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Workshop: AI for Science: Mind the Gaps

3D Pre-training improves GNNs for Molecular Property Prediction

Hannes Stärk · Dominique Beaini · Gabriele Corso · Prudencio Tossou · Christian Dallago · Stephan Günnemann · Pietro Lió


Molecular property prediction is one of the fastest-growing applications of deep learning with critical real-world impacts. Including 3D molecular structure as input to learned models improves their predictions for many molecular properties. However, this information is infeasible to compute at the scale required by most real-world applications. We propose pre-training a model to understand the geometry of molecules given only their 2D molecular graph. Using methods from self-supervised learning, we maximize the mutual information between a 3D summary vector and the representations of a Graph Neural Network (GNN) such that they contain latent 3D information. During fine-tuning on molecules with unknown geometry, the GNN still generates implicit 3D information and can use it to inform downstream tasks. We show that 3D pre-training provides significant improvements for a wide range of molecular properties, such as a 22% average MAE reduction on eight quantum mechanical properties. Crucially, the learned representations can be effectively transferred between datasets with vastly different molecules.