Compressed graph representation for scalable molecular graph generation

• Main Authors: Youngchun Kwon, Dongseon Lee, Youn-Suk Choi, Kyoham Shin, Seokho Kang
• Format: Article
• Language: English
• Published: BMC 2020-09-01
• Series: Journal of Cheminformatics
• Subjects: Molecular graph generation; Compressed graph representation; Graph variational autoencoder; Deep learning
• Online Access: http://link.springer.com/article/10.1186/s13321-020-00463-2

Abstract Recently, deep learning has been successfully applied to molecular graph generation. Nevertheless, mitigating the computational complexity, which increases with the number of nodes in a graph, has been a major challenge. This has hindered the application of deep learning-based molecular graph generation to large molecules with many heavy atoms. In this study, we present a molecular graph compression method to alleviate the complexity while maintaining the capability of generating chemically valid and diverse molecular graphs. We designate six small substructural patterns that are prevalent between two atoms in real-world molecules. These relevant substructures in a molecular graph are then converted to edges by regarding them as additional edge features along with the bond types. This reduces the number of nodes significantly without any information loss. Consequently, a generative model can be constructed in a more efficient and scalable manner with large molecules on a compressed graph representation. We demonstrate the effectiveness of the proposed method for molecules with up to 88 heavy atoms using the GuacaMol benchmark.