Graph-based Molecular Representation Learning

Zhichun Guo, Kehan Guo, Bozhao Nan, Yijun Tian, Roshni G. Iyer, Yihong Ma, Olaf Wiest, Xiangliang Zhang, Wei Wang, Chuxu Zhang, Nitesh V. Chawla

Research output: Chapter in Book/Report/Conference proceedingConference contribution


Molecular representation learning (MRL) is a key step to build the connection between machine learning and chemical science. In particular, it encodes molecules as numerical vectors preserving the molecular structures and features, on top of which the downstream tasks (e.g., property prediction) can be performed. Recently, MRL has achieved considerable progress, especially in methods based on deep molecular graph learning. In this survey, we systematically review these graph-based molecular representation techniques, especially the methods incorporating chemical domain knowledge. Specifically, we first introduce the features of 2D and 3D molecular graphs. Then we summarize and categorize MRL methods into three groups based on their input. Furthermore, we discuss some typical chemical applications supported by MRL. To facilitate studies in this fast-developing area, we also list the benchmarks and commonly used datasets in the paper. Finally, we share our thoughts on future research directions.
Original languageEnglish (US)
Title of host publicationIJCAI International Joint Conference on Artificial Intelligence
PublisherInternational Joint Conferences on Artificial Intelligence
Number of pages9
ISBN (Print)9781956792034
StatePublished - Jan 1 2023
Externally publishedYes

Bibliographical note

Generated from Scopus record by KAUST IRTS on 2023-09-20


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