Related papers: ProteinAE: Protein Diffusion Autoencoders for Stru…
Recent work leverages Vision Foundation Models as image encoders to boost the generative performance of latent diffusion models (LDMs), as their semantic feature distributions are easy to learn. However, such semantic features often lack…
Designing new protein structures is fundamental to computational biology, enabling advances in therapeutic molecule discovery and enzyme engineering. Existing diffusion-based generative models typically operate in Cartesian coordinate…
Neural network approaches to single-channel speech enhancement have received much recent attention. In particular, mask-based architectures have achieved significant performance improvements over conventional methods. This paper proposes a…
Variational auto-encoders (VAEs) have proven to be a well suited tool for performing dimensionality reduction by extracting latent variables lying in a potentially much smaller dimensional space than the data. Their ability to capture…
In this paper we study generative modeling via autoencoders while using the elegant geometric properties of the optimal transport (OT) problem and the Wasserstein distances. We introduce Sliced-Wasserstein Autoencoders (SWAE), which are…
The dominant approach for music representation learning involves the deep unsupervised model family variational autoencoder (VAE). However, most, if not all, viable attempts on this problem have largely been limited to monophonic music.…
We present a novel masked image modeling (MIM) approach, context autoencoder (CAE), for self-supervised representation pretraining. We pretrain an encoder by making predictions in the encoded representation space. The pretraining tasks…
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,…
The interaction of a protein with its environment can be understood and controlled via its 3D structure. Experimental methods for protein structure determination, such as X-ray crystallography or cryogenic electron microscopy, shed light on…
Recently, molecule generation using deep learning has been actively investigated in drug discovery. In this field, Transformer and VAE are widely used as powerful models, but they are rarely used in combination due to structural and…
Directed evolution is a molecular biology technique that is transforming protein engineering by creating proteins with desirable properties and functions. However, it is experimentally impossible to perform the deep mutational scanning of…
Integrated sensing and communication and millimeter wave (mmWave) have emerged as pivotal technologies for 6G networks. However, the narrow nature of mmWave beams requires precise alignments that typically necessitate large training…
We propose Tree Variational Autoencoder (TreeVAE), a new generative hierarchical clustering model that learns a flexible tree-based posterior distribution over latent variables. TreeVAE hierarchically divides samples according to their…
This paper investigates a novel algorithmic approach to data representation based on kernel methods. Assuming that the observations lie in a Hilbert space X, the introduced Kernel Autoencoder (KAE) is the composition of mappings from…
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…
Extensive research has produced robust methods for unsupervised data visualization. Yet supervised visualization$\unicode{x2013}$where expert labels guide representations$\unicode{x2013}$remains underexplored, as most supervised approaches…
Autoencoders (AE) provide a useful method for nonlinear dimensionality reduction but are ill-suited for low data regimes. Conversely, Principal Component Analysis (PCA) is data-efficient but is limited to linear dimensionality reduction,…
In recent years, studies on image generation models of spiking neural networks (SNNs) have gained the attention of many researchers. Variational autoencoders (VAEs), as one of the most popular image generation models, have attracted a lot…
Despite their ubiquity, variational autoencoders (VAEs) inherently suffer from posterior collapse, a failure mode in which latent variables are effectively ignored. This failure arises because explicit prior imposition drives optimization…
The prediction of protein 3D structure from amino acid sequence is a computational grand challenge in biophysics, and plays a key role in robust protein structure prediction algorithms, from drug discovery to genome interpretation. The…