• Section image

    研究方向

    我的研究方向是医学图像处理，特别是基于深度学习的弥散磁共振图像处理方法，包括组织微观结构重建、白质纤维束重建与分割、脑连接计算、脑病灶分割等，以及这些方法在临床中的应用。

  • 教育背景

    2009 - 2014

    约翰霍普金斯大学，电子与计算机工程系，博士

    导师：Jerry L Prince

    2005 - 2009

    北京大学，信息科学技术学院，学士

  • 工作经历

    2021.9 - 今

    北京理工大学，集成电路与电子学院，副教授（特别研究员）

    2018.4 - 2019.9

    北京理工大学，信息与电子学院，副教授（特别研究员）

    2016.12 - 2018.3

    中国科学院，自动化研究所，副研究员

    2015.3 - 2016.11

    中国科学院，自动化研究所，助理研究员

  • 部分发表论文

    （*代表通讯作者；#代表共同一作）

    期刊论文

    • Xin Gao#, Meihui Zhang#,*, Junjie Li#, Shanbo Zhao, Zhizheng Zhuo, Liying Qu, Jinyuan Weng, Li Chai, Yunyun Duan, Chuyang Ye*, Yaou Liu*, “Anatomy-guided slice-description interaction for multimodal brain disease diagnosis based on 3D image and radiological report”, Computerized Medical Imaging and Graphics 123, 102556, 2025.
    • Xinru Zhang, Ni Ou, Chenghao Liu, Zhizheng Zhuo, Paul M. Matthews, Yaou Liu*, Chuyang Ye*, Wenjia Bai*, “Unsupervised brain MRI tumour segmentation via two-stage image synthesis”, Medical Image Analysis 102, 103568, 2025.
    • Tianshu Zheng, Chuyang Ye, Zhaopeng Cui, Hui Zhang, Daniel C. Alexander, Dan Wu*, “An extragradient and noise-tuning adaptive iterative network for diffusion MRI-based microstructural estimation”, Medical Image Analysis 102, 103535, 2025.
    • Yueyan Bian, Jin Li, Chuyang Ye, Xiuqin Jia, Qi Yang*, “Artificial intelligence in medical imaging: From task-specific models to large-scale foundation models”, Chinese Medical Journal, early access, 2025.
    • Xinru Zhang, Ni Ou, Berke Doga Basaran, Marco Visentin, Mengyun Qiao, Renyang Gu, Paul M. Matthews, Yaou Liu*, Chuyang Ye*, Wenjia Bai*, “A Foundation Model for Lesion Segmentation on Brain MRI with Mixture of Modality Experts”, IEEE Transactions on Medical Imaging, early access, 2025.
    • Fei Peng#, Jiaxiang Xia#, Fandong Zhang, Shiyu Lu, Hao Wang, Jiashu Li, Xinmin Liu, Yao Zhong, Jiahuan Guo, Yonghong Duan, Binbin Sui, Chuyang Ye, Yi Ju, Shuai Kang, Yizhou Yu, Xin Feng*, Xingquan Zhao*, Rui Li*, Aihua Liu*, “Intracranial aneurysm instability prediction model based on 4D-Flow MRI and HR-MRI”, Neurotherapeutics 22, e00505, 2025.
    • Mengmeng Wu, Tiantian Liu*, Xin Dai, Chuyang Ye, Jinglong Wu, Shintaro Funahashi, Tianyi Yan*, “HMDA: A Hybrid Model with Multi-scale Deformable Attention for Medical Image Segmentation”, IEEE Journal of Biomedical and Health Informatics 29, 1243-1255, 2025.
    • Fangrong Zong, Zaimin Zhu, Jiayi Zhang, Xiaofeng Deng, Zhuangzhuang Li, Chuyang Ye, Yong Liu*, “Attention-based q-space Deep Learning Generalized for Accelerated Diffusion Magnetic Resonance Imaging”, IEEE Journal of Biomedical and Health Informatics 29, 1176-1188, 2025.
    • Yuxing Li#, Zhizheng Zhuo#, Chenghao Liu, Yunyun Duan, Yulu Shi, Tingting Wang, Runzhi Li, Yanli Wang, Jiwei Jiang, Jun Xu, Decai Tian, Xinghu Zhang, Fudong Shi, Xiaofeng Zhang, Aaron Carass, Frederik Barkhof, Jerry L Prince, Chuyang Ye*, Yaou Liu*, “Deep learning enables accurate brain tissue microstructure analysis based on clinically feasible diffusion magnetic resonance imaging”, NeuroImage 300, 120858, 2024.
    • Chundan Xu#, Jie Li#, Yakui Wang, Lixue Wang, Yizhe Wang, Xiaofeng Zhang, Weiqi Liu, Jingang Chen, Aleksandra Vatian, Natalia Gusarova, Chuyang Ye*, Zhuozhao Zheng*, “SiMix: A domain generalization method for cross-site brain MRI harmonization via site mixing”, NeuroImage 299, 120812, 2024.
    • Evi M.C. Huijben#, Maarten L. Terpstra#, Arthur Jr. Galapon, Suraj Pai, Adrian Thummerer, Peter Koopmans, Manya Afonso, Maureen van Eijnatten, Oliver Gurney-Champion, Zeli Chen, Yiwen Zhang, Kaiyi Zheng, Chuanpu Li, Haowen Pang, Chuyang Ye, Runqi Wang, Tao Song, Fuxin Fan, Jingna Qiu, Yixing Huang, Juhyung Ha, Jong Sung Park, Alexandra Alain-Beaudoin, Silvain Bériault, Pengxin Yu, Hongbin Guo, Zhanyao Huang, Gengwan Li, Xueru Zhang, Yubo Fan, Han Liu, Bowen Xin, Aaron Nicolson, Lujia Zhong, Zhiwei Deng, Gustav Müller-Franzes, Firas Khader, Xia Li, Ye Zhang, Cédric Hémon, Valentin Boussot, Zhihao Zhang, Long Wang, Lu Bai, Shaobin Wang, Derk Mus, Bram Kooiman, Chelsea A.H. Sargeant, Edward G.A. Henderson, Satoshi Kondo, Satoshi Kasai, Reza Karimzadeh, Bulat Ibragimov, Thomas Helfer, Jessica Dafflon, Zijie Chen, Enpei Wang, Zoltan Perko, Matteo Maspero*, “Generating synthetic computed tomography for radiotherapy: SynthRAD2023 challenge report”, Medical Image Analysis 97, 103276, 2024.
    • Chenghao Liu#, Zhizheng Zhuo#, Liying Qu, Ying Jin, Tiantian Hua, Jun Xu, Guirong Tan, Yuna Li, Yunyun Duan, Tingting Wang, Zaiqiang Zhang, Yanling Zhang, Rui Chen, Pinnan Yu, Peixin Zhang, Yulu Shi, Jianguo Zhang, Decai Tian, Runzhi Li, Xinghu Zhang, Fudong Shi, Yanli Wang, Jiwei Jiang, Aaron Carass, Yaou Liu*, Chuyang Ye*, “DeepWMH: A deep learning tool for accurate white matter hyperintensity segmentation without requiring manual annotations for training”, Science Bulletin 69, 872-875, 2024.
    • Wan Liu, Zhizheng Zhuo, Yaou Liu*, Chuyang Ye*, “One-shot segmentation of novel white matter tracts via extensive data augmentation and adaptive knowledge transfer”, Medical Image Analysis 90, 102968, 2023
    • Xinru Zhang, Chenghao Liu, Ni Ou, Xiangzhu Zeng, Zhizheng Zhuo, Yunyun Duan, Xiaoliang Xiong, Yizhou Yu, Zhiwen Liu*, Yaou Liu*, Chuyang Ye*, “CarveMix: a simple data augmentation method for brain lesion segmentation”, NeuroImage 271, 120041, 2023.
    • Tianshu Zheng, Guohui Yan, Haotian Li, Weihao Zheng, Wen Shi, Yi Zhang, Chuyang Ye, Dan Wu*, “A microstructure estimation Transformer inspired by sparse representation for diffusion MRI”, Medical Image Analysis 79, 102454, 2023.
    • Zipei Zhao#, Fengqian Pang#, Yaou Liu, Zhiwen Liu*, Chuyang Ye*, “Positive-unlabeled learning for binary and multi-class cell detection in histopathology images with incomplete annotations”, Machine Learning for Biomedical Imaging 1, 1-30, 2022.
    • Junjie Li#, Peng Zhang#, Liying Qu#, Ting Sun, Yunyun Duan, Minghao Wu, Jinyuan Weng, Zhaohui Li, Xiaodong Gong, Xing Liu, Yongzhi Wang, Wenqing Jia, Xiaorui Su, Qiang Yue, Jianrui Li, Zhiqiang Zhang, Frederik Barkhof, Raymond Y Huang, Ken Chang, Haris Sair, Chuyang Ye, Liwei Zhang, Zhizheng Zhuo, Yaou Liu*, “Deep learning for noninvasive assessment of H3 K27M mutation status in diffuse midline gliomas using MR imaging”, Journal of Magnetic Resonance Imaging 58, 850-861, 2023.
    • Qi Lu#, Wan Liu#, Zhizheng Zhuo#, Yuxing Li, Yunyun Duan, Pinnan Yu, Liying Qu, Chuyang Ye*, Yaou Liu*, “A transfer learning approach to few-shot segmentation of novel white matter tracts”, Medical Image Analysis 79, 102454, 2022.
    • Zhizheng Zhuo#, Jie Zhang#, Yunyun Duan, Liying Qu, Chenlu Feng, Xufang Huang, Dan Cheng, Xiaolu Xu, Ting Sun, Zhaohui Li, Xiaopeng Guo, Xiaodong Gong, Yongzhi Wang, Wenqing Jia, Decai Tian, Xinghu Zhang, Fudong Shi, Sven Haller, Frederik Barkhof, Chuyang Ye, Yaou Liu*, “Automated Classification of Intramedullary Spinal Cord Tumors and Inflammatory Demyelinating Lesions Using Deep Learning”, Radiology: Artificial Intelligence, e210292, 2022.
    • Wan Liu, Qi Lu, Zhizheng Zhuo, Yuxing Li, Yunyun Duan, Pinnan Yu, Liying Qu, Chuyang Ye*, Yaou Liu*, “Volumetric segmentation of white matter tracts with label embedding”, NeuroImage 250, 118934, 2022.
    • Qi Lu, Yuxing Li, Chuyang Ye*, “Volumetric white matter tract segmentation with nested self-supervised learning using sequential pretext tasks”, Medical Image Analysis 72, 102094, 2021.
    • Yu Qin, Yuxing Li, Zhizheng Zhuo, Zhiwen Liu*, Yaou Liu*, Chuyang Ye*, “Multimodal super-resolved q-space deep learning”, Medical Image Analysis 71, 102085, 2021.
    • Yanlin Liu#, Wenhui Cui#, Qing Ha, Xiaoliang Xiong, Xiangzhu Zeng, Chuyang Ye*, “Knowledge transfer between brain lesion segmentation tasks with increased model capacity”, Computerized Medical Imaging and Graphics 88, 101842, 2021.
    • Yu Qin, Zhiwen Liu, Chenghao Liu, Yuxing Li, Xiangzhu Zeng, Chuyang Ye*, “Super-resolved q-space deep learning with uncertainty quantification”, Medical Image Analysis 67, 101885, 2021.
    • Chuyang Ye*, Yuxing Li, Xiangzhu Zeng, "An improved deep network for tissue microstructure estimation with uncertainty quantification", Medical Image Analysis 61, 101650, 2020.
    • Bin He, Zhengyi Yang, Lingzhong Fan, Bin Gao, Hai Li, Chuyang Ye, Bo You*, Tianzi Jiang*, “MonkeyCBP: A toolbox for connectivity-based parcellation of monkey brain”, Frontiers in Neuroinformatics 14, 14, 2020.
    • Chuyang Ye, Xiuli Li, Jingnan Chen*, "A deep network for tissue microstructure estimation using modified LSTM units", Medical Image Analysis 55, Pages 49-64, 2019.
    • Yue Cui#, Ming Song#, Darren M. Lipnicki, Yi Yang, Chuyang Ye, Lingzhong Fan, Jing Sui, Tianzi Jiang*, Jianghong He*, "Subdivisions of the posteromedial cortex in disorders of consciousness", NeuroImage: Clinical 20, Pages 260-266, 2018.
    • Chuyang Ye*, Jerry L. Prince, “Dictionary-based fiber orientation estimation with improved spatial consistency”, Medical Image Analysis 44, Pages 41-53, 2018.
    • Chuyang Ye*, “Tissue microstructure estimation using a deep network inspired by a dictionary-based framework”, Medical Image Analysis 42, Pages 288-299, 2017.
    • Chuyang Ye*, Jerry L. Prince, “Probabilistic tractography using Lasso bootstrap”, Medical Image Analysis 35, Pages 544-553, 2017.
    • Chuyang Ye*, Jiachen Zhuo, Rao P. Gullapalli, Jerry L. Prince, “Estimation of fiber orientations using neighborhood information”, Medical Image Analysis 32, Pages 243-256, 2016.
    • Chuyang Ye*, Jerry L. Prince, “A Bayesian approach to fiber orientation estimation guided by volumetric tract segmentation”, Computerized Medical Imaging and Graphics 54, Pages 35-47, 2016.
    • Zhen Yang*, Chuyang Ye, John A. Bogovic, Aaron Carass, Bruno M. Jedynak, Sarah H. Ying, Jerry L. Prince, “Automated cerebellar lobule segmentation with application to cerebellar structural analysis in cerebellar disease”, NeuroImage 127, Pages 435-444, 2016.
    • Chuyang Ye*, Emi Murano, Maureen Stone, Jerry L. Prince, “A Bayesian approach to distinguishing interdigitated muscles in the tongue from limited diffusion magnetic resonance imaging”, Computerized Medical Imaging and Graphics 45, Pages 63-74, 2015.
    • Chuyang Ye*, Zhen Yang, Sarah H. Ying, Jerry L. Prince, “Segmentation of the cerebellar peduncles using a random forest classifier and a multi-object geometric deformable model: Application to spinocerebellar ataxia type 6”, Neuroinformatics 13(3), Pages 367-381, 2015.
    • Navid Shiee*, Pierre-Louis Bazin, Jennifer L Cuzzocreo, Chuyang Ye, Bhaskar Kishore, Aaron Carass, Peter A. Calabresi, Daniel S. Reich, Jerry L. Prince, Dzung L. Pham, “Reconstruction of the human cerebral cortex robust to white matter lesions: Method and validation”, Human Brain Mapping 35(7), Pages 3385-3401, 2014.
    • Pierre-Louis Bazin*, Chuyang Ye, John A. Bogovic, Navid Shiee, Daniel S. Reich, Jerry L. Prince, Dzung L. Pham, “Direct segmentation of the major white matter tracts in diffusion tensor images”, NeuroImage 58(2), Pages 458-468, 2011.

    会议论文（MICCAI、IPMI）

    • Haowen Pang, Peng Zhang, Xiaoming Hong, Shannan Chen, Chuyang Ye*, “D3M: Deformation-Driven Diffusion Model for Synthesis of Contrast-Enhanced MRI with Brain Tumors”, Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2025.
    • Yuxing Li, Chuyang Ye*, “Hierarchical Anatomy-Aware Guidance for Brain Tissue Microstructure Reconstruction from T1-weighted MRI”, Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2025.
    • Lisong Yin#, Chuyang Ye#, Tiantian Liu*, Jinglong Wu, Tianyi Yan*, U”niCross: Balanced Multimodal Learning for Alzheimer's Disease Diagnosis by Uni-modal Separation and Metadata-guided Cross-modal Interaction”, Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2025.
    • Ruiqing Sun#, Zeng Fan#, Boyang Dai#, Yiyan Su, Qun Hao*, Chuyang Ye*, Shaohui Zhang*, “Towards Accurate Tumor Budding Detection: A Benchmark Dataset and A Detection Approach Based on Implicit Annotation Standardization and Positive-Negative Feature Coupling”, Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2025.
    • Haowen Pang, Xiaoming Hong, Peng Zhang, Chuyang Ye*, “Cascaded Diffusion Model and Segment Anything Model for Medical Image Synthesis via Uncertainty-Guided Prompt Generation”, Information Processing in Medical Imaging (IPMI), 2025.
    • Xinru Zhang, Ni Ou, Berke Doga Basaran, Marco Visentin, Mengyun Qiao, Renyang Gu, Cheng Ouyang, Yaou Liu, Paul M. Matthews, Chuyang Ye*, Wenjia Bai*, “A Foundation Model for Brain Lesion Segmentation with Mixture of Modality Experts”, Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2024.
    • Lujun Gui#, Chuyang Ye#, Tianyi Yan*, “CAVM: Conditional Autoregressive Vision Model for Contrast-Enhanced Brain Tumor MRI Synthesis”, Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2024.
    • Ziqi Wen, Xinru Zhang, Chuyang Ye*, “Source-Free Domain Adaptation for Medical Image Segmentation via Selectively Updated Mean Teacher”, Information Processing in Medical Imaging (IPMI), 2023.
    • Wan Liu, Chuyang Ye*, “Better Generalization of White Matter Tract Segmentation to Arbitrary Datasets with Scaled Residual Bootstrap”, Information Processing in Medical Imaging (IPMI), 2023.
    • Wan Liu, Qi Lu, Zhizheng Zhuo, Yaou Liu, Chuyang Ye*, “One-Shot Segmentation of Novel White Matter Tracts via Extensive Data Augmentation”, Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2022.
    • Chundan Xu#, Ziqi Wen#, Zhiwen Liu*, Chuyang Ye*, “Improved Domain Generalization for Cell Detection in Histopathology Images via Test-Time Stain Augmentation”, Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2022.
    • Tianshu Zheng, Weihao Zheng, Yi Sun, Yi Zhang, Chuyang Ye, Dan Wu*, “An Adaptive Network with Extragradient for Diffusion MRI-Based Microstructure Estimation”, Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2022.
    • Zipei Zhao#, Fengqian Pang#, Zhiwen Liu*, Chuyang Ye*, “Positive-unlabeled Learning for Cell Detection in Histopathology Images with Incomplete Annotations”, Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2021.
    • Chenghao Liu, Xiangzhu Zeng, Kongming Liang, Yizhou Yu, Chuyang Ye*, “Improved Brain Lesion Segmentation with Anatomical Priors from Healthy Subjects”, Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2021.
    • Xinru Zhang#, Chenghao Liu#, Ni Ou, Xiangzhu Zeng, Xiaoliang Xiong, Yizhou Yu, Zhiwen Liu*, Chuyang Ye*, “CarveMix: A Simple Data Augmentation Method for Brain Lesion Segmentation”, Medical Image Computing and Computer Assisted Intervention (MICCAI), 2021.
    • Qi Lu, Chuyang Ye*, “Knowledge Transfer for Few-shot Segmentation of Novel White Matter Tracts”, Information Processing in Medical Imaging (IPMI), 2021.
    • Qi Lu, Yuxing Li, Chuyang Ye*, “White Matter Tract Segmentation with Self-supervised Learning”, Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2020.
    • Chuyang Ye*, Yu Qin, Chenghao Liu, Yuxing Li, Xiangzhu Zeng, Zhiwen Liu, “Super-Resolved q-Space Deep Learning", Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2019.
    • Wenhui Cui, Yanlin Liu, Yuxing Li, Menghao Guo, Yiming Li, Xiuli Li, Tianle Wang, Xiangzhu Zeng, Chuyang Ye*, “Semi-Supervised Brain Lesion Segmentation with an Adapted Mean Teacher Model”, Information Processing in Medical Imaging (IPMI), 2019.
    • Chuyang Ye*, Jerry L. Prince, “Fiber Orientation Estimation Guided by a Deep Network", Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2017.
    • Chuyang Ye*, “Learning-based Ensemble Average Propagator Estimation", Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2017.
    • Chuyang Ye*, “Estimation of Tissue Microstructure Using a Deep Network Inspired by a Sparse Reconstruction Framework”, Information Processing in Medical Imaging (IPMI), 2017.
    • Chuyang Ye*, “Fiber orientation estimation using nonlocal and local information", Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2016.
    • Joshua V. Stough*, Jeffrey Glaister, Chuyang Ye, Sarah H. Ying, Jerry L. Prince, Aaron Carass, “Automatic method for thalamus parcellation using multi-modal feature classification”, Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2014.

  • 获得奖项

    • 2022年度北京市科学技术进步奖一等奖，脑和脊髓影像学标志物体系构建及在神经免疫系统疾病的应用推广，刘亚欧、施福东、叶初阳、李坤成、李郁欣、田德财、金薇娜、杨春生、黄靖、段云云、卓芝政（2023）

    • 小米青年学者（2023）

    • IEEE Transactions on Medical Imaging 优秀审稿人 Silver Level（2023）

    • IEEE Transactions on Medical Imaging 优秀审稿人 Silver Level（2022）

    • IEEE Transactions on Medical Imaging 优秀审稿人 Bronze Level（2021.2.21）

    • 第十四届“挑战杯”中国大学生创业计划竞赛“秦创原”创新挑战赛，金奖，“慧心晰影”—智能数字放射科医生辅助诊断系统，赵山博、庞浩文、陈龙飞、侯皓天、武志强、刘紫馨、高鑫、石一鑫、李雨星、陈钰豪、徐皓晨、张欣茹、张驰、王华章，指导教师：张美慧、叶初阳、史继筠、袁野、王国仁 （2024）

    • MICCAI BraTS Clusters of Challenges 2024 (BraTS-Synthesis (Global) Challenge) 挑战赛，亚军，庞浩文、郭威严、叶初阳（2024）

    • Synthesizing computed tomography for radiotherapy (SynthRAD 2023) 挑战赛，亚军，庞浩文、叶初阳 （2023）

    • 第六届图像计算与数字医学国际研讨会（ISICDM 2023）挑战赛胶质瘤分割，二等奖，庞浩文、刘紫馨、姜润泽，指导教师：叶初阳 （2023）

  • 指导学生

    博士生

    • 李雨星，2019 - 2025
    • 刘婉，2020 - 2024
    • 刘成浩，2021 - 2025
    • 张欣茹，2022 - 今
    • 庞浩文，2023 - 今
    • 洪晓明，2024 - 今
    • 刘晓英，2024 - 今
    • 郭威严，2025 - 今

    硕士生

    • 刘妍麟，2018 - 2021
    • 林梓，2018 - 2021（共同指导）
    • 秦余，2018 - 2021（共同指导）
    • 刘成浩，2019 - 2021
    • 卢琪，2019 - 2022
    • 赵梓培，2019 - 2022（共同指导）
    • 赵心怡，2020 - 2023
    • 卢世宇，2020 - 2023
    • 张欣茹，2020 - 2022（共同指导）
    • 曾译加，2020 - 2024（共同指导）
    • 文梓棋，2021 - 2024
    • 高炳楠，2021 - 2024（共同指导）
    • 杨雨晴，2021 - 2024（共同指导）
    • 郭威严，2021 - 2025
    • 徐春丹，2022 - 2025
    • 刘紫馨，2022 - 2025
    • 贾智皓，2022 - 2025
    • 焦瑞柯，2022 - 2025
    • 姜润泽，2023 - 今
    • 刘美辰，2023 - 今
    • 孙雨飞，2023 - 今
    • 张鹏，2024 - 今
    • 李常凯，2025 - 今
    • 张硕，2025 - 今
    • 杨嘉凝，2025 - 今
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