Literature DB >> 34645850

On the statistical significance of communities from weighted graphs.

Zengyou He1,2, Wenfang Chen3, Xiaoqi Wei3, Yan Liu3.   

Abstract

Community detection is a fundamental procedure in the analysis of network data. Despite decades of research, there is still no consensus on the definition of a community. To analytically test the realness of a candidate community in weighted networks, we present a general formulation from a significance testing perspective. In this new formulation, the edge-weight is modeled as a censored observation due to the noisy characteristics of real networks. In particular, the edge-weights of missing links are incorporated as well, which are specified to be zeros based on the assumption that they are truncated or unobserved. Thereafter, the community significance assessment issue is formulated as a two-sample test problem on censored data. More precisely, the Logrank test is employed to conduct the significance testing on two sets of augmented edge-weights: internal weight set and external weight set. The presented approach is evaluated on both weighted networks and un-weighted networks. The experimental results show that our method can outperform prior widely used evaluation metrics on the task of individual community validation.
© 2021. The Author(s).

Entities:  

Year:  2021        PMID: 34645850      PMCID: PMC8514603          DOI: 10.1038/s41598-021-99175-2

Source DB:  PubMed          Journal:  Sci Rep        ISSN: 2045-2322            Impact factor:   4.379


  17 in total

Review 1.  Community structure in social and biological networks.

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3.  A comparison of tests for the k-sample, non-decreasing alternative.

Authors:  J M Mahrer; R C Magel
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Authors:  John Palowitch; Shankar Bhamidi; Andrew B Nobel
Journal:  J Mach Learn Res       Date:  2018-04       Impact factor: 3.654

5.  Computing the statistical significance of optimized communities in networks.

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Journal:  Sci Rep       Date:  2019-12-05       Impact factor: 4.379

6.  MIPS: analysis and annotation of proteins from whole genomes.

Authors:  H W Mewes; C Amid; R Arnold; D Frishman; U Güldener; G Mannhaupt; M Münsterkötter; P Pagel; N Strack; V Stümpflen; J Warfsmann; A Ruepp
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

7.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

Authors:  Nevan J Krogan; Gerard Cagney; Haiyuan Yu; Gouqing Zhong; Xinghua Guo; Alexandr Ignatchenko; Joyce Li; Shuye Pu; Nira Datta; Aaron P Tikuisis; Thanuja Punna; José M Peregrín-Alvarez; Michael Shales; Xin Zhang; Michael Davey; Mark D Robinson; Alberto Paccanaro; James E Bray; Anthony Sheung; Bryan Beattie; Dawn P Richards; Veronica Canadien; Atanas Lalev; Frank Mena; Peter Wong; Andrei Starostine; Myra M Canete; James Vlasblom; Samuel Wu; Chris Orsi; Sean R Collins; Shamanta Chandran; Robin Haw; Jennifer J Rilstone; Kiran Gandi; Natalie J Thompson; Gabe Musso; Peter St Onge; Shaun Ghanny; Mandy H Y Lam; Gareth Butland; Amin M Altaf-Ul; Shigehiko Kanaya; Ali Shilatifard; Erin O'Shea; Jonathan S Weissman; C James Ingles; Timothy R Hughes; John Parkinson; Mark Gerstein; Shoshana J Wodak; Andrew Emili; Jack F Greenblatt
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8.  Finding statistically significant communities in networks.

Authors:  Andrea Lancichinetti; Filippo Radicchi; José J Ramasco; Santo Fortunato
Journal:  PLoS One       Date:  2011-04-29       Impact factor: 3.240

9.  Up-to-date catalogues of yeast protein complexes.

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10.  Gene Ontology annotations at SGD: new data sources and annotation methods.

Authors:  Eurie L Hong; Rama Balakrishnan; Qing Dong; Karen R Christie; Julie Park; Gail Binkley; Maria C Costanzo; Selina S Dwight; Stacia R Engel; Dianna G Fisk; Jodi E Hirschman; Benjamin C Hitz; Cynthia J Krieger; Michael S Livstone; Stuart R Miyasato; Robert S Nash; Rose Oughtred; Marek S Skrzypek; Shuai Weng; Edith D Wong; Kathy K Zhu; Kara Dolinski; David Botstein; J Michael Cherry
Journal:  Nucleic Acids Res       Date:  2007-11-03       Impact factor: 16.971

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