15,419 research outputs found
Searching for Communities in Bipartite Networks
Bipartite networks are a useful tool for representing and investigating
interaction networks. We consider methods for identifying communities in
bipartite networks. Intuitive notions of network community groups are made
explicit using Newman's modularity measure. A specialized version of the
modularity, adapted to be appropriate for bipartite networks, is presented; a
corresponding algorithm is described for identifying community groups through
maximizing this measure. The algorithm is applied to networks derived from the
EU Framework Programs on Research and Technological Development. Community
groups identified are compared using information-theoretic methods.Comment: 12 pages, 4 figures, to appear in "Proceedings of the 5th Jagna
International Workshop: Stochastic and Quantum Dynamics of Biomolecular
Systems," C. C. Bernido and M. V. Carpio-Bernido, editors. A version with
full-quality figures and larger file size is available at
http://ccm.uma.pt/publications/Barber-Faria-Streit-Strogan-2008.pd
Parallel Toolkit for Measuring the Quality of Network Community Structure
Many networks display community structure which identifies groups of nodes
within which connections are denser than between them. Detecting and
characterizing such community structure, which is known as community detection,
is one of the fundamental issues in the study of network systems. It has
received a considerable attention in the last years. Numerous techniques have
been developed for both efficient and effective community detection. Among
them, the most efficient algorithm is the label propagation algorithm whose
computational complexity is O(|E|). Although it is linear in the number of
edges, the running time is still too long for very large networks, creating the
need for parallel community detection. Also, computing community quality
metrics for community structure is computationally expensive both with and
without ground truth. However, to date we are not aware of any effort to
introduce parallelism for this problem. In this paper, we provide a parallel
toolkit to calculate the values of such metrics. We evaluate the parallel
algorithms on both distributed memory machine and shared memory machine. The
experimental results show that they yield a significant performance gain over
sequential execution in terms of total running time, speedup, and efficiency.Comment: 8 pages; in Network Intelligence Conference (ENIC), 2014 Europea
Yeast Protein Interactome Topology Provides Framework for Coordinated-Functionality
The architecture of the network of protein-protein physical interactions in
Saccharomyces cerevisiae is exposed through the combination of two
complementary theoretical network measures, betweenness centrality and
`Q-modularity'. The yeast interactome is characterized by well-defined
topological modules connected via a small number of inter-module protein
interactions. Should such topological inter-module connections turn out to
constitute a form of functional coordination between the modules, we speculate
that this coordination is occurring typically in a pair-wise fashion, rather
than by way of high-degree hub proteins responsible for coordinating multiple
modules. The unique non-hub-centric hierarchical organization of the
interactome is not reproduced by gene duplication-and-divergence stochastic
growth models that disregard global selective pressures.Comment: Final, revised version. 13 pages. Please see Nucleic Acids open
access article for higher resolution figure
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