GP on SPMD parallel graphics hardware for mega Bioinformatics data mining
Department of Computer Science, King’s College, London, Strand, London, WC2R 2LS, UK
Soft Computing – A Fusion of Foundations, Methodologies and Applications, Volume 12, Number 12, 1169-1183
@article{langdon2008gp,
title={GP on SPMD parallel graphics hardware for mega bioinformatics data mining},
author={Langdon, W.B. and Harrison, A.P.},
journal={Soft Computing-A Fusion of Foundations, Methodologies and Applications},
volume={12},
number={12},
pages={1169–1183},
issn={1432-7643},
year={2008},
publisher={Springer}
}
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.
January 21, 2011 by hgpu
