Ziqi Chen

Frazier N. Baker, Ziqi Chen, Daniel Adu-Ampratwum et al.

Retrosynthesis is the process of determining the set of reactant molecules that can react to form a desired product. Semi-template-based retrosynthesis methods, which imitate the reverse logic of synthesis reactions, first predict the reaction centers in the products, and then complete the resulting synthons back into reactants. We develop a new offline-online reinforcement learning method RLSynC for synthon completion in semi-template-based methods. RLSynC assigns one agent to each synthon, all of which complete the synthons by conducting actions step by step in a synchronized fashion. RLSynC learns the policy from both offline training episodes and online interactions, which allows RLSynC to explore new reaction spaces. RLSynC uses a standalone forward synthesis model to evaluate the likelihood of the predicted reactants in synthesizing a product, and thus guides the action search. Our results demonstrate that RLSynC can outperform state-of-the-art synthon completion methods with improvements as high as 14.9%, highlighting its potential in synthesis planning.

Ziqi Chen, Oluwatosin R. Ayinde, James R. Fuchs et al.

Retrosynthesis is a procedure where a target molecule is transformed into potential reactants and thus the synthesis routes can be identified. Recently, computational approaches have been developed to accelerate the design of synthesis routes. In this paper, we develop a generative framework $\mathsf{G^2Retro}$ for one-step retrosynthesis prediction. $\mathsf{G^2Retro}$ imitates the reversed logic of synthetic reactions. It first predicts the reaction centers in the target molecules (products), identifies the synthons needed to assemble the products, and transforms these synthons into reactants. $\mathsf{G^2Retro}$ defines a comprehensive set of reaction center types, and learns from the molecular graphs of the products to predict potential reaction centers. To complete synthons into reactants, $\mathsf{G^2Retro}$ considers all the involved synthon structures and the product structures to identify the optimal completion paths, and accordingly attaches small substructures sequentially to the synthons. Here we show that $\mathsf{G^2Retro}$ is able to better predict the reactants for given products in the benchmark dataset than the state-of-the-art methods.