Implicit Geometry and Interaction Embeddings Improve Few-Shot Molecular Property Prediction

Abstract: Few-shot learning is a promising approach to molecular property prediction as supervised data is often very limited. However, many important molecular properties depend on complex molecular characteristics -- such as the various 3D geometries a molecule may adopt or the types of chemical interactions it can form -- that are not explicitly encoded in the feature space and must be approximated from low amounts of data. Learning these characteristics can be difficult, especially for few-shot learning algorithms that are designed for fast adaptation to new tasks. In this work, we develop molecular embeddings that encode complex molecular characteristics to improve the performance of few-shot molecular property prediction. Our approach leverages large amounts of synthetic data, namely the results of molecular docking calculations, and a multi-task learning paradigm to structure the embedding space. On multiple molecular property prediction benchmarks, training from the embedding space substantially improves Multi-Task, MAML, and Prototypical Network few-shot learning performance. Our code is available at https://github.com/cfifty/IGNITE.