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The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…

Biomolecules · Quantitative Biology 2022-11-28 Kevin E. Wu , Kevin K. Yang , Rianne van den Berg , James Y. Zou , Alex X. Lu , Ava P. Amini

Investigating conformational landscapes of proteins is a crucial way to understand their biological functions and properties. AlphaFlow stands out as a sequence-conditioned generative model that introduces flexibility into structure…

Machine Learning · Computer Science 2024-07-18 Shaoning Li , Mingyu Li , Yusong Wang , Xinheng He , Nanning Zheng , Jian Zhang , Pheng-Ann Heng

Sampling useful three-dimensional molecular structures along with their most favorable conformations is a key challenge in drug discovery. Current state-of-the-art 3D de-novo design flow matching or diffusion-based models are limited to…

Machine Learning · Computer Science 2025-11-24 Riccardo Tedoldi , Ola Engkvist , Patrick Bryant , Hossein Azizpour , Jon Paul Janet , Alessandro Tibo

New technologies such as Rectified Flow and Flow Matching have significantly improved the performance of generative models in the past two years, especially in terms of control accuracy, generation quality, and generation efficiency.…

Computer Vision and Pattern Recognition · Computer Science 2026-01-09 Sen Fang , Hongbin Zhong , Yalin Feng , Yanxin Zhang , Dimitris N. Metaxas

Recent advancements in generative modeling have significantly enhanced the reconstruction of audio waveforms from various representations. While diffusion models are adept at this task, they are hindered by latency issues due to their…

Sound · Computer Science 2024-10-08 Peng Liu , Dongyang Dai , Zhiyong Wu

AlphaFold3 introduces a diffusion-based architecture that elevates protein structure prediction to all-atom resolution with improved accuracy. This state-of-the-art performance has established AlphaFold3 as a foundation model for diverse…

Machine Learning · Computer Science 2026-05-19 Zhe Zhang , Yuanning Feng , Yuxuan Song , Keyue Qiu , Hao Zhou , Wei-Ying Ma

Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…

Machine Learning · Computer Science 2024-12-30 Kaihui Cheng , Ce Liu , Qingkun Su , Jun Wang , Liwei Zhang , Yining Tang , Yao Yao , Siyu Zhu , Yuan Qi

The growing significance of RNA engineering in diverse biological applications has spurred interest in developing AI methods for structure-based RNA design. While diffusion models have excelled in protein design, adapting them for RNA…

Biomolecules · Quantitative Biology 2024-06-11 Divya Nori , Wengong Jin

Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…

Machine Learning · Computer Science 2025-10-01 Yogesh Verma , Markus Heinonen , Vikas Garg

Accurate and real-time radio map (RM) generation is crucial for next-generation wireless systems, yet diffusion-based approaches often suffer from large model sizes, slow iterative denoising, and high inference latency, which hinder…

Computer Vision and Pattern Recognition · Computer Science 2025-10-13 Haozhe Jia , Wenshuo Chen , Xiucheng Wang , Nan Cheng , Hongbo Zhang , Kuimou Yu , Songning Lai , Nanjian Jia , Bowen Tian , Hongru Xiao , Yutao Yue

Designing novel proteins that bind to small molecules is a long-standing challenge in computational biology, with applications in developing catalysts, biosensors, and more. Current computational methods rely on the assumption that the…

Biomolecules · Quantitative Biology 2024-09-19 Junqi Liu , Shaoning Li , Chence Shi , Zhi Yang , Jian Tang

Proteins are complex biomolecules that perform a variety of crucial functions within living organisms. Designing and generating novel proteins can pave the way for many future synthetic biology applications, including drug discovery.…

Robotic manipulation in unstructured environments requires the generation of robust and long-horizon trajectory-level policy with conditions of perceptual observations and benefits from the advantages of SE(3)-equivariant diffusion models…

Robotics · Computer Science 2025-09-30 Zhitao Wang , Yanke Wang , Jiangtao Wen , Roberto Horowitz , Yuxing Han

Diffusion- and flow-based generative models have recently demonstrated strong performance in protein backbone generation tasks, offering unprecedented capabilities for de novo protein design. However, while achieving notable performance in…

Machine Learning · Computer Science 2025-10-29 Liyang Xie , Haoran Zhang , Zhendong Wang , Wesley Tansey , Mingyuan Zhou

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

Flow matching models have emerged as a powerful framework for realistic image generation by learning to reverse a corruption process that progressively adds Gaussian noise. However, because noise is injected in the latent domain, its impact…

Computer Vision and Pattern Recognition · Computer Science 2026-04-20 Sucheng Ren , Qihang Yu , Ju He , Xiaohui Shen , Alan Yuille , Liang-Chieh Chen

How can we design protein sequences folding into the desired structures effectively and efficiently? AI methods for structure-based protein design have attracted increasing attention in recent years; however, few methods can simultaneously…

Artificial Intelligence · Computer Science 2023-04-14 Zhangyang Gao , Cheng Tan , Pablo Chacón , Stan Z. Li

We introduce a generative model for protein backbone design utilizing geometric products and higher order message passing. In particular, we propose Clifford Frame Attention (CFA), an extension of the invariant point attention (IPA)…

Machine Learning · Computer Science 2024-11-11 Simon Wagner , Leif Seute , Vsevolod Viliuga , Nicolas Wolf , Frauke Gräter , Jan Stühmer

Image restoration aims to recover high-quality (HQ) images from degraded low-quality (LQ) ones by reversing the effects of degradation. Existing generative models for image restoration, including diffusion and score-based models, often…

Computer Vision and Pattern Recognition · Computer Science 2025-06-23 Haina Qin , Wenyang Luo , Libin Wang , Dandan Zheng , Jingdong Chen , Ming Yang , Bing Li , Weiming Hu

We propose ReinFlow, a simple yet effective online reinforcement learning (RL) framework that fine-tunes a family of flow matching policies for continuous robotic control. Derived from rigorous RL theory, ReinFlow injects learnable noise…

Robotics · Computer Science 2026-01-09 Tonghe Zhang , Chao Yu , Sichang Su , Yu Wang