Optimization of Molecules via Deep Reinforcement Learning

19 Oct 2018  ·  Zhenpeng Zhou, Steven Kearnes, Li Li, Richard N. Zare, Patrick Riley ·

We present a framework, which we call Molecule Deep $Q$-Networks (MolDQN), for molecule optimization by combining domain knowledge of chemistry and state-of-the-art reinforcement learning techniques (double $Q$-learning and randomized value functions). We directly define modifications on molecules, thereby ensuring 100\% chemical validity. Further, we operate without pre-training on any dataset to avoid possible bias from the choice of that set. Inspired by problems faced during medicinal chemistry lead optimization, we extend our model with multi-objective reinforcement learning, which maximizes drug-likeness while maintaining similarity to the original molecule. We further show the path through chemical space to achieve optimization for a molecule to understand how the model works.

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Results from the Paper


 Ranked #1 on Molecular Graph Generation on ZINC (QED Top-3 metric)

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Task Dataset Model Metric Name Metric Value Global Rank Result Benchmark
Molecular Graph Generation ZINC MolDQN QED Top-3 0.948, 0.948, 0.948 # 1
PlogP Top-3 8.93, 8.93, 8.91 # 1

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