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ReGen: Optimizing Genetic Selection Algorithms for Heterogeneous Computing

Scott Kenneth Winkleblack
California Polytechnic State University
California Polytechnic State University, 2014

@article{winkleblack2014regen,

   title={ReGen: Optimizing Genetic Selection Al},

   author={Winkleblack, Scott},

   year={2014}

}

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GenSel is a genetic selection analysis tool used to determine which genetic markers are informational for a given trait. Performing genetic selection related analyses is a time consuming and computationally expensive task. Due to an expected increase in the number of genotyped individuals, analysis times will increase dramatically. Therefore, optimization efforts must be made to keep analysis times reasonable. This thesis focuses on optimizing one of GenSel’s underlying algorithms for heterogeneous computing. The resulting algorithm exposes task-level parallelism and data-level parallelism present but inaccessible in the original algorithm. The heterogeneous computing solution, ReGen, outperforms the optimized CPU implementation achieving a 1.84 times speedup.
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