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221
Comparing community structure identification
 Journal of Statistical Mechanics: Theory and Experiment
, 2005
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Graph Clustering Based on Structural/Attribute Similarities
"... The goal of graph clustering is to partition vertices in a large graph into different clusters based on various criteria such as vertex connectivity or neighborhood similarity. Graph clustering techniques are very useful for detecting densely connected groups in a large graph. Many existing graph cl ..."
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Cited by 95 (8 self)
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The goal of graph clustering is to partition vertices in a large graph into different clusters based on various criteria such as vertex connectivity or neighborhood similarity. Graph clustering techniques are very useful for detecting densely connected groups in a large graph. Many existing graph clustering methods mainly focus on the topological structure for clustering, but largely ignore the vertex properties which are often heterogenous. In this paper, we propose a novel graph clustering algorithm, SACluster, based on both structural and attribute similarities through a unified distance measure. Our method partitions a large graph associated with attributes into k clusters so that each cluster contains a densely connected subgraph with homogeneous attribute values. An effective method is proposed to automatically learn the degree of contributions of structural similarity and attribute similarity. Theoretical analysis is provided to show that SACluster is converging. Extensive experimental results demonstrate the effectiveness of SACluster through comparison with the stateoftheart graph clustering and summarization methods. 1.
WEBbased GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res. 2013;41(Web Server issue):W77–83
"... Functional enrichment analysis is an essential task for the interpretation of gene lists derived from largescale genetic, transcriptomic and proteomic studies. WebGestalt (WEBbased GEne SeT AnaLysis Toolkit) has become one of the popular software tools in this field since its publication in 2005. ..."
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Cited by 85 (0 self)
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Functional enrichment analysis is an essential task for the interpretation of gene lists derived from largescale genetic, transcriptomic and proteomic studies. WebGestalt (WEBbased GEne SeT AnaLysis Toolkit) has become one of the popular software tools in this field since its publication in 2005. For the last 7 years, WebGestalt data holdings have grown substantially to satisfy the requirements of users from different research areas. The current version of WebGestalt supports 8 organisms and 201 gene identifiers from various databases and different technology platforms, making it directly available to the fast growing omics community. Meanwhile, by integrating functional categories derived from centrally and publicly curated databases as well as computational analyses, WebGestalt has significantly increased the coverage of functional categories in various biological contexts including Gene Ontology, pathway, network module, gene–phenotype association, gene–disease association, gene–drug association and chromosomal location, leading to a total of 78 612 functional categories. Finally, new interactive features, such as pathway map, hierarchical network visualization and phenotype ontology visualization have been added to WebGestalt to help users better understand the enrichment results. WebGestalt can be freely accessed through
Community Structure in Graphs
, 2007
"... Graph vertices are often organized into groups that seem to live fairly independently of the rest of the graph, with which they share but a few edges, whereas the relationships between group members are stronger, as shown by the large number of mutual connections. Such groups of vertices, or communi ..."
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Cited by 44 (0 self)
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Graph vertices are often organized into groups that seem to live fairly independently of the rest of the graph, with which they share but a few edges, whereas the relationships between group members are stronger, as shown by the large number of mutual connections. Such groups of vertices, or communities, can be considered as independent compartments of a graph. Detecting communities is of great importance in sociology, biology and computer science, disciplines where systems are often represented as graphs. The task is very hard, though, both conceptually, due to the ambiguity in the definition of community and in the discrimination of different partitions and practically, because algorithms must find “good ” partitions among an exponentially large number of them. Other complications are represented by the possible occurrence of hierarchies, i.e. communities which are nested inside larger communities, and by the existence of overlaps between communities, due to the presence of nodes belonging to more groups. All these aspects are dealt with in some detail and many methods are described, from traditional approaches used in computer science and sociology to recent techniques developed mostly within statistical physics.
Multilevel algorithms for modularity clustering
"... been adapted to modularity clustering. Section 4 details the singlelevel and multilevel refinement heuristics, and Section 5.3 compares them experimentally. Because the effectiveness of (particularly multilevel) refinement may depend on the coarsening algorithm, Section 5.4 examines various combi ..."
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Cited by 41 (0 self)
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been adapted to modularity clustering. Section 4 details the singlelevel and multilevel refinement heuristics, and Section 5.3 compares them experimentally. Because the effectiveness of (particularly multilevel) refinement may depend on the coarsening algorithm, Section 5.4 examines various combinations of coarsening and refinement heuristics. Section 6 compares public implementations and benchmark results of modularity clustering heuristics, without a restriction to coarsening and refinement algorithms. While this is one of the most extensive comparisons in the literature, it is far from exhaustive, because implementations and sufficient experimental results have not been published for some proposed heurisarXiv:0812.4073v1
Laplacian dynamics and multiscale modular structure in networks
 ArXiv
, 2009
"... Most methods proposed to uncover communities in complex networks rely on their structural properties. Here we introduce the stability of a network partition, a measure of its quality defined in terms of the statistical properties of a dynamical process taking place on the graph. The timescale of th ..."
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Cited by 33 (3 self)
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Most methods proposed to uncover communities in complex networks rely on their structural properties. Here we introduce the stability of a network partition, a measure of its quality defined in terms of the statistical properties of a dynamical process taking place on the graph. The timescale of the process acts as an intrinsic parameter that uncovers community structures at different resolutions. The stability extends and unifies standard notions for community detection: modularity and spectral partitioning can be seen as limiting cases of our dynamic measure. Similarly, recently proposed multiresolution methods correspond to linearisations of the stability at short times. The connection between community detection and Laplacian dynamics enables us to establish dynamically motivated stability measures linked to distinct null models. We apply our method to find multiscale partitions for different networks and show that the stability can be computed efficiently for large networks with extended versions of current algorithms. The relation between the structure of a network and the dynamics that takes place on it 1 Lambiotte et al. has been studied extensively in the last years 1,2,3. A growing body of research has shown how
An experimental investigation of graph kernels on a collaborative recommendation task
 Proceedings of the 6th International Conference on Data Mining (ICDM 2006
, 2006
"... This paper presents a survey as well as a systematic empirical comparison of seven graph kernels and two related similarity matrices (simply referred to as graph kernels), namely the exponential diffusion kernel, the Laplacian exponential diffusion kernel, the von Neumann diffusion kernel, the regul ..."
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Cited by 27 (7 self)
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This paper presents a survey as well as a systematic empirical comparison of seven graph kernels and two related similarity matrices (simply referred to as graph kernels), namely the exponential diffusion kernel, the Laplacian exponential diffusion kernel, the von Neumann diffusion kernel, the regularized Laplacian kernel, the commutetime kernel, the randomwalkwithrestart similarity matrix, and finally, three graph kernels introduced in this paper: the regularized commutetime kernel, the Markov diffusion kernel, and the crossentropy diffusion matrix. The kernelonagraph approach is simple and intuitive. It is illustrated by applying the nine graph kernels to a collaborativerecommendation task and to a semisupervised classification task, both on several databases. The graph methods compute proximity measures between nodes that help study the structure of the graph. Our comparisons suggest that the regularized commutetime and the Markov diffusion kernels perform best, closely followed by the regularized Laplacian kernel. 1
A fast algorithm to find overlapping communities in networks
 In Proc. of ECML/PKDD 2008
, 2008
"... Abstract. Many networks possess a community structure, such that vertices form densely connected groups which are more sparsely linked to other groups. In some cases these groups overlap, with some vertices shared between two or more communities. Discovering communities in networks is a computationa ..."
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Cited by 26 (1 self)
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Abstract. Many networks possess a community structure, such that vertices form densely connected groups which are more sparsely linked to other groups. In some cases these groups overlap, with some vertices shared between two or more communities. Discovering communities in networks is a computationally challenging task, especially if they overlap. In previous work we proposed an algorithm, CONGA, that could detect overlapping communities using the new concept of split betweenness. Here we present an improved algorithm based on a local form of betweenness, which yields good results but is much faster. It is especially effective in discovering smalldiameter communities in large networks, and has a time complexity of only O(n log n) for sparse networks. 1 Introduction and Related Work In recent years, networks (graphs) have increasingly been used to represent various kinds of complex system in the real world. Many networks exhibit community structure: the tendency of vertices to form communities (or modules) such that intracommunity edges are denser than the edges between communities. Communities often
A family of dissimilarity measures between nodes generalizing both the shortestpath and the commutetime distances
 in Proceedings of the 14th SIGKDD International Conference on Knowledge Discovery and Data Mining
"... This work introduces a new family of linkbased dissimilarity measures between nodes of a weighted directed graph. This measure, called the randomized shortestpath (RSP) dissimilarity, depends on a parameter θ and has the interesting property of reducing, on one end, to the standard shortestpath d ..."
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Cited by 25 (11 self)
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This work introduces a new family of linkbased dissimilarity measures between nodes of a weighted directed graph. This measure, called the randomized shortestpath (RSP) dissimilarity, depends on a parameter θ and has the interesting property of reducing, on one end, to the standard shortestpath distance when θ is large and, on the other end, to the commutetime (or resistance) distance when θ is small (near zero). Intuitively, it corresponds to the expected cost incurred by a random walker in order to reach a destination node from a starting node while maintaining a constant entropy (related to θ) spread in the graph. The parameter θ is therefore biasing gradually the simple random walk on the graph towards the shortestpath policy. By adopting a statistical physics approach and computing a sum over all the possible paths (discrete path integral), it is shown that the RSP dissimilarity from every node to a particular node of interest can be computed efficiently by solving two linear systems of n equations, where n is the number of nodes. On the other hand, the dissimilarity between every couple of nodes is obtained by inverting an n × n matrix. The proposed measure can be used for various graph mining tasks such as computing betweenness centrality, finding dense communities, etc, as shown in the experimental section.
Graph nodes clustering with the sigmoid commutetime kernel: A . . .
 DATA & KNOWLEDGE ENGINEERING
, 2009
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