GPU accelerated support vector machines for mining high-throughput screening data.
Support Vector Machine (SVM), one of the most promising tools in chemical informatics, is time-consuming for mining large high-throughput screening (HTS) data sets. Here, we describe a parallelization of SVM-light algorithm on a graphic processor unit (GPU), using molecular fingerprints as descriptors and the Tanimoto index as kernel function. Comparison experiments based on six PubChem Bioassay data sets show that the GPU version is 43-104x faster than SVM-light for building classification models and 112-212x over SVM-light for building regression models.
Liao
Quan
Q
ChemExplorer Co. Ltd., 965 Halei Road, Shanghai 201203, People's Republic of China.
Wang
Jibo
J
Webster
Yue
Y
Watson
Ian A
IA
D000465:Algorithms; D001185:Artificial Intelligence; D003201:Computers; D057225:Data Mining / Q000379:methods*; D055808:Drug Discovery; D057166:High-Throughput Screening Assays / Q000379:methods*; D013997:Time Factors