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Adeno-associated viral (AAV) vectors are widely used delivery platforms in gene therapy, and the design of improved capsids is key to expanding their therapeutic potential. A central challenge in AAV bioengineering, as in protein design…

Variational auto-encoders (VAEs) are an influential and generally-used class of likelihood-based generative models in unsupervised learning. The likelihood-based generative models have been reported to be highly robust to the…

Structure-based drug design is drawing growing attentions in computer-aided drug discovery. Compared with the virtual screening approach where a pre-defined library of compounds are computationally screened, de novo drug design based on the…

We investigate deep generative models that can exchange multiple modalities bi-directionally, e.g., generating images from corresponding texts and vice versa. A major approach to achieve this objective is to train a model that integrates…

Recently, self-supervised pre-training has advanced Vision Transformers on various tasks w.r.t. different data modalities, e.g., image and 3D point cloud data. In this paper, we explore this learning paradigm for 3D mesh data analysis based…

Unsupervised representation learning holds the promise of exploiting large amounts of unlabeled data to learn general representations. A promising technique for unsupervised learning is the framework of Variational Auto-encoders (VAEs).…

Recent studies have shown that autoencoder-based models can achieve superior performance on anomaly detection tasks due to their excellent ability to fit complex data in an unsupervised manner. In this work, we propose a novel…

The ability to accurately model random fields plays a critical role in science and engineering for problems involving uncertain, spatially-varying quantities such as heterogeneous material properties and turbulent flows. Deep generative…

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based…

Variational auto-encoders (VAEs) provide an attractive solution to image generation problem. However, they tend to produce blurred and over-smoothed images due to their dependence on pixel-wise reconstruction loss. This paper introduces a…

Protein representation learning is critical for numerous biological tasks. Recently, large transformer-based protein language models (pLMs) pretrained on large scale protein sequences have demonstrated significant success in sequence-based…

Variant effect predictors (VEPs) aim to assess the functional impact of protein variants, traditionally relying on multiple sequence alignments (MSAs). This approach assumes that naturally occurring variants are fit, an assumption…

Variational autoencoders (VAEs), that are built upon deep neural networks have emerged as popular generative models in computer vision. Most of the work towards improving variational autoencoders has focused mainly on making the…

Semi-supervised learning is sought for leveraging the unlabelled data when labelled data is difficult or expensive to acquire. Deep generative models (e.g., Variational Autoencoder (VAE)) and semisupervised Generative Adversarial Networks…

Video Variational Autoencoder (VAE) enables latent video generative modeling by mapping the visual world into compact spatiotemporal latent spaces, improving training efficiency and stability. While existing video VAEs achieve commendable…

Generative modeling and self-supervised learning have in recent years made great strides towards learning from data in a completely unsupervised way. There is still however an open area of investigation into guiding a neural network to…

Design of new drug compounds with target properties is a key area of research in generative modeling. We present a small drug molecule design pipeline based on graph-generative models and a comparison study of two state-of-the-art graph…

The generation of small molecule candidate (ligand) binding poses in its target protein pocket is important for computer-aided drug discovery. Typical rigid-body docking methods ignore the pocket flexibility of protein, while the more…

Generative models able to synthesize layouts of different kinds (e.g. documents, user interfaces or furniture arrangements) are a useful tool to aid design processes and as a first step in the generation of synthetic data, among other…

Deep learning on graphs has become a popular research topic with many applications. However, past work has concentrated on learning graph embedding tasks, which is in contrast with advances in generative models for images and text. Is it…