Deep Molecular Representation Learning via Fusing Physical and Chemical Information

Molecular representation learning is the first yet vital step in combining deep learning and molecular science. To push the boundaries of molecular representation learning, we present PhysChem, a novel neural architecture that learns molecular representations via fusing physical and chemical information of molecules. PhysChem is composed of a physicist network (PhysNet) and a chemist network (ChemNet). PhysNet is a neural physical engine that learns molecular conformations through simulating molecular dynamics with parameterized forces; ChemNet implements geometry-aware deep message-passing to learn chemical / biomedical properties of molecules. Two networks specialize in their own tasks and cooperate by providing expertise to each other. By fusing physical and chemical information, PhysChem achieved state-of-the-art performances on MoleculeNet, a standard molecular machine learning benchmark. The effectiveness of PhysChem was further corroborated on cutting-edge datasets of SARS-CoV-2. * Equal Contribution. † Corresponding Author. 3 SMILES (Simplified Molecular Input Line Entry Specification [35] ) is a widely used protocol that specifies (non-unique) line notations for molecules, CCO for ethanol, for example. 35th Conference on Neural Information Processing Systems (NeurIPS 2021).