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

Machine learning in drug discovery has been focused on virtual screening of molecular libraries using discriminative models. Generative models are an entirely different approach that learn to represent and optimize molecules in a continuous…

We propose the Binary Diffusion Probabilistic Model (BDPM), a generative framework specifically designed for data representations in binary form. Conventional denoising diffusion probabilistic models (DDPMs) assume continuous inputs, use…

Remote sensing change detection is crucial for understanding the dynamics of our planet's surface, facilitating the monitoring of environmental changes, evaluating human impact, predicting future trends, and supporting decision-making. In…

Free-form image inpainting is the task of reconstructing parts of an image specified by an arbitrary binary mask. In this task, it is typically desired to generalize model capabilities to unseen mask types, rather than learning certain mask…

Designing molecules that bind to specific target proteins is a fundamental task in drug discovery. Recent models leverage geometric constraints to generate ligand molecules that bind cohesively with specific protein pockets. However, these…

The gradient discretisation method (GDM) is a generic framework for designing and analysing numerical schemes for diffusion models. In this paper, we study the GDM for the porous medium equation, including fast diffusion and slow diffusion…

Diffusion models are among the most effective methods for image generation. This is in particular because, unlike GANs, they can be easily conditioned during training to produce elements with desired class or properties. However, guiding a…

Developing bioactive molecules remains a central, time- and cost-heavy challenge in drug discovery, particularly for novel targets lacking structural or functional data. Pharmacophore modeling presents an alternative for capturing the key…

Deep learning for molecular science has so far mainly focused on 2D molecular graphs. Recently, however, there has been work to extend it to 3D molecular geometry, due to its scientific significance and critical importance in real-world…

Diffusion-based generative models have recently emerged as powerful solutions for high-quality synthesis in multiple domains. Leveraging the bidirectional Markov chains, diffusion probabilistic models generate samples by inferring the…

This paper investigates how diffusion generative models leverage (unknown) low-dimensional structure to accelerate sampling. Focusing on two mainstream samplers -- the denoising diffusion implicit model (DDIM) and the denoising diffusion…

Methods for out-of-distribution (OOD) detection that scale to 3D data are crucial components of any real-world clinical deep learning system. Classic denoising diffusion probabilistic models (DDPMs) have been recently proposed as a robust…

Advances in deep generative models shed light on de novo molecule generation with desired properties. However, molecule generation targeted for dual protein targets still faces formidable challenges including protein 3D structure data…

A common starting point for drug design is to find small chemical groups or "fragments" that form interactions with distinct subregions in a protein binding pocket. The subsequent challenge is to assemble these fragments into a molecule…

Temporal volume images with 3D+t (4D) information are often used in medical imaging to statistically analyze temporal dynamics or capture disease progression. Although deep-learning-based generative models for natural images have been…

We propose a novel approach for probabilistic generative modeling of 3D shapes. Unlike most existing models that learn to deterministically translate a latent vector to a shape, our model, Point-Voxel Diffusion (PVD), is a unified,…

Text-guided molecule generation is a task where molecules are generated to match specific textual descriptions. Recently, most existing SMILES-based molecule generation methods rely on an autoregressive architecture. In this work, we…

Diffusion probabilistic models have quickly become a major approach for generative modeling of images, 3D geometry, video and other domains. However, to adapt diffusion generative modeling to these domains the denoising network needs to be…

The scarcity of large-scale 3D-text paired data poses a great challenge on open vocabulary 3D scene understanding, and hence it is popular to leverage internet-scale 2D data and transfer their open vocabulary capabilities to 3D models…

Accurate molecular geometries are a prerequisite for reliable quantum-chemical predictions, yet density functional theory (DFT) optimization remains a major bottleneck for high-throughput molecular screening. Here we present GeoOpt-Net, a…