TY - CONF
T1 - CHEMICAL-REACTION-AWARE MOLECULE REPRESENTATION LEARNING
AU - Wang, Hongwei
AU - Li, Weijiang
AU - Jin, Xiaomeng
AU - Cho, Kyunghyun
AU - Ji, Heng
AU - Han, Jiawei
AU - Burke, Martin D.
N1 - Funding Information:
This research is based upon work supported by the Molecule Maker Lab Institute: an AI research institute program supported by NSF under award No. 2019897 and No. 2034562. The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for governmental purposes notwithstanding any copyright annotation therein.
Publisher Copyright:
© 2022 ICLR 2022 - 10th International Conference on Learning Representationss. All rights reserved.
PY - 2022
Y1 - 2022
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85150351182&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85150351182&partnerID=8YFLogxK
M3 - Paper
AN - SCOPUS:85150351182
T2 - 10th International Conference on Learning Representations, ICLR 2022
Y2 - 25 April 2022 through 29 April 2022
ER -