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Efficiently Detecting Protein Complexes from Protein Interaction Networks via Alternating Direction Method of Multipliers

文献类型：期刊论文

作者Hu, Lun3; Yuan, Xiaohui3; Liu, Xing3; Xiong, Shengwu3; Luo, Xin1,2
刊名IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
出版日期2019-11-01
卷号16期号:6页码:1922-1935
关键词Protein complex protein interaction network alternating direction method of multipliers efficiency
ISSN号1545-5963
DOI10.1109/TCBB.2018.2844256
通讯作者Xiong, Shengwu(xiongsw@whut.edu.cn) ; Luo, Xin(luoxin21@cigit.ac.cn)
英文摘要Protein complexes are crucial in improving our understanding of the mechanisms employed by proteins. Various computational algorithms have thus been proposed to detect protein complexes from protein interaction networks. However, given massive protein interactome data obtained by high-throughput technologies, existing algorithms, especially those with additionally consideration of biological information of proteins, either have low efficiency in performing their tasks or suffer from limited effectiveness. For addressing this issue, this work proposes to detect protein complexes from a protein interaction network with high efficiency and effectiveness. To do so, the original detection task is first formulated into an optimization problem according to the intuitive properties of protein complexes. After that, the framework of alternating direction method of multipliers is applied to decompose this optimization problem into several subtasks, which can be subsequently solved in a separate and parallel manner. An algorithm for implementing this solution is then developed. Experimental results on five large protein interaction networks demonstrated that compared to state-of-the-art protein complex detection algorithms, our algorithm outperformed them in terms of both effectiveness and efficiency. Moreover, as number of parallel processes increases, one can expect an even higher computational efficiency for the proposed algorithm with no compromise on effectiveness.
资助项目National Natural Science Foundation of China[61602352] ; National Natural Science Foundation of China[61772493] ; National Natural Science Foundation of China[61702387] ; Hubei Natural Science Foundation[2016CFB173] ; Hubei Natural Science Foundation[2017CFB302] ; Pioneer Hundred Talents Program of the Chinese Academy of Sciences ; Key Technical Innovation Project of Hubei[2017AAA122]
WOS研究方向Biochemistry & Molecular Biology ; Computer Science ; Mathematics
语种英语
WOS记录号WOS:000507924300014
出版者IEEE COMPUTER SOC
源URL[http://119.78.100.138/handle/2HOD01W0/10219]  
专题中国科学院重庆绿色智能技术研究院
通讯作者Xiong, Shengwu; Luo, Xin
作者单位1.Chinese Acad Sci, Chongqing Inst Green & Intelligent Technol, Chongqing Key Lab Big Data & Intelligent Comp, Chongqing 400714, Peoples R China
2.Chinese Acad Sci, Chongqing Engn Res Ctr Big Data Applicat Smart Ci, Chongqing Inst Green & Intelligent Technol, Chongqing 400714, Peoples R China
3.Wuhan Univ Technol, Sch Comp Sci & Technol, Wuhan 430070, Peoples R China
推荐引用方式
GB/T 7714		 Hu, Lun,Yuan, Xiaohui,Liu, Xing,et al. Efficiently Detecting Protein Complexes from Protein Interaction Networks via Alternating Direction Method of Multipliers[J]. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,2019,16(6):1922-1935.
APA Hu, Lun,Yuan, Xiaohui,Liu, Xing,Xiong, Shengwu,&Luo, Xin.(2019).Efficiently Detecting Protein Complexes from Protein Interaction Networks via Alternating Direction Method of Multipliers.IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,16(6),1922-1935.
MLA Hu, Lun,et al."Efficiently Detecting Protein Complexes from Protein Interaction Networks via Alternating Direction Method of Multipliers".IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 16.6(2019):1922-1935.

入库方式： OAI收割

来源：重庆绿色智能技术研究院

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