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Gene selection using pyramid gravitational search algorithm

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  • Amirhossein Tahmouresi
  • Esmat Rashedi
  • Mohammad Mehdi Yaghoobi
  • Masoud Rezaei

Abstract

Genetics play a prominent role in the development and progression of malignant neoplasms. Identification of the relevant genes is a high-dimensional data processing problem. Pyramid gravitational search algorithm (PGSA), a hybrid method in which the number of genes is cyclically reduced is proposed to conquer the curse of dimensionality. PGSA consists of two elements, a filter and a wrapper method (inspired by the gravitational search algorithm) which iterates through cycles. The genes selected in each cycle are passed on to the subsequent cycles to further reduce the dimension. PGSA tries to maximize the classification accuracy using the most informative genes while reducing the number of genes. Results are reported on a multi-class microarray gene expression dataset for breast cancer. Several feature selection algorithms have been implemented to have a fair comparison. The PGSA ranked first in terms of accuracy (84.5%) with 73 genes. To check if the selected genes are meaningful in terms of patient’s survival and response to therapy, protein-protein interaction network analysis has been applied on the genes. An interesting pattern was emerged when examining the genetic network. HSP90AA1, PTK2 and SRC genes were amongst the top-rated bottleneck genes, and DNA damage, cell adhesion and migration pathways are highly enriched in the network.

Suggested Citation

  • Amirhossein Tahmouresi & Esmat Rashedi & Mohammad Mehdi Yaghoobi & Masoud Rezaei, 2022. "Gene selection using pyramid gravitational search algorithm," PLOS ONE, Public Library of Science, vol. 17(3), pages 1-15, March.
    • Handle: RePEc:plo:pone00:0265351
    DOI: 10.1371/journal.pone.0265351
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    References listed on IDEAS

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    1. Shams, Masumeh & Rashedi, Esmat & Hakimi, Ahmad, 2015. "Clustered-gravitational search algorithm and its application in parameter optimization of a low noise amplifier," Applied Mathematics and Computation, Elsevier, vol. 258(C), pages 436-453.
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