Conditional $β$-VAE for De Novo Molecular Generation
This work addresses limitations in molecular generation for pharmaceutical applications, though it is incremental as it builds on existing VAE methods with specific enhancements.
The paper tackled the problem of generating and optimizing molecules for drug discovery by introducing a conditional β-VAE that disentangles the latent space, achieving state-of-the-art results on penalized LogP (104.29, 90.12, 69.68) and QED (0.948) scores while matching SOTA in validity, novelty, and uniqueness.
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 which limit their ability to both optimize properties and decode syntactically valid molecules. We present a recurrent, conditional $β$-VAE which 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.