Dataset Information

Multi-resolution community detection in massive networks.

ABSTRACT: Aiming at improving the efficiency and accuracy of community detection in complex networks, we proposed a new algorithm, which is based on the idea that communities could be detected from subnetworks by comparing the internal and external cohesion of each subnetwork. In our method, similar nodes are firstly gathered into meta-communities, which are then decided to be retained or merged through a multilevel label propagation process, until all of them meet our community criterion. Our algorithm requires neither any priori information of communities nor optimization of any objective function. Experimental results on both synthetic and real-world networks show that, our algorithm performs quite well and runs extremely fast, compared with several other popular algorithms. By tuning a resolution parameter, we can also observe communities at different scales, so this could reveal the hierarchical structure of the network. To further explore the effectiveness of our method, we applied it to the E-Coli transcriptional regulatory network, and found that all the identified modules have strong structural and functional coherence.

SUBMITTER: Han J

PROVIDER: S-EPMC5154182 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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Publications

Multi-resolution community detection in massive networks.

Han Jihui J Li Wei W Deng Weibing W

Scientific reports 20161213

Aiming at improving the efficiency and accuracy of community detection in complex networks, we proposed a new algorithm, which is based on the idea that communities could be detected from subnetworks by comparing the internal and external cohesion of each subnetwork. In our method, similar nodes are firstly gathered into meta-communities, which are then decided to be retained or merged through a multilevel label propagation process, until all of them meet our community criterion. Our algorithm r ...[more]

PMID: 27958395

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Project description:The visual exploration and analysis of biomolecular networks is of paramount importance for identifying hidden and complex interaction patterns among proteins. Although many tools have been proposed for this task, they are mainly focused on the query and visualization of a single protein with its neighborhood. The global exploration of the entire network and the interpretation of its underlying structure still remains difficult, mainly due to the excessively large size of the biomolecular networks. In this paper we propose a novel multi-resolution representation and exploration approach that exploits hierarchical community detection algorithms for the identification of communities occurring in biomolecular networks. The proposed graphical rendering combines two types of nodes (protein and communities) and three types of edges (protein-protein, community-community, protein-community), and displays communities at different resolutions, allowing the user to interactively zoom in and out from different levels of the hierarchy. Links among communities are shown in terms of relationships and functional correlations among the biomolecules they contain. This form of navigation can be also combined by the user with a vertex centric visualization for identifying the communities holding a target biomolecule. Since communities gather limited-size groups of correlated proteins, the visualization and exploration of complex and large networks becomes feasible on off-the-shelf computer machines. The proposed graphical exploration strategies have been implemented and integrated in UNIPred-Web, a web application that we recently introduced for combining the UNIPred algorithm, able to address both integration and protein function prediction in an imbalance-aware fashion, with an easy to use vertex-centric exploration of the integrated network. The tool has been deeply amended from different standpoints, including the prediction core algorithm. Several tests on networks of different size and connectivity have been conducted to show off the vast potential of our methodology; moreover, enrichment analyses have been performed to assess the biological meaningfulness of detected communities. Finally, a CoV-human network has been embedded in the system, and a corresponding case study presented, including the visualization and the prediction of human host proteins that potentially interact with SARS-CoV2 proteins.

Project description:MotivationWith the wide availability of single-cell RNA-seq (scRNA-seq) technology, population-scale scRNA-seq datasets across multiple individuals and time points are emerging. While the initial investigations of these datasets tend to focus on standard analysis of clustering and differential expression, leveraging the power of scRNA-seq data at the personalized dynamic gene co-expression network level has the potential to unlock subject and/or time-specific network-level variation, which is critical for understanding phenotypic differences. Community detection from co-expression networks of multiple time points or conditions has been well-studied; however, none of the existing settings included networks from multiple subjects and multiple time points simultaneously. To address this, we develop Multi-subject Dynamic Community Detection (MuDCoD) for multi-subject community detection in personalized dynamic gene networks from scRNA-seq. MuDCoD builds on the spectral clustering framework and promotes information sharing among the networks of the subjects as well as networks at different time points. It clusters genes in the personalized dynamic gene networks and reveals gene communities that are variable or shared not only across time but also among subjects.ResultsEvaluation and benchmarking of MuDCoD against existing approaches reveal that MuDCoD effectively leverages apparent shared signals among networks of the subjects at individual time points, and performs robustly when there is no or little information sharing among the networks. Applications to population-scale scRNA-seq datasets of human-induced pluripotent stem cells during dopaminergic neuron differentiation and CD4+ T cell activation indicate that MuDCoD enables robust inference for identifying time-varying personalized gene modules. Our results illustrate how personalized dynamic community detection can aid in the exploration of subject-specific biological processes that vary across time.Availability and implementationMuDCoD is publicly available at https://github.com/bo1929/MuDCoD as a Python package. Implementation includes simulation and real-data experiments together with extensive documentation.

Dataset Information

Multi-resolution community detection in massive networks.

Publications

Multi-resolution community detection in massive networks.

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