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Publication Detail
Improving CUDA DNA Analysis Software with Genetic Programming
  • Publication Type:
    Conference
  • Authors:
    Langdon WB, Lam BYH, Petke J, Harman M
  • Publisher:
    ACM
  • Publication date:
    2015
  • Pagination:
    1063, 1070
  • Published proceedings:
    GECCO ’15: Proceedings of the 2015 on Genetic and Evolutionary Computation Conference
  • Editors:
    Silva S,Esparcia-Alcazar AI,Lopez-Ibanez M,Mostaghim S,Timmis J,Zarges C,Correia L,Soule T,Giacobini M,Urbanowicz R,Akimoto Y,Glasmachers T,Vega FFD,Hoover A,Larranaga P,Soto M,Cotta C,Pereira FB,Handl J,Koutnik J,Gaspar-Cunha A,Trautmann H,Mouret J-B,Risi S,Costa E,Schuetze O,Krawiec K,Moraglio A,Miller JF,Widera P,Cagnoni S,Merelo JJ,Hart E,Trujillo L,Kessentini M,Ochoa G,Chicano F,Doerr C
  • ISBN-13:
    978-1-4503-3472-3
  • Addresses:
    Madrid
  • Notes:
    organisation: SIGEVO publisher_address: New York, NY, USA keywords: genetic algorithms, genetic programming, genetic improvement, SBSE, Artificial Intelligence; Automatic Programming; Testing, Performance, Speedup, BarraCUDA, DNA sequence mapping, software, NVIDIA Tesla K40, CUDA, C++, GPU, Burrows-Wheeler algorithm, BWA, parallel computing, SIMD, phenotypic tabu search, genotypic tabu search, GPGPU, Bioinformatics, Software engineering, GP, GI, GGGP, Grow and Graft Genetic programming, Man and Machine Collaborative Development, Tabu, BNF grammar notes: See also \citeLangdon:RN1503. Slides: http://geneticimprovement2015.com/wp-content/uploads/2015/07/gi4gi.pdf http://www.cs.ucl.ac.uk/staff/W.Langdon/gecco2015/langdon_2015_gecco_slides.pdf Code http://www.cs.ucl.ac.uk/staff/W.Langdon/ftp/gp-code/barracuda_gp.tar.gz Incorporated code as barracuda release 0.7.105 can be downloaded from SourceForge: http://sourceforge.net/projects/seqbarracuda/ Also known as \cite2754652 GECCO-2015 A joint meeting of the twenty fourth international conference on genetic algorithms (ICGA-2015) and the twentith annual genetic programming conference (GP-2015)
Abstract
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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