Related papers: Geometry-Complete Diffusion for 3D Molecule Genera…

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…

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…

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…

Deep generative models that produce novel molecular structures have the potential to facilitate chemical discovery. Diffusion models currently achieve state of the art performance for 3D molecule generation. In this work, we explore the use…

Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…

Shape-based virtual screening is widely employed in ligand-based drug design to search chemical libraries for molecules with similar 3D shapes yet novel 2D chemical structures compared to known ligands. 3D deep generative models have the…

Denoising diffusion probabilistic models (DDPMs) have emerged as competitive generative models yet brought challenges to efficient sampling. In this paper, we propose novel bilateral denoising diffusion models (BDDMs), which take…

Denoising Diffusion Probabilistic Models (DDPMs) are powerful generative deep learning models that have been very successful at image generation, and, very recently, in path planning and control. In this paper, we investigate how to…

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…

Recently, 3D generative models have shown promising performances in structure-based drug design by learning to generate ligands given target binding sites. However, only modeling the target-ligand distribution can hardly fulfill one of the…

Denoising diffusion probabilistic models (DDPMs) have achieved high quality image generation without adversarial training, yet they require simulating a Markov chain for many steps to produce a sample. To accelerate sampling, we present…

The introduction of diffusion models in anomaly detection has paved the way for more effective and accurate image reconstruction in pathologies. However, the current limitations in controlling noise granularity hinder diffusion models'…

We introduce DD3G, a formulation that Distills a multi-view Diffusion model (MV-DM) into a 3D Generator using gaussian splatting. DD3G compresses and integrates extensive visual and spatial geometric knowledge from the MV-DM by simulating…

Molecular conformation generation poses a significant challenge in the field of computational chemistry. Recently, Diffusion Probabilistic Models (DPMs) and Score-Based Generative Models (SGMs) are effectively used due to their capacity for…

Geometric representation-conditioned molecule generation provides an effective paradigm that decouples molecule representation modeling from structure generation. By decoupling molecule generation into two stages-first generating a…

Due to the three-dimensional nature of CT- or MR-scans, generative modeling of medical images is a particularly challenging task. Existing approaches mostly apply patch-wise, slice-wise, or cascaded generation techniques to fit the…

Graph Neural Networks (GNNs) are highly vulnerable to adversarial attacks, which can greatly degrade their performance. Existing graph purification methods attempt to address this issue by filtering attacked graphs. However, they struggle…

Qualifying the discrepancy between 3D geometric models, which could be represented with either point clouds or triangle meshes, is a pivotal issue with board applications. Existing methods mainly focus on directly establishing the…

In recent years, AI-assisted drug design methods have been proposed to generate molecules given the pockets' structures of target proteins. Most of them are atom-level-based methods, which consider atoms as basic components and generate…

Computational imaging is crucial in many disciplines from autonomous driving to life sciences. However, traditional model-driven and iterative methods consume large computational power and lack scalability for imaging. Deep learning (DL) is…