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IEEE Transactions on Evolutionary Computation | Vol.20, Issue.6 | | Pages 874-891

IEEE Transactions on Evolutionary Computation

Cooperative Co-Evolutionary Module Identification With Application to Cancer Disease Module Discovery

Mirco Musolesi   John K. Heath   Qiang Huang   Shan He   Guanbo Jia   Zexuan Zhu   Daniel A. Tennant   Xin Yao   Ke Tang   Jing Liu  
Abstract

Module identification or community detection in complex networks has become increasingly important in many scientific fields because it provides insight into the relationship and interaction between network function and topology. In recent years, module identification algorithms based on stochastic optimization algorithms such as evolutionary algorithms have been demonstrated to be superior to other algorithms on small- to medium-scale networks. However, the scalability and resolution limit (RL) problems of these module identification algorithms have not been fully addressed, which impeded their application to real-world networks. This paper proposes a novel module identification algorithm called cooperative co-evolutionary module identification to address these two problems. The proposed algorithm employs a cooperative co-evolutionary framework to handle large-scale networks. We also incorporate a recursive partitioning scheme into the algorithm to effectively address the RL problem. The performance of our algorithm is evaluated on 12 benchmark complex networks. As a medical application, we apply our algorithm to identify disease modules that differentiate low- and high-grade glioma tumors to gain insights into the molecular mechanisms that underpin the progression of glioma. Experimental results show that the proposed algorithm has a very competitive performance compared with other state-of-the-art module identification algorithms.

Original Text (This is the original text for your reference.)

Cooperative Co-Evolutionary Module Identification With Application to Cancer Disease Module Discovery

Module identification or community detection in complex networks has become increasingly important in many scientific fields because it provides insight into the relationship and interaction between network function and topology. In recent years, module identification algorithms based on stochastic optimization algorithms such as evolutionary algorithms have been demonstrated to be superior to other algorithms on small- to medium-scale networks. However, the scalability and resolution limit (RL) problems of these module identification algorithms have not been fully addressed, which impeded their application to real-world networks. This paper proposes a novel module identification algorithm called cooperative co-evolutionary module identification to address these two problems. The proposed algorithm employs a cooperative co-evolutionary framework to handle large-scale networks. We also incorporate a recursive partitioning scheme into the algorithm to effectively address the RL problem. The performance of our algorithm is evaluated on 12 benchmark complex networks. As a medical application, we apply our algorithm to identify disease modules that differentiate low- and high-grade glioma tumors to gain insights into the molecular mechanisms that underpin the progression of glioma. Experimental results show that the proposed algorithm has a very competitive performance compared with other state-of-the-art module identification algorithms.

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Mirco Musolesi, John K. Heath, Qiang Huang,Shan He, Guanbo Jia, Zexuan Zhu, Daniel A. Tennant, Xin Yao, Ke Tang, Jing Liu,.Cooperative Co-Evolutionary Module Identification With Application to Cancer Disease Module Discovery. 20 (6),874-891.

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