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Journal Articles
- 2024
[j25]Evi M. C. Huijben
, Maarten L. Terpstra, Arthur Jr Galapon, Suraj Pai, Adrian Thummerer, Peter Koopmans, Manya Afonso, Maureen A. J. M. van Eijnatten, Oliver J. 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, Zoltán Perkó, Matteo Maspero:
Generating synthetic computed tomography for radiotherapy: SynthRAD2023 challenge report. Medical Image Anal. 97: 103276 (2024)- [j24]Chundan Xu, Jie Li, Yakui Wang, Lixue Wang, Yizhe Wang, Xiaofeng Zhang, Weiqi Liu, Jingang Chen, Aleksandra Vatian, Natalia F. Gusarova, Chuyang Ye, Zhuozhao Zheng:
SiMix: A domain generalization method for cross-site brain MRI harmonization via site mixing. NeuroImage 299: 120812 (2024) - [j23]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) - [j22]Ning Jiang, Gongshu Wang, Chuyang Ye, Tiantian Liu, Tianyi Yan:
Multi-Task Collaborative Pre-Training and Adaptive Token Selection: A Unified Framework for Brain Representation Learning. IEEE J. Biomed. Health Informatics 28(9): 5528-5539 (2024) - 2023
- [j21]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 Anal. 86: 102788 (2023) - [j20]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 Anal. 90: 102968 (2023) - [j19]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) - 2022
- [j18]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 Anal. 79: 102454 (2022) - [j17]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) - 2021
- [j16]Yanlin Liu, Wenhui Cui, Qing Ha, Xiaoliang Xiong, Xiangzhu Zeng, Chuyang Ye:
Knowledge transfer between brain lesion segmentation tasks with increased model capacity. Comput. Medical Imaging Graph. 88: 101842 (2021) - [j15]Yu Qin, Zhiwen Liu, Chenghao Liu, Yuxing Li, Xiangzhu Zeng, Chuyang Ye:
Super-Resolved q-Space deep learning with uncertainty quantification. Medical Image Anal. 67: 101885 (2021) - [j14]Yu Qin, Yuxing Li, Zhizheng Zhuo, Zhiwen Liu, Yaou Liu, Chuyang Ye:
Multimodal super-resolved q-space deep learning. Medical Image Anal. 71: 102085 (2021) - [j13]Qi Lu, Yuxing Li, Chuyang Ye:
Volumetric white matter tract segmentation with nested self-supervised learning using sequential pretext tasks. Medical Image Anal. 72: 102094 (2021) - 2020
- [j12]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 Neuroinformatics 14: 14 (2020) - [j11]Chuyang Ye, Yuxing Li, Xiangzhu Zeng:
An improved deep network for tissue microstructure estimation with uncertainty quantification. Medical Image Anal. 61: 101650 (2020) - 2019
- [j10]Chuyang Ye, Xiuli Li, Jingnan Chen:
A deep network for tissue microstructure estimation using modified LSTM units. Medical Image Anal. 55: 49-64 (2019) - 2018
- [j9]Chuyang Ye, Jerry L. Prince:
Dictionary-based fiber orientation estimation with improved spatial consistency. Medical Image Anal. 44: 41-53 (2018) - 2017
- [j8]Chuyang Ye, Jerry L. Prince:
Probabilistic tractography using Lasso bootstrap. Medical Image Anal. 35: 544-553 (2017) - [j7]Chuyang Ye:
Tissue microstructure estimation using a deep network inspired by a dictionary-based framework. Medical Image Anal. 42: 288-299 (2017) - 2016
- [j6]Chuyang Ye, Jerry L. Prince:
A Bayesian approach to fiber orientation estimation guided by volumetric tract segmentation. Comput. Medical Imaging Graph. 54: 35-47 (2016) - [j5]Chuyang Ye, Jiachen Zhuo, Rao P. Gullapalli, Jerry L. Prince:
Estimation of fiber orientations using neighborhood information. Medical Image Anal. 32: 243-256 (2016) - [j4]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: 435-444 (2016) - 2015
- [j3]Chuyang Ye, Emi Z. Murano, Maureen L. Stone, Jerry L. Prince:
A Bayesian approach to distinguishing interdigitated tongue muscles from limited diffusion magnetic resonance imaging. Comput. Medical Imaging Graph. 45: 63-74 (2015) - [j2]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): 367-381 (2015) - 2011
- [j1]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): 458-468 (2011)
Conference and Workshop Papers
- 2024
- [c41]Lujun Gui, Chuyang Ye, Tianyi Yan:
CAVM: Conditional Autoregressive Vision Model for Contrast-Enhanced Brain Tumor MRI Synthesis. MICCAI (7) 2024: 161-170 - [c40]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. MICCAI (12) 2024: 379-389 - 2023
- [c39]Chuyang Ye, Zhizi Liu, Sihan Dong, Xueying Shao, Hongyu Chen, Honghai Zhu, Liang Zhang:
Measurements of Complexity in Vehicle Dashboards: Revision and Validation of the Perceived Visual Complexity Scale. HCI (1) 2023: 327-335 - [c38]Ziqi Wen, Xinru Zhang, Chuyang Ye:
Source-Free Domain Adaptation for Medical Image Segmentation via Selectively Updated Mean Teacher. IPMI 2023: 225-236 - [c37]Wan Liu, Chuyang Ye:
Better Generalization of White Matter Tract Segmentation to Arbitrary Datasets with Scaled Residual Bootstrap. IPMI 2023: 629-640 - [c36]Huazhang Wang, Zhaojing Luo, James Wei Luen Yip, Chuyang Ye, Meihui Zhang:
ECGGAN: A Framework for Effective and Interpretable Electrocardiogram Anomaly Detection. KDD 2023: 5071-5081 - [c35]Tianshu Zheng, Ruicheng Ba, Xiaoli Wang, Chuyang Ye, Dan Wu:
AUA-dE: An Adaptive Uncertainty Guided Attention for Diffusion MRI Models Estimation. MICCAI (8) 2023: 142-151 - [c34]Ziqi Wen, Chuyang Ye:
A Robust Mean Teacher Framework for Semi-Supervised Cell Detection in Histopathology Images. MIDL 2023: 643-652 - 2022
- [c33]Shiyu Lu, Hao Wang, Chuyang Ye:
Semi-supervised Intracranial Aneurysm Segmentation with Selected Unlabeled Data. BrainLes@MICCAI 2022: 115-123 - [c32]Yijia Zeng, Wan Liu, Zhiwen Liu, Chuyang Ye:
Improved White Matter Tract Segmentation for Unannotated Dataset. CSSE 2022: 388-392 - [c31]Wan Liu, Qi Lu, Zhizheng Zhuo, Yaou Liu, Chuyang Ye:
One-Shot Segmentation of Novel White Matter Tracts via Extensive Data Augmentation. MICCAI (1) 2022: 133-142 - [c30]Chundan Xu, Ziqi Wen, Zhiwen Liu, Chuyang Ye:
Improved Domain Generalization for Cell Detection in Histopathology Images via Test-Time Stain Augmentation. MICCAI (2) 2022: 150-159 - [c29]Tianshu Zheng, Weihao Zheng, Yi Sun, Yi Zhang, Chuyang Ye, Dan Wu:
An Adaptive Network with Extragradient for Diffusion MRI-Based Microstructure Estimation. MICCAI (1) 2022: 153-162 - 2021
- [c28]Qi Lu, Chuyang Ye:
Knowledge Transfer for Few-Shot Segmentation of Novel White Matter Tracts. IPMI 2021: 216-227 - [c27]Chenghao Liu, Xiangzhu Zeng, Kongming Liang, Yizhou Yu, Chuyang Ye:
Improved Brain Lesion Segmentation with Anatomical Priors from Healthy Subjects. MICCAI (1) 2021: 186-195 - [c26]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. MICCAI (1) 2021: 196-205 - [c25]Zipei Zhao, Fengqian Pang, Zhiwen Liu, Chuyang Ye:
Positive-Unlabeled Learning for Cell Detection in Histopathology Images with Incomplete Annotations. MICCAI (8) 2021: 509-518 - 2020
- [c24]Yanlin Liu, Xiangzhu Zeng, Chuyang Ye:
Volume Preserving Brain Lesion Segmentation. BrainLes@MICCAI (1) 2020: 60-69 - [c23]Chenghao Liu, Fengqian Pang, Yanlin Liu, Kongming Liang, Xiuli Li, Xiangzhu Zeng, Chuyang Ye:
Semi-Supervised Brain Lesion Segmentation Using Training Images with and Without Lesions. ISBI 2020: 279-282 - [c22]Shen Wang, Kongming Liang, Chengwei Pan, Chuyang Ye, Xiuli Li, Feng Liu, Yizhou Yu, Yizhou Wang:
Segmentation-Based Method Combined with Dynamic Programming for Brain Midline Delineation. ISBI 2020: 772-776 - [c21]Yu Qin, Yuxing Li, Zhiwen Liu, Chuyang Ye:
Knowledge Transfer Between Datasets for Learning-Based Tissue Microstructure Estimation. ISBI 2020: 1530-1533 - [c20]Zi Lin, Manli Zhong, Xiangzhu Zeng, Chuyang Ye:
Frequency-Selective Learning for CT to MR Synthesis. SASHIMI@MICCAI 2020: 101-109 - [c19]Qi Lu, Yuxing Li, Chuyang Ye:
White Matter Tract Segmentation with Self-supervised Learning. MICCAI (7) 2020: 270-279 - 2019
- [c18]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. IPMI 2019: 554-565 - [c17]Chuyang Ye, Yu Qin, Chenghao Liu, Yuxing Li, Xiangzhu Zeng, Zhiwen Liu:
Super-Resolved q-Space Deep Learning. MICCAI (3) 2019: 582-589 - 2017
- [c16]Chuyang Ye:
Estimation of Tissue Microstructure Using a Deep Network Inspired by a Sparse Reconstruction Framework. IPMI 2017: 466-477 - [c15]Chuyang Ye, Jerry L. Prince:
Fiber Orientation Estimation Guided by a Deep Network. MICCAI (1) 2017: 575-583 - [c14]Chuyang Ye:
Learning-Based Ensemble Average Propagator Estimation. MICCAI (1) 2017: 593-601 - 2016
- [c13]Chuyang Ye:
Fiber Orientation Estimation Using Nonlocal and Local Information. MICCAI (1) 2016: 97-105 - [c12]Ke Li, Chuyang Ye, Zhen Yang, Aaron Carass, Sarah H. Ying, Jerry L. Prince:
Quality assurance using outlier detection on an automatic segmentation method for the cerebellar peduncles. Medical Imaging: Image Processing 2016: 97841H - 2015
- [c11]Chuyang Ye, Jeffrey Glaister, Jerry L. Prince:
Probabilistic fiber tracking using a modified Lasso bootstrap method. ISBI 2015: 943-946 - [c10]Fangxu Xing, Chuyang Ye, Jonghye Woo, Maureen L. Stone, Jerry L. Prince:
Relating speech production to tongue muscle compressions using tagged and high-resolution magnetic resonance imaging. Medical Imaging: Image Processing 2015: 94131L - 2014
- [c9]Chuyang Ye, Aaron Carass, Emi Z. Murano, Maureen L. Stone, Jerry L. Prince:
A Bayesian Approach to Distinguishing Interdigitated Muscles in the Tongue from Limited Diffusion Weighted Imaging. BAMBI 2014: 13-24 - [c8]Chuyang Ye, Vivek Vaidya, Fei Zhao:
Improved mass detection in 3D automated breast ultrasound using region based features and multi-view information. EMBC 2014: 2865-2868 - [c7]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. MICCAI (3) 2014: 169-176 - 2013
- [c6]Chuyang Ye, John A. Bogovic, Sarah H. Ying, Jerry L. Prince:
Segmentation of the complete superior cerebellar peduncles using a multi-object geometric deformable model. ISBI 2013: 49-52 - [c5]Joshua V. Stough, Chuyang Ye, Sarah H. Ying, Jerry L. Prince:
Thalamic parcellation from multi-modal data using random forest learning. ISBI 2013: 852-855 - [c4]Chuyang Ye, John A. Bogovic, Sarah H. Ying, Jerry L. Prince:
Parcellation of the thalamus using diffusion tensor images and a multi-object geometric deformable model. Medical Imaging: Image Processing 2013: 866909 - 2012
- [c3]Chuyang Ye, John A. Bogovic, Pierre-Louis Bazin, Jerry L. Prince, Sarah H. Ying:
Fully automatic segmentation of the dentate nucleus using diffusion weighted images. ISBI 2012: 1128-1131 - [c2]Chuyang Ye, Pierre-Louis Bazin, John A. Bogovic, Sarah H. Ying, Jerry L. Prince:
Labeling of the cerebellar peduncles using a supervised Gaussian classifier with volumetric tract segmentation. Medical Imaging: Image Processing 2012: 831447 - [c1]Chuyang Ye, Pierre-Louis Bazin, Sarah H. Ying, Jerry L. Prince:
A fiber tracking method guided by volumetric tract segmentation. MMBIA 2012: 137-142
Informal and Other Publications
- 2024
- [i21]Ruizhi Zhu, Xinru Zhang, Haowen Pang, Chundan Xu, Chuyang Ye:
Advancing Brain Tumor Inpainting with Generative Models. CoRR abs/2402.01509 (2024) - [i20]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. CoRR abs/2405.10246 (2024) - [i19]Qinting Jiang, Chuyang Ye, Dongyan Wei, Yuan Xue, Jingyan Jiang, Zhi Wang:
Discover Your Neighbors: Advanced Stable Test-Time Adaptation in Dynamic World. CoRR abs/2406.05413 (2024) - [i18]Lujun Gui, Chuyang Ye, Tianyi Yan:
CAVM: Conditional Autoregressive Vision Model for Contrast-Enhanced Brain Tumor MRI Synthesis. CoRR abs/2406.16074 (2024) - [i17]Chuyang Ye, Dongyan Wei, Zhendong Liu, Yuanyi Pang, Yixi Lin, Jiarong Liao, Qinting Jiang, Xianghua Fu, Qing Li, Jingyan Jiang:
DATTA: Towards Diversity Adaptive Test-Time Adaptation in Dynamic Wild World. CoRR abs/2408.08056 (2024) - 2023
- [i16]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. CoRR abs/2302.08050 (2023) - [i15]Wan Liu, Qi Lu, Zhizheng Zhuo, Yaou Liu, Chuyang Ye:
One-Shot Segmentation of Novel White Matter Tracts via Extensive Data Augmentation. CoRR abs/2303.06852 (2023) - [i14]Wan Liu, Yuqian Chen, Chuyang Ye, Nikos Makris, Yogesh Rathi, Weidong Cai, Fan Zhang, Lauren J. O'Donnell:
Fiber Tract Shape Measures Inform Prediction of Non-Imaging Phenotypes. CoRR abs/2303.09124 (2023) - [i13]Xinru Zhang, Ni Ou, Chenghao Liu, Zhizheng Zhuo, Yaou Liu, Chuyang Ye:
Unsupervised Brain Tumor Segmentation with Image-based Prompts. CoRR abs/2304.01472 (2023) - [i12]Wan Liu, Chuyang Ye:
Better Generalization of White Matter Tract Segmentation to Arbitrary Datasets with Scaled Residual Bootstrap. CoRR abs/2309.13980 (2023) - 2022
- [i11]Tianshu Zheng, Cong Sun, Weihao Zheng, Wen Shi, Haotian Li, Yi Sun, Yi Zhang, Guangbin Wang, Chuyang Ye, Dan Wu:
A microstructure estimation Transformer inspired by sparse representation for diffusion MRI. CoRR abs/2205.06450 (2022) - 2021
- [i10]Qi Lu, Chuyang Ye:
Knowledge Transfer for Few-shot Segmentation of Novel White Matter Tracts. CoRR abs/2105.14513 (2021) - [i9]Zipei Zhao, Fengqian Pang, Zhiwen Liu, Chuyang Ye:
Positive-unlabeled Learning for Cell Detection in Histopathology Images with Incomplete Annotations. CoRR abs/2106.15918 (2021) - [i8]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. CoRR abs/2108.06883 (2021) - 2020
- [i7]Shen Wang, Kongming Liang, Chengwei Pan, Chuyang Ye, Xiuli Li, Feng Liu, Yizhou Yu, Yizhou Wang:
Segmentation-based Method combined with Dynamic Programming for Brain Midline Delineation. CoRR abs/2002.11918 (2020) - 2019
- [i6]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. CoRR abs/1903.01248 (2019) - [i5]Yu Qin, Yuxing Li, Zhiwen Liu, Chuyang Ye:
Knowledge Transfer between Datasets for Learning-based Tissue Microstructure Estimation. CoRR abs/1910.10930 (2019) - 2017
- [i4]Chuyang Ye:
Estimation of Tissue Microstructure Using a Deep Network Inspired by a Sparse Reconstruction Framework. CoRR abs/1704.01246 (2017) - [i3]Chuyang Ye, Jerry L. Prince:
Fiber Orientation Estimation Guided by a Deep Network. CoRR abs/1705.06870 (2017) - [i2]Chuyang Ye:
Learning-based Ensemble Average Propagator Estimation. CoRR abs/1706.06258 (2017) - 2016
- [i1]Chuyang Ye, Jiachen Zhuo, Rao P. Gullapalli, Jerry L. Prince:
Estimation of Fiber Orientations Using Neighborhood Information. CoRR abs/1601.04115 (2016)
Coauthor Index
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