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FAACOSE: A Fast Adaptive Ant Colony Optimization Algorithm for Detecting SNP Epistasis

Author

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  • Lin Yuan
  • Chang-An Yuan
  • De-Shuang Huang

Abstract

The epistasis is prevalent in the SNP interactions. Some of the existing methods are focused on constructing models for two SNPs. Other methods only find the SNPs in consideration of one-objective function. In this paper, we present a unified fast framework integrating adaptive ant colony optimization algorithm with multiobjective functions for detecting SNP epistasis in GWAS datasets. We compared our method with other existing methods using synthetic datasets and applied the proposed method to Late-Onset Alzheimer’s Disease dataset. Our experimental results show that the proposed method outperforms other methods in epistasis detection, and the result of real dataset contributes to the research of mechanism underlying the disease.

Suggested Citation

  • Lin Yuan & Chang-An Yuan & De-Shuang Huang, 2017. "FAACOSE: A Fast Adaptive Ant Colony Optimization Algorithm for Detecting SNP Epistasis," Complexity, Hindawi, vol. 2017, pages 1-10, September.
    • Handle: RePEc:hin:complx:5024867
    DOI: 10.1155/2017/5024867
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    References listed on IDEAS

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    1. Lin Zhu & Zhu-Hong You & De-Shuang Huang & Bing Wang, 2013. "t-LSE: A Novel Robust Geometric Approach for Modeling Protein-Protein Interaction Networks," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-13, April.
    2. Teri A. Manolio & Francis S. Collins & Nancy J. Cox & David B. Goldstein & Lucia A. Hindorff & David J. Hunter & Mark I. McCarthy & Erin M. Ramos & Lon R. Cardon & Aravinda Chakravarti & Judy H. Cho &, 2009. "Finding the missing heritability of complex diseases," Nature, Nature, vol. 461(7265), pages 747-753, October.
    3. Wei Zhang & Jun Zhu & Eric E Schadt & Jun S Liu, 2010. "A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules," PLOS Computational Biology, Public Library of Science, vol. 6(1), pages 1-10, January.
    4. Bryan N Howie & Peter Donnelly & Jonathan Marchini, 2009. "A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies," PLOS Genetics, Public Library of Science, vol. 5(6), pages 1-15, June.
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    Cited by:

    1. Fang Liu & Hua Gong & Ligang Cai & Ke Xu, 2019. "Prediction of Ammunition Storage Reliability Based on Improved Ant Colony Algorithm and BP Neural Network," Complexity, Hindawi, vol. 2019, pages 1-13, March.

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