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A De Novo Molecular Generation Method Using Latent Vector Based Generative Adversarial Network

preprint
revised on 18.09.2019, 09:14 and posted on 23.09.2019, 14:38 by Oleksii Prykhodko, Simon Viet Johansson, Panagiotis-Christos Kotsias, Josep Arús-Pous, Esben Jannik Bjerrum, Ola Engkvist, Hongming Chen

Deep learning methods applied to drug discovery have been used to generate novel structures. In this study, we propose a new deep learning architecture, LatentGAN, which combines an autoencoder and a generative adversarial neural network for de novo molecular design. We applied the method in two scenarios: one to generate random drug-like compounds and another to generate target-biased compounds. Our results show that the method works well in both cases: sampled compounds from the trained model can largely occupy the same chemical space as the training set and also generate a substantial fraction of novel compounds. Moreover, the drug-likeness score of compounds sampled from LatentGAN is also similar to that of the training set. Lastly, generated compounds differ from those obtained with a Recurrent Neural Network-based generative model approach, indicating that both methods can be used complementarily.

Funding

Josep Arús-Pous is supported financially by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 676434, “Big Data in Chemistry” (“BIGCHEM,” http://bigchem.eu).

History

Email Address of Submitting Author

simon.johansson@astrazeneca.com

Institution

AstraZeneca AB

Country

Sweden

ORCID For Submitting Author

0000-0001-9139-6378

Declaration of Conflict of Interest

No conflict of interest.

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