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Recent advances in machine learning for molecules exhibit great potential for facilitating drug discovery from in silico predictions. Most models for molecule generation rely on the decomposition of molecules into frequently occurring…

Chemical Physics · Physics 2023-11-08 Leon Hetzel , Johanna Sommer , Bastian Rieck , Fabian Theis , Stephan Günnemann

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

Generating ligand molecules for specific protein targets, known as structure-based drug design, is a fundamental problem in therapeutics development and biological discovery. Recently, target-aware generative models, especially diffusion…

Biomolecules · Quantitative Biology 2024-10-29 Siyi Gu , Minkai Xu , Alexander Powers , Weili Nie , Tomas Geffner , Karsten Kreis , Jure Leskovec , Arash Vahdat , Stefano Ermon

Molecular conformer generation is a fundamental task in computational chemistry. Several machine learning approaches have been developed, but none have outperformed state-of-the-art cheminformatics methods. We propose torsional diffusion, a…

Chemical Physics · Physics 2023-03-02 Bowen Jing , Gabriele Corso , Jeffrey Chang , Regina Barzilay , Tommi Jaakkola

Diffusion models have emerged as the best approach for generative modeling of 2D images. Part of their success is due to the possibility of training them on millions if not billions of images with a stable learning objective. However,…

Computer Vision and Pattern Recognition · Computer Science 2023-05-23 Animesh Karnewar , Andrea Vedaldi , David Novotny , Niloy Mitra

Recent 3D large reconstruction models typically employ a two-stage process, including first generate multi-view images by a multi-view diffusion model, and then utilize a feed-forward model to reconstruct images to 3D content.However,…

Computer Vision and Pattern Recognition · Computer Science 2024-07-30 Zhenyu Tang , Junwu Zhang , Xinhua Cheng , Wangbo Yu , Chaoran Feng , Yatian Pang , Bin Lin , Li Yuan

The paradigm shift toward structure-driven molecule generation has been propelled by advances in deep generative models, such as variational auto-encoders and diffusion models. However, these generative models for molecular design remain…

Machine Learning · Computer Science 2026-04-17 Peidong Liu , Wenbo Zhang , Wei Ju , Jiancheng Lv , Xianggen Liu

3D building generation with low data acquisition costs, such as single image-to-3D, becomes increasingly important. However, most of the existing single image-to-3D building creation works are restricted to those images with specific…

Computer Vision and Pattern Recognition · Computer Science 2023-09-04 Yao Wei , George Vosselman , Michael Ying Yang

It is inherently ambiguous to lift 2D results from pre-trained diffusion models to a 3D world for text-to-3D generation. 2D diffusion models solely learn view-agnostic priors and thus lack 3D knowledge during the lifting, leading to the…

Computer Vision and Pattern Recognition · Computer Science 2023-10-23 Weiyu Li , Rui Chen , Xuelin Chen , Ping Tan

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…

Machine Learning · Computer Science 2025-03-04 Austin Cheng , Alston Lo , Kin Long Kelvin Lee , Santiago Miret , Alán Aspuru-Guzik

Recent 3D molecular generation methods primarily use asynchronous auto-regressive or synchronous diffusion models. While auto-regressive models build molecules sequentially, they're limited by a short horizon and a discrepancy between…

Machine Learning · Computer Science 2026-04-27 Junyi An , Chao Qu , Yun-Fei Shi , Zhijian Zhou , Fenglei Cao , Yuan Qi

Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to…

Biomolecules · Quantitative Biology 2024-03-01 Zhilin Huang , Ling Yang , Zaixi Zhang , Xiangxin Zhou , Yu Bao , Xiawu Zheng , Yuwei Yang , Yu Wang , Wenming Yang

We address the problem of 3D inconsistency of image inpainting based on diffusion models. We propose a generative model using image pairs that belong to the same scene. To achieve the 3D-consistent and semantically coherent inpainting, we…

Computer Vision and Pattern Recognition · Computer Science 2024-12-10 Leonid Antsfeld , Boris Chidlovskii

The diffusion model is widely leveraged for either video generation or video editing. As each field has its task-specific problems, it is difficult to merely develop a single diffusion for completing both tasks simultaneously. Video…

Computer Vision and Pattern Recognition · Computer Science 2024-07-16 Haoyu Zhao , Tianyi Lu , Jiaxi Gu , Xing Zhang , Qingping Zheng , Zuxuan Wu , Hang Xu , Yu-Gang Jiang

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,…

In the past decade, Artificial Intelligence driven drug design and discovery has been a hot research topic, where an important branch is molecule generation by generative models, from GAN-based models and VAE-based models to the latest…

Biomolecules · Quantitative Biology 2023-10-10 Siyuan Guo , Jihong Guan , Shuigeng Zhou

Structure-based drug design (SBDD) leverages the 3D structure of biomolecular targets to guide the creation of new therapeutic agents. Recent advances in generative models, including diffusion models and geometric deep learning, have…

Biomolecules · Quantitative Biology 2025-01-28 Ali Khodabandeh Yalabadi , Mehdi Yazdani-Jahromi , Ozlem Ozmen Garibay

Generative models of macromolecules carry abundant and impactful implications for industrial and biomedical efforts in protein engineering. However, existing methods are currently limited to modeling protein structures or sequences,…

Biomolecules · Quantitative Biology 2024-01-15 Alex Morehead , Jeffrey Ruffolo , Aadyot Bhatnagar , Ali Madani

Masked diffusion models (MDMs) have achieved notable progress in modeling discrete data, while their potential in molecular generation remains underexplored. In this work, we explore their potential and introduce the surprising result that…

Machine Learning · Computer Science 2025-09-29 Hyunjin Seo , Taewon Kim , Sihyun Yu , SungSoo Ahn

The performance of anomaly inspection in industrial manufacturing is constrained by the scarcity of anomaly data. To overcome this challenge, researchers have started employing anomaly generation approaches to augment the anomaly dataset.…

Computer Vision and Pattern Recognition · Computer Science 2025-04-30 Ying Jin , Jinlong Peng , Qingdong He , Teng Hu , Jiafu Wu , Hao Chen , Haoxuan Wang , Wenbing Zhu , Mingmin Chi , Jun Liu , Yabiao Wang