Abstract

Molecule representation learning (MRL) methods aim to embed molecules into a real vector space. However, existing SMILES-based (Simplified Molecular-Input Line-Entry System) or GNN-based (Graph Neural Networks) MRL methods either take SMILES strings as input that have difficulty in encoding molecule structure information, or over-emphasize the importance of GNN architectures but neglect their generalization ability. Here we propose using chemical reactions to assist learning molecule representation. The key idea of our approach is to preserve the equivalence of molecules with respect to chemical reactions in the embedding space, i.e., forcing the sum of reactant embeddings and the sum of product embeddings to be equal for each chemical equation. This constraint is proven effective to 1) keep the embedding space well-organized and 2) improve the generalization ability of molecule embeddings. Moreover, our model can use any GNN as the molecule encoder and is thus agnostic to GNN architectures. Experimental results demonstrate that our method achieves state-of-the-art performance in a variety of downstream tasks, e.g., reaction product prediction, molecule property prediction, reaction classification, and graph-edit-distance prediction. The code is available at https://github.com/hwwang55/MolR.

Original languageEnglish (US)
StatePublished - 2022
Event10th International Conference on Learning Representations, ICLR 2022 - Virtual, Online
Duration: Apr 25 2022Apr 29 2022

Conference

Conference10th International Conference on Learning Representations, ICLR 2022
CityVirtual, Online
Period4/25/224/29/22

ASJC Scopus subject areas

  • Language and Linguistics
  • Computer Science Applications
  • Education
  • Linguistics and Language

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