Incorporating domain knowledge into evolutionary computing for discovering gene-gene interaction

Stephen D. Turner, Scott M. Dudek, Marylyn Deriggi Ritchie

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Understanding the genetic underpinnings of common heritable human traits has enormous public health benefits with implications for risk prediction, development of novel drugs, and personalized medicine. Many complex human traits are highly heritable, yet little of the variability in such traits can be accounted for by examining single DNA variants at a time. Seldom explored non-additive gene-gene interactions are thought to be one source of this "missing" heritability. Approaches that can account for this complexity are more aptly suited to find combinations of genetic and environmental exposures that can lead to disease. Stochastic methods employing evolutionary algorithms have demonstrated promise in being able to detect and model gene-gene interactions that influence human traits, yet the search space is nearly infinite because of the vast number of variables collected in contemporary human genetics studies. In this work we assess the performance and feasibility of sensible initialization of an evolutionary algorithm using domain knowledge.

Original languageEnglish (US)
Title of host publicationParallel Problem Solving from Nature, PPSN XI - 11th International Conference, Proceedings
Pages394-403
Number of pages10
EditionPART 1
DOIs
StatePublished - Nov 12 2010
Event11th International Conference on Parallel Problem Solving from Nature, PPSN 2010 - Krakow, Poland
Duration: Sep 11 2010Sep 15 2010

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
NumberPART 1
Volume6238 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other11th International Conference on Parallel Problem Solving from Nature, PPSN 2010
CountryPoland
CityKrakow
Period9/11/109/15/10

Fingerprint

Evolutionary Computing
Domain Knowledge
Genes
Gene
Interaction
Evolutionary algorithms
Evolutionary Algorithms
Heritability
Stochastic Methods
Public Health
Public health
Initialization
Medicine
Search Space
Drugs
DNA
Human
Prediction

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Turner, S. D., Dudek, S. M., & Ritchie, M. D. (2010). Incorporating domain knowledge into evolutionary computing for discovering gene-gene interaction. In Parallel Problem Solving from Nature, PPSN XI - 11th International Conference, Proceedings (PART 1 ed., pp. 394-403). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6238 LNCS, No. PART 1). https://doi.org/10.1007/978-3-642-15844-5_40
Turner, Stephen D. ; Dudek, Scott M. ; Ritchie, Marylyn Deriggi. / Incorporating domain knowledge into evolutionary computing for discovering gene-gene interaction. Parallel Problem Solving from Nature, PPSN XI - 11th International Conference, Proceedings. PART 1. ed. 2010. pp. 394-403 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); PART 1).
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Turner, SD, Dudek, SM & Ritchie, MD 2010, Incorporating domain knowledge into evolutionary computing for discovering gene-gene interaction. in Parallel Problem Solving from Nature, PPSN XI - 11th International Conference, Proceedings. PART 1 edn, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), no. PART 1, vol. 6238 LNCS, pp. 394-403, 11th International Conference on Parallel Problem Solving from Nature, PPSN 2010, Krakow, Poland, 9/11/10. https://doi.org/10.1007/978-3-642-15844-5_40

Incorporating domain knowledge into evolutionary computing for discovering gene-gene interaction. / Turner, Stephen D.; Dudek, Scott M.; Ritchie, Marylyn Deriggi.

Parallel Problem Solving from Nature, PPSN XI - 11th International Conference, Proceedings. PART 1. ed. 2010. p. 394-403 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6238 LNCS, No. PART 1).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Turner SD, Dudek SM, Ritchie MD. Incorporating domain knowledge into evolutionary computing for discovering gene-gene interaction. In Parallel Problem Solving from Nature, PPSN XI - 11th International Conference, Proceedings. PART 1 ed. 2010. p. 394-403. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); PART 1). https://doi.org/10.1007/978-3-642-15844-5_40