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arXiv · 1905.13372

MolecularRNN: Generating realistic molecular graphs with optimized properties

Mariya Popova·Mykhailo Shvets·Junier Oliva·Olexandr Isayev
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Abstract

Designing new molecules with a set of predefined properties is a core problem in modern drug discovery and development. There is a growing need for de-novo design methods that would address this problem. We present MolecularRNN, the graph recurrent generative model for molecular structures. Our model generates diverse realistic molecular graphs after likelihood pretraining on a big database of molecules. We perform an analysis of our pretrained models on large-scale generated datasets of 1 million samples. Further, the model is tuned with policy gradient algorithm, provided a critic that estimates the reward for the property of interest. We show a significant distribution shift to the desired range for lipophilicity, drug-likeness, and melting point outperforming state-of-the-art works. With the use of rejection sampling based on valency constraints, our model yields 100% validity. Moreover, we show that invalid molecules provide a rich signal to the model through the use of structure penalty in our reinforcement learning pipeline.

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BibTeXRIS

Mariya Popova, Mykhailo Shvets, Junier Oliva, Olexandr Isayev. 2019-05-31. MolecularRNN: Generating realistic molecular graphs with optimized properties. https://arxiv.org/abs/1905.13372

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