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Improving CUDA DNA Analysis Software with Genetic Programming

William B. Langdon, Brian Yee Hong Lam, Justyna Petke, Mark Harman
Department of Computer Science, University College London Gower Street, WC1E 6BT, UK
Genetic and Evolutionary Computation Conference (GECCO), 2015

@inproceedings{langdon2015improving,

   title={Improving CUDA DNA Analysis Software with Genetic Programming},

   author={Langdon, William B and Lam, Brian Yee Hong and Petke, Justyna and Harman, Mark},

   organization={GECCO},

   year={2015}

}

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We genetically improve BarraCUDA using a BNF grammar incorporating C scoping rules with GP. Barracuda maps next generation DNA sequences to the human genome using the Burrows-Wheeler algorithm (BWA) on nVidia Tesla parallel graphics hardware (GPUs). GI using phenotypic tabu search with manually grown code can graft new features giving more than 100 fold speed up on a performance critical kernel without loss of accuracy.
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  • Oleg John Konings

    Another great paper with well commented source code!

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