Improved Ant Colony Optimization for Detecting Functional Modules in Protein-Protein Interaction Networks

Ji, Junzhong; Liu, Zhijun; Zhang, Aidong; Jiao, Lang; Liu, Chunnian

doi:10.1007/978-3-642-34041-3_57

Cited by 14 publications

(2 citation statements)

References 21 publications

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“…In 2012, Ji introduced a new heuristic function, namely, the NACO-FDM [25] algorithm, to improve the process of ACO in searching for the optimal path. However, this algorithm easily falls into the local optimum.…”

Section: Existing Workmentioning

confidence: 99%

Simplified Swarm Optimization Based Function Modules Detection in Protein-to-Protein Interaction Networks

Zheng¹,

Wu²,

Shao-zhen

et al. 2017

Preprint

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Abstract. Proteomics research has become one of the most important topics in the fields of life science and natural science. At present, research on protein-protein interaction networks (PPINs) mainly focuses on detecting protein complexes or function modules. However, existing approaches are either ineffective or incomplete. In this paper, we investigate function module detection mechanisms in PPIN, including open databases, existing detection algorithms and recent solutions. After that, we describe the proposed solution based on simplified swarm optimization (SSO) algorithm and gene ontology knowledge. The proposed solution implements 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 dataset 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.

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Section: Existing Workmentioning

confidence: 99%

Simplified Swarm Optimization Based Function Modules Detection in Protein-to-Protein Interaction Networks

Zheng¹,

Wu²,

Shao-zhen

et al. 2017

Preprint

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show abstract

“…The detection of protein function modules is an NP hard problem [28]. Since the PSO-related solution is efficient and has been implemented in different kinds of NP hard problems, we propose the enhancement of PSO, Simplified Swarm Optimization (SSO) algorithms, for implementation in the detection of protein function modules.…”

Section: Interaction Modelmentioning

confidence: 99%

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

Zheng

Shao-zhen

et al. 2017

Applied Sciences

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Abstract: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.

show abstract

Evolutionary Algorithms for Applications of Biological Networks: A Review

Liu

et al. 2021

Lecture Notes in Computer Science

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Improved Ant Colony Optimization for Detecting Functional Modules in Protein-Protein Interaction Networks

Cited by 14 publications

References 21 publications

Simplified Swarm Optimization Based Function Modules Detection in Protein-to-Protein Interaction Networks

Simplified Swarm Optimization Based Function Modules Detection in Protein-to-Protein Interaction Networks

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

Evolutionary Algorithms for Applications of Biological Networks: A Review

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