Related papers: D3MES: Diffusion Transformer with multihead equiva…

This work introduces a diffusion model for molecule generation in 3D that is equivariant to Euclidean transformations. Our E(3) Equivariant Diffusion Model (EDM) learns to denoise a diffusion process with an equivariant network that jointly…

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…

Rich data and powerful machine learning models allow us to design drugs for a specific protein target \textit{in silico}. Recently, the inclusion of 3D structures during targeted drug design shows superior performance to other target-free…

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…

Equivariant diffusion models have achieved impressive performance in 3D molecule generation. These models incorporate Euclidean symmetries of 3D molecules by utilizing an SE(3)-equivariant denoising network. However, specialized equivariant…

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…

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…

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…

Molecular conformation generation plays key roles in computational drug design. Recently developed deep learning methods, particularly diffusion models have reached competitive performance over traditional cheminformatical approaches.…

Deep generative diffusion models are a promising avenue for 3D de novo molecular design in materials science and drug discovery. However, their utility is still limited by suboptimal performance on large molecular structures and limited…

3D molecule generation is crucial for drug discovery and material science, requiring models to process complex multi-modalities, including atom types, chemical bonds, and 3D coordinates. A key challenge is integrating these modalities of…

Diffusion-based generative models have reformed generative AI, and also enabled new capabilities in the science domain, e.g., fast generation of 3D structures of molecules. In such tasks, there is often a symmetry in the system, identifying…

Recent 3D molecular generation methods primarily use asynchronous auto-regressive or synchronous diffusion models. While auto-regressive models build molecules sequentially, they're limited by a short horizon and a discrepancy between…

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…

Creating diverse and high-quality 3D assets with an automatic generative model is highly desirable. Despite extensive efforts on 3D generation, most existing works focus on the generation of a single category or a few categories. In this…

Denoising diffusion models have shown great potential in multiple research areas. Existing diffusion-based generative methods on de novo 3D molecule generation face two major challenges. Since majority heavy atoms in molecules allow…

We introduce Equivariant Neural Diffusion (END), a novel diffusion model for molecule generation in 3D that is equivariant to Euclidean transformations. Compared to current state-of-the-art equivariant diffusion models, the key innovation…

How can diffusion models process 3D geometries in a coarse-to-fine manner, akin to our multiscale view of the world? In this paper, we address the question by focusing on a fundamental biochemical problem of generating 3D molecular…

Recent methods for molecular generation face a trade-off: they either enforce strict equivariance with costly architectures or relax it to gain scalability and flexibility. We propose a frame-based diffusion paradigm that achieves…

Diffusion-based models have shown great promise in molecular generation but often require a large number of sampling steps to generate valid samples. In this paper, we introduce a novel Straight-Line Diffusion Model (SLDM) to tackle this…