Evaluation of Reinforcement Learning in Transformer-based Molecular Design

10 July 2024, Version 2
This content is a preprint and has not undergone peer review at the time of posting.


Designing compounds with a range of desirable properties is a fundamental challenge in drug discovery. In pre-clinical early drug discovery, novel compounds are often designed based on an already existing promising starting compound through structural modifications for further property optimization. Recently, transformer-based deep learning models have been explored for the task of molecular optimization by training on pairs of similar molecules. This provides a starting point for generating similar molecules to a given input molecule, but has limited flexibility regarding user-defined property profiles. Here, we evaluate the effect of reinforcement learning on transformer-based molecular generative models. The generative model can be considered as a pre-trained model with knowledge of the chemical space close to an input compound, while reinforcement learning can be viewed as a tuning phase, steering the model towards chemical space with user-specific desirable properties. The evaluation of two distinct tasks - molecular optimization and scaffold discovery - suggest that reinforcement learning could guide the transformer-based generative model towards the generation of more compounds of interest. Additionally, the impact of pre-trained models, learning steps and learning rates are investigated. Scientific Contribution: Our study investigates the effect of reinforcement learning on a transformer-based generative model initially trained for generating molecules similar to starting molecules. The reinforcement learning framework is applied to facilitate multiparameter optimisation of starting molecules. This approach allows for more flexibility for optimizing user-specific property profiles and helps finding more ideas of interest.


reinforcement learning
generative model
molecular optimization

Supplementary materials

Supplementary figures
This file contains supplementary figures to the main manuscript.


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