Particle swarm optimization artificial intelligence technique for gene signature discovery in transcriptomic cohorts

Ross G. Murphy, Alan Gilmore, Seedevi Senevirathne, Paul G. O'Reilly, Melissa LaBonte Wilson, Suneil Jain, Darragh G. McArt

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)
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Abstract

The development of gene signatures is key for delivering personalized medicine, despite only a few signatures being available for use in the clinic for cancer patients. Gene signature discovery tends to revolve around identifying a single signature. However, it has been shown that various highly predictive signatures can be produced from the same dataset. This study assumes that the presentation of top ranked signatures will allow greater efforts in the selection of gene signatures for validation on external datasets and for their clinical translation. Particle swarm optimization (PSO) is an evolutionary algorithm often used as a search strategy and largely represented as binary PSO (BPSO) in this domain. BPSO, however, fails to produce succinct feature sets for complex optimization problems, thus affecting its overall runtime and optimization performance. Enhanced BPSO (EBPSO) was developed to overcome these shortcomings. Thus, this study will validate unique candidate gene signatures for different underlying biology from EBPSO on transcriptomics cohorts. EBPSO was consistently seen to be as accurate as BPSO with substantially smaller feature signatures and significantly faster runtimes. 100% accuracy was achieved in all but two of the selected data sets. Using clinical transcriptomics cohorts, EBPSO has demonstrated the ability to identify accurate, succinct, and significantly prognostic signatures that are unique from one another. This has been proposed as a promising alternative to overcome the issues regarding traditional single gene signature generation. Interpretation of key genes within the signatures provided biological insights into the associated functions that were well correlated to their cancer type.
Original languageEnglish
Pages (from-to)5547-5563
Number of pages17
JournalComputational and Structural Biotechnology Journal
Volume20
Early online date26 Sept 2022
DOIs
Publication statusPublished (in print/issue) - 11 Oct 2022

Keywords

  • Particle swarm optimisat
  • Artificial Intelligence
  • Machine Learning
  • Cancer
  • Transcriptomics
  • Biomarker discovery

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