Journal
JOURNAL OF CHEMICAL INFORMATION AND MODELING
Volume 49, Issue 12, Pages 2718-2725Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ci900337f
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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.
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