Kernel-Elastic Autoencoder for Molecular Design
This addresses the problem of generating diverse and valid molecules for drug discovery and materials science, representing a strong incremental advance in generative models for molecular design.
The paper tackles the challenge of achieving both valid generation and accurate reconstruction in molecular design by introducing the Kernel-Elastic Autoencoder (KAE), which achieves remarkable diversity in molecule generation while maintaining near-perfect reconstructions on independent testing datasets, outperforming previous models.
We introduce the Kernel-Elastic Autoencoder (KAE), a self-supervised generative model based on the transformer architecture with enhanced performance for molecular design. KAE is formulated based on two novel loss functions: modified maximum mean discrepancy and weighted reconstruction. KAE addresses the long-standing challenge of achieving valid generation and accurate reconstruction at the same time. KAE achieves remarkable diversity in molecule generation while maintaining near-perfect reconstructions on the independent testing dataset, surpassing previous molecule-generating models. KAE enables conditional generation and allows for decoding based on beam search resulting in state-of-the-art performance in constrained optimizations. Furthermore, KAE can generate molecules conditional to favorable binding affinities in docking applications as confirmed by AutoDock Vina and Glide scores, outperforming all existing candidates from the training dataset. Beyond molecular design, we anticipate KAE could be applied to solve problems by generation in a wide range of applications.