20,464 research outputs found
Evidential Communities for Complex Networks
Community detection is of great importance for understand-ing graph structure
in social networks. The communities in real-world networks are often
overlapped, i.e. some nodes may be a member of multiple clusters. How to
uncover the overlapping communities/clusters in a complex network is a general
problem in data mining of network data sets. In this paper, a novel algorithm
to identify overlapping communi-ties in complex networks by a combination of an
evidential modularity function, a spectral mapping method and evidential
c-means clustering is devised. Experimental results indicate that this
detection approach can take advantage of the theory of belief functions, and
preforms good both at detecting community structure and determining the
appropri-ate number of clusters. Moreover, the credal partition obtained by the
proposed method could give us a deeper insight into the graph structure
Median evidential c-means algorithm and its application to community detection
Median clustering is of great value for partitioning relational data. In this
paper, a new prototype-based clustering method, called Median Evidential
C-Means (MECM), which is an extension of median c-means and median fuzzy
c-means on the theoretical framework of belief functions is proposed. The
median variant relaxes the restriction of a metric space embedding for the
objects but constrains the prototypes to be in the original data set. Due to
these properties, MECM could be applied to graph clustering problems. A
community detection scheme for social networks based on MECM is investigated
and the obtained credal partitions of graphs, which are more refined than crisp
and fuzzy ones, enable us to have a better understanding of the graph
structures. An initial prototype-selection scheme based on evidential
semi-centrality is presented to avoid local premature convergence and an
evidential modularity function is defined to choose the optimal number of
communities. Finally, experiments in synthetic and real data sets illustrate
the performance of MECM and show its difference to other methods
Identifying Overlapping and Hierarchical Thematic Structures in Networks of Scholarly Papers: A Comparison of Three Approaches
We implemented three recently proposed approaches to the identification of
overlapping and hierarchical substructures in graphs and applied the
corresponding algorithms to a network of 492 information-science papers coupled
via their cited sources. The thematic substructures obtained and overlaps
produced by the three hierarchical cluster algorithms were compared to a
content-based categorisation, which we based on the interpretation of titles
and keywords. We defined sets of papers dealing with three topics located on
different levels of aggregation: h-index, webometrics, and bibliometrics. We
identified these topics with branches in the dendrograms produced by the three
cluster algorithms and compared the overlapping topics they detected with one
another and with the three pre-defined paper sets. We discuss the advantages
and drawbacks of applying the three approaches to paper networks in research
fields.Comment: 18 pages, 9 figure
A similarity-based community detection method with multiple prototype representation
Communities are of great importance for understanding graph structures in
social networks. Some existing community detection algorithms use a single
prototype to represent each group. In real applications, this may not
adequately model the different types of communities and hence limits the
clustering performance on social networks. To address this problem, a
Similarity-based Multi-Prototype (SMP) community detection approach is proposed
in this paper. In SMP, vertices in each community carry various weights to
describe their degree of representativeness. This mechanism enables each
community to be represented by more than one node. The centrality of nodes is
used to calculate prototype weights, while similarity is utilized to guide us
to partitioning the graph. Experimental results on computer generated and
real-world networks clearly show that SMP performs well for detecting
communities. Moreover, the method could provide richer information for the
inner structure of the detected communities with the help of prototype weights
compared with the existing community detection models
Searching for network modules
When analyzing complex networks a key target is to uncover their modular
structure, which means searching for a family of modules, namely node subsets
spanning each a subnetwork more densely connected than the average. This work
proposes a novel type of objective function for graph clustering, in the form
of a multilinear polynomial whose coefficients are determined by network
topology. It may be thought of as a potential function, to be maximized, taking
its values on fuzzy clusterings or families of fuzzy subsets of nodes over
which every node distributes a unit membership. When suitably parametrized,
this potential is shown to attain its maximum when every node concentrates its
all unit membership on some module. The output thus is a partition, while the
original discrete optimization problem is turned into a continuous version
allowing to conceive alternative search strategies. The instance of the problem
being a pseudo-Boolean function assigning real-valued cluster scores to node
subsets, modularity maximization is employed to exemplify a so-called quadratic
form, in that the scores of singletons and pairs also fully determine the
scores of larger clusters, while the resulting multilinear polynomial potential
function has degree 2. After considering further quadratic instances, different
from modularity and obtained by interpreting network topology in alternative
manners, a greedy local-search strategy for the continuous framework is
analytically compared with an existing greedy agglomerative procedure for the
discrete case. Overlapping is finally discussed in terms of multiple runs, i.e.
several local searches with different initializations.Comment: 10 page
Methods for protein complex prediction and their contributions towards understanding the organization, function and dynamics of complexes
Complexes of physically interacting proteins constitute fundamental
functional units responsible for driving biological processes within cells. A
faithful reconstruction of the entire set of complexes is therefore essential
to understand the functional organization of cells. In this review, we discuss
the key contributions of computational methods developed till date
(approximately between 2003 and 2015) for identifying complexes from the
network of interacting proteins (PPI network). We evaluate in depth the
performance of these methods on PPI datasets from yeast, and highlight
challenges faced by these methods, in particular detection of sparse and small
or sub- complexes and discerning of overlapping complexes. We describe methods
for integrating diverse information including expression profiles and 3D
structures of proteins with PPI networks to understand the dynamics of complex
formation, for instance, of time-based assembly of complex subunits and
formation of fuzzy complexes from intrinsically disordered proteins. Finally,
we discuss methods for identifying dysfunctional complexes in human diseases,
an application that is proving invaluable to understand disease mechanisms and
to discover novel therapeutic targets. We hope this review aptly commemorates a
decade of research on computational prediction of complexes and constitutes a
valuable reference for further advancements in this exciting area.Comment: 1 Tabl
Recommended from our members
Artificial Immune Systems - Models, algorithms and applications
Copyright © 2010 Academic Research Publishing Agency.This article has been made available through the Brunel Open Access Publishing Fund.Artificial Immune Systems (AIS) are computational paradigms that belong to the computational intelligence family and are inspired by the biological immune system. During the past decade, they have attracted a lot of interest from researchers aiming to develop immune-based models and techniques to solve complex computational or engineering problems. This work presents a survey of existing AIS models and algorithms with a focus on the last five years.This article is available through the Brunel Open Access Publishing Fun
- …