Evolving GeneChip correlation predictors on parallel graphics hardware

—A GPU is used to datamine five million correlations between probes within Affymetrix HG-U133A probesets across 6685 human tissue samples from NCBI’s GEO database. These concordances are used as machine learning training data for genetic programming running on a Linux PC with a RapidMind OpenGL GLSL backend. GPGPU is used to identify technological factors influencing High Density Oligonuclotide Arrays (HDONA) performance. GP suggests mismatch (PM/MM) and Adenosine/Guanine ratio influence microarray quality. Initial results hint that Watson-Crick probe self hybridisation or folding is not important. Under GPGPGPU an nVidia GeForce 8800 GTX interprets 300 million GP primitives/second (300 MGPops, approx 8 GFLOPS).

• Type: Conference
• Year: 2008
• Where: CEC
• Authors: William B. Langdon
• Keywords: Artificial Intelligence, CEC 2008, Geforce 8800 Gtx, GP Suggests Mismatch, five Million Correlations