Identifying interacting SNPs with parallel fish-agent based logic regression

Jiayin Wang, Jin Zhang, Yufeng Wu

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

3 Scopus citations

Abstract

Understanding the genotype-phenotype association is a fundamental problem in genetics. A major open problem in mapping complex traits is identifying a set of interacting genetic variants (such as single nucleotide polymorphisms or SNPs) that influence disease susceptibility. Logic regression (LR) is a statistical approach that has been proposed to model interactions of SNPs. Several LR-based association detection approaches have been developed in the past. However, existing LR-based approaches are insufficient in handling noisy and increasingly larger data. In this paper, we first develop a relational clustering approach for handling noisy data, where we reduce noise by filtering out unrelated SNPs. We then propose a parallel fish-agent LR approach to speed up the computation. The basic idea of our approach is using multiple fish-agents that explore the model space independently. At each iteration, agents in the same or different clusters communicate with others to achieve faster convergence to the global optimal solutions. Simulation results show that our approach significantly speeds up the LR computation over existing approaches. Also, our results show that our approach achieves good performance in dealing with noise.

Original languageEnglish
Title of host publication2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011
Pages171-177
Number of pages7
DOIs
StatePublished - Apr 14 2011
Externally publishedYes
Event1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011 - Orlando, FL, United States
Duration: Feb 3 2011Feb 5 2011

Publication series

Name2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011

Conference

Conference1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011
CountryUnited States
CityOrlando, FL
Period02/3/1102/5/11

Keywords

  • Clustering
  • Genotype-phenotype association
  • Logic regression
  • Parallel computing
  • Swarm intelligence method

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  • Cite this

    Wang, J., Zhang, J., & Wu, Y. (2011). Identifying interacting SNPs with parallel fish-agent based logic regression. In 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011 (pp. 171-177). [5729874] (2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011). https://doi.org/10.1109/ICCABS.2011.5729874