Conditional 𝛽-VAE for De Novo Molecular Generation

02 May 2022, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


Deep learning has significantly advanced and accelerated de novo molecular generation. Generative networks, namely Variational Autoencoders (VAEs) can not only randomly generate new molecules but also alter molecular structures to optimize specific chemical properties which are pivotal for drug-discovery. While VAEs have been proposed and researched in the past for pharmaceutical applications, they possess deficiencies that limit their ability to both optimize properties and decode syntactically valid molecules. We present a recurrent, conditional 𝛽-VAE that disentangles the latent space to enhance post hoc molecule optimization. We create a mutual information driven training protocol and data augmentations to both increase molecular validity and promote longer sequence generation. We demonstrate the efficacy of our framework on the ZINC-250k dataset, achieving SOTA unconstrained optimization results on the penalized LogP (pLogP) and QED scores, while also matching current SOTA results for validity, novelty, and uniqueness scores for random generation. We match the current SOTA on QED for top-3 molecules at 0.948, while setting a new SOTA for pLogP optimization at 104.29, 90.12, 69.68 and demonstrating improved results on the constrained optimization task.


deep learning
de novo molecule generation
machine learning
variational autoencoder
molecular generation
drug discovery


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