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Diffusion models have emerged as a leading framework in generative modeling, poised to transform the traditionally slow and costly process of drug discovery. This review provides a systematic comparison of their application in designing two…

Machine Learning · Computer Science 2025-11-27 Yiquan Wang , Yahui Ma , Yuhan Chang , Jiayao Yan , Jialin Zhang , Minnuo Cai , Kai Wei

Molecular property prediction, crucial for early drug candidate screening and optimization, has seen advancements with deep learning-based methods. While deep learning-based methods have advanced considerably, they often fall short in fully…

Biomolecules · Quantitative Biology 2024-07-01 Taojie Kuang , Yiming Ren , Zhixiang Ren

Diffusion Transformers (DiTs) have demonstrated strong performance in generative modeling, particularly in image synthesis, making them a compelling choice for molecular conformer generation. However, applying DiTs to molecules introduces…

Machine Learning · Computer Science 2025-11-12 J. Thorben Frank , Winfried Ripken , Gregor Lied , Klaus-Robert Müller , Oliver T. Unke , Stefan Chmiela

Structure-based drug discovery, encompassing the tasks of protein-ligand docking and pocket-aware 3D drug design, represents a core challenge in drug discovery. However, no existing work can deal with both tasks to effectively leverage the…

Computational Engineering, Finance, and Science · Computer Science 2025-02-10 Xiuyuan Hu , Guoqing Liu , Can Chen , Yang Zhao , Hao Zhang , Xue Liu

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…

Machine Learning · Computer Science 2025-08-27 Wenyin Zhou , Christopher Iliffe Sprague , Vsevolod Viliuga , Matteo Tadiello , Arne Elofsson , Hossein Azizpour

Drug discovery projects entail cycles of design, synthesis, and testing that yield a series of chemically related small molecules whose properties, such as binding affinity to a given target protein, are progressively tailored to a…

Machine Learning · Computer Science 2020-02-10 Paul Maragakis , Hunter Nisonoff , Brian Cole , David E. Shaw

The increased demand for 3D data in AR/VR, robotics and gaming applications, gave rise to powerful generative pipelines capable of synthesizing high-quality 3D objects. Most of these models rely on the Score Distillation Sampling (SDS)…

Computer Vision and Pattern Recognition · Computer Science 2023-12-12 Ziyu Wan , Despoina Paschalidou , Ian Huang , Hongyu Liu , Bokui Shen , Xiaoyu Xiang , Jing Liao , Leonidas Guibas

Disordered metamaterials are promising for programming physical properties across diverse applications, yet their inverse design remains challenging due to the non-intuitive structure-property relationships and large design spaces. Recent…

Computational Engineering, Finance, and Science · Computer Science 2026-03-18 Ziyuan Xie , Weipeng Xu , Dazhi Zhao , Wenchang Zhang , Daoyang Dong , Bingbing Xu , Ning Liu , Sheng Mao , Tianju Xue

Generative AI has redefined artificial intelligence, enabling the creation of innovative content and customized solutions that drive business practices into a new era of efficiency and creativity. In this paper, we focus on diffusion…

Machine Learning · Computer Science 2024-03-21 Zihao Li , Hui Yuan , Kaixuan Huang , Chengzhuo Ni , Yinyu Ye , Minshuo Chen , Mengdi Wang

Structure-based drug design (SBDD) leverages the three-dimensional geometry of proteins to identify potential drug candidates. Traditional approaches, rooted in physicochemical modeling and domain expertise, are often resource-intensive.…

Quantitative Methods · Quantitative Biology 2024-11-19 Zaixi Zhang , Jiaxian Yan , Yining Huang , Qi Liu , Enhong Chen , Mengdi Wang , Marinka Zitnik

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…

Computer Vision and Pattern Recognition · Computer Science 2024-07-19 Mateusz Poleski , Jacek Tabor , Przemysław Spurek

Discrete diffusion models form a powerful class of generative models across diverse domains, including text and graphs. However, existing approaches face fundamental limitations. Masked diffusion models suffer from irreversible errors due…

Machine Learning · Computer Science 2026-04-21 Marcel Kollovieh , Sirine Ayadi , Stephan Günnemann

The rapid evolution of the fashion industry increasingly intersects with technological advancements, particularly through the integration of generative AI. This study introduces a novel generative pipeline designed to transform the fashion…

Computer Vision and Pattern Recognition · Computer Science 2024-04-30 Abhishek Kumar Singh , Ioannis Patras

The Gaussian diffusion model, initially designed for image generation, has recently been adapted for 3D point cloud generation. However, these adaptations have not fully considered the intrinsic geometric characteristics of 3D shapes,…

Graphics · Computer Science 2024-08-01 Dengsheng Chen , Jie Hu , Xiaoming Wei , Enhua Wu

The integration of artificial intelligence (AI) in early-stage drug discovery offers unprecedented opportunities for exploring chemical space and accelerating hit-to-lead optimization. However, docking optimization in generative approaches…

Quantitative Methods · Quantitative Biology 2025-10-03 Ekaterina Podplutova , Anastasia Vepreva , Olga A. Konovalova , Vladimir Vinogradov , Dmitrii O. Shkil , Andrei Dmitrenko

Recently, deep generative models have revealed itself as a promising way of performing de novo molecule design. However, previous research has focused mainly on generating SMILES strings instead of molecular graphs. Although current graph…

Quantitative Methods · Quantitative Biology 2018-04-24 Yibo Li , Liangren Zhang , Zhenming Liu

Synthesizability remains a critical bottleneck in generative molecular design. While recent advances have addressed synthesizability in 2D graphs, extending these constraints to 3D for geometry-based conditional generation remains largely…

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…

Machine Learning · Computer Science 2025-05-27 Danny Reidenbach , Filipp Nikitin , Olexandr Isayev , Saee Paliwal

Recent text-to-3D methods employing diffusion models have made significant advancements in 3D human generation. However, these approaches face challenges due to the limitations of text-to-image diffusion models, which lack an understanding…

Computer Vision and Pattern Recognition · Computer Science 2023-11-30 Xin Huang , Ruizhi Shao , Qi Zhang , Hongwen Zhang , Ying Feng , Yebin Liu , Qing Wang

Dataset distillation has emerged as an effective strategy, significantly reducing training costs and facilitating more efficient model deployment. Recent advances have leveraged generative models to distill datasets by capturing the…

Computer Vision and Pattern Recognition · Computer Science 2025-05-27 Jeffrey A. Chan-Santiago , Praveen Tirupattur , Gaurav Kumar Nayak , Gaowen Liu , Mubarak Shah
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