Proteins are complex biomolecules that perform a variety of crucial functions within living organisms. Designing and generating novel proteins can pave the way for many future synthetic biology applications, including drug discovery. However, it remains a challenging computational task due to the large modeling space of protein structures. In this study, we propose a latent diffusion model that can reduce the complexity of protein modeling while flexibly capturing the distribution of natural protein structures in a condensed latent space. Specifically, we propose an equivariant protein autoencoder that embeds proteins into a latent space and then uses an equivariant diffusion model to learn the distribution of the latent protein representations. Experimental results demonstrate that our method can effectively generate novel protein backbone structures with high designability and efficiency.

Data augmentations are effective in improving the invariance of learning machines. We argue that the core challenge of data augmentations lies in designing data transformations that preserve labels. This is relatively straightforward for images, but much more challenging for graphs. In this work, we propose GraphAug, a novel automated data augmentation method aiming at computing label-invariant augmentations for graph classification. Instead of using uniform transformations as in existing studies, GraphAug uses an automated augmentation model to avoid compromising critical label-related information of the graph, thereby producing label-invariant augmentations at most times. To ensure label-invariance, we develop a training method based on reinforcement learning to maximize an estimated label-invariance probability. Experiments show that GraphAug outperforms previous graph augmentation methods on various graph classification tasks.