Parallel multi-objective optimization for high-order epistasis detection

Daniel Gallego-Sánchez, José M. Granado-Criado, Sergio Santander-Jiménez, Álvaro Rubio-Largo, Miguel A. Vega-Rodríguez

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

3 Citations (Scopus)

Abstract

Many studies have shown that there is a direct relationship between Single Nucleotide Polymorphisms (SNPs) and the appearance of complex diseases, such as Alzheimer’s or Parkinson’s. However, recent advances in the Study of the Complete Genome Association indicate that the relationship between SNPs and these diseases goes beyond a simple one-to-one relationship, that is, the appearance of multiple SNPs (epistasis) influences the appearance of these diseases. In this sense, this work proposes the application of the NSGA-II multi-objective algorithm for the detection of epistasis of multiple loci in a database with 31,341 SNPs. Moreover, a parallel study has been performed to reduce the execution time of this problem. Our implementation not only achieves a reasonable good parallel performance and scalability, but also its biological significance overcomes other approaches published in the literature.

Original languageEnglish
Title of host publicationAlgorithms and Architectures for Parallel Processing - 17th International Conference, ICA3PP 2017, Proceedings
EditorsShadi Ibrahim, Zheng Yan, Kim-Kwang Raymond Choo, Witold Pedrycz
PublisherSpringer Verlag
Pages523-532
Number of pages10
ISBN (Print)9783319654812
DOIs
Publication statusPublished - 1 Jan 2017
Event17th International Conference on Algorithms and Architectures for Parallel Processing, ICA3PP 2017 - Helsinki, Finland
Duration: 21 Aug 201723 Aug 2017

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10393 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference17th International Conference on Algorithms and Architectures for Parallel Processing, ICA3PP 2017
CountryFinland
CityHelsinki
Period21/08/1723/08/17

Keywords

  • Epistasis
  • NSGA-II
  • Parallelism
  • SNP

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