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GP on SPMD parallel graphics hardware for mega Bioinformatics data mining

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Abstract

We demonstrate a SIMD C++ genetic programming system on a single 128 node parallel nVidia GeForce 8800 GTX GPU under RapidMind’s GPGPU Linux software by predicting ten year+ outcome of breast cancer from a dataset containing a million inputs. NCBI GEO GSE3494 contains hundreds of Affymetrix HG-U133A and HG-U133B GeneChip biopsies. Multiple GP runs each with a population of 5 million programs winnow useful variables from the chaff at more than 500 million GPops per second. Sources available via FTP.

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  1. Mathematical and Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK

    W. B. Langdon & A. P. Harrison

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  1. W. B. Langdon
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  2. A. P. Harrison
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Correspondence to W. B. Langdon.

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Langdon, W.B., Harrison, A.P. GP on SPMD parallel graphics hardware for mega Bioinformatics data mining. Soft Comput 12, 1169–1183 (2008). https://doi.org/10.1007/s00500-008-0296-x

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