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Grammars and reinforcement learning for molecule optimization

Machine Learning 2018-11-29 v1 Chemical Physics Machine Learning

Abstract

We seek to automate the design of molecules based on specific chemical properties. Our primary contributions are a simpler method for generating SMILES strings guaranteed to be chemically valid, using a combination of a new context-free grammar for SMILES and additional masking logic; and casting the molecular property optimization as a reinforcement learning problem, specifically best-of-batch policy gradient applied to a Transformer model architecture. This approach uses substantially fewer model steps per atom than earlier approaches, thus enabling generation of larger molecules, and beats previous state-of-the art baselines by a significant margin. Applying reinforcement learning to a combination of a custom context-free grammar with additional masking to enforce non-local constraints is applicable to any optimization of a graph structure under a mixture of local and nonlocal constraints.

Keywords

Cite

@article{arxiv.1811.11222,
  title  = {Grammars and reinforcement learning for molecule optimization},
  author = {Egor Kraev},
  journal= {arXiv preprint arXiv:1811.11222},
  year   = {2018}
}

Comments

3 figures

R2 v1 2026-06-23T06:22:38.028Z