GP on SPMD parallel graphics hardware for mega Bioinformatics data mining

Authors:
W. B. Langdon;A. P. Harrison
Affiliations:
University of Essex, Mathematical and Biological Sciences, Wivenhoe Park, CO4 3SQ, Colchester, UK;University of Essex, Mathematical and Biological Sciences, Wivenhoe Park, CO4 3SQ, Colchester, UK
Venue:
Soft Computing - A Fusion of Foundations, Methodologies and Applications - Special issue (1143 - 1198) " Distributed Bioinspired Algorithms"; Guest editors: F. Fernández de Vega, E. Cantú-Paz
Year:
2008

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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.