5,830 research outputs found
Identifying network communities with a high resolution
Community structure is an important property of complex networks. An
automatic discovery of such structure is a fundamental task in many
disciplines, including sociology, biology, engineering, and computer science.
Recently, several community discovery algorithms have been proposed based on
the optimization of a quantity called modularity (Q). However, the problem of
modularity optimization is NP-hard, and the existing approaches often suffer
from prohibitively long running time or poor quality. Furthermore, it has been
recently pointed out that algorithms based on optimizing Q will have a
resolution limit, i.e., communities below a certain scale may not be detected.
In this research, we first propose an efficient heuristic algorithm, Qcut,
which combines spectral graph partitioning and local search to optimize Q.
Using both synthetic and real networks, we show that Qcut can find higher
modularities and is more scalable than the existing algorithms. Furthermore,
using Qcut as an essential component, we propose a recursive algorithm, HQcut,
to solve the resolution limit problem. We show that HQcut can successfully
detect communities at a much finer scale and with a higher accuracy than the
existing algorithms. Finally, we apply Qcut and HQcut to study a
protein-protein interaction network, and show that the combination of the two
algorithms can reveal interesting biological results that may be otherwise
undetectable.Comment: 14 pages, 5 figures. 1 supplemental file at
http://cic.cs.wustl.edu/qcut/supplemental.pd
A Method Based on Total Variation for Network Modularity Optimization using the MBO Scheme
The study of network structure is pervasive in sociology, biology, computer
science, and many other disciplines. One of the most important areas of network
science is the algorithmic detection of cohesive groups of nodes called
"communities". One popular approach to find communities is to maximize a
quality function known as {\em modularity} to achieve some sort of optimal
clustering of nodes. In this paper, we interpret the modularity function from a
novel perspective: we reformulate modularity optimization as a minimization
problem of an energy functional that consists of a total variation term and an
balance term. By employing numerical techniques from image processing
and compressive sensing -- such as convex splitting and the
Merriman-Bence-Osher (MBO) scheme -- we develop a variational algorithm for the
minimization problem. We present our computational results using both synthetic
benchmark networks and real data.Comment: 23 page
Finding community structure in networks using the eigenvectors of matrices
We consider the problem of detecting communities or modules in networks,
groups of vertices with a higher-than-average density of edges connecting them.
Previous work indicates that a robust approach to this problem is the
maximization of the benefit function known as "modularity" over possible
divisions of a network. Here we show that this maximization process can be
written in terms of the eigenspectrum of a matrix we call the modularity
matrix, which plays a role in community detection similar to that played by the
graph Laplacian in graph partitioning calculations. This result leads us to a
number of possible algorithms for detecting community structure, as well as
several other results, including a spectral measure of bipartite structure in
networks and a new centrality measure that identifies those vertices that
occupy central positions within the communities to which they belong. The
algorithms and measures proposed are illustrated with applications to a variety
of real-world complex networks.Comment: 22 pages, 8 figures, minor corrections in this versio
Network Community Detection on Metric Space
Community detection in a complex network is an important problem of much
interest in recent years. In general, a community detection algorithm chooses
an objective function and captures the communities of the network by optimizing
the objective function, and then, one uses various heuristics to solve the
optimization problem to extract the interesting communities for the user. In
this article, we demonstrate the procedure to transform a graph into points of
a metric space and develop the methods of community detection with the help of
a metric defined for a pair of points. We have also studied and analyzed the
community structure of the network therein. The results obtained with our
approach are very competitive with most of the well-known algorithms in the
literature, and this is justified over the large collection of datasets. On the
other hand, it can be observed that time taken by our algorithm is quite less
compared to other methods and justifies the theoretical findings
Community Detection via Maximization of Modularity and Its Variants
In this paper, we first discuss the definition of modularity (Q) used as a
metric for community quality and then we review the modularity maximization
approaches which were used for community detection in the last decade. Then, we
discuss two opposite yet coexisting problems of modularity optimization: in
some cases, it tends to favor small communities over large ones while in
others, large communities over small ones (so called the resolution limit
problem). Next, we overview several community quality metrics proposed to solve
the resolution limit problem and discuss Modularity Density (Qds) which
simultaneously avoids the two problems of modularity. Finally, we introduce two
novel fine-tuned community detection algorithms that iteratively attempt to
improve the community quality measurements by splitting and merging the given
network community structure. The first of them, referred to as Fine-tuned Q, is
based on modularity (Q) while the second one is based on Modularity Density
(Qds) and denoted as Fine-tuned Qds. Then, we compare the greedy algorithm of
modularity maximization (denoted as Greedy Q), Fine-tuned Q, and Fine-tuned Qds
on four real networks, and also on the classical clique network and the LFR
benchmark networks, each of which is instantiated by a wide range of
parameters. The results indicate that Fine-tuned Qds is the most effective
among the three algorithms discussed. Moreover, we show that Fine-tuned Qds can
be applied to the communities detected by other algorithms to significantly
improve their results
A Unified Community Detection, Visualization and Analysis method
Community detection in social graphs has attracted researchers' interest for
a long time. With the widespread of social networks on the Internet it has
recently become an important research domain. Most contributions focus upon the
definition of algorithms for optimizing the so-called modularity function. In
the first place interest was limited to unipartite graph inputs and partitioned
community outputs. Recently bipartite graphs, directed graphs and overlapping
communities have been investigated. Few contributions embrace at the same time
the three types of nodes. In this paper we present a method which unifies
commmunity detection for the three types of nodes and at the same time merges
partitionned and overlapping communities. Moreover results are visualized in
such a way that they can be analyzed and semantically interpreted. For
validation we experiment this method on well known simple benchmarks. It is
then applied to real data in three cases. In two examples of photos sets with
tagged people we reveal social networks. A second type of application is of
particularly interest. After applying our method to Human Brain Tractography
Data provided by a team of neurologists, we produce clusters of white fibers in
accordance with other well known clustering methods. Moreover our approach for
visualizing overlapping clusters allows better understanding of the results by
the neurologist team. These last results open up the possibility of applying
community detection methods in other domains such as data analysis with
original enhanced performances.Comment: Submitted to Advances in Complex System
Simplified Energy Landscape for Modularity Using Total Variation
Networks capture pairwise interactions between entities and are frequently
used in applications such as social networks, food networks, and protein
interaction networks, to name a few. Communities, cohesive groups of nodes,
often form in these applications, and identifying them gives insight into the
overall organization of the network. One common quality function used to
identify community structure is modularity. In Hu et al. [SIAM J. App. Math.,
73(6), 2013], it was shown that modularity optimization is equivalent to
minimizing a particular nonconvex total variation (TV) based functional over a
discrete domain. They solve this problem, assuming the number of communities is
known, using a Merriman, Bence, Osher (MBO) scheme.
We show that modularity optimization is equivalent to minimizing a convex
TV-based functional over a discrete domain, again, assuming the number of
communities is known. Furthermore, we show that modularity has no convex
relaxation satisfying certain natural conditions. We therefore, find a
manageable non-convex approximation using a Ginzburg Landau functional, which
provably converges to the correct energy in the limit of a certain parameter.
We then derive an MBO algorithm with fewer hand-tuned parameters than in Hu et
al. and which is 7 times faster at solving the associated diffusion equation
due to the fact that the underlying discretization is unconditionally stable.
Our numerical tests include a hyperspectral video whose associated graph has
2.9x10^7 edges, which is roughly 37 times larger than was handled in the paper
of Hu et al.Comment: 25 pages, 3 figures, 3 tables, submitted to SIAM J. App. Mat
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