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ChuyangYe.JPG

ABOUT ME

I am currently an Associate Professor at the School of Integrated Circuits and Electronics, Beijing Institute of Technology. Before joining Beijing Institute of Technology, I was an Associate Professor at the Brainnetome Center, Institute of Automation, Chinese Academy of Sciences. I received my Ph.D. degree from the Johns Hopkins University. My current research interest is medical image computing and its application to clinical and basic neuroscience.

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RESEARCH

My primary research interests include tissue microstructure estimation, white matter tract reconstruction, and brain connectivity computation from diffusion MRI. In particular, I am working on developing deep learning based approaches to solving inverse problems in diffusion MRI. My research interests also include application of deep learning to brain MRI processing and analysis for clinical practice.

EDUCATION

2009 - 2014

Ph.D. in the Department of Electrical and Computer Engineering, Johns Hopkins University. Advisor: Dr. Jerry L Prince

2005 - 2009

B.S. in the School of Electronic Engineering and Computer Science, Peking University

WORK EXPERIENCE

September 2021 - Present

Associate Professor, School of Integrated Circuits and Electronics, Beijing Institute of Technology

April 2018 - September 2021

Associate Professor, School of Information and Electronics, Beijing Institute of Technology

December 2016 - March 2018

Associate Professor, Institute of Automation, Chinese Academy of Sciences

March 2015 - November 2016

Assistant Professor, Institute of Automation, Chinese Academy of Sciences

SELECTED PUBLICATIONS

(*: corresponding authors; #: co-first authors)

JOURNAL PAPERS

  • 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.

CONFERENCE PAPERS (MICCAI AND IPMI)

  • 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.

  • Tianshu Zheng, Ruicheng Ba, Xiaoli Wang, Chuyang Ye, Dan Wu*, “AUA-dE: An Adaptive Uncertainty Guided Attention for Diffusion MRI Models Estimation”, Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2023.

  • 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.

OTHERS

For a complete list of papers, please refer to my google scholar page: https://scholar.google.com/citations?user=N0qJQQ4AAAAJ

AWARDS

  • 2022 Beijing Science and Technology Progress Award (rank 3/11)

  • IEEE Transactions on Medical Imaging Distinguished Reviewer Silver Level (10/1/2023)

  • IEEE Transactions on Medical Imaging Distinguished Reviewer Silver Level (08/27/2022)

  • IEEE Transactions on Medical Imaging Distinguished Reviewer Bronze Level (02/21/2021)

STUDENTS

PHD STUDENTS

  • Yuxing Li (Started 2019)

  • Wan Liu (2020 - 2024)

  • Chenghao Liu (Started 2021)

  • Xinru Zhang (Started 2022)

  • Haowen Pang (Started 2023)

  • Xiaoming Hong (Started 2024)

MASTER STUDENTS

  • Yanlin Liu (2018 - 2021)

  • Zi Lin (2018 - 2021, Co-advised)

  • Yu Qin (2018- 2021, Co-advised)

  • Chenghao Liu (2019 - 2021)

  • Qi Lu (2019 - 2022)

  • Zipei Zhao (2019 - 2022, Co-advised)

  • Xinyi Zhao (2020 - 2023)

  • Shiyu Lu (2020 - 2023)

  • Xinru Zhang (2020-2022)

  • Yijia Zeng (2020 - 2023, Co-advised)

  • Ziqi Wen (2021 - 2024)

  • Bingnan Gao (2021 - 2024, Co-advised)

  • Yuqing Yang (2021 - 2024, Co-advised)

  • Chundan Xu (Started 2022)

  • Zixin Liu (Started 2022)

  • Ruike Jiao (Started 2022)

  • Zhihao Jia (Started 2022)

  • Runze Jiang (Started 2023)

  • Meichen Liu (Started 2023)

  • Yufei Sun (Started 2023)

  • Peng Zhang (Started 2024)

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