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Enrichment of Extremely Noisy High-Throughput Screening Data Using a Naïve Bayes Classifier

Novartis Institute for Biomedical Research, Cambridge, MA meir.glick{at}pharma.novartis.com

Anthony E. Klon

Novartis Institute for Biomedical Research, Cambridge, MA

Pierre Acklin

Novartis Institute for Biomedical Research, Cambridge, MA

John W. Davies

Novartis Institute for Biomedical Research, Cambridge, MA

The noise level of a high-throughput screening (HTS) experiment depends on various factors such as the quality and robustness of the assay itself and the quality of the robotic platform. Screening of compound mixtures is noisier than screening single compounds per well. A classification model based on naïve Bayes (NB) may be used to enrich such data. The authors studied the ability of the NB classifier to prioritize noisy primary HTS data of compound mixtures (5 compounds/well) in 4 campaigns in which the percentage of noise presumed to be inactive compounds ranged between 81% and 91%. The top 10% of the compounds suggested by the classifier captured between 26% and 45% of the active compounds. These results are reasonable and useful, considering the poor quality of the training set and the short computing time that is needed to build and deploy the classifier. (Journal of Biomolecular Screening 2004:32-36)

Key Words: high-throughput screening • compound mixtures • molecular similarity • extended-connectivity fingerprints • naïve Bayes

Journal of Biomolecular Screening, Vol. 9, No. 1, 32-36 (2004)
DOI: 10.1177/1087057103260590


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