24,893 research outputs found
Generating realistic scaled complex networks
Research on generative models is a central project in the emerging field of
network science, and it studies how statistical patterns found in real networks
could be generated by formal rules. Output from these generative models is then
the basis for designing and evaluating computational methods on networks, and
for verification and simulation studies. During the last two decades, a variety
of models has been proposed with an ultimate goal of achieving comprehensive
realism for the generated networks. In this study, we (a) introduce a new
generator, termed ReCoN; (b) explore how ReCoN and some existing models can be
fitted to an original network to produce a structurally similar replica, (c)
use ReCoN to produce networks much larger than the original exemplar, and
finally (d) discuss open problems and promising research directions. In a
comparative experimental study, we find that ReCoN is often superior to many
other state-of-the-art network generation methods. We argue that ReCoN is a
scalable and effective tool for modeling a given network while preserving
important properties at both micro- and macroscopic scales, and for scaling the
exemplar data by orders of magnitude in size.Comment: 26 pages, 13 figures, extended version, a preliminary version of the
paper was presented at the 5th International Workshop on Complex Networks and
their Application
Tunable and Growing Network Generation Model with Community Structures
Recent years have seen a growing interest in the modeling and simulation of
social networks to understand several social phenomena. Two important classes
of networks, small world and scale free networks have gained a lot of research
interest. Another important characteristic of social networks is the presence
of community structures. Many social processes such as information diffusion
and disease epidemics depend on the presence of community structures making it
an important property for network generation models to be incorporated. In this
paper, we present a tunable and growing network generation model with small
world and scale free properties as well as the presence of community
structures. The major contribution of this model is that the communities thus
created satisfy three important structural properties: connectivity within each
community follows power-law, communities have high clustering coefficient and
hierarchical community structures are present in the networks generated using
the proposed model. Furthermore, the model is highly robust and capable of
producing networks with a number of different topological characteristics
varying clustering coefficient and inter-cluster edges. Our simulation results
show that the model produces small world and scale free networks along with the
presence of communities depicting real world societies and social networks.Comment: Social Computing and Its Applications, SCA 13, Karlsruhe : Germany
(2013
Towards realistic artificial benchmark for community detection algorithms evaluation
Assessing the partitioning performance of community detection algorithms is
one of the most important issues in complex network analysis. Artificially
generated networks are often used as benchmarks for this purpose. However,
previous studies showed their level of realism have a significant effect on the
algorithms performance. In this study, we adopt a thorough experimental
approach to tackle this problem and investigate this effect. To assess the
level of realism, we use consensual network topological properties. Based on
the LFR method, the most realistic generative method to date, we propose two
alternative random models to replace the Configuration Model originally used in
this algorithm, in order to increase its realism. Experimental results show
both modifications allow generating collections of community-structured
artificial networks whose topological properties are closer to those
encountered in real-world networks. Moreover, the results obtained with eleven
popular community identification algorithms on these benchmarks show their
performance decrease on more realistic networks
Benchmarks for testing community detection algorithms on directed and weighted graphs with overlapping communities
Many complex networks display a mesoscopic structure with groups of nodes
sharing many links with the other nodes in their group and comparatively few
with nodes of different groups. This feature is known as community structure
and encodes precious information about the organization and the function of the
nodes. Many algorithms have been proposed but it is not yet clear how they
should be tested. Recently we have proposed a general class of undirected and
unweighted benchmark graphs, with heterogenous distributions of node degree and
community size. An increasing attention has been recently devoted to develop
algorithms able to consider the direction and the weight of the links, which
require suitable benchmark graphs for testing. In this paper we extend the
basic ideas behind our previous benchmark to generate directed and weighted
networks with built-in community structure. We also consider the possibility
that nodes belong to more communities, a feature occurring in real systems,
like, e. g., social networks. As a practical application, we show how
modularity optimization performs on our new benchmark.Comment: 9 pages, 13 figures. Final version published in Physical Review E.
The code to create the benchmark graphs can be freely downloaded from
http://santo.fortunato.googlepages.com/inthepress
Centrality Measures for Networks with Community Structure
Understanding the network structure, and finding out the influential nodes is
a challenging issue in the large networks. Identifying the most influential
nodes in the network can be useful in many applications like immunization of
nodes in case of epidemic spreading, during intentional attacks on complex
networks. A lot of research is done to devise centrality measures which could
efficiently identify the most influential nodes in the network. There are two
major approaches to the problem: On one hand, deterministic strategies that
exploit knowledge about the overall network topology in order to find the
influential nodes, while on the other end, random strategies are completely
agnostic about the network structure. Centrality measures that can deal with a
limited knowledge of the network structure are required. Indeed, in practice,
information about the global structure of the overall network is rarely
available or hard to acquire. Even if available, the structure of the network
might be too large that it is too much computationally expensive to calculate
global centrality measures. To that end, a centrality measure is proposed that
requires information only at the community level to identify the influential
nodes in the network. Indeed, most of the real-world networks exhibit a
community structure that can be exploited efficiently to discover the
influential nodes. We performed a comparative evaluation of prominent global
deterministic strategies together with stochastic strategies with an available
and the proposed deterministic community-based strategy. Effectiveness of the
proposed method is evaluated by performing experiments on synthetic and
real-world networks with community structure in the case of immunization of
nodes for epidemic control.Comment: 30 pages, 4 figures. Accepted for publication in Physica A. arXiv
admin note: text overlap with arXiv:1411.627
Consensus clustering in complex networks
The community structure of complex networks reveals both their organization
and hidden relationships among their constituents. Most community detection
methods currently available are not deterministic, and their results typically
depend on the specific random seeds, initial conditions and tie-break rules
adopted for their execution. Consensus clustering is used in data analysis to
generate stable results out of a set of partitions delivered by stochastic
methods. Here we show that consensus clustering can be combined with any
existing method in a self-consistent way, enhancing considerably both the
stability and the accuracy of the resulting partitions. This framework is also
particularly suitable to monitor the evolution of community structure in
temporal networks. An application of consensus clustering to a large citation
network of physics papers demonstrates its capability to keep track of the
birth, death and diversification of topics.Comment: 11 pages, 12 figures. Published in Scientific Report
ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra
Background: Many biological systems are modeled qualitatively with discrete
models, such as probabilistic Boolean networks, logical models, Petri nets, and
agent-based models, with the goal to gain a better understanding of the system.
The computational complexity to analyze the complete dynamics of these models
grows exponentially in the number of variables, which impedes working with
complex models. Although there exist sophisticated algorithms to determine the
dynamics of discrete models, their implementations usually require
labor-intensive formatting of the model formulation, and they are oftentimes
not accessible to users without programming skills. Efficient analysis methods
are needed that are accessible to modelers and easy to use. Method: By
converting discrete models into algebraic models, tools from computational
algebra can be used to analyze their dynamics. Specifically, we propose a
method to identify attractors of a discrete model that is equivalent to solving
a system of polynomial equations, a long-studied problem in computer algebra.
Results: A method for efficiently identifying attractors, and the web-based
tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other
analysis methods for discrete models. ADAM converts several discrete model
types automatically into polynomial dynamical systems and analyzes their
dynamics using tools from computer algebra. Based on extensive experimentation
with both discrete models arising in systems biology and randomly generated
networks, we found that the algebraic algorithms presented in this manuscript
are fast for systems with the structure maintained by most biological systems,
namely sparseness, i.e., while the number of nodes in a biological network may
be quite large, each node is affected only by a small number of other nodes,
and robustness, i.e., small number of attractors
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