Molecular Generative Model Based on an Adversarially Regularized Autoencoder

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Deep generative models are attracting great attention as a new promising approach for molecular design. A variety of models reported so far are based on either a variational autoencoder (VAE) or a generative adversarial network (GAN), but they have limitations such as low validity and uniqueness. Here, we propose a new type of model based on an adversarially regularized autoencoder (ARAE). It basically uses latent variables like VAE, but the distribution of the latent variables is estimated by adversarial training like in GAN. The latter is intended to avoid both the insufficiently flexible approximation of posterior distribution in VAE and the difficulty in handling discrete variables in GAN. Our benchmark study showed that ARAE indeed outperformed conventional models in terms of validity, uniqueness, and novelty per generated molecule. We also demonstrated a successful conditional generation of drug-like molecules with ARAE for the control of both cases of single and multiple properties. As a potential real-world application, we could generate epidermal growth factor receptor inhibitors sharing the scaffolds of known active molecules while satisfying drug-like conditions simultaneously.
Publisher
AMER CHEMICAL SOC
Issue Date
2020-01
Language
English
Article Type
Article
Citation

JOURNAL OF CHEMICAL INFORMATION AND MODELING, v.60, no.1, pp.29 - 36

ISSN
1549-9596
DOI
10.1021/acs.jcim.9b00694
URI
http://hdl.handle.net/10203/272594
Appears in Collection
CH-Journal Papers(저널논문)
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