Pre-training Molecular Graph Representation with 3D GeometryDownload PDF

Sep 29, 2021 (edited Mar 15, 2022)ICLR 2022 PosterReaders: Everyone
  • Keywords: Pre-training, SSL, Molecule, 3D Geometry, 2D representation
  • Abstract: Molecular graph representation learning is a fundamental problem in modern drug and material discovery. Molecular graphs are typically modeled by their 2D topological structures, but it has been recently discovered that 3D geometric information plays a more vital role in predicting molecular functionalities. However, the lack of 3D information in real-world scenarios has significantly impeded the learning of geometric graph representation. To cope with this challenge, we propose the Graph Multi-View Pre-training (GraphMVP) framework where self-supervised learning (SSL) is performed by leveraging the correspondence and consistency between 2D topological structures and 3D geometric views. GraphMVP effectively learns a 2D molecular graph encoder that is enhanced by richer and more discriminative 3D geometry. We further provide theoretical insights to justify the effectiveness of GraphMVP. Finally, comprehensive experiments show that GraphMVP can consistently outperform existing graph SSL methods. Code is available on GitHub: https://github.com/chao1224/GraphMVP.
  • One-sentence Summary: We proposed a new SSL framework to make 3D geomety information helpful for 2D representation, in terms of the downstream tasks with 2D info only.
  • Supplementary Material: zip
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