An enhancement of binary particle swarm optimization for gene selection in classifying cancer classes

Mohd Saberi Mohamad, Sigeru Omatu, Safaai Deris, Michifumi Yoshioka, Afnizanfaizal Abdullah, Zuwairie Ibrahim

Research output: Contribution to journalArticlepeer-review

40 Citations (Scopus)

Abstract

Background: Gene expression data could likely be a momentous help in the progress of proficient cancer diagnoses and classification platforms. Lately, many researchers analyze gene expression data using diverse computational intelligence methods, for selecting a small subset of informative genes from the data for cancer classification. Many computational methods face difficulties in selecting small subsets due to the small number of samples compared to the huge number of genes (high-dimension), irrelevant genes, and noisy genes.Methods: We propose an enhanced binary particle swarm optimization to perform the selection of small subsets of informative genes which is significant for cancer classification. Particle speed, rule, and modified sigmoid function are introduced in this proposed method to increase the probability of the bits in a particle's position to be zero. The method was empirically applied to a suite of ten well-known benchmark gene expression data sets.Results: The performance of the proposed method proved to be superior to other previous related works, including the conventional version of binary particle swarm optimization (BPSO) in terms of classification accuracy and the number of selected genes. The proposed method also requires lower computational time compared to BPSO.

Original languageEnglish
Article number15
JournalAlgorithms for Molecular Biology
Volume8
Issue number1
DOIs
Publication statusPublished - Apr 24 2013
Externally publishedYes

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology
  • Computational Theory and Mathematics
  • Applied Mathematics

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