6,013 research outputs found
Spectral and Dynamical Properties in Classes of Sparse Networks with Mesoscopic Inhomogeneities
We study structure, eigenvalue spectra and diffusion dynamics in a wide class
of networks with subgraphs (modules) at mesoscopic scale. The networks are
grown within the model with three parameters controlling the number of modules,
their internal structure as scale-free and correlated subgraphs, and the
topology of connecting network. Within the exhaustive spectral analysis for
both the adjacency matrix and the normalized Laplacian matrix we identify the
spectral properties which characterize the mesoscopic structure of sparse
cyclic graphs and trees. The minimally connected nodes, clustering, and the
average connectivity affect the central part of the spectrum. The number of
distinct modules leads to an extra peak at the lower part of the Laplacian
spectrum in cyclic graphs. Such a peak does not occur in the case of
topologically distinct tree-subgraphs connected on a tree. Whereas the
associated eigenvectors remain localized on the subgraphs both in trees and
cyclic graphs. We also find a characteristic pattern of periodic localization
along the chains on the tree for the eigenvector components associated with the
largest eigenvalue equal 2 of the Laplacian. We corroborate the results with
simulations of the random walk on several types of networks. Our results for
the distribution of return-time of the walk to the origin (autocorrelator)
agree well with recent analytical solution for trees, and it appear to be
independent on their mesoscopic and global structure. For the cyclic graphs we
find new results with twice larger stretching exponent of the tail of the
distribution, which is virtually independent on the size of cycles. The
modularity and clustering contribute to a power-law decay at short return
times
Communities in Networks
We survey some of the concepts, methods, and applications of community
detection, which has become an increasingly important area of network science.
To help ease newcomers into the field, we provide a guide to available
methodology and open problems, and discuss why scientists from diverse
backgrounds are interested in these problems. As a running theme, we emphasize
the connections of community detection to problems in statistical physics and
computational optimization.Comment: survey/review article on community structure in networks; published
version is available at
http://people.maths.ox.ac.uk/~porterm/papers/comnotices.pd
Bi-Objective Community Detection (BOCD) in Networks using Genetic Algorithm
A lot of research effort has been put into community detection from all
corners of academic interest such as physics, mathematics and computer science.
In this paper I have proposed a Bi-Objective Genetic Algorithm for community
detection which maximizes modularity and community score. Then the results
obtained for both benchmark and real life data sets are compared with other
algorithms using the modularity and MNI performance metrics. The results show
that the BOCD algorithm is capable of successfully detecting community
structure in both real life and synthetic datasets, as well as improving upon
the performance of previous techniques.Comment: 11 pages, 3 Figures, 3 Tables. arXiv admin note: substantial text
overlap with arXiv:0906.061
Partitioning networks into cliques: a randomized heuristic approach
In the context of community detection in social networks, the term community can be grounded in the strict way that simply everybody should know each other within the community. We consider the corresponding community detection problem. We search for a partitioning of a network into the minimum number of non-overlapping cliques, such that the cliques cover all vertices. This problem is called the clique covering problem (CCP) and is one of the classical NP-hard problems. For CCP, we propose a randomized heuristic approach. To construct a high quality solution to CCP, we present an iterated greedy (IG) algorithm. IG can also be combined with a heuristic used to determine how far the algorithm is from the optimum in the worst case. Randomized local search (RLS) for maximum independent set was proposed to find such a bound. The experimental results of IG and the bounds obtained by RLS indicate that IG is a very suitable technique for solving CCP in real-world graphs. In addition, we summarize our basic rigorous results, which were developed for analysis of IG and understanding of its behavior on several relevant graph classes
Community detection in multiplex networks using locally adaptive random walks
Multiplex networks, a special type of multilayer networks, are increasingly
applied in many domains ranging from social media analytics to biology. A
common task in these applications concerns the detection of community
structures. Many existing algorithms for community detection in multiplexes
attempt to detect communities which are shared by all layers. In this article
we propose a community detection algorithm, LART (Locally Adaptive Random
Transitions), for the detection of communities that are shared by either some
or all the layers in the multiplex. The algorithm is based on a random walk on
the multiplex, and the transition probabilities defining the random walk are
allowed to depend on the local topological similarity between layers at any
given node so as to facilitate the exploration of communities across layers.
Based on this random walk, a node dissimilarity measure is derived and nodes
are clustered based on this distance in a hierarchical fashion. We present
experimental results using networks simulated under various scenarios to
showcase the performance of LART in comparison to related community detection
algorithms
Clustering and Community Detection in Directed Networks: A Survey
Networks (or graphs) appear as dominant structures in diverse domains,
including sociology, biology, neuroscience and computer science. In most of the
aforementioned cases graphs are directed - in the sense that there is
directionality on the edges, making the semantics of the edges non symmetric.
An interesting feature that real networks present is the clustering or
community structure property, under which the graph topology is organized into
modules commonly called communities or clusters. The essence here is that nodes
of the same community are highly similar while on the contrary, nodes across
communities present low similarity. Revealing the underlying community
structure of directed complex networks has become a crucial and
interdisciplinary topic with a plethora of applications. Therefore, naturally
there is a recent wealth of research production in the area of mining directed
graphs - with clustering being the primary method and tool for community
detection and evaluation. The goal of this paper is to offer an in-depth review
of the methods presented so far for clustering directed networks along with the
relevant necessary methodological background and also related applications. The
survey commences by offering a concise review of the fundamental concepts and
methodological base on which graph clustering algorithms capitalize on. Then we
present the relevant work along two orthogonal classifications. The first one
is mostly concerned with the methodological principles of the clustering
algorithms, while the second one approaches the methods from the viewpoint
regarding the properties of a good cluster in a directed network. Further, we
present methods and metrics for evaluating graph clustering results,
demonstrate interesting application domains and provide promising future
research directions.Comment: 86 pages, 17 figures. Physics Reports Journal (To Appear
Detection of regulator genes and eQTLs in gene networks
Genetic differences between individuals associated to quantitative phenotypic
traits, including disease states, are usually found in non-coding genomic
regions. These genetic variants are often also associated to differences in
expression levels of nearby genes (they are "expression quantitative trait
loci" or eQTLs for short) and presumably play a gene regulatory role, affecting
the status of molecular networks of interacting genes, proteins and
metabolites. Computational systems biology approaches to reconstruct causal
gene networks from large-scale omics data have therefore become essential to
understand the structure of networks controlled by eQTLs together with other
regulatory genes, and to generate detailed hypotheses about the molecular
mechanisms that lead from genotype to phenotype. Here we review the main
analytical methods and softwares to identify eQTLs and their associated genes,
to reconstruct co-expression networks and modules, to reconstruct causal
Bayesian gene and module networks, and to validate predicted networks in
silico.Comment: minor revision with typos corrected; review article; 24 pages, 2
figure
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