Author(s)

Wei Hu

Department of Computer Science, Houghton College, Houghton, NY, USA.

Creating new molecules with desired properties is a fundamental and challenging problem in chemistry. Reinforcement learning (RL) has shown its utility in this area where the target chemical property values can serve as a reward signal. At each step of making a new molecule, the RL agent learns selecting an action from a list of many chemically valid actions for a given molecule, implying a great uncertainty associated with its learning. In a traditional implementation of deep RL algorithms, deterministic neural networks are typically employed, thus allowing the agent to choose one action from one sampled action at each step. In this paper, we proposed a new strategy of applying Bayesian neural networks to RL to reduce uncertainty so that the agent can choose one action from a pool of sampled actions at each step, and investigated its benefits in molecule design. Our experiments suggested the Bayesian approach could create molecules of desirable chemical quality while maintained their diversity, a very difficult goal to achieve in machine learning of molecules. We further exploited their diversity by using them to train a generative model to yield more novel drug-like molecules, which were absent in the training molecules as we know novelty is essential for drug candidate molecules. In conclusion, Bayesian approach could offer a balance between exploitation and exploration in RL, and a balance between optimization and diversity in molecule design.

Molecule Design, Bayesian Neural Networks, Reinforcement Learning

Hu, W. (2021) Reinforcement Learning of Molecule Optimization with Bayesian Neural Networks. Computational Molecular Bioscience, 11, 69-83. doi: 10.4236/cmb.2021.114005.