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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…

Optimizing conflicting molecular properties while strictly adhering to complex 3D structural constraints constitutes a challenging Constrained Multi-Objective Optimization Problem (CMOP). Traditional Evolutionary Algorithms (EAs) destroy…

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…

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…

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…

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…

Can we train a 3D molecule generator using data from dense regions to generate samples in sparse regions? This challenge can be framed as an out-of-distribution (OOD) generation problem. While prior research on OOD generation predominantly…

In materials science and particularly electron microscopy, Electron Back-scatter Diffraction (EBSD) is a common and powerful mapping technique for collecting local crystallographic data at the sub-micron scale. The quality of 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…

Structure-based drug design (SBDD) aims to design small-molecule ligands that bind with high affinity and specificity to pre-determined protein targets. Generative SBDD methods leverage structural data of drugs in complex with their protein…

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…

Geometric diffusion models have shown remarkable success in molecular dynamics and structure generation. However, efficiently fine-tuning them for downstream tasks with varying geometric controls remains underexplored. In this work, we…

Molecular conformation generation, a critical aspect of computational chemistry, involves producing the three-dimensional conformer geometry for a given molecule. Generating molecular conformation via diffusion requires learning to reverse…

Embodied agents operate in a structured world, often solving tasks with spatial, temporal, and permutation symmetries. Most algorithms for planning and model-based reinforcement learning (MBRL) do not take this rich geometric structure into…

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…

Predicting molecular conformations (or 3D structures) from molecular graphs is a fundamental problem in many applications. Most existing approaches are usually divided into two steps by first predicting the distances between atoms and then…

Molecular conformer generation (MCG) is an important task in cheminformatics and drug discovery. The ability to efficiently generate low-energy 3D structures can avoid expensive quantum mechanical simulations, leading to accelerated virtual…

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…

Designing new molecules is essential for drug discovery and material science. Recently, deep generative models that aim to model molecule distribution have made promising progress in narrowing down the chemical research space and generating…

We propose enforcing constraints on Model-Based Diffusion by introducing emerging barrier functions inspired by interior point methods. We demonstrate that the standard Model-Based Diffusion algorithm can lead to catastrophic performance…