Overlapping Structures Detection in Protein-Protein Interaction Networks Using Community Detection Algorithm Based on Neighbor Clustering Coefficient

With the rapid development of bioinformatics, researchers have applied community detection algorithms to detect functional modules in protein-protein interaction (PPI) networks that can predict the function of unknown proteins at the molecular level and further reveal the regularity of cell activity. Clusters in a PPI network may overlap where a protein is involved in multiple functional modules. To identify overlapping structures in protein functional modules, this paper proposes a novel overlapping community detection algorithm based on the neighboring local clustering coefficient (NLC). The contributions of the NLC algorithm are threefold: (i) Combine the edge-based community detection method with local expansion in seed selection and the local clustering coefficient of neighboring nodes to improve the accuracy of seed selection; (ii) A method of measuring the distance between edges is improved to make the result of community division more accurate; (iii) A community optimization strategy for the excessive overlapping nodes makes the overlapping structure more reasonable. The experimental results on standard networks, Lancichinetti-Fortunato-Radicchi (LFR) benchmark networks and PPI networks show that the NLC algorithm can improve the Extended modularity (EQ) value and Normalized Mutual Information (NMI) value of the community division, which verifies that the algorithm can not only detect reasonable communities but also identify overlapping structures in networks

Fast Multi-Scale Community Detection based on Local Criteria within a Multi-Threaded Algorithm

Many systems can be described using graphs, or networks. Detecting communities in these networks can provide information about the underlying structure and functioning of the original systems. Yet this detection is a complex task and a large amount of work was dedicated to it in the past decade. One important feature is that communities can be found at several scales, or levels of resolution, indicating several levels of organisations. Therefore solutions to the community structure may not be unique. Also networks tend to be large and hence require efficient processing. In this work, we present a new algorithm for the fast detection of communities across scales using a local criterion. We exploit the local aspect of the criterion to enable parallel computation and improve the algorithm's efficiency further. The algorithm is tested against large generated multi-scale networks and experiments demonstrate its efficiency and accuracy.Comment: arXiv admin note: text overlap with arXiv:1204.100

Detecting highly overlapping community structure by greedy clique expansion

In complex networks it is common for each node to belong to several communities, implying a highly overlapping community structure. Recent advances in benchmarking indicate that existing community assignment algorithms that are capable of detecting overlapping communities perform well only when the extent of community overlap is kept to modest levels. To overcome this limitation, we introduce a new community assignment algorithm called Greedy Clique Expansion (GCE). The algorithm identifies distinct cliques as seeds and expands these seeds by greedily optimizing a local fitness function. We perform extensive benchmarks on synthetic data to demonstrate that GCE's good performance is robust across diverse graph topologies. Significantly, GCE is the only algorithm to perform well on these synthetic graphs, in which every node belongs to multiple communities. Furthermore, when put to the task of identifying functional modules in protein interaction data, and college dorm assignments in Facebook friendship data, we find that GCE performs competitively.Comment: 10 pages, 7 Figures. Implementation source and binaries available at http://sites.google.com/site/greedycliqueexpansion

Fast community structure local uncovering by independent vertex-centred process

This paper addresses the task of community detection and proposes a local approach based on a distributed list building, where each vertex broadcasts basic information that only depends on its degree and that of its neighbours. A decentralised external process then unveils the community structure. The relevance of the proposed method is experimentally shown on both artificial and real data.Comment: 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, Aug 2015, Paris, France. Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Minin