Direct segmentation of the major white matter tracts in diffusion tensor images. - Pierre-Louis Bazin; Chuyang Ye; John A. Bogovic; Navid Shiee; Daniel S. Reich; Jerry L. Prince; Dzung L. Pham (NeuroImage, 2011)

Fully automatic segmentation of the dentate nucleus using diffusion weighted images. - Chuyang Ye; John A. Bogovic; Pierre-Louis Bazin; Jerry L. Prince; Sarah H. Ying (ISBI, 2012)

Labeling of the cerebellar peduncles using a supervised Gaussian classifier with volumetric tract segmentation. - Chuyang Ye; Pierre-Louis Bazin; John A. Bogovic; Sarah H. Ying; Jerry L. Prince (Image Processing, 2012)

A fiber tracking method guided by volumetric tract segmentation. - Chuyang Ye; Pierre-Louis Bazin; Sarah H. Ying; Jerry L. Prince (MMBIA, 2012)

Thalamic parcellation from multi-modal data using random forest learning. - Joshua V. Stough; Chuyang Ye; Sarah H. Ying; Jerry L. Prince (ISBI, 2013)

Segmentation of the complete superior cerebellar peduncles using a multi-object geometric deformable model. - Chuyang Ye; John A. Bogovic; Sarah H. Ying; Jerry L. Prince (ISBI, 2013)

Parcellation of the thalamus using diffusion tensor images and a multi-object geometric deformable model. - Chuyang Ye; John A. Bogovic; Sarah H. Ying; Jerry L. Prince (Image Processing, 2013)

A Bayesian Approach to Distinguishing Interdigitated Muscles in the Tongue from Limited Diffusion Weighted Imaging. - Chuyang Ye; Aaron Carass; Emi Z. Murano; Maureen L. Stone; Jerry L. Prince (BAMBI, 2014)

Improved mass detection in 3D automated breast ultrasound using region based features and multi-view information. - Chuyang Ye; Vivek Vaidya 001; Fei Zhao (EMBC, 2014)

Automatic Method for Thalamus Parcellation Using Multi-modal Feature Classification. - Joshua V. Stough; Jeffrey Glaister; Chuyang Ye; Sarah H. Ying; Jerry L. Prince; Aaron Carass (MICCAI (3), 2014)

Probabilistic fiber tracking using a modified Lasso bootstrap method. - Chuyang Ye; Jeffrey Glaister; Jerry L. Prince (ISBI, 2015)

Relating speech production to tongue muscle compressions using tagged and high-resolution magnetic resonance imaging. - Fangxu Xing; Chuyang Ye; Jonghye Woo; Maureen L. Stone; Jerry L. Prince (Image Processing, 2015)

A Bayesian approach to distinguishing interdigitated tongue muscles from limited diffusion magnetic resonance imaging. - Chuyang Ye; Emi Z. Murano; Maureen L. Stone; Jerry L. Prince (Comput. Medical Imaging Graph., 2015)

Segmentation of the Cerebellar Peduncles Using a Random Forest Classifier and a Multi-object Geometric Deformable Model: Application to Spinocerebellar Ataxia Type 6. - Chuyang Ye; Zhen Yang 002; Sarah H. Ying; Jerry L. Prince (Neuroinformatics, 2015)

Fiber Orientation Estimation Using Nonlocal and Local Information. - Chuyang Ye (MICCAI (1), 2016)

Quality assurance using outlier detection on an automatic segmentation method for the cerebellar peduncles. - Ke Li; Chuyang Ye; Zhen Yang 002; Aaron Carass; Sarah H. Ying; Jerry L. Prince (Image Processing, 2016)

A Bayesian approach to fiber orientation estimation guided by volumetric tract segmentation. - Chuyang Ye; Jerry L. Prince (Comput. Medical Imaging Graph., 2016)

Estimation of fiber orientations using neighborhood information. - Chuyang Ye; Jiachen Zhuo; Rao P. Gullapalli; Jerry L. Prince (Medical Image Anal., 2016)

Automated cerebellar lobule segmentation with application to cerebellar structural analysis in cerebellar disease. - Zhen Yang 002; Chuyang Ye; John A. Bogovic; Aaron Carass; Bruno M. Jedynak; Sarah H. Ying; Jerry L. Prince (NeuroImage, 2016)

Estimation of Tissue Microstructure Using a Deep Network Inspired by a Sparse Reconstruction Framework. - Chuyang Ye (IPMI, 2017)

Learning-Based Ensemble Average Propagator Estimation. - Chuyang Ye (MICCAI (1), 2017)

Fiber Orientation Estimation Guided by a Deep Network. - Chuyang Ye; Jerry L. Prince (MICCAI (1), 2017)

Tissue microstructure estimation using a deep network inspired by a dictionary-based framework. - Chuyang Ye (Medical Image Anal., 2017)

Probabilistic tractography using Lasso bootstrap. - Chuyang Ye; Jerry L. Prince (Medical Image Anal., 2017)

Dictionary-based fiber orientation estimation with improved spatial consistency. - Chuyang Ye; Jerry L. Prince (Medical Image Anal., 2018)

Semi-supervised Brain Lesion Segmentation with an Adapted Mean Teacher Model. - Wenhui Cui; Yanlin Liu; Yuxing Li; Menghao Guo; Yiming Li; Xiuli Li; Tianle Wang 002; Xiangzhu Zeng; Chuyang Ye (IPMI, 2019)

Super-Resolved q-Space Deep Learning. - Chuyang Ye; Yu Qin; Chenghao Liu; Yuxing Li; Xiangzhu Zeng; Zhiwen Liu (MICCAI (3), 2019)

A deep network for tissue microstructure estimation using modified LSTM units. - Chuyang Ye; Xiuli Li; Jingnan Chen (Medical Image Anal., 2019)

Volume Preserving Brain Lesion Segmentation. - Yanlin Liu; Xiangzhu Zeng; Chuyang Ye (BrainLes@MICCAI (1), 2020)

Semi-Supervised Brain Lesion Segmentation Using Training Images with and Without Lesions. - Chenghao Liu; Fengqian Pang; Yanlin Liu; Kongming Liang; Xiuli Li; Xiangzhu Zeng; Chuyang Ye (ISBI, 2020)

Knowledge Transfer Between Datasets for Learning-Based Tissue Microstructure Estimation. - Yu Qin; Yuxing Li; Zhiwen Liu; Chuyang Ye (ISBI, 2020)

Segmentation-Based Method Combined with Dynamic Programming for Brain Midline Delineation. - Shen Wang; Kongming Liang; Chengwei Pan; Chuyang Ye; Xiuli Li; Feng Liu 036; Yizhou Yu; Yizhou Wang 001 (ISBI, 2020)

Frequency-Selective Learning for CT to MR Synthesis. - Zi Lin; Manli Zhong; Xiangzhu Zeng; Chuyang Ye (SASHIMI@MICCAI, 2020)

White Matter Tract Segmentation with Self-supervised Learning. - Qi Lu; Yuxing Li; Chuyang Ye (MICCAI (7), 2020)

MonkeyCBP: A Toolbox for Connectivity-Based Parcellation of Monkey Brain. - Bin He; Zhengyi Yang 002; Lingzhong Fan; Bin Gao; Hai Li; Chuyang Ye; Bo You; Tianzi Jiang (Frontiers Neuroinformatics, 2020)

An improved deep network for tissue microstructure estimation with uncertainty quantification. - Chuyang Ye; Yuxing Li; Xiangzhu Zeng (Medical Image Anal., 2020)

Knowledge Transfer for Few-Shot Segmentation of Novel White Matter Tracts. - Qi Lu; Chuyang Ye (IPMI, 2021)

Improved Brain Lesion Segmentation with Anatomical Priors from Healthy Subjects. - Chenghao Liu; Xiangzhu Zeng; Kongming Liang; Yizhou Yu; Chuyang Ye (MICCAI (1), 2021)

CarveMix: A Simple Data Augmentation Method for Brain Lesion Segmentation. - Xinru Zhang; Chenghao Liu; Ni Ou; Xiangzhu Zeng; Xiaoliang Xiong; Yizhou Yu; Zhiwen Liu; Chuyang Ye (MICCAI (1), 2021)

Positive-Unlabeled Learning for Cell Detection in Histopathology Images with Incomplete Annotations. - Zipei Zhao; Fengqian Pang; Zhiwen Liu; Chuyang Ye (MICCAI (8), 2021)

Knowledge transfer between brain lesion segmentation tasks with increased model capacity. - Yanlin Liu; Wenhui Cui; Qing Ha; Xiaoliang Xiong; Xiangzhu Zeng; Chuyang Ye (Comput. Medical Imaging Graph., 2021)

Volumetric white matter tract segmentation with nested self-supervised learning using sequential pretext tasks. - Qi Lu; Yuxing Li; Chuyang Ye (Medical Image Anal., 2021)

Super-Resolved q-Space deep learning with uncertainty quantification. - Yu Qin; Zhiwen Liu; Chenghao Liu; Yuxing Li; Xiangzhu Zeng; Chuyang Ye (Medical Image Anal., 2021)

Multimodal super-resolved q-space deep learning. - Yu Qin; Yuxing Li; Zhizheng Zhuo; Zhiwen Liu; Yaou Liu; Chuyang Ye (Medical Image Anal., 2021)

Semi-supervised Intracranial Aneurysm Segmentation with Selected Unlabeled Data. - Shiyu Lu; Hao Wang; Chuyang Ye (BrainLes@MICCAI, 2022)

Improved White Matter Tract Segmentation for Unannotated Dataset. - Yijia Zeng; Wan Liu 001; Zhiwen Liu; Chuyang Ye (CSSE, 2022)

One-Shot Segmentation of Novel White Matter Tracts via Extensive Data Augmentation. - Wan Liu 001; Qi Lu; Zhizheng Zhuo; Yaou Liu; Chuyang Ye (MICCAI (1), 2022)

Improved Domain Generalization for Cell Detection in Histopathology Images via Test-Time Stain Augmentation. - Chundan Xu; Ziqi Wen; Zhiwen Liu; Chuyang Ye (MICCAI (2), 2022)

An Adaptive Network with Extragradient for Diffusion MRI-Based Microstructure Estimation. - Tianshu Zheng; Weihao Zheng; Yi Sun; Yi Zhang 080; Chuyang Ye; Dan Wu (MICCAI (1), 2022)

A microstructure estimation Transformer inspired by sparse representation for diffusion MRI. - Tianshu Zheng; Cong Sun; Weihao Zheng; Wen Shi; Haotian Li; Yi Sun; Yi Zhang 080; Guangbin Wang; Chuyang Ye; Dan Wu (CoRR, 2022)

A transfer learning approach to few-shot segmentation of novel white matter tracts. - Qi Lu; Wan Liu 001; Zhizheng Zhuo; Yuxing Li; Yunyun Duan; Pinnan Yu; Liying Qu; Chuyang Ye; Yaou Liu (Medical Image Anal., 2022)

Volumetric segmentation of white matter tracts with label embedding. - Wan Liu 001; Qi Lu; Zhizheng Zhuo; Yuxing Li; Yunyun Duan; Pinnan Yu; Liying Qu; Chuyang Ye; Yaou Liu (NeuroImage, 2022)

Measurements of Complexity in Vehicle Dashboards: Revision and Validation of the Perceived Visual Complexity Scale. - Chuyang Ye; Zhizi Liu; Sihan Dong; Xueying Shao; Hongyu Chen; Honghai Zhu; Liang Zhang (HCI (1), 2023)

Better Generalization of White Matter Tract Segmentation to Arbitrary Datasets with Scaled Residual Bootstrap. - Wan Liu 001; Chuyang Ye (IPMI, 2023)

Source-Free Domain Adaptation for Medical Image Segmentation via Selectively Updated Mean Teacher. - Ziqi Wen; Xinru Zhang; Chuyang Ye (IPMI, 2023)

ECGGAN: A Framework for Effective and Interpretable Electrocardiogram Anomaly Detection. - Huazhang Wang; Zhaojing Luo; James Wei Luen Yip; Chuyang Ye; Meihui Zhang 001 (KDD, 2023)

AUA-dE: An Adaptive Uncertainty Guided Attention for Diffusion MRI Models Estimation. - Tianshu Zheng; Ruicheng Ba; Xiaoli Wang; Chuyang Ye; Dan Wu (MICCAI (8), 2023)

A Robust Mean Teacher Framework for Semi-Supervised Cell Detection in Histopathology Images. - Ziqi Wen; Chuyang Ye (MIDL, 2023)

Positive-unlabeled learning for binary and multi-class cell detection in histopathology images with incomplete annotations. - Zipei Zhao; Fengqian Pang; Yaou Liu; Zhiwen Liu; Chuyang Ye (CoRR, 2023)

Fiber Tract Shape Measures Inform Prediction of Non-Imaging Phenotypes. - Wan Liu 001; Yuqian Chen; Chuyang Ye; Nikos Makris; Yogesh Rathi; Weidong Cai 001; Fan Zhang 013; Lauren J. O'Donnell (CoRR, 2023)

Unsupervised Brain Tumor Segmentation with Image-based Prompts. - Xinru Zhang; Ni Ou; Chenghao Liu; Zhizheng Zhuo; Yaou Liu; Chuyang Ye (CoRR, 2023)

A microstructure estimation Transformer inspired by sparse representation for diffusion MRI. - Tianshu Zheng; Guohui Yan; Haotian Li; Weihao Zheng; Wen Shi; Yi Zhang 080; Chuyang Ye; Dan Wu (Medical Image Anal., 2023)

CarveMix: A simple data augmentation method for brain lesion segmentation. - Xinru Zhang; Chenghao Liu; Ni Ou; Xiangzhu Zeng; Zhizheng Zhuo; Yunyun Duan; Xiaoliang Xiong; Yizhou Yu; Zhiwen Liu; Yaou Liu; Chuyang Ye (NeuroImage, 2023)

One-shot segmentation of novel white matter tracts via extensive data augmentation and adaptive knowledge transfer. - Wan Liu 001; Zhizheng Zhuo; Yaou Liu; Chuyang Ye (Medical Image Anal., 2023)

MedMM: A Multimodal Fusion Framework for 3D Medical Image Classification with Multigranular Text Guidance. - Shanbo Zhao; Meihui Zhang 001; Xiaoqin Zhu; Junjie Li; Yunyun Duan; Zhizheng Zhuo; Yaou Liu; Chuyang Ye (BigCom, 2024)

Intracranial Steno-Occlusive Lesion Detection on Magnetic Resonance Angiography Images. - Zhihao Jia; Chuyang Ye; Youyuan Zhao; Jingang Chen; Jiande Ouyang; Xuesheng Ma (ICBBT, 2024)

CAVM: Conditional Autoregressive Vision Model for Contrast-Enhanced Brain Tumor MRI Synthesis. - Lujun Gui; Chuyang Ye; Tianyi Yan (MICCAI (7), 2024)

Improved Stroke Lesion Segmentation via Cross-Model Knowledge Distillation. - Zixin Liu; Haowen Pang; Xinru Zhang; Chuyang Ye (SWITCH/ISLES@MICCAI, 2024)

A Foundation Model for Brain Lesion Segmentation with Mixture of Modality Experts. - Xinru Zhang; Ni Ou; Berke Doga Basaran; Marco Visentin; Mengyun Qiao; Renyang Gu; Cheng Ouyang; Yaou Liu; Paul M. Matthews; Chuyang Ye; Wenjia Bai (MICCAI (12), 2024)

Advancing Brain Tumor Inpainting with Generative Models. - Ruizhi Zhu; Xinru Zhang; Haowen Pang; Chundan Xu; Chuyang Ye (CoRR, 2024)

Discover Your Neighbors: Advanced Stable Test-Time Adaptation in Dynamic World. - Qinting Jiang; Chuyang Ye; Dongyan Wei; Yuan Xue; Jingyan Jiang; Zhi Wang (CoRR, 2024)

DATTA: Towards Diversity Adaptive Test-Time Adaptation in Dynamic Wild World. - Chuyang Ye; Dongyan Wei; Zhendong Liu; Yuanyi Pang; Yixi Lin; Jiarong Liao; Qinting Jiang; Xianghua Fu; Qing Li; Jingyan Jiang (CoRR, 2024)

Generating synthetic computed tomography for radiotherapy: SynthRAD2023 challenge report. - 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; et al. (Medical Image Anal., 2024)

Deep learning enables accurate brain tissue microstructure analysis based on clinically feasible diffusion magnetic resonance imaging. - Yuxing Li; Zhizheng Zhuo; Chenghao Liu; Yunyun Duan; Yulu Shi; Tingting Wang; Runzhi Li; Yanli Wang; Jiwei Jiang; Jun Xu; Decai Tian; Xinghu Zhang; et al. (NeuroImage, 2024)

SiMix: A domain generalization method for cross-site brain MRI harmonization via site mixing. - 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 (NeuroImage, 2024)

Multi-Task Collaborative Pre-Training and Adaptive Token Selection: A Unified Framework for Brain Representation Learning. - Ning Jiang; Gongshu Wang; Chuyang Ye; Tiantian Liu; Tianyi Yan (IEEE J. Biomed. Health Informatics, 2024)

Cascaded Diffusion Model and Segment Anything Model for Medical Image Synthesis via Uncertainty-Guided Prompt Generation. - Haowen Pang; Xiaoming Hong; Peng Zhang; Chuyang Ye (IPMI (1), 2025)

Anatomy-guided slice-description interaction for multimodal brain disease diagnosis based on 3D image and radiological report. - Xin Gao; Meihui Zhang 001; Junjie Li; Shanbo Zhao; Zhizheng Zhuo; Liying Qu; Jinyuan Weng; Li Chai 009; Yunyun Duan; Chuyang Ye; Yaou Liu (Comput. Medical Imaging Graph., 2025)

An extragradient and noise-tuning adaptive iterative network for diffusion MRI-based microstructural estimation. - Tianshu Zheng; Chuyang Ye; Zhaopeng Cui; Hui Zhang 005; Daniel C. Alexander; Dan Wu (Medical Image Anal., 2025)

HMDA: A Hybrid Model With Multi-Scale Deformable Attention for Medical Image Segmentation. - Mengmeng Wu; Tiantian Liu; Xin Dai; Chuyang Ye; Jinglong Wu; Shintaro Funahashi; Tianyi Yan (IEEE J. Biomed. Health Informatics, 2025)

Attention-Based Q-Space Deep Learning Generalized for Accelerated Diffusion Magnetic Resonance Imaging. - Fangrong Zong; Zaimin Zhu; Jiayi Zhang; Xiaofeng Deng; Zhuangzhuang Li; Chuyang Ye; Yong Liu 002 (IEEE J. Biomed. Health Informatics, 2025)

Multi-modal brain MRI synthesis based on SwinUNETR. - Haowen Pang; Weiyan Guo; Chuyang Ye (CoRR, 2025)

Feature-Based Instance Neighbor Discovery: Advanced Stable Test-Time Adaptation in Dynamic World. - Qinting Jiang; Chuyang Ye; Dongyan Wei; Bingli Wang; Yuan Xue; Jingyan Jiang; Zhi Wang (CoRR, 2025)

A Foundation Model for Lesion Segmentation on Brain MRI With Mixture of Modality Experts. - Xinru Zhang; Ni Ou; Berke Doga Basaran; Marco Visentin; Mengyun Qiao; Renyang Gu; Paul M. Matthews; Yaou Liu; Chuyang Ye; Wenjia Bai (IEEE Trans. Medical Imaging, 2025)

MolCLIP: A Molecular-Auxiliary CLIP Framework for Identifying Drug Mechanism of Action Based on Time-Lapsed Mitochondrial Images. - Fengqian Pang; Chunyue Lei; Hongfei Zhao; Chenghao Liu; Zhiqiang Xing; Huafeng Wang; Chuyang Ye (CoRR, 2025)