Related papers: FlowMol3: Flow Matching for 3D De Novo Small-Molec…

Molecule generation is advancing rapidly in chemical discovery and drug design. Flow matching methods have recently set the state of the art (SOTA) in unconditional molecule generation, surpassing score-based diffusion models. However,…

We present FLOWR.root, an SE(3)-equivariant flow-matching model for pocket-aware 3D ligand generation with joint potency and binding affinity prediction and confidence estimation. The model supports de novo generation, interaction- and…

Many generative applications, such as synthesis-based 3D molecular design, involve constructing compositional objects with continuous features. Here, we introduce Compositional Generative Flows (CGFlow), a novel framework that extends flow…

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…

Generative models for molecules based on sequential line notation (e.g. SMILES) or graph representation have attracted an increasing interest in the field of structure-based drug design, but they struggle to capture important 3D spatial…

Robots can acquire complex manipulation skills by learning policies from expert demonstrations, which is often known as vision-based imitation learning. Generating policies based on diffusion and flow matching models has been shown to be…

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…

Elucidating reaction mechanisms hinges on efficiently generating transition states (TSs), products, and complete reaction networks. Recent generative models, such as diffusion models for TS sampling and sequence-based architectures for…

Generating molecular graphs with desired chemical properties driven by deep graph generative models provides a very promising way to accelerate drug discovery process. Such graph generative models usually consist of two steps: learning…

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…

With the recent advances in machine learning for quantum chemistry, it is now possible to predict the chemical properties of compounds and to generate novel molecules. Existing generative models mostly use a string- or graph-based…

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…

We introduce a new representation for 3D molecules based on their continuous atomic density fields. Using this representation, we propose a new model based on walk-jump sampling for unconditional 3D molecule generation in the continuous…

The generation of 3D molecules requires simultaneously deciding the categorical features~(atom types) and continuous features~(atom coordinates). Deep generative models, especially Diffusion Models (DMs), have demonstrated effectiveness in…

We introduce a new graph diffusion model for small molecule generation, DMol, which outperforms the state-of-the-art DiGress model in terms of validity by roughly 1.5% across all benchmarking datasets while reducing the number of diffusion…

Unconditional molecular generation is a stepping stone for conditional molecular generation, which is important in \emph{de novo} drug design. Recent unconditional 3D molecular generation methods report saturated benchmarks, suggesting it…

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…

Amorphous molecular solids offer a promising alternative to inorganic semiconductors, owing to their mechanical flexibility and solution processability. The packing structure of these materials plays a crucial role in determining their…

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…

Designing metal-organic frameworks (MOFs) with novel chemistries is a longstanding challenge due to their large combinatorial space and complex 3D arrangements of the building blocks. While recent deep generative models have enabled…