Molecular Graph Enhanced Transformer for Retrosynthesis PredictionDownload PDF

25 Sept 2019, 19:22 (modified: 24 Dec 2019, 06:16)ICLR 2020 Conference Blind SubmissionReaders: Everyone
Original Pdf: pdf
Abstract: With massive possible synthetic routes in chemistry, retrosynthesis prediction is still a challenge for researchers. Recently, retrosynthesis prediction is formulated as a Machine Translation (MT) task. Namely, since each molecule can be represented as a Simplified Molecular-Input Line-Entry System (SMILES) string, the process of synthesis is analogized to a process of language translation from reactants to products. However, the MT models that applied on SMILES data usually ignore the information of natural atomic connections and the topology of molecules. In this paper, we propose a Graph Enhanced Transformer (GET) framework, which adopts both the sequential and graphical information of molecules. Four different GET designs are proposed, which fuse the SMILES representations with atom embedding learned from our improved Graph Neural Network (GNN). Empirical results show that our model significantly outperforms the Transformer model in test accuracy.
7 Replies