Related papers: Geometric-Facilitated Denoising Diffusion Model fo…

Denoising diffusion probabilistic models (DDPMs) have pioneered new state-of-the-art results in disciplines such as computer vision and computational biology for diverse tasks ranging from text-guided image generation to structure-guided…

Predicting molecular conformations from molecular graphs is a fundamental problem in cheminformatics and drug discovery. Recently, significant progress has been achieved with machine learning approaches, especially with deep generative…

Molecule generation is a very important practical problem, with uses in drug discovery and material design, and AI methods promise to provide useful solutions. However, existing methods for molecule generation focus either on 2D graph…

Molecule generation, especially generating 3D molecular geometries from scratch (i.e., 3D \textit{de novo} generation), has become a fundamental task in drug designs. Existing diffusion-based 3D molecule generation methods could suffer from…

Generative models, especially diffusion models (DMs), have achieved promising results for generating feature-rich geometries and advancing foundational science problems such as molecule design. Inspired by the recent huge success of Stable…

Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…

Deep generative models have recently achieved superior performance in 3D molecule generation. Most of them first generate atoms and then add chemical bonds based on the generated atoms in a post-processing manner. However, there might be no…

Molecular representation learning has shown great success in advancing AI-based drug discovery. The core of many recent works is based on the fact that the 3D geometric structure of molecules provides essential information about their…

The task of deducing three-dimensional molecular configurations from their two-dimensional graph representations holds paramount importance in the fields of computational chemistry and pharmaceutical development. The rapid advancement of…

We introduce PolyDiff, the first diffusion-based approach capable of directly generating realistic and diverse 3D polygonal meshes. In contrast to methods that use alternate 3D shape representations (e.g. implicit representations), our…

Generative models of graphs based on discrete Denoising Diffusion Probabilistic Models (DDPMs) offer a principled approach to molecular generation by systematically removing structural noise through iterative atom and bond adjustments.…

Advanced generative model (e.g., diffusion model) derived from simplified continuity assumptions of data distribution, though showing promising progress, has been difficult to apply directly to geometry generation applications due to the…

This work introduces MiDi, a novel diffusion model for jointly generating molecular graphs and their corresponding 3D arrangement of atoms. Unlike existing methods that rely on predefined rules to determine molecular bonds based on the 3D…

We propose a new score-based approach to generate 3D molecules represented as atomic densities on regular grids. First, we train a denoising neural network that learns to map from a smooth distribution of noisy molecules to the distribution…

Generating molecules that bind to specific proteins is an important but challenging task in drug discovery. Previous works usually generate atoms in an auto-regressive way, where element types and 3D coordinates of atoms are generated one…

Diffusion models have emerged as a leading framework in generative modeling, poised to transform the traditionally slow and costly process of drug discovery. This review provides a systematic comparison of their application in designing two…

Diffusion models have emerged as powerful tools for molecular generation, particularly in the context of 3D molecular structures. Inspired by non-equilibrium statistical physics, these models can generate 3D molecular structures with…

Probabilistic denoising diffusion models (DDMs) have set a new standard for 2D image generation. Extending DDMs for 3D content creation is an active field of research. Here, we propose TetraDiffusion, a diffusion model that operates on a…

Developing bioactive molecules remains a central, time- and cost-heavy challenge in drug discovery, particularly for novel targets lacking structural or functional data. Pharmacophore modeling presents an alternative for capturing the key…

Understanding and predicting the diverse conformational states of molecules is crucial for advancing fields such as chemistry, material science, and drug development. Despite significant progress in generative models, accurately generating…