Practical Applications of Deep Learning To Impute Heterogeneous Drug Discovery Data

Contemporary deep learning approaches still struggle to bring a useful improvement in the field of drug discovery because of the challenges of sparse, noisy, and heterogeneous data that are typically encountered in this context. We use a state-of-the-art deep learning method, Alchemite, to impute da...

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Bibliographic Details
Published in:Journal of chemical information and modeling 2020-06, Vol.60 (6), p.2848-2857
Main Authors: Irwin, Benedict W J, Levell, Julian R, Whitehead, Thomas M, Segall, Matthew D, Conduit, Gareth J
Format: Article
Language:English
Subjects:
Deep learning
Machine learning
Model accuracy
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Summary:Contemporary deep learning approaches still struggle to bring a useful improvement in the field of drug discovery because of the challenges of sparse, noisy, and heterogeneous data that are typically encountered in this context. We use a state-of-the-art deep learning method, Alchemite, to impute data from drug discovery projects, including multitarget biochemical activities, phenotypic activities in cell-based assays, and a variety of absorption, distribution, metabolism, and excretion (ADME) endpoints. The resulting model gives excellent predictions for activity and ADME endpoints, offering an average increase in of 0.22 versus quantitative structure-activity relationship methods. The model accuracy is robust to combining data across uncorrelated endpoints and projects with different chemical spaces, enabling a single model to be trained for all compounds and endpoints. We demonstrate improvements in accuracy on the latest chemistry and data when updating models with new data as an ongoing medicinal chemistry project progresses.
ISSN:1549-9596
1549-960X
DOI:10.1021/acs.jcim.0c00443