相关论文: GeoDiff: a Geometric Diffusion Model for Molecular…

Generative models have shown great promise in generating 3D geometric systems, which is a fundamental problem in many natural science domains such as molecule and protein design. However, existing approaches only operate on static…

This work introduces GeoDirDock (GDD), a novel approach to molecular docking that enhances the accuracy and physical plausibility of ligand docking predictions. GDD guides the denoising process of a diffusion model along geodesic paths…

In this paper, we introduce a denoising diffusion algorithm to discover microstructures with nonlinear fine-tuned properties. Denoising diffusion probabilistic models are generative models that use diffusion-based dynamics to gradually…

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…

Effective generation of molecular structures, or new chemical entities, that bind to target proteins is crucial for lead identification and optimization in drug discovery. Despite advancements in atom- and motif-wise deep learning models…

Denoising diffusions are state-of-the-art generative models exhibiting remarkable empirical performance. They work by diffusing the data distribution into a Gaussian distribution and then learning to reverse this noising process to obtain…

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…

Denoising diffusion probabilistic models and score-matching models have proven to be very powerful for generative tasks. While these approaches have also been applied to the generation of discrete graphs, they have, so far, relied on…

Coarse-grained (CG) models play a crucial role in the study of protein structures, protein thermodynamic properties, and protein conformation dynamics. Due to the information loss in the coarse-graining process, backmapping from CG to…

We propose SymDiff, a method for constructing equivariant diffusion models using the framework of stochastic symmetrisation. SymDiff resembles a learned data augmentation that is deployed at sampling time, and is lightweight,…

Crystalline materials often exhibit a high level of symmetry. However, most generative models do not account for symmetry, but rather model each atom without any constraints on its position or element. We propose a generative model, Wyckoff…

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…

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…

Diffusion models generate data by learning to reverse a forward process, where samples are progressively perturbed with Gaussian noise according to a predefined noise schedule. From a geometric perspective, each noise schedule corresponds…

The paradigm shift toward structure-driven molecule generation has been propelled by advances in deep generative models, such as variational auto-encoders and diffusion models. However, these generative models for molecular design remain…

Denoising diffusion models have proven to be a flexible and effective paradigm for generative modelling. Their recent extension to infinite dimensional Euclidean spaces has allowed for the modelling of stochastic processes. However, many…

Structure-based drug design (SBDD), which aims to generate molecules that can bind tightly to the target protein, is an essential problem in drug discovery, and previous approaches have achieved initial success. However, most existing…

We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning…

Diffusion models have emerged as a promising approach for text generation, with recent works falling into two main categories: discrete and continuous diffusion models. Discrete diffusion models apply token corruption independently using…

The discovery and study of new material systems rely on molecular simulations that often come with significant computational expense. We propose MDDM, a Molecular Dynamics Diffusion Model, which is capable of predicting a valid output…