Related papers: SemlaFlow -- Efficient 3D Molecular Generation wit…

Generating molecular structures with desired properties is a critical task with broad applications in drug discovery and materials design. We propose 3M-Diffusion, a novel multi-modal molecular graph generation method, to generate diverse,…

Structure-based drug design (SBDD), aiming to generate 3D molecules with high binding affinity toward target proteins, is a vital approach in novel drug discovery. Although recent generative models have shown great potential, they suffer…

State-of-the-art models for 3D molecular generation are based on significant inductive biases, SE(3), permutation equivariance to respect symmetry and graph message-passing networks to capture local chemistry, yet the generated molecules…

We introduce a new framework for molecular graph generation with 3D molecular generative models. Our Synthetic Coordinate Embedding (SyCo) framework maps molecular graphs to Euclidean point clouds via synthetic conformer coordinates and…

We suggest a new multi-modal algorithm for joint inference of paired structurally aligned samples with Rectified Flow models. While some existing methods propose a codependent generation process, they do not view the problem of joint…

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…

Sampling useful three-dimensional molecular structures along with their most favorable conformations is a key challenge in drug discovery. Current state-of-the-art 3D de-novo design flow matching or diffusion-based models are limited to…

Three-dimensional molecular structure generation is typically performed at the level of individual atoms, yet molecular graph generation techniques often consider fragments as their structural units. Building on the advances in frame-based…

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…

Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent…

Flow Matching has emerged as a powerful framework for learning continuous transformations between distributions, enabling high-fidelity generative modeling. This work introduces Symmetrical Flow Matching (SymmFlow), a new formulation that…

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…

Estimating three-dimensional conformations of a molecular graph allows insight into the molecule's biological and chemical functions. Fast generation of valid conformations is thus central to molecular modeling. Recent advances in…

In the real world, a molecule is a 3D geometric structure. Compared to 1D SMILES sequences and 2D molecular graphs, 3D molecules represent the most informative molecular modality. Despite the rapid progress of autoregressive-based language…

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…

Molecular structure elucidation is a fundamental step in understanding chemical phenomena, with applications in identifying molecules in natural products, lab syntheses, forensic samples, and the interstellar medium. We consider the task of…

De novo 3D molecule generation is a pivotal task in drug discovery. However, many recent geometric generative models struggle to produce high-quality 3D structures, even if they maintain 2D validity and topological stability. To tackle this…

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…

Diffusion-based generative models in SE(3)-invariant space have demonstrated promising performance in molecular conformation generation, but typically require solving stochastic differential equations (SDEs) with thousands of update steps.…

Molecular 3D conformations play a key role in determining how molecules interact with other molecules or protein surfaces. Recent deep learning advancements have improved conformation prediction, but slow training speeds and difficulties in…