Related papers: Manipulating 3D Molecules in a Fixed-Dimensional E…

Vector-Quantized Variational Autoencoders (VQ-VAE)[1] provide an unsupervised model for learning discrete representations by combining vector quantization and autoencoders. In this paper, we study the use of VQ-VAE for representation…

The dynamics of biomolecules are crucial for our understanding of their functioning in living systems. However, current 3D imaging techniques, such as cryogenic electron microscopy (cryo-EM), require freezing the sample, which limits the…

Generative models for molecules based on sequential line notation (e.g. SMILES) or graph representation have attracted an increasing interest in the field of structure-based drug design, but they struggle to capture important 3D spatial…

Using the information theory, this study provides insights into how the construction of latent space of autoencoder (AE) using deep neural network (DNN) training finds a smooth low-dimensional manifold in the stiff dynamical system. Our…

Recently, deep generative models for molecular graphs are gaining more and more attention in the field of de novo drug design. A variety of models have been developed to generate topological structures of drug-like molecules, but…

The integrative analysis of histopathological images and genomic data has received increasing attention for survival prediction of human cancers. However, the existing studies always hold the assumption that full modalities are available.…

The application of language models (LMs) to molecular structure generation using line notations such as SMILES and SELFIES has been well-established in the field of cheminformatics. However, extending these models to generate 3D molecular…

Variational Autoencoders (VAE) and their variants have been widely used in a variety of applications, such as dialog generation, image generation and disentangled representation learning. However, the existing VAE models have some…

In many imaging modalities, objects of interest can occur in a variety of locations and poses (i.e. are subject to translations and rotations in 2d or 3d), but the location and pose of an object does not change its semantics (i.e. the…

Neural implicit surface reconstruction has become a new trend in reconstructing a detailed 3D shape from images. In previous methods, however, the 3D scene is only encoded by the MLPs which do not have an explicit 3D structure. To better…

Variational autoencoders are prominent generative models for modeling discrete data. However, with flexible decoders, they tend to ignore the latent codes. In this paper, we study a VAE model with a deterministic decoder (DD-VAE) for…

Deep learning (DL) methods where interpretability is intrinsically considered as part of the model are required to better understand the relationship of clinical and imaging-based attributes with DL outcomes, thus facilitating their use in…

We introduce a Three-Dimensional Convolutional Variational Autoencoder (3D-CVAE) for automated anomaly detection in Electron Energy Loss Spectroscopy Spectrum Imaging (EELS-SI) data. Our approach leverages the full three-dimensional…

Generative autoencoders offer a promising approach for controllable text generation by leveraging their latent sentence representations. However, current models struggle to maintain coherent latent spaces required to perform meaningful text…

A molecule's 2D representation consists of its atoms, their attributes, and the molecule's covalent bonds. A 3D (geometric) representation of a molecule is called a conformer and consists of its atom types and Cartesian coordinates. Every…

High-throughput approximations of quantum mechanics calculations and combinatorial experiments have been traditionally used to reduce the search space of possible molecules, drugs and materials. However, the interplay of structural and…

Medical images are acquired at high resolutions with large fields of view in order to capture fine-grained features necessary for clinical decision-making. Consequently, training deep learning models on medical images can incur large…

With the advent of affordable depth sensors, 3D capture becomes more and more ubiquitous and already has made its way into commercial products. Yet, capturing the geometry or complete shapes of everyday objects using scanning devices (e.g.…

Deep latent variable models, trained using variational autoencoders or generative adversarial networks, are now a key technique for representation learning of continuous structures. However, applying similar methods to discrete structures,…

Recent advancements in multimodal large language models (MLLMs) have demonstrated considerable potential for comprehensive 3D scene understanding. However, existing approaches typically utilize only one or a limited subset of 3D modalities,…