative “forest fire” burning process, is able to produce graphs exhibiting a network community structure similar to our observations.

Each complex network (or class of networks) presents specific topological features which characterize its connectivity and highly influence the dynamics and function of processes executed on the network. The analysis, discrimination, and synthesis of complex networks therefore rely on the use of measurements capable of expressing the most relevant topological features. This article presents a survey of such measurements. It includes general considerations about complex network characterization, a brief review of the principal models, and the presentation of the main existing measurements organized into classes. Special attention is given to relating complex network analysis with the areas of pattern recognition and feature selection, as well as on surveying some concepts and measurements from traditional graph theory which are potentially useful for complex network research. Depending on the network and the analysis task one has in mind, a specific set of features may be chosen. It is hoped that the present survey will help the

A large body of work has been devoted to defining and identifying clusters or communities in social and information networks, i.e., in graphs in which the nodes represent underlying social entities and the edges represent some sort of interaction between pairs of nodes. Most such research begins with the premise that a community or a cluster should be thought of as a set of nodes that has more and/or better connections between its members than to the remainder of the network. In this paper, we explore from a novel perspective several questions related to identifying meaningful communities in large social and information networks, and we come to several striking conclusions. Rather than defining a procedure to extract sets of nodes from a graph and then attempt to interpret these sets as a “real ” communities, we employ approximation algorithms for the graph partitioning problem to characterize as a function of size the statistical and structural properties of partitions of graphs that could plausibly be interpreted as communities. In particular, we define the network community profile plot, which characterizes the “best ” possible community—according to the conductance measure—over a wide range of size scales. We study over 100 large real-world networks, ranging from traditional and on-line social networks, to technological and information networks and

Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or logical approaches. We propose a new modeling framework for gene regulatory networks, that combines the intuitive appeal of a qualitative description of gene states with a high flexibility in incorporating stochasticity in the duration of cellular processes. We apply our methods to the regulatory network of the segment polarity genes, thus gaining novel insights into the development of gene expression patterns. For example, we show that very short synthesis and decay times can perturb the wild type pattern. On the other hand, separation of timescales between pre- and posttranslational processes and a minimal prepattern ensure convergence to the wild type expression pattern regardless of fluctuations.

Motivation: High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions but it is often difficult to decide which proteins to probe as interaction partners. Developing reliable computational methods assisting this decision process is a pressing need in bioinformatics. Results: We show that we can use the conserved properties of the protein network to identify and validate interaction candidates. We apply a number of machine learning algorithms to the protein connectivity information and achieve a surprisingly good overall performance in predicting interacting proteins. Using a ‘leave-one-out ’ approach we find average success rates between 20 and 40 % for predicting the correct interaction partner of a protein. We demonstrate that the success of these methods is based on the presence of conserved interaction motifs within the network. Availability: A reference implementation and a table with candidate interacting partners for each yeast protein are available

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Traditionally, proteins have been viewed as a construct based on elements of secondary structure and their arrangement in three-dimensional space. In a departure from this perspective we show that protein structures can be modelled as network systems that exhibit small-world, single-scale, and to some degree, scale-free properties. The phenomenological network concept of degrees of separation is applied to three-dimensional protein structure networks and reveals how amino acid residues can be connected to each other within six degrees of separation. This work also illuminates the unique features of protein networks in comparison to other networks currently studied. Recognising that proteins are networks provides a means of rationalising the robustness in the overall three-dimensional fold of a protein against random mutations and suggests an alternative avenue to investigate the determinants of protein structure, function and folding. q 2003 Published by Elsevier Ltd.

Betweenness is a centrality measure based on shortest paths, widely used in complex network analysis. It is computationally-expensive to exactly determine betweenness; currently the fastest-known algorithm by Brandes requires O(nm) time for unweighted graphs and O(nm + n 2 log n) time for weighted graphs, where n is the number of vertices and m is the number of edges in the network. These are also the worstcase time bounds for computing the betweenness score of a single vertex. In this paper, we present a novel approximation algorithm for computing betweenness centrality of a given vertex, for both weighted and unweighted graphs. Our approximation algorithm is based on an adaptive sampling technique that significantly reduces the number of single-source shortest path computations for vertices with high centrality. We conduct an extensive experimental study on real-world graph instances, and observe that our random sampling algorithm gives very good betweenness approximations for biological networks, road networks and web crawls.