Graph Neural Networks Pretraining Through Inherent Supervision for Molecular Property Prediction

Abstract

Recent global events have emphasized the importance of accelerating the drug discovery process. A way to deal with the issue is to use machine learning to increase the rate at which drugs are made available to the public. However, chemical labeled data for real-world applications is extremely scarce making traditional approaches less effective. A fruitful course of action for this challenge is to pretrain a model using related tasks with large enough datasets, with the next step being finetuning it for the desired task. This is challenging as creating these datasets requires labeled data or expert knowledge. To aid in solving this pressing issue, we introduce MISU - Molecular Inherent SUpervision, a unique method for pretraining graph neural networks for molecular property prediction. Our method leapfrogs past the need for labeled data or any expert knowledge by introducing three innovative components that utilize inherent properties of molecular graphs to induce information extraction at different scales, from the local neighborhood of an atom to substructures in the entire molecule. Our empirical results for six chemical-property-prediction tasks show that our method reaches state-of-the-art results compared to numerous baselines.