Community Landscapes: An Integrative Approach to Determine Overlapping Network Module Hierarchy, Identify Key Nodes and Predict Network Dynamics
PLoS ONEPublished 2 September 2010Open access
I. Kovács, Robin Palotai, Máté Szalay, Péter Csermely
Citations341
SJR quartileQ1
SJR score0.80
SNIP1.07
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
TL;DR
A new restricted SVD-based CUR (RSVD-CUR) factorization for matrix triplets that aims to extract meaningful information by providing a low-rank approximation of the three matrices using a subset of their rows and columns using the discrete empirical interpolation method.
Abstract
The concept opens a wide range of possibilities to develop new approaches and applications including network routing, classification, comparison and prediction.
Keywords
Biochemistry, Genetics and Molecular BiologyPhysics and Astronomy
Genome ResearchCytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
54,321 Citations2003Paul Shannon, Andrew Markiel +7 more
Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
NatureCollective dynamics of ‘small-world’ networks
43,160 Citations1998Duncan J. Watts, Steven H. Strogatz
Simple models of networks that can be tuned through this middle ground: regular networks ‘rewired’ to introduce increasing amounts of disorder are explored, finding that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs.
Munich Personal RePEc Archive (Ludwig Maximilian University of Munich)Some methods for classification and analysis of multivariate observations
22,787 Citations1967James B. MacQueen
SIAM ReviewThe Structure and Function of Complex Networks
18,742 Citations2003Michael Newman
Developments in this field are reviewed, 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.
Social NetworksCentrality in social networks conceptual clarification
16,883 Citations1978Linton C. Freeman
Three distinct intuitive conceptions of centrality are uncovered and existing measures are refined to embody these conceptions, one absolute and one relative measure of the centrality of positions in a network and one reflecting the degree of centralization of the entire network.
Computer Networks and ISDN SystemsThe anatomy of a large-scale hypertextual Web search engine
15,828 Citations1998Sergey Brin, Lawrence M. Page
This paper provides an in-depth description of Google, a prototype of a large-scale search engine which makes heavy use of the structure present in hypertext and looks at the problem of how to effectively deal with uncontrolled hypertext collections where anyone can publish anything they want.
Proceedings of the National Academy of SciencesCommunity structure in social and biological networks
15,656 Citations2002Michelle Girvan, M. E. J. Newman
This article proposes a method for detecting communities, built around the idea of using centrality indices to find community boundaries, and tests it on computer-generated and real-world graphs whose community structure is already known and finds that the method detects this known structure with high sensitivity and reliability.
Physical Review EFinding and evaluating community structure in networks
13,892 Citations2004Michelle G. Newman, Michelle Girvan
It is demonstrated that the algorithms proposed are highly effective at discovering community structure in both computer-generated and real-world network data, and can be used to shed light on the sometimes dauntingly complex structure of networked systems.
Physics ReportsCommunity detection in graphs
11,324 Citations2009Santo Fortunato
A thorough exposition of community structure, or clustering, is attempted, from the definition of the main elements of the problem, to the presentation of most methods developed, with a special focus on techniques designed by statistical physicists.
Physics ReportsComplex networks: Structure and dynamics
11,022 Citations2006Stefano Boccaletti, Vito Latora +3 more
The major concepts and results recently achieved in the study of the structure and dynamics of complex networks are reviewed, and the relevant applications of these ideas in many different disciplines are summarized, ranging from nonlinear science to biology, from statistical mechanics to medicine and engineering.
Journal of the ACMAuthoritative sources in a hyperlinked environment
9,060 Citations1999Jon Kleinberg
This work proposes and test an algorithmic formulation of the notion of authority, based on the relationship between a set of relevant authoritative pages and the set of “hub pages” that join them together in the link structure, and has connections to the eigenvectors of certain matrices associated with the link graph.
Journal of the Operational Research SocietyNetwork Flows: Theory, Algorithms, and Applications.
8,138 Citations1994David K. Smith, Ravindra K. Ahuja +2 more
In-depth, self-contained treatments of shortest path, maximum flow, and minimum cost flow problems, including descriptions of polynomial-time algorithms for these core models are presented.
Nature Reviews GeneticsNetwork biology: understanding the cell's functional organization
7,878 Citations2004Albert-Ĺaszló Barabási, Zoltán N. Oltvai
This work states that rapid advances in network biology indicate that cellular networks are governed by universal laws and offer a new conceptual framework that could potentially revolutionize the view of biology and disease pathologies in the twenty-first century.
Physical Review EFinding community structure in very large networks
7,484 Citations2004Aaron Clauset, M. E. J. Newman +1 more
A hierarchical agglomeration algorithm for detecting community structure which is faster than many competing algorithms: its running time on a network with n vertices and m edges is O (md log n) where d is the depth of the dendrogram describing the community structure.
ScienceClustering by Passing Messages Between Data Points
6,876 Citations2007Brendan J. Frey, Delbert Dueck
A method called “affinity propagation,” which takes as input measures of similarity between pairs of data points, which found clusters with much lower error than other methods, and it did so in less than one-hundredth the amount of time.
Journal of CyberneticsA Fuzzy Relative of the ISODATA Process and Its Use in Detecting Compact Well-Separated Clusters
6,548 Citations1973J. C. Dunn
Two fuzzy versions of the k-means optimal, least squared error partitioning problem are formulated for finite subsets X of a general inner product space; in both cases, the extremizing solutions are shown to be fixed points of a certain operator T on the class of fuzzy, k-partitions of X, and simple iteration of T provides an algorithm which has the descent property relative to the least squarederror criterion function.
BMC BioinformaticsAn automated method for finding molecular complexes in large protein interaction networks
6,293 Citations2003Gary D. Bader, Christopher W.V. Hogue
A novel graph theoretic clustering algorithm, "Molecular Complex Detection" (MCODE), that detects densely connected regions in large protein-protein interaction networks that may represent molecular complexes is described.
Statistical Applications in Genetics and Molecular BiologyA General Framework for Weighted Gene Co-Expression Network Analysis
6,035 Citations2005Bin Zhang, Steve Horvath
A general framework for `soft' thresholding that assigns a connection weight to each gene pair is described and several node connectivity measures are introduced and provided empirical evidence that they can be important for predicting the biological significance of a gene.
Physical Review EFast algorithm for detecting community structure in networks
5,491 Citations2004M. E. J. Newman
An algorithm is described which gives excellent results when tested on both computer-generated and real-world networks and is much faster, typically thousands of times faster, than previous algorithms.
American Journal of SociologyPower and Centrality: A Family of Measures
5,205 Citations1987Phillip Bonacich
Physical Review EFinding community structure in networks using the eigenvectors of matrices
4,801 Citations2006M. E. J. Newman
A modularity matrix plays a role in community detection similar to that played by the graph Laplacian in graph partitioning calculations, and a spectral measure of bipartite structure in networks and a centrality measure that identifies vertices that occupy central positions within the communities to which they belong are proposed.
Proceedings of the National Academy of SciencesMaps of random walks on complex networks reveal community structure
4,688 Citations2008Martin Rosvall, Carl T. Bergstrom
An information theoretic approach is introduced that reveals community structure in weighted and directed networks of large-scale biological and social systems and reveals a directional pattern of citation from the applied fields to the basic sciences.
Journal of Anthropological ResearchAn Information Flow Model for Conflict and Fission in Small Groups
4,661 Citations1977Wayne Zachary
NatureFunctional cartography of complex metabolic networks
4,013 Citations2005Roger Guimerà, Luı́s A. Nunes Amaral
A methodology is proposed that can find functional modules in complex networks, and classify nodes into universal roles according to their pattern of intra- and inter-module connections, which yields a ‘cartographic representation’ of complex networks.
PsychometrikaA New Status Index Derived from Sociometric Analysis
3,863 Citations1953Leo Katz
A new method of computation which takes into account who chooses as well as how many choose is presented, which introduces the concept of attenuation in influence transmitted through intermediaries.
Nucleic Acids ResearchAn efficient algorithm for large-scale detection of protein families
3,788 Citations2002Anton J. Enright
This work presents a novel approach called TRIBE-MCL for rapid and accurate clustering of protein sequences into families based on precomputed sequence similarity information that has been rigorously tested and validated on a number of very large databases.
NatureFrom molecular to modular cell biology
3,691 Citations1999Leland H. Hartwell, J. J. Hopfield +2 more
General principles that govern the structure and behaviour of modules may be discovered with help from synthetic sciences such as engineering and computer science, from stronger interactions between experiment and theory in cell biology, and from an appreciation of evolutionary constraints.
Physical Review ENear linear time algorithm to detect community structures in large-scale networks
3,542 Citations2007Usha Nandini Raghavan, Réka Albert +1 more
This paper investigates a simple label propagation algorithm that uses the network structure alone as its guide and requires neither optimization of a predefined objective function nor prior information about the communities.
Journal of Mathematical SociologyFactoring and weighting approaches to status scores and clique identification
3,129 Citations1972Phillip Bonacich
Physical Review EBenchmark graphs for testing community detection algorithms
3,077 Citations2008Andrea Lancichinetti, Santo Fortunato +1 more
This work introduces a class of benchmark graphs, that account for the heterogeneity in the distributions of node degrees and of community sizes, and uses this benchmark to test two popular methods of community detection, modularity optimization, and Potts model clustering.
Proceedings of the National Academy of SciencesResolution limit in community detection
3,045 Citations2006Santo Fortunato, Marc Barthélemy
It is found that modularity optimization may fail to identify modules smaller than a scale which depends on the total size of the network and on the degree of interconnectedness of the modules, even in cases where modules are unambiguously defined.
Journal of Statistical Mechanics Theory and ExperimentComparing community structure identification
2,877 Citations2005León Danon, Albert Dı́az-Guilera +2 more
It is found that the most accurate methods tend to be more computationally expensive, and that both aspects need to be considered when choosing a method for practical purposes.
Graduate texts in mathematicsModern Graph Theory
2,844 Citations1998Béla Bollobás
This book presents an account of newer topics, including Szemer'edi's Regularity Lemma and its use; Shelah's extension of the Hales-Jewett Theorem; the precise nature of the phase transition in a random graph process; the connection between electrical networks and random walks on graphs; and the Tutte polynomial and its cousins in knot theory.
Physical Review EAnalysis of weighted networks
2,451 Citations2004M. E. J. Newman
It is pointed out that weighted networks can in many cases be analyzed using a simple mapping from a weighted network to an unweighted multigraph, allowing us to apply standard techniques for unweighting graphs to weighted ones as well.
Choice Reviews OnlineSmall worlds: the dynamics of networks between order and randomness
2,393 Citations2000
Physical Review ECommunity detection algorithms: A comparative analysis
2,218 Citations2009Andrea Lancichinetti, Santo Fortunato
Three recent algorithms introduced by Rosvall and Bergstrom and Ronhovde and Nussinov have an excellent performance, with the additional advantage of low computational complexity, which enables one to analyze large systems.
ScienceCommunity Structure in Time-Dependent, Multiscale, and Multiplex Networks
2,213 Citations2010Peter J. Mucha, Thomas Richardson +3 more
A generalized framework of network quality functions was developed that allowed us to study the community structure of arbitrary multislice networks, which are combinations of individual networks coupled through links that connect each node in one network slice to itself in other slices.
NatureHierarchical structure and the prediction of missing links in networks
2,198 Citations2008Aaron Clauset, Cristopher Moore +1 more
This work presents a general technique for inferring hierarchical structure from network data and shows that the existence of hierarchy can simultaneously explain and quantitatively reproduce many commonly observed topological properties of networks.
Physical Review EStatistical mechanics of community detection
2,119 Citations2006Jörg Reichardt, Stefan Bornholdt
The properties of the ground state configuration are elucidated to give a concise definition of communities as cohesive subgroups in networks that is adaptive to the specific class of network under study.
New Journal of PhysicsDetecting the overlapping and hierarchical community structure in complex networks
1,960 Citations2009Andrea Lancichinetti, Santo Fortunato +1 more
The first algorithm that finds both overlapping communities and the hierarchical structure is presented, based on the local optimization of a fitness function, enabling different hierarchical levels of organization to be investigated.
NatureLink communities reveal multiscale complexity in networks
1,941 Citations2010Yong‐Yeol Ahn, James P. Bagrow +1 more
It is implied that link communities are fundamental building blocks that reveal overlap and hierarchical organization in networks to be two aspects of the same phenomenon.
Social NetworksNetwork structure and minimum degree
1,873 Citations1983Stephen B. Seidman
An approach to network cohesion is proposed that is based on minimum degree and which produces a sequence of subgraphs of gradually increasing cohesion that associates with any network measures of local density which promise to be useful both in characterizing network structures and in comparing networks.
NatureEvidence for dynamically organized modularity in the yeast protein–protein interaction network
1,845 Citations2004Jing‐Dong J. Han, Nicolas Bertin +9 more
This work investigated how hubs might contribute to robustness and other cellular properties for protein–protein interactions dynamically regulated both in time and in space, and uncovered two types of hub: ‘party’ hubs, which interact with most of their partners simultaneously, and ‘date’ Hubs, which bind their different partners at different times or locations.
NatureQuantifying social group evolution
1,657 Citations2007Gergely Palla, Albert-Ĺaszló Barabási +1 more
The focus is on networks capturing the collaboration between scientists and the calls between mobile phone users, and it is found that large groups persist for longer if they are capable of dynamically altering their membership, suggesting that an ability to change the group composition results in better adaptability.
Direct Methods for Sparse Matrices
1,612 Citations2017Iain Duff, A. M. Erisman +1 more
This book aims to be suitable also for a student course, probably at MSc level, and the subject is intensely practical and this book is written with practicalities ever in mind.
NatureSelf-similarity of complex networks
1,525 Citations2005Chaoming Song, Shlomo Havlin +1 more
A power-law relation is identified between the number of boxes needed to cover the network and the size of the box, defining a finite self-similar exponent to explain the scale-free nature of complex networks and suggest a common self-organization dynamics.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topicsSelf-similar community structure in a network of human interactions
1,491 Citations2003Roger Guimerà, León Danon +3 more
The results reveal the self-organization of the network into a state where the distribution of community sizes is self-similar, suggesting that a universal mechanism, responsible for emergence of scaling in other self-organized complex systems, as, for instance, river networks, could also be the underlying driving force in the formation and evolution of social networks.
Proceedings of the National Academy of SciencesProtein complexes and functional modules in molecular networks
1,472 Citations2003Victor Spirin, Leonid A. Mirny
The results provide strong support for the network modularity principle introduced by Hartwell et al. (1999), suggesting that found modules constitute the “building blocks” of molecular networks.
Journal of Graph Algorithms and ApplicationsComputing Communities in Large Networks Using Random Walks
1,461 Citations2006Pascal Pons, Matthieu Latapy
ScienceHigh-Quality Binary Protein Interaction Map of the Yeast Interactome Network
1,428 Citations2008Haiyuan Yu, Pascal Falter‐Braun +32 more
A comparative quality assessment of current yeast interactome data sets is carried out, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information.
American Journal of SociologyRace, School Integration, and Friendship Segregation in America
1,345 Citations2001James Moody
Proceedings of the National Academy of SciencesThe maturing architecture of the brain's default network
1,337 Citations2008Damien A. Fair, Alexander L. Cohen +7 more
This study used resting-state functional connectivity MRI (rs-fcMRI) to characterize the development of the brain's default network and found that the default regions are only sparsely functionally connected at early school age; over development, these regions integrate into a cohesive, interconnected network.
Physical Review ESubgraph centrality in complex networks
1,257 Citations2005Ernesto Estrada, Juan A. Rodríguez‐Velázquez
A new centrality measure that characterizes the participation of each node in all subgraphs in a network, C(S)(i), which is better able to discriminate the nodes of a network than alternate measures such as degree, closeness, betweenness, and eigenvector centralities.
IEEE Transactions on Pattern Analysis and Machine IntelligenceA Maximum Likelihood Approach to Continuous Speech Recognition
1,220 Citations1983L.R. Bahl, Frederick Jelinek +1 more
This paper describes a number of statistical models for use in speech recognition, with special attention to determining the parameters for such models from sparse data, and describes two decoding methods appropriate for constrained artificial languages and one appropriate for more realistic decoding tasks.
KOPS (University of Konstanz)An efficient approach to clustering in large multimedia databases with noise
1,168 Citations1998Alexander Hinneburg, Daniel A. Keim
A new algorithm to clustering in large multimedia databases called DENCLUE (DENsity-based CLUstEring) is introduced, which has a firm mathematical basis, has good clustering properties in data sets with large amounts of noise, allows a compact mathematical description of arbitrarily shaped clusters in high-dimensional data sets and is significantly faster than existing algorithms.
Physical Review LettersCommunity Structure in Directed Networks
1,144 Citations2008E. A. Leicht, M. E. J. Newman
This work describes an explicit algorithm based on spectral optimization of the modularity and shows that it gives demonstrably better results than previous methods on a variety of test networks, both real and computer generated.
Software Practice and ExperienceAn open graph visualization system and its applications to software engineering
1,103 Citations2000Emden R. Gansner, Stephen C. North
A package of practical tools and libraries for manipulating graphs and their drawings that includes stream and event interfaces for graph operations, high‐quality static and dynamic layout algorithms, and the ability to handle sizeable graphs is described.
Machine LearningCorrelation Clustering
1,091 Citations2004Nikhil Bansal, Avrim Blum +1 more
This formulation is motivated from a document clustering problem in which one has a pairwise similarity function f learned from past data, and the goal is to partition the current set of documents in a way that correlates with f as much as possible; it can also be viewed as a kind of “agnostic learning” problem.
Physical Review EBenchmarks for testing community detection algorithms on directed and weighted graphs with overlapping communities
1,041 Citations2009Andrea Lancichinetti, Santo Fortunato
The basic ideas behind the previous benchmark are extended to generate directed and weighted networks with built-in community structure, and the possibility that nodes belong to more communities is considered, a feature occurring in real systems, such as social networks.
Nature PhysicsDetecting rich-club ordering in complex networks
1,021 Citations2006Vittoria Colizza, Alessandro Flammini +2 more
The presented analysis enables the measurement of the rich-club ordering and its relation with the function and dynamics of networks in examples drawn from the biological, social and technological domains.
ComputerSelf-organization and identification of Web communities
1,007 Citations2002Gary William Flake, Sandra Lawrence +2 more
This work shows that the Web self-organizes and its link structure allows efficient identification of communities and is significant because no central authority or process governs the formation and structure of hyperlinks.
PsychometrikaA Method of Matrix Analysis of Group Structure
984 Citations1949R. Duncan Luce, Albert D. Perry
This paper describes a matrix method, n-chain and clique, which has simple relationships to the powers of certain matrices and applies it to the analysis of practical examples of group structure.
Physical Review EPerformance of modularity maximization in practical contexts
950 Citations2010Benjamin H. Good, Yves-Alexandre de Montjoye +1 more
It is shown that the modularity function Q exhibits extreme degeneracies: it typically admits an exponential number of distinct high-scoring solutions and typically lacks a clear global maximum, implying that the output of any modularity maximization procedure should be interpreted cautiously in scientific contexts.
Physical Review EVertex similarity in networks
914 Citations2006E. A. Leicht, Petter Holme +1 more
A measure of similarity based on the concept that two vertices are similar if their immediate neighbors in the network are themselves similar is proposed, which leads to a self-consistent matrix formulation of similarity that can be evaluated iteratively using only a knowledge of the adjacency matrix of the network.
Physical Review EModularity from fluctuations in random graphs and complex networks
905 Citations2004Roger Guimerà, Marta Sales‐Pardo +1 more
It is shown both numerically and analytically that random graphs and scale-free networks have modularity and it is argued that this fact must be taken into consideration to define statistically significant modularity in complex networks.
Physical Review LettersSynchronization Reveals Topological Scales in Complex Networks
854 Citations2006Àlex Arenas, Albert Dı́az-Guilera +1 more
The analysis is based on the full dynamics towards synchronization of a system of coupled oscillators and provides a useful connection between synchronization dynamics, complex networks topology, and spectral graph analysis.
Proceedings of the National Academy of SciencesAn information-theoretic framework for resolving community structure in complex networks
822 Citations2007Martin Rosvall, Carl T. Bergstrom
An information-theoretic foundation for the concept of modularity in networks is developed and the modules of which the network is composed are identified by finding an optimal compression of its topology, capitalizing on regularities in its structure.
Physical Review EFinding local community structure in networks
789 Citations2005Aaron Clauset
This work defines both a measure of local community structure and an algorithm that infers the hierarchy of communities that enclose a given vertex by exploring the graph one vertex at a time, and uses this algorithm to extract meaningful local clustering information in the large recommender network of an online retailer.
Proceedings of the National Academy of SciencesA model of Internet topology using <i>k</i> -shell decomposition
771 Citations2007Shai Carmi, Shlomo Havlin +3 more
This analysis uses information on the connectivity of the network shells to separate, in a unique (no parameters) way, the Internet into three subcomponents: a nucleus that is a small, very well connected globally distributed subgraph; a fractal subcomponent that is able to connect the bulk of the Internet without congesting the nucleus, with self-similar properties and critical exponents predicted from percolation theory.
Physical Review ECommunicability in complex networks
765 Citations2008Ernesto Estrada, Naomichi Hatano
A new measure of the communicability of a complex network is proposed, which is a broad generalization of the concept of the shortest path and able to distinguish finer structures of networks, such as communities into which a network is divided.
Physical Review EModularity and community detection in bipartite networks
751 Citations2007Michael Barber
The bipartite modularity is presented in terms of a modularity matrix B; some key properties of the eigenspectrum of B are identified and used to describe an algorithm for identifying modules in bipartites networks.
Physica A Statistical Mechanics and its ApplicationsDetect overlapping and hierarchical community structure in networks
714 Citations2008Huawei Shen, Xueqi Cheng +2 more
This paper proposes an algorithm (EAGLE) to detect both the overlapping and hierarchical properties of complex community structure together and deals with the set of maximal cliques and adopts an agglomerative framework.
Proceedings of the National Academy of SciencesModular organization of cellular networks
708 Citations2003Alexander Rives, Timothy Galitski
This work investigated the organization of interacting proteins and protein complexes into networks of modules and identified module-organizer proteins and module-connector proteins that suggest that they are important for module function and intermodule communication.
Physical Review Letters<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>k</mml:mi></mml:math>-Core Organization of Complex Networks
687 Citations2006S. N. Dorogovt︠s︡ev, A. V. Goltsev +1 more
It is shown that in networks with a finite mean number zeta2 of the second-nearest neighbors, the emergence of a k-core is a hybrid phase transition, and in contrast, ifZeta2 diverges, the networks contain an infinite sequence of k-cores which are ultrarobust against random damage.
BioinformaticsProtein complex prediction via cost-based clustering
668 Citations2004Andrew D. King, Nataša Pržulj +1 more
The RNSC algorithm is developed to efficiently partition networks into clusters using a cost function and provides an accurate and scalable method of detecting and predicting protein complexes within a PPI network.
Current BiologyUse of an oriented peptide library to determine the optimal substrates of protein kinases
666 Citations1994Zhou Songyang, Steven Blechner +4 more
Using the new technique developed, the sequence specificity of protein kinases can rapidly be predicted and, from this information, potential targets of the kinase can be identified.
PLoS ONEMapping Change in Large Networks
650 Citations2010Martin Rosvall, Carl T. Bergstrom
It is shown that bootstrap resampling accompanied by significance clustering provides a solution to the problem of distinguishing meaningful structural changes from random fluctuations and is realized de Solla Price's vision of mapping change in science.
Software Practice and ExperienceAn open graph visualization system and its applications to software engineering
610 Citations2000Emden R. Gansner, Stephen C. North
Physical Review LettersDetecting Fuzzy Community Structures in Complex Networks with a Potts Model
599 Citations2004Jörg Reichardt, Stefan Bornholdt
A fast community detection algorithm based on a q-state Potts model that allows for the detection of overlapping ("fuzzy") communities and quantifying the association of nodes with multiple communities as well as the robustness of a community.
Proceedings of the National Academy of SciencesMixture models and exploratory analysis in networks
567 Citations2007M. E. J. Newman, E. A. Leicht
A general technique for detecting structural features in large-scale network data that works by dividing the nodes of a network into classes such that the members of each class have similar patterns of connection to other nodes is described.
Proceedings of the National Academy of SciencesExtracting the hierarchical organization of complex systems
552 Citations2007Marta Sales‐Pardo, Roger Guimerà +2 more
An unsupervised method for extracting the hierarchical organization of complex biological, social, and technological networks is introduced and validated and an ensemble of hierarchically nested random graphs is defined, which is used to validate the method.
Physical Review LettersSuperparamagnetic Clustering of Data
544 Citations1996Marcelo Blatt, Shai Wiseman +1 more
This work presents a new approach for clustering, based on the physical properties of an inhomogeneous ferromagnetic model, which outperforms other algorithms for toy problems as well as for real data.
Physica A Statistical Mechanics and its ApplicationsIdentification of overlapping community structure in complex networks using fuzzy -means clustering
521 Citations2006Shihua Zhang, Rui‐Sheng Wang +1 more
A novel algorithm to identify overlapping communities in complex networks by the combination of a new modularity function based on generalizing NG's Q function, an approximation mapping of network nodes into Euclidean space and fuzzy c-means clustering is devised.
BMC BioinformaticsDevelopment and implementation of an algorithm for detection of protein complexes in large interaction networks
500 Citations2006Md. Altaf‐Ul‐Amin, Yoko Shinbo +3 more
The proposed algorithm makes it possible to detect clusters of proteins in PPI networks which mostly represent molecular biological functional units, and they are also useful to understand and explain certain biological processes.
Journal of Mathematical SociologyA graph‐theoretic definition of a sociometric clique†
495 Citations1973Richard Alba
The intent of this paper is to provide a definition of a socioraetric clique in the language of graph theory, using Luce's (1950) concept of an n‐clique, but further qualifications are added.
Proceedings of the National Academy of SciencesStability of graph communities across time scales
490 Citations2010Jean‐Charles Delvenne, Sophia N. Yaliraki +1 more
The stability of a partition is introduced, a measure of its quality as a community structure based on the clustered autocovariance of a dynamic Markov process taking place on the network, and the dynamical definition provides a unifying framework for several standard partitioning measures.
ScienceRelating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights
476 Citations2006Philip M. Kim, Long Lu +2 more
This work characterize interactions of protein networks by using atomic-resolution information from three-dimensional protein structures to find that some previously recognized relationships between network topology and genomic features are actually more reflective of a structural quantity, the number of distinct binding interfaces.
Molecular Biology of the CellGlucose Depletion Rapidly Inhibits Translation Initiation in Yeast
457 Citations2000Mark Ashe, Susan K. De Long +1 more
It is discovered that glucose withdrawal from the growth medium led to a rapid inhibition of protein synthesis and that this effect was readily reversed upon readdition of glucose, highlighting the intimate connection between the nutrient status of the cell and its translational capacity.
The European Physical Journal BFinding communities in linear time: a physics approach
456 Citations2004F. Wu, Bernardo A. Huberman
The European Physical Journal B (EPJ B) publishes regular articles and colloquia in Condensed Matter and Complex Systems on the range of topics including Solid State and Materials, Computational Methods, Statistical and Nonlinear Physics, and Interdisciplinary Physics.
Journal of Mathematical SociologyA graph‐theoretic generalization of the clique concept
449 Citations1978Stephen B. Seidman, Brian L. Foster
A family of new clique‐like structures is proposed which captures an aspect of cliques which is seldom treated in the existing literature and provides a new means of tapping several important properties of social networks.
Physical Review ECommunity detection in networks with positive and negative links
440 Citations2009Vincent Traag, Jeroen Bruggeman
An existing Potts model is extended to incorporate negative links as well, resulting in a method similar to the clustering of signed graphs, as dealt with in social balance theory, but more general.
Nature PhysicsClasses of complex networks defined by role-to-role connectivity profiles
432 Citations2006Roger Guimerà, Marta Sales‐Pardo +1 more
It is reported that networks with different functions, including the Internet, metabolic, air transportation and protein interaction networks, have distinct patterns of connections among nodes with different roles, and that, as a consequence, complex networks can be classified into two distinct functional classes on the basis of their link type frequency.
Physical Review EFuzzy communities and the concept of bridgeness in complex networks
410 Citations2008Tamás Nepusz, Andrea Petróczi +2 more
An algorithm for determining the optimal membership degrees with respect to a given goal function is created, and a measure is introduced that is able to identify outlier vertices that do not belong to any of the communities, bridges that have significant membership in more than one single community, and regular Vertices that fundamentally restrict their interactions within their own community.
New Journal of PhysicsA measure of centrality based on network efficiency
391 Citations2007Vito Latora, Massimo Marchiori
Proceedings of the National Academy of SciencesRevealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data
384 Citations2004Amos Tanay, Roded Sharan +2 more
This work performs analysis of a highly diverse collection of genomewide data sets to reveal the modular organization of the yeast system, and uses the identified modules to study the yeast transcriptional network and predict the function of >800 uncharacterized genes.
Genome biologyWhat properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?
378 Citations2006Diana Ekman, Sara Light +2 more
The results indicate that multiple and repeated domains are enriched in hub proteins and, further, that long disordered regions, which are common in date hubs, are particularly important for flexible binding.
Proceedings of the National Academy of SciencesCurvature of co-links uncovers hidden thematic layers in the World Wide Web
353 Citations2002Jean‐Pierre Eckmann, Elisha Moses
It is demonstrated here how thematic relationships can be located precisely by looking only at the graph of hyperlinks, gleaning content and context from the Web without having to read what is in the pages.
Physical Review ERobustness of community structure in networks
350 Citations2008Brian Karrer, Elizaveta Levina +1 more
It is shown that the significance of community structure can be effectively quantified by measuring its robustness to small perturbations in network structure.
…