ATHENA optimization: The effect of initial parameter settings across different genetic models

Emily R. Holzinger, Scott M. Dudek, Eric C. Torstenson, Marylyn D. Ritchie

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

5 Citations (Scopus)

Abstract

Rapidly advancing technology has allowed for the generation of massive amounts data assessing variation across the human genome. One analysis method for this type of data is the genome-wide association study (GWAS) where each variation is assessed individually for association to disease. While these studies have elucidated novel etiology, much of the variation due to genetics remains unexplained. One hypothesis is that some of the variation lies in gene-gene interactions. An impediment to testing for interactions is the infeasibility of exhaustively searching all multi-locus models. Novel methods are being developed that perform a non-exhaustive search. Because these methods are new to genetic studies, rigorous parameter optimization is necessary. Here, we assess genotype encodings, function sets, and cross-over in two algorithms which use grammatical evolution to optimize neural networks or symbolic regression formulas in the ATHENA software package. Our results show that the effect of these parameters is highly dependent on the underlying disease model.

Original languageEnglish (US)
Title of host publicationEvolutionary Computation, Machine Learning and Data Mining in Bioinformatics - 9th European Conference, EvoBIO 2011, Proceedings
Pages48-58
Number of pages11
DOIs
StatePublished - May 13 2011
Event9th European Conference on Evolutionary Computation, Machine Learning, and Data Mining in Bioinformatics, EvoBIO 2011 - Torino, Italy
Duration: Apr 27 2011Apr 29 2011

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6623 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other9th European Conference on Evolutionary Computation, Machine Learning, and Data Mining in Bioinformatics, EvoBIO 2011
CountryItaly
CityTorino
Period4/27/114/29/11

Fingerprint

Genes
Optimization
Genome
Grammatical Evolution
Gene
Symbolic Regression
Infeasibility
Parameter Optimization
Genotype
Interaction
Software Package
Software packages
Model
Crossover
Locus
Encoding
Optimise
Neural Networks
Neural networks
Testing

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Holzinger, E. R., Dudek, S. M., Torstenson, E. C., & Ritchie, M. D. (2011). ATHENA optimization: The effect of initial parameter settings across different genetic models. In Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics - 9th European Conference, EvoBIO 2011, Proceedings (pp. 48-58). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6623 LNCS). https://doi.org/10.1007/978-3-642-20389-3_5
Holzinger, Emily R. ; Dudek, Scott M. ; Torstenson, Eric C. ; Ritchie, Marylyn D. / ATHENA optimization : The effect of initial parameter settings across different genetic models. Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics - 9th European Conference, EvoBIO 2011, Proceedings. 2011. pp. 48-58 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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Holzinger, ER, Dudek, SM, Torstenson, EC & Ritchie, MD 2011, ATHENA optimization: The effect of initial parameter settings across different genetic models. in Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics - 9th European Conference, EvoBIO 2011, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 6623 LNCS, pp. 48-58, 9th European Conference on Evolutionary Computation, Machine Learning, and Data Mining in Bioinformatics, EvoBIO 2011, Torino, Italy, 4/27/11. https://doi.org/10.1007/978-3-642-20389-3_5

ATHENA optimization : The effect of initial parameter settings across different genetic models. / Holzinger, Emily R.; Dudek, Scott M.; Torstenson, Eric C.; Ritchie, Marylyn D.

Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics - 9th European Conference, EvoBIO 2011, Proceedings. 2011. p. 48-58 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6623 LNCS).

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

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Holzinger ER, Dudek SM, Torstenson EC, Ritchie MD. ATHENA optimization: The effect of initial parameter settings across different genetic models. In Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics - 9th European Conference, EvoBIO 2011, Proceedings. 2011. p. 48-58. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-642-20389-3_5