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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).…

While traditional self-supervised learning methods improve performance and robustness across various medical tasks, they rely on single-vector embeddings that may not capture fine-grained concepts such as anatomical structures or organs.…

Part-level features are crucial for image understanding, but few studies focus on them because of the lack of fine-grained labels. Although unsupervised part discovery can eliminate the reliance on labels, most of them cannot maintain…

The ultimate aim of the study is to explore the inverse design of porous metamaterials using a deep learning-based generative framework. Specifically, we develop a property-variational autoencoder (pVAE), a variational autoencoder (VAE)…

Peptides, short chains of amino acids, interact with target proteins, making them a unique class of protein-based therapeutics for treating human diseases. Recently, deep generative models have shown great promise in peptide generation.…

Motivation: PCR is more economical and quicker than Next Generation Sequencing for detecting target organisms, with primer design being a critical step. In epidemiology with rapidly mutating viruses, designing effective primers is…

Unsupervised learning can leverage large-scale data sources without the need for annotations. In this context, deep learning-based autoencoders have shown great potential in detecting anomalies in medical images. However, especially…

In this paper we present a new approach to solve semi-supervised classification tasks for biomedical applications, involving a supervised autoencoder network. We create a network architecture that encodes labels into the latent space of an…

We propose an algorithm, guided variational autoencoder (Guided-VAE), that is able to learn a controllable generative model by performing latent representation disentanglement learning. The learning objective is achieved by providing…

Accumulated clinical studies show that microbes living in humans interact closely with human hosts, and get involved in modulating drug efficacy and drug toxicity. Microbes have become novel targets for the development of antibacterial…

Recently, deep learning has made rapid progress in antibody design, which plays a key role in the advancement of therapeutics. A dominant paradigm is to train a model to jointly generate the antibody sequence and the structure as a…

Peptides offer great biomedical potential and serve as promising drug candidates. Currently, the majority of approved peptide drugs are directly derived from well-explored natural human peptides. It is quite necessary to utilize advanced…

As in many fields of medical research, survival analysis has witnessed a growing interest in the application of deep learning techniques to model complex, high-dimensional, heterogeneous, incomplete, and censored medical data. Current…

Peptide-based drugs can bind to protein interaction sites that small molecules often cannot, and are easier to produce than large protein drugs. However, designing effective peptide binders is difficult. A typical peptide has an enormous…

Density estimation, compression and data generation are crucial tasks in artificial intelligence. Variational Auto-Encoders (VAEs) constitute a single framework to achieve these goals. Here, we present a novel class of generative models,…

Diffusion and flow matching models have recently emerged as promising approaches for peptide binder design. Despite their progress, these models still face two major challenges. First, categorical sampling of discrete residue types…

Identifying molecules that exhibit some pre-specified properties is a difficult problem to solve. In the last few years, deep generative models have been used for molecule generation. Deep Graph Variational Autoencoders are among the most…

The use of well-disentangled representations offers many advantages for downstream tasks, e.g. an increased sample efficiency, or better interpretability. However, the quality of disentangled interpretations is often highly dependent on the…

Recent state-of-the-art autoencoder based generative models have an encoder-decoder structure and learn a latent representation with a pre-defined distribution that can be sampled from. Implementing the encoder networks of these models in a…

Generative models of graphs are well-known, but many existing models are limited in scalability and expressivity. We present a novel sequential graphical variational autoencoder operating directly on graphical representations of data. In…