A gene selection algorithm using simplified swarm optimization with multi-filter ensemble technique

• Published in: Applied soft computing Vol. 100; p. 106994
• Main Authors: Lai, Chyh-Ming, Huang, Hsin-Ping
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.03.2021
• Subjects: Classification; Gene selection; MRMR; Multi-filter ensemble technique; Simplified swarm optimization; Support vector machine; Gene selection; Support vector machine; MRMR; Simplified swarm optimization; Multi-filter ensemble technique; Classification
• ISSN: 1568-4946; 1872-9681
• DOI: 10.1016/j.asoc.2020.106994

Gene expression data has been successfully applied to various purposes, especially for cancer classification. The challenges confronted by the development of effective classifiers for expression data are the curse of dimensionality and over-fitting. Gene selection is an efficient and effective method for overcoming the above difficulties and enhancing the predictive accuracy of a classifier. This work presents a hybrid gene selection method based on a novel multi-filter ensemble technique and simplified swarm optimization (SSO). This proposed method was comprised of two phases. In the first phase, the ensemble technique was developed via VIKOR to integrate the outcomes of multiple filters to preselect the most informative gene subset from the original dataset. In the second phase, SSO was tailored with a new gene pruning strategy, re-initialization scheme, and support vector machine as a wrapper to further search the optimal gene subset on the space of the candidate genes selected in the first phase. As evidence of the performance of the proposed method, extensive experiments on nineteen microarray datasets were carried out. The computational results compared favorably with well-known methods in the literature. Statistical analysis indicated that the proposed method was highly competitive and could be an effective tool for microarray analysis. •A VIKOR based multi-filter ensemble technique was proposed to preselect a compact gene subset.•A tailored simplified swarm optimization was proposed for solving the gene selection problem.•A gene pruning strategy was proposed to reinforce the local search ability of SSO.•Extensive experiments on nineteen microarray datasets were conducted.