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2025

Editorial for Special Issue on Foundation Models for Medical Image AnalysisXiaosong Wang 0001, Dequan Wang, Xiaoxiao Li, Jens Rittscher, Dimitris N. Metaxas, Shaoting Zhang 0001. mia, 100:103389, 2025. [doi]

ECGFM: A foundation model for ECG analysis trained on a multi-center million-ECG datasetShaoting Zhang 0001, Yishan Du, Wenji Wang, Xianying He, Fangfang Cui, Liang Zhao 0018, Bei Wang, Zhiqiang Hu, Ziqiang Wang, Qing Xia 0002, Tian Shen, Jie Zhao 0014. inffus, 124:103363, 2025. [doi]

Unleashing the Potential of Vision-Language Pre-Training for 3D Zero-Shot Lesion Segmentation via Mask-Attribute AlignmentYankai Jiang 0003, Wenhui Lei, Xiaofan Zhang 0002, Shaoting Zhang 0001. iclr 2025: [doi]

Improving Foundation Model for Endoscopy Video Analysis via Representation Learning on Long SequencesZhao Wang 0006, Chang Liu, Lingting Zhu, Tongtong Wang, Shaoting Zhang 0001, Qi Dou 0001. titb, 29(5):3526-3536, May 2025. [doi]

MedOdyssey: A Medical Domain Benchmark for Long Context Evaluation Up to 200K TokensYongqi Fan, Hongli Sun, Kui Xue, Xiaofan Zhang 0002, Shaoting Zhang 0001, Tong Ruan. naacl 2025: 32-56 [doi]

UM-CAM: Uncertainty-weighted multi-resolution class activation maps for weakly-supervised segmentationJia Fu, Guotai Wang, Tao Lu, Qiang Yue, Tom Vercauteren, Sébastien Ourselin, Shaoting Zhang 0001. PR, 160:111204, 2025. [doi]

A-Eval: A benchmark for cross-dataset and cross-modality evaluation of abdominal multi-organ segmentationZiyan Huang, Zhongying Deng, Jin Ye, Haoyu Wang, Yanzhou Su, Tianbin Li, Hui Sun, Junlong Cheng, Jianpin Chen, Junjun He, Yun Gu, Shaoting Zhang 0001, Lixu Gu, Yu Qiao 0001. mia, 101:103499, 2025. [doi]

MedLSAM: Localize and segment anything model for 3D CT imagesWenhui Lei, Wei Xu, Kang Li 0004, Xiaofan Zhang 0002, Shaoting Zhang 0001. mia, 99:103370, 2025. [doi]

Interactive Evaluation for Medical LLMs via Task-oriented Dialogue SystemRuoyu Liu, Kui Xue, Xiaofan Zhang 0002, Shaoting Zhang 0001. COLING 2025: 4871-4896 [doi]

Fairness Analysis of Clip-Based Foundation Models for X-Ray Image ClassificationXiangyu Sun, Xiaoguang Zou, Yuanquan Wu, Guotai Wang, Shaoting Zhang 0001. isbi 2025: 1-5 [doi]

Fine-grained medical image out-of-distribution detection through multi-view feature uncertainty and adversarial sample generationJie Wei, Guotai Wang, Shaoting Zhang 0001. PR, 162:111401, 2025. [doi]

Slice2Mesh: 3D Surface Reconstruction From Sparse Slices of Images for the Left VentricleJia Xiao, Wen Zheng, Wenji Wang, Qing Xia 0002, Zhennan Yan, Qian Guo, Xiao Wang, Shaoping Nie, Shaoting Zhang 0001. tmi, 44(3):1541-1555, March 2025. [doi]

Segmentation and Vascular Vectorization for Coronary Artery by Geometry-Based Cascaded Neural NetworkXiaoyu Yang, Lijian Xu, Simon C. H. Yu, Qing Xia 0002, Hongsheng Li 0001, Shaoting Zhang 0001. tmi, 44(1):259-269, January 2025. [doi]

Rethinking the generalization of drug target affinity prediction algorithms via similarity aware evaluationChenbin Zhang, Zhiqiang Hu, Chuchu Jiang, Wen Chen 0022, Jie Xu, Shaoting Zhang 0001. iclr 2025: [doi]

Guiding Medical Vision-Language Models with Diverse Visual Prompts: Framework Design and Comprehensive Exploration of Prompt VariationsKangyu Zhu, Ziyuan Qin 0001, Huahui Yi, Zekun Jiang, Qicheng Lao, Shaoting Zhang 0001, Kang Li 0004. naacl 2025: 11726-11739 [doi]

MeNTi: Bridging Medical Calculator and LLM Agent with Nested Tool CallingYakun Zhu, Shaohang Wei, Xu Wang, Kui Xue, Shaoting Zhang 0001, Xiaofan Zhang 0002. naacl 2025: 5097-5116 [doi]

2024

On the challenges and perspectives of foundation models for medical image analysisShaoting Zhang 0001, Dimitris N. Metaxas. mia, 91:102996, January 2024. [doi]

ZePT: Zero-Shot Pan-Tumor Segmentation via Query-Disentangling and Self-PromptingYankai Jiang 0003, Zhongzhen Huang, Rongzhao Zhang, Xiaofan Zhang 0002, Shaoting Zhang 0001. cvpr 2024: 11386-11397 [doi]

SAM-Med3D: Towards General-Purpose Segmentation Models for Volumetric Medical ImagesHaoyu Wang 0010, Sizheng Guo, Jin Ye 0002, Zhongying Deng, Junlong Cheng, Tianbin Li, Jianpin Chen, Yanzhou Su, Ziyan Huang, Yiqing Shen 0003, Bin Fu, Shaoting Zhang 0001, Junjun He, Yu Qiao 0001. eccv 2025: 51-67 [doi]

TransUNet: Rethinking the U-Net architecture design for medical image segmentation through the lens of transformersJieneng Chen, Jieru Mei, Xianhang Li, Yongyi Lu, Qihang Yu, QingYue Wei, Xiangde Luo, Yutong Xie, Ehsan Adeli 0001, Yan Wang 0033, Matthew P. Lungren, Shaoting Zhang 0001, Lei Xing 0001, Le Lu 0001, Alan L. Yuille, Yuyin Zhou. mia, 97:103280, 2024. [doi]

Boosting Dermatoscopic Lesion Segmentation Via Diffusion Models With Visual And Textual PromptsShiyi Du, Xiaosong Wang, Yongyi Lu, Yuyin Zhou, Shaoting Zhang 0001, Alan L. Yuille, Kang Li 0004, Zongwei Zhou. isbi 2024: 1-5 [doi]

DMSPS: Dynamically mixed soft pseudo-label supervision for scribble-supervised medical image segmentationMeng Han, Xiangde Luo, Xiangjiang Xie, Wenjun Liao, Shichuan Zhang, Tao Song, Guotai Wang, Shaoting Zhang 0001. mia, 97:103274, 2024. [doi]

CAT: Coordinating Anatomical-Textual Prompts for Multi-Organ and Tumor SegmentationZhongzhen Huang, Yankai Jiang 0003, Rongzhao Zhang, Shaoting Zhang 0001, Xiaofan Zhang 0002. nips 2024: [doi]

Modality-Aware and Shift Mixer for Multi-Modal Brain Tumor SegmentationZhongzhen Huang, Linda Wei, Shaoting Zhang 0001, Xiaofan Zhang 0002. ecai 2024: 306-313 [doi]

One-Shot Weakly-Supervised Segmentation in 3D Medical ImagesWenhui Lei, Qi Su, Tianyu Jiang, Ran Gu, Na Wang, Xinglong Liu, Guotai Wang, Xiaofan Zhang 0002, Shaoting Zhang 0001. tmi, 43(1):175-189, January 2024. [doi]

One-to-Normal: Anomaly Personalization for Few-shot Anomaly DetectionYiyue Li, Shaoting Zhang 0001, Kang Li 0004, Qicheng Lao. nips 2024: [doi]

Hierarchical-Instance Contrastive Learning for Minority Detection on Imbalanced Medical DatasetsYiyue Li, Guangwu Qian, Xiaoshuang Jiang, Zekun Jiang, Wen Wen, Shaoting Zhang 0001, Kang Li 0004, Qicheng Lao. tmi, 43(1):416-426, January 2024. [doi]

RPL-SFDA: Reliable Pseudo Label-Guided Source-Free Cross-Modality Adaptation for NPC GTV SegmentationXinya Liu, Jianghao Wu, Xiangde Luo, Wenjun Liao, Shichuan Zhang, Shaoting Zhang 0001, Guotai Wang. isbi 2024: 1-5 [doi]

Swin-UMamba: Mamba-Based UNet with ImageNet-Based PretrainingJiarun Liu, Hao Yang 0026, Hong-Yu Zhou, Yan-xi, Lequan Yu, Cheng Li 0008, Yong Liang, Guangming Shi, Yizhou Yu, Shaoting Zhang 0001, Hairong Zheng, Shanshan Wang 0002. miccai 2024: 615-625 [doi]

Domain composition and attention network trained with synthesized unlabeled images for generalizable medical image segmentationJiangshan Lu, Ran Gu, Wenjun Liao, Shichuan Zhang, Huijun Yu, Shaoting Zhang 0001, Guotai Wang. ijon, 599:128115, 2024. [doi]

PathoTune: Adapting Visual Foundation Model to Pathological SpecialistsJiaxuan Lu, Fang Yan, Xiaofan Zhang 0002, Yue Gao 0002, Shaoting Zhang 0001. miccai 2024: 395-406 [doi]

Rethinking Abdominal Organ Segmentation (RAOS) in the Clinical Scenario: A Robustness Evaluation Benchmark with Challenging CasesXiangde Luo, Zihan Li, Shaoting Zhang 0001, Wenjun Liao, Guotai Wang. miccai 2024: 531-541 [doi]

DA-Tran: Multiphase liver tumor segmentation with a domain-adaptive transformer networkYangfan Ni, Geng Chen, Zhan Feng, Heng Cui, Dimitris N. Metaxas, Shaoting Zhang 0001, Wentao Zhu. PR, 149:110233, 2024. [doi]

Multi-modal Data Binding for Survival Analysis Modeling with Incomplete Data and AnnotationsLinhao Qu, Dan Huang, Shaoting Zhang 0001, Xiaosong Wang. miccai 2024: 501-510 [doi]

ScribSD+: Scribble-supervised medical image segmentation based on simultaneous multi-scale knowledge distillation and class-wise contrastive regularizationYijie Qu, Tao Lu, Shaoting Zhang 0001, Guotai Wang. cmig, 116:102416, 2024. [doi]

Pathology-Knowledge Enhanced Multi-instance Prompt Learning for Few-Shot Whole Slide Image ClassificationLinhao Qu, Dingkang Yang, Dan Huang, Qinhao Guo, Rongkui Luo, Shaoting Zhang 0001, Xiaosong Wang 0001. eccv 2025: 196-212 [doi]

Medical Dialogue System: A Survey of Categories, Methods, Evaluation and ChallengesXiaoming Shi, Zeming Liu, Li Du, Yuxuan Wang 0001, Hongru Wang 0003, Yuhang Guo 0001, Tong Ruan, Jie Xu, Xiaofan Zhang 0002, Shaoting Zhang 0001. acl 2014: 2840-2861 [doi]

BrainSCK: Brain Structure and Cognition Alignment via Knowledge Injection and Reactivation for Diagnosing Brain DisordersLilong Wang, Mianxin Liu, Shaoting Zhang 0001, Xiaosong Wang. miccai 2024: 45-55 [doi]

Dual-Perspective Label Smoothing for Accurate Tumor SegmentationLilong Wang, Xuan Wang, Yali Xu, Xiangan Wu, Shunda Du, Shaoting Zhang 0001, Qiang Sun, Xiaosong Wang. isbi 2024: 1-5 [doi]

AVDNet: Joint coronary artery and vein segmentation with topological consistencyWenji Wang, Qing Xia 0002, Zhennan Yan, Zhiqiang Hu, Yinan Chen, Wen Zheng, Xiao Wang, Shaoping Nie, Dimitris N. Metaxas, Shaoting Zhang 0001. mia, 91:102999, January 2024. [doi]

FPL+: Filtered Pseudo Label-Based Unsupervised Cross-Modality Adaptation for 3D Medical Image SegmentationJianghao Wu, Dong Guo, Guotai Wang, Qiang Yue, Huijun Yu, Kang Li 0004, Shaoting Zhang 0001. tmi, 43(9):3098-3109, September 2024. [doi]

Pattern-Aware Transformer: Hierarchical Pattern Propagation in Sequential Medical ImagesLingyun Wu, Xiang Gao, Zhiqiang Hu, Shaoting Zhang 0001. tmi, 43(1):405-415, January 2024. [doi]

GECSum: Generative Evaluation-Driven Sequence Level Contrastive Learning for Abstractive SummarizationJiawen Xie, Shaoting Zhang 0001, Xiaofan Zhang 0002. COLING 2024: 7581-7595 [doi]

Semi-Supervised Medical Image Segmentation via Multi-Group Network with Consistency Among Heterogeneous Loss SupervisionPing Ye, He Li, Shaoting Zhang 0001, Guotai Wang. isbi 2024: 1-5 [doi]

Semi-supervised pathological image segmentation via cross distillation of multiple attentions and Seg-CAM consistencyLanfeng Zhong, Xiangde Luo, Xin Liao, Shaoting Zhang 0001, Guotai Wang. PR, 152:110492, 2024. [doi]

Self-Supervised Pre-Training Based On Contrastive Complementary Masking for Semi-Supervised Cardiac Image SegmentationYubo Zhou, Ran Gu, Shaoting Zhang 0001, Guotai Wang. isbi 2024: 1-5 [doi]

Classification of lung cancer subtypes on CT images with synthetic pathological priorsWentao Zhu, Yuan Jin, Gege Ma, Geng Chen, Jan Egger, Shaoting Zhang 0001, Dimitris N. Metaxas. mia, 95:103199, 2024. [doi]

2023

Pathology-and-Genomics Multimodal Transformer for Survival Outcome PredictionKexin Ding, Mu Zhou, Dimitris N. Metaxas, Shaoting Zhang 0001. miccai 2023: 622-631 [doi]

UM-CAM: Uncertainty-weighted Multi-resolution Class Activation Maps for Weakly-supervised Fetal Brain SegmentationJia Fu, Tao Lu, Shaoting Zhang 0001, Guotai Wang. miccai 2023: 315-324 [doi]

CDDSA: Contrastive domain disentanglement and style augmentation for generalizable medical image segmentationRan Gu, Guotai Wang, Jiangshan Lu, Jingyang Zhang, Wenhui Lei, Yinan Chen, Wenjun Liao, Shichuan Zhang, Kang Li 0004, Dimitris N. Metaxas, Shaoting Zhang 0001. mia, 89:102904, October 2023. [doi]

Scribble-Based 3D Multiple Abdominal Organ Segmentation via Triple-Branch Multi-Dilated Network with Pixel- and Class-Wise ConsistencyMeng Han, Xiangde Luo, Wenjun Liao, Shichuan Zhang, Shaoting Zhang 0001, Guotai Wang. miccai 2023: 33-42 [doi]

Predicting cancer outcomes from whole slide images via hybrid supervision learningXianying He, Jiahui Li 0005, Fang Yan, Linlin Wang, Wen Chen 0001, Xiaodi Huang, Zhiqiang Hu, Qi Duan, Hongsheng Li 0001, Shaoting Zhang 0001, Jie Zhao. ijon, 557:126736, November 2023. [doi]

Automatic Lung Cancer Subtypes Classification on CT Images with Self-generated Multi-modality Hybrid FeaturesGege Ma, Yuan Jin, Jianhu Pan, Shaoting Zhang 0001, Dimitris N. Metaxas, Wentao Zhu. embc 2023: 1-6 [doi]

Voxel2Hemodynamics: An End-to-End Deep Learning Method for Predicting Coronary Artery HemodynamicsZiyu Ni, Linda Wei, Lijian Xu, Qing Xia 0002, Hongsheng Li, Shaoting Zhang 0001, Dimitris N. Metaxas. stacom-ws 2024: 15-24 [doi]

Domain-Adversarial Transformer Network for Multiphase Liver Tumor SegmentationYangfan Ni, Geng Chen, Zhan Feng, Heng Cui, Dimitris N. Metaxas, Shaoting Zhang 0001, Wentao Zhu. embc 2023: 1-4 [doi]

ScribSD: Scribble-Supervised Fetal MRI Segmentation Based on Simultaneous Feature and Prediction Self-distillationYijie Qu, Qianfei Zhao, Linda Wei, Tao Lu, Shaoting Zhang 0001, Guotai Wang. miccai 2023: 14-23 [doi]

Foundation Model for Endoscopy Video Analysis via Large-Scale Self-supervised Pre-trainZhao Wang, Chang Liu, Shaoting Zhang 0001, Qi Dou 0001. miccai 2023: 101-111 [doi]

UPL-SFDA: Uncertainty-Aware Pseudo Label Guided Source-Free Domain Adaptation for Medical Image SegmentationJianghao Wu, Guotai Wang, Ran Gu, Tao Lu, Yinan Chen, Wentao Zhu, Tom Vercauteren, Sébastien Ourselin, Shaoting Zhang 0001. tmi, 42(12):3932-3943, December 2023. [doi]

Text-Guided Foundation Model Adaptation for Pathological Image ClassificationYunkun Zhang, Jin Gao, Mu Zhou, Xiaosong Wang, Yu Qiao, Shaoting Zhang 0001, Dequan Wang. miccai 2023: 272-282 [doi]

Semi-supervised Pathological Image Segmentation via Cross Distillation of Multiple AttentionsLanfeng Zhong, Xin Liao, Shaoting Zhang 0001, Guotai Wang. miccai 2023: 570-579 [doi]

HAMIL: High-Resolution Activation Maps and Interleaved Learning for Weakly Supervised Segmentation of Histopathological ImagesLanfeng Zhong, Guotai Wang, Xin Liao, Shaoting Zhang 0001. tmi, 42(10):2912-2923, October 2023. [doi]

2022

Efficient Federated Tumor Segmentation via Parameter Distance Weighted Aggregation and Client PruningMeirui Jiang, Hongzheng Yang, Xiaofan Zhang, Shaoting Zhang 0001, Qi Dou 0001. brainles-ws 2023: 161-172 [doi]

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