7,873 research outputs found
Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm
Peer reviewedPublisher PD
Overlapping modularity at the critical point of k-clique percolation
One of the most remarkable social phenomena is the formation of communities
in social networks corresponding to families, friendship circles, work teams,
etc. Since people usually belong to several different communities at the same
time, the induced overlaps result in an extremely complicated web of the
communities themselves. Thus, uncovering the intricate community structure of
social networks is a non-trivial task with great potential for practical
applications, gaining a notable interest in the recent years. The Clique
Percolation Method (CPM) is one of the earliest overlapping community finding
methods, which was already used in the analysis of several different social
networks. In this approach the communities correspond to k-clique percolation
clusters, and the general heuristic for setting the parameters of the method is
to tune the system just below the critical point of k-clique percolation.
However, this rule is based on simple physical principles and its validity was
never subject to quantitative analysis. Here we examine the quality of the
partitioning in the vicinity of the critical point using recently introduced
overlapping modularity measures. According to our results on real social- and
other networks, the overlapping modularities show a maximum close to the
critical point, justifying the original criteria for the optimal parameter
settings.Comment: 20 pages, 6 figure
Link communities reveal multiscale complexity in networks
Networks have become a key approach to understanding systems of interacting
objects, unifying the study of diverse phenomena including biological organisms
and human society. One crucial step when studying the structure and dynamics of
networks is to identify communities: groups of related nodes that correspond to
functional subunits such as protein complexes or social spheres. Communities in
networks often overlap such that nodes simultaneously belong to several groups.
Meanwhile, many networks are known to possess hierarchical organization, where
communities are recursively grouped into a hierarchical structure. However, the
fact that many real networks have communities with pervasive overlap, where
each and every node belongs to more than one group, has the consequence that a
global hierarchy of nodes cannot capture the relationships between overlapping
groups. Here we reinvent communities as groups of links rather than nodes and
show that this unorthodox approach successfully reconciles the antagonistic
organizing principles of overlapping communities and hierarchy. In contrast to
the existing literature, which has entirely focused on grouping nodes, link
communities naturally incorporate overlap while revealing hierarchical
organization. We find relevant link communities in many networks, including
major biological networks such as protein-protein interaction and metabolic
networks, and show that a large social network contains hierarchically
organized community structures spanning inner-city to regional scales while
maintaining pervasive overlap. Our results imply that link communities are
fundamental building blocks that reveal overlap and hierarchical organization
in networks to be two aspects of the same phenomenon.Comment: Main text and supplementary informatio
The Architecture of a Proteomic Network in the Yeast
We describe an approach to clustering the yeast protein-protein inter-action network in order to identify functional modules, groups of proteins forming multi-protein complexes accomplishing various functions in the cell. We have developed a clustering method that accounts for the small-world nature of the network. The algorithm makes use of the concept of k-cores in a graph, and employs recursive spectral clustering to compute the functional modules. The computed clusters are annotated using their protein memberships into known multi-protein complexes in the yeast. We also dissect the protein interaction network into a global subnetwork of hub proteins (connected to several clusters), and a local network consisting of cluster proteins
Link-Prediction Enhanced Consensus Clustering for Complex Networks
Many real networks that are inferred or collected from data are incomplete
due to missing edges. Missing edges can be inherent to the dataset (Facebook
friend links will never be complete) or the result of sampling (one may only
have access to a portion of the data). The consequence is that downstream
analyses that consume the network will often yield less accurate results than
if the edges were complete. Community detection algorithms, in particular,
often suffer when critical intra-community edges are missing. We propose a
novel consensus clustering algorithm to enhance community detection on
incomplete networks. Our framework utilizes existing community detection
algorithms that process networks imputed by our link prediction based
algorithm. The framework then merges their multiple outputs into a final
consensus output. On average our method boosts performance of existing
algorithms by 7% on artificial data and 17% on ego networks collected from
Facebook
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