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G2GT: Retrosynthesis Prediction with Graph to Graph Attention Neural Network and Self-Training

Retrosynthesis prediction, the task of identifying reactant molecules that can be used to synthesize product molecules, is a fundamental challenge in organic chemistry and related fields. To address this challenge,… Click to show full abstract

Retrosynthesis prediction, the task of identifying reactant molecules that can be used to synthesize product molecules, is a fundamental challenge in organic chemistry and related fields. To address this challenge, we propose a novel graph-to-graph transformation model, G2GT. The model is built on the standard transformer structure and utilizes graph encoders and decoders. Additionally, we demonstrate the effectiveness of self-training, a data augmentation technique that utilizes unlabeled molecular data, in improving the performance of the model. To further enhance diversity, we propose a weak ensemble method, inspired by reaction-type labels and ensemble learning. This method incorporates beam search, nucleus sampling, and top-k sampling to improve inference diversity. A simple ranking algorithm is employed to retrieve the final top-10 results. We achieved new state-of-the-art results on both the USPTO-50K data set, with a top-1 accuracy of 54%, and the larger more challenging USPTO-Full data set, with a top-1 accuracy of 49.3% and competitive top-10 results. Our model can also be generalized to all other graph-to-graph transformation tasks. Data and code are available at https://github.com/Anonnoname/G2GT_2.

Keywords: retrosynthesis prediction; graph; self training; graph graph

Journal Title: Journal of chemical information and modeling
Year Published: 2022

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