Active module identification in intracellular networks using a memetic algorithm with a new binary decoding scheme

BMC Genomics

Research

Zexuan Zhu¹  Guyu Hu²  Zhisong Pan²  Shan He³  Dong Li³ 

[1] College of Computer Science and Software Engineering, Shenzhen University, 518060, Shenzhen, China;PLA University of Science and Technology, 210007, Nanjing, China;School of Computer Science, University of Birmingham, B15 2TT, Birmingham, UK;

关键词: Memetic algorithm;    Module identification;    Connectedness;    Module size;   

DOI  :  10.1186/s12864-017-3495-y

来源: Springer

【 摘 要 】

BackgroundActive modules are connected regions in biological network which show significant changes in expression over particular conditions. The identification of such modules is important since it may reveal the regulatory and signaling mechanisms that associate with a given cellular response.ResultsIn this paper, we propose a novel active module identification algorithm based on a memetic algorithm. We propose a novel encoding/decoding scheme to ensure the connectedness of the identified active modules. Based on the scheme, we also design and incorporate a local search operator into the memetic algorithm to improve its performance.ConclusionThe effectiveness of proposed algorithm is validated on both small and large protein interaction networks.

【 授权许可】

CC BY   
© The Author(s) 2017

【 图 表 】

Fig. 2