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Hu K, Xiang J, Yu YX, Tang L, Xiang Q, Li JM, Tang YH, Chen YJ, Zhang Y. Significance-based multi-scale method for network community detection and its application in disease-gene prediction. PLoS One 2020; 15:e0227244. [PMID: 32196490 PMCID: PMC7083276 DOI: 10.1371/journal.pone.0227244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/16/2019] [Indexed: 11/18/2022] Open
Abstract
Community detection in complex networks is an important issue in network science. Several statistical measures have been proposed and widely applied to detecting the communities in various complex networks. However, due to the lack of flexibility resolution, some of them have to encounter the resolution limit and thus are not compatible with multi-scale structures of complex networks. In this paper, we investigated a statistical measure of interest for community detection, Significance [Sci. Rep. 3 (2013) 2930], and analyzed its critical behaviors based on the theoretical derivation of critical number of communities and the phase diagram in community-partition transition. It was revealed that Significance exhibits far higher resolution than the traditional Modularity when the intra- and inter-link densities of communities are obviously different. Following the critical analysis, we developed a multi-resolution version of Significance for identifying communities in the multi-scale networks. Experimental tests in several typical networks have been performed and confirmed that the generalized Significance can be competent for the multi-scale communities detection. Moreover, it can effectively relax the first- and second-type resolution limits. Finally, we displayed an important potential application of the multi-scale Significance in computational biology: disease-gene identification, showing that extracting information from the perspective of multi-scale module mining is helpful for disease gene prediction.
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Affiliation(s)
- Ke Hu
- School of Physics and Optoelectronic Engineering, Xiangtan University, Xiangtan, Hunan, People’s Republic of China
| | - Ju Xiang
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, People’s Republic of China
- School of Basic Medical Sciences, Changsha Medical University, Changsha, Hunan, People’s Republic of China
| | - Yun-Xia Yu
- School of Physics and Optoelectronic Engineering, Xiangtan University, Xiangtan, Hunan, People’s Republic of China
| | - Liang Tang
- School of Basic Medical Sciences, Changsha Medical University, Changsha, Hunan, People’s Republic of China
| | - Qin Xiang
- School of Basic Medical Sciences, Changsha Medical University, Changsha, Hunan, People’s Republic of China
| | - Jian-Ming Li
- School of Basic Medical Sciences, Changsha Medical University, Changsha, Hunan, People’s Republic of China
- Department of Neurology, Xiang-ya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Department of Rehabilitation, Xiangya Boai Rehabilitation Hospital, Changsha, Hunan, People’s Republic of China
- Department of Neurology, Nanhua Affiliated Hospital, University of South China, Hengyang, Hunan, People’s Republic of China
| | - Yong-Hong Tang
- Department of Neurology, Nanhua Affiliated Hospital, University of South China, Hengyang, Hunan, People’s Republic of China
| | - Yong-Jun Chen
- Department of Neurology, Nanhua Affiliated Hospital, University of South China, Hengyang, Hunan, People’s Republic of China
| | - Yan Zhang
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, People’s Republic of China
- School of Basic Medical Sciences, Changsha Medical University, Changsha, Hunan, People’s Republic of China
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