Theoretical and Computational Chemistry

Building Attention and Edge Convolution Neural Networks for Bioactivity and Physical-Chemical Property Prediction

Abstract

We introduce Attention and Edge Memory schemes to the existing Message Passing Neural Network framework for graph convolution, and benchmark our approaches against eight different physical-chemical and bioactivity datasets from the literature. We remove the need to introduce a priori knowledge of the task and chemical descriptor calculation by using only fundamental graph-derived properties. Our results consistently perform on-par with other state-of-the-art machine learning approaches, and set a new standard on sparse multi-task virtual screening targets. We also investigate model performance as a function of dataset preprocessing, and make some suggestions regarding hyperparameter selection.

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Updated author contributions.

Content

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Supplementary material

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Supplemental Information