Imputation of Assay Bioactivity Data using Deep Learning
This paper was printed in the Journal of Chemical Information and Modeling.
Imputation of Assay Bioactivity Data Using Deep Learning
Whitehead TM*, Irwin BWJ, Hunt P, Segall MD, Conduit GJ** (*Intellegens, **Cavendish Laboratory)
J. Chem. Inf. Model. (2019) 59(3) pp. 1197-1204
We describe a novel deep learning neural network method and its application to impute assay pIC50 values. Unlike conventional machine learning approaches, this method is trained on sparse bioactivity data as input, typical of that found in public and commercial databases, enabling it to learn directly from correlations between activities measured in different assays.
In two case studies on public domain data sets we show that the neural network method outperforms traditional quantitative structure-activity relationship (QSAR) models and other leading approaches. Furthermore, by focussing on only the most confident predictions the accuracy is increased to R² > 0.9 using our method, as compared to R² = 0.44 when reporting all predictions.
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