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192
The structure and function of complex networks
 SIAM REVIEW
, 2003
"... 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, ..."
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Cited by 1407 (9 self)
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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 smallworld effect, degree distributions, clustering, network correlations, random graph models, models of network growth and preferential attachment, and dynamical processes taking place on networks.
Comparing community structure identification
 Journal of Statistical Mechanics: Theory and Experiment
, 2005
"... ..."
Nunes Amaral. Functional cartography of complex metabolic networks
 Nature
, 2005
"... Highthroughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major scientific challenge. Here, we propose a methodology that enab ..."
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Cited by 129 (3 self)
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Highthroughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major scientific challenge. Here, we propose a methodology that enables us to extract and display information contained in complex networks 1,2,3. Specifically, we demonstrate that one can (i) find functional modules 4,5 in complex networks, and (ii) classify nodes into universal roles according to their pattern of intra and intermodule connections. The method thus yields a “cartographic representation ” of complex networks. Metabolic networks 6,7,8 are among the most challenging biological networks and, arguably, the ones with more potential for immediate applicability 9. We use our method to analyze the metabolic networks of twelve organisms from three different superkingdoms. We find that, typically, 80 % of the nodes are only connected to other nodes within their respective modules, and that nodes with different roles are affected by different evolutionary constraints and pressures. Remarkably, we
Statistical properties of community structure in large social and information networks
"... 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 structur ..."
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Cited by 120 (10 self)
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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 realworld networks taken from a wide range of application domains. Our results suggest a significantly more refined picture of community structure in large realworld 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 “communitylike.” This behavior is not explained, even at a qualitative level, by any of the commonlyused 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 wellembeddable in a lowdimensional 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.
Computing communities in large networks using random walks
 J. of Graph Alg. and App. bf
, 2004
"... Dense subgraphs of sparse graphs (communities), which appear in most realworld complex networks, play an important role in many contexts. Computing them however is generally expensive. We propose here a measure of similarities between vertices based on random walks which has several important advan ..."
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Cited by 94 (2 self)
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Dense subgraphs of sparse graphs (communities), which appear in most realworld complex networks, play an important role in many contexts. Computing them however is generally expensive. We propose here a measure of similarities between vertices based on random walks which has several important advantages: it captures well the community structure in a network, it can be computed efficiently, and it can be used in an agglomerative algorithm to compute efficiently the community structure of a network. We propose such an algorithm, called Walktrap, which runs in time O(mn 2) and space O(n 2) in the worst case, and in time O(n 2 log n) and space O(n 2) in most realworld cases (n and m are respectively the number of vertices and edges in the input graph). Extensive comparison tests show that our algorithm surpasses previously proposed ones concerning the quality of the obtained community structures and that it stands among the best ones concerning the running time.
Community structure in large networks: Natural cluster sizes and the absence of large welldefined clusters
, 2008
"... 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 wit ..."
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Cited by 79 (6 self)
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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 realworld networks, ranging from traditional and online social networks, to technological and information networks and
Modeling interactome: scalefree or geometric
 Bioinformatics
, 2004
"... doi:10.1093/bioinformatics/bth436 ..."
Kronecker Graphs: An Approach to Modeling Networks
 JOURNAL OF MACHINE LEARNING RESEARCH 11 (2010) 9851042
, 2010
"... How can we generate realistic networks? In addition, how can we do so with a mathematically tractable model that allows for rigorous analysis of network properties? Real networks exhibit a long list of surprising properties: Heavy tails for the in and outdegree distribution, heavy tails for the ei ..."
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Cited by 48 (2 self)
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How can we generate realistic networks? In addition, how can we do so with a mathematically tractable model that allows for rigorous analysis of network properties? Real networks exhibit a long list of surprising properties: Heavy tails for the in and outdegree distribution, heavy tails for the eigenvalues and eigenvectors, small diameters, and densification and shrinking diameters over time. Current network models and generators either fail to match several of the above properties, are complicated to analyze mathematically, or both. Here we propose a generative model for networks that is both mathematically tractable and can generate networks that have all the above mentioned structural properties. Our main idea here is to use a nonstandard matrix operation, the Kronecker product, to generate graphs which we refer to as “Kronecker graphs”. First, we show that Kronecker graphs naturally obey common network properties. In fact, we rigorously prove that they do so. We also provide empirical evidence showing that Kronecker graphs can effectively model the structure of real networks. We then present KRONFIT, a fast and scalable algorithm for fitting the Kronecker graph generation model to large real networks. A naive approach to fitting would take superexponential
Evolving protein interaction networks through gene duplication
 J. Theor. Biol
"... The topology of the proteome map revealed by recent largescale hybridization methods has shown that the distribution of proteinprotein interactions is highly heterogeneous, with many proteins having few links while a few of them are heavily connected. This particular topology is shared by other ce ..."
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Cited by 45 (2 self)
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The topology of the proteome map revealed by recent largescale hybridization methods has shown that the distribution of proteinprotein interactions is highly heterogeneous, with many proteins having few links while a few of them are heavily connected. This particular topology is shared by other cellular networks, such as metabolic pathways, and it has been suggested to be responsible for the high mutational homeostasis displayed by the genome of some organisms. In this paper we explore a recent model of proteome evolution that has been shown to reproduce many of the features displayed by its real counterparts. The model is based on gene duplication plus rewiring of the newly created genes. The statistical features displayed by the proteome of wellknown organisms are reproduced, suggesting that the overall topology of the protein maps naturally emerges from the two leading mechanisms considered by the model. I.
Uncovering network systems within protein structures
 Journal of Molecular Biology
"... Traditionally, proteins have been viewed as a construct based on elements of secondary structure and their arrangement in threedimensional space. In a departure from this perspective we show that protein structures can be modelled as network systems that exhibit smallworld, singlescale, and to so ..."
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Cited by 41 (0 self)
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Traditionally, proteins have been viewed as a construct based on elements of secondary structure and their arrangement in threedimensional space. In a departure from this perspective we show that protein structures can be modelled as network systems that exhibit smallworld, singlescale, and to some degree, scalefree properties. The phenomenological network concept of degrees of separation is applied to threedimensional 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 threedimensional 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.