Data-driven approaches for identifying hyperparameters in multi-step retrosynthesis

Abstract

The multi-step retrosynthesis problem can be solved by a search algorithm, such as Monte Carlo tree search (MCTS). The performance of multistep retrosynthesis, as measured by a trade-off in search time and route solvability, therefore depends on the hyperparameters of the search algorithm. In this paper, we demonstrated the effect of three MCTS hyperparameters (number of iterations, tree depth, and tree width) on metrics such as Linear integrated speed-accuracy score (LISAS) and Inverse efficiency score which consider both route solvability and search time. This exploration was conducted by employing three data-driven approaches, namely a systematic grid search, Bayesian optimization over an ensemble of molecules to obtain static MCTS hyperparameters, and a machine learning approach to dynamically predict optimal MCTS hyperparameters given an input target molecule. With the obtained results on the internal dataset, we demonstrated that it is possible to identify a hyperparameter set which outperforms the current AiZynthFinder default setting. It appeared optimal across a variety of target input molecules, both on proprietary and public datasets. The settings identified with the in-house dataset reached a solvability of 93 % and median search time of 151 s for the in-house dataset, and a 74 % solvability and 114 s for the ChEMBL dataset. These numbers can be compared to the current default settings which solved 85 % and 73 % during a median time of 110s and 84 s, for in-house and ChEMBL, respectively.