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Simplified Swarm Optimization-Based Function Module Detection in Protein–Protein Interaction Networks

College of Mathematics and Computer Science, Fuzhou University, Fuzhou 350116, China
Fujian Key Laboratory of Network Computing and Intelligent Information Processing, Fuzhou 350116, China
College of Computer and Information, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Author to whom correspondence should be addressed.
Academic Editors: Wenbing Zhao, Xiong Luo and Tie Qiu
Appl. Sci. 2017, 7(4), 412;
Received: 12 February 2017 / Revised: 13 April 2017 / Accepted: 14 April 2017 / Published: 19 April 2017
(This article belongs to the Special Issue Smart Healthcare)
PDF [1284 KB, uploaded 19 April 2017]


Proteomics research has become one of the most important topics in the field of life science and natural science. At present, research on protein–protein interaction networks (PPIN) mainly focuses on detecting protein complexes or function modules. However, existing approaches are either ineffective or incomplete. In this paper, we investigate detection mechanisms of functional modules in PPIN, including open database, existing detection algorithms, and recent solutions. After that, we describe the proposed approach based on the simplified swarm optimization (SSO) algorithm and the knowledge of Gene Ontology (GO). The proposed solution implements the SSO algorithm for clustering proteins with similar function, and imports biological gene ontology knowledge for further identifying function complexes and improving detection accuracy. Furthermore, we use four different categories of species datasets for experiment: fruitfly, mouse, scere, and human. The testing and analysis result show that the proposed solution is feasible, efficient, and could achieve a higher accuracy of prediction than existing approaches. View Full-Text
Keywords: protein–protein interaction networks; protein function module; simplified swarm optimization protein–protein interaction networks; protein function module; simplified swarm optimization

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Zheng, X.; Wu, L.; Ye, S.; Chen, R. Simplified Swarm Optimization-Based Function Module Detection in Protein–Protein Interaction Networks. Appl. Sci. 2017, 7, 412.

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