Mothra: Multi-objective de novo Molecular Generation using Monte Carlo Tree Search

02 April 2024, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


In the field of drug discovery, identifying compounds that satisfy multiple criteria, such as target protein affinity, pharmacokinetics, and membrane permeability, is challenging because of the vast chemical space. Until now, multi-objective optimization using generative models has often involved linear combinations of different reward functions, turning multi-objective optimization into a single-objective task and causing problems with weighting for each individual objective. Herein we propose a scalable multi-objective molecular generative model developed using deep learning techniques. This model integrates the capabilities of recurrent neural networks for molecular generation and Pareto multi-objective Monte Carlo tree search to determine the optimal search direction. Through this integration, our model can generate compounds using enhanced evaluation functions that include important aspects like target protein affinity, drug similarity, and toxicity. The proposed model addresses the limitations of previous linear combination methods, and its effectiveness is demonstrated via extensive experimentation. The improvements achieved in the evaluation metrics underscore the potential utility of our approach toward drug discovery applications. In addition, we provide the source code for our model such that researchers can easily access and use our framework in their own investigations. The source code is available at


in-silico drug discovery
molecular generative models


Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.