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

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
Published on April 2, 2024
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