publications

2026

1. Arxiv

   

   TubeMLLM: A Foundation Model for Topology Knowledge Exploration in Vessel-like Anatomy

   Yaoyu Liu^*, Minghui Zhang^*, Kefan Wang, Xin You, Hanxiao Zhang, Qingbiao Liu, Yirong Chen, and Yun Gu

   Under Review, 2026

   * Equal Contribution

   arXiv Bib

   @article{liu2026tubemllm,
     title = {TubeMLLM: A Foundation Model for Topology Knowledge Exploration in Vessel-like Anatomy},
     author = {Liu, Yaoyu and Zhang, Minghui and Wang, Kefan and You, Xin and Zhang, Hanxiao and Liu, Qingbiao and Chen, Yirong and Gu, Yun},
     note = {* Equal Contribution},
     journal = {Under Review},
     year = {2026}
   }

2. NEJM AI

   

   Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA

   Kaiyuan Yang, Fabio Musio, Yihui Ma, others, Minghui Zhang, Xin You, Hanxiao Zhang, Guang-Zhong Yang, Yun Gu, others, Sven Hirsch, Susanne Wegener, and Bjoern Menze

   The New England Journal of Medicine AI, Accepted, 2026

   Awarded arXiv Bib HTML Website

   We ranked the 1st place of one track, 2nd place of two tracks, 3rd place of three tracks, hosted in MICCAI 2024.

   @article{yang2024benchmarking,
     title = {Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA},
     author = {Yang, Kaiyuan and Musio, Fabio and Ma, Yihui and others and Zhang, Minghui and You, Xin and Zhang, Hanxiao and Yang, Guang-Zhong and Gu, Yun and others and Hirsch, Sven and Wegener, Susanne and Menze, Bjoern},
     journal = {The New England Journal of Medicine AI, Accepted},
     year = {2026},
   }

3. NMI

   

   TriALS: Triphasic-Aided Liver Lesion Segmentation Benchmark in Non-Contrast CT

   Marawan Elbatel, Mohamed Ghonim, others, Hanxiao Zhang, Minghui Zhang, Xin You, others, Aya Yassin, and Xiaomeng Li

   Nature Machine Intelligence (Under Review), 2026

   arXiv Bib HTML

   @article{elbatel2026trials,
     title = {TriALS: Triphasic-Aided Liver Lesion Segmentation Benchmark in Non-Contrast CT},
     author = {Elbatel, Marawan and Ghonim, Mohamed and others and Zhang, Hanxiao and Zhang, Minghui and You, Xin and others and Yassin, Aya and Li, Xiaomeng},
     journal = {Nature Machine Intelligence (Under Review)},
     year = {2026}
   }

4. Arxiv

   

   Long-Short Term Agents for Pure-Vision Bronchoscopy Robotic Autonomy

   Junyang Wu, Mingyi Luo, Fangfang Xie, Minghui Zhang, Hanxiao Zhang, Chunxi Zhang, Junhao Wang, Jiayuan Sun, Yun Gu, and Guang-Zhong Yang

   Under Review, 2026

   arXiv Bib

   @article{wu2026long,
     title = {Long-Short Term Agents for Pure-Vision Bronchoscopy Robotic Autonomy},
     author = {Wu, Junyang and Luo, Mingyi and Xie, Fangfang and Zhang, Minghui and Zhang, Hanxiao and Zhang, Chunxi and Wang, Junhao and Sun, Jiayuan and Gu, Yun and Yang, Guang-Zhong},
     journal = {Under Review},
     year = {2026},
   }

5. MedIA

   

   Multi-Class Segmentation of Aortic Branches and Zones in Computed Tomography Angiography: The AortaSeg24 Challenge

   Muhammad Imran, Jonathan R Krebs, Vishal Balaji Sivaraman, Teng Zhang, others, Minghui Zhang, Hanxiao Zhang, Xin You, Yun Gu, others, Michol A Cooper, and Wei Shao

   Medical Image Analysis, 2026

   arXiv Bib HTML Website

   @article{imran2025multi,
     title = {Multi-Class Segmentation of Aortic Branches and Zones in Computed Tomography Angiography: The AortaSeg24 Challenge},
     author = {Imran, Muhammad and Krebs, Jonathan R and Sivaraman, Vishal Balaji and Zhang, Teng and others and Zhang, Minghui and Zhang, Hanxiao and You, Xin and Gu, Yun and others and Cooper, Michol A and Shao, Wei},
     journal = {Medical Image Analysis},
     year = {2026},
   }

6. IEEE TMI

   

   EndoSERV: A Vision-based Endoluminal Robot Navigation System

   Junyang Wu, Fangfang Xie, Minghui Zhang, Hanxiao Zhang, Jiayuan Sun, Yun Gu, and Guang-Zhong Yang

   IEEE Transactions on Medical Imaging (Revision), 2026

   arXiv Bib

   @article{wu2025EndoSERV,
     title = {EndoSERV: A Vision-based Endoluminal Robot Navigation System},
     author = {Wu, Junyang and Xie, Fangfang and Zhang, Minghui and Zhang, Hanxiao and Sun, Jiayuan and Gu, Yun and Yang, Guang-Zhong},
     journal = {IEEE Transactions on Medical Imaging (Revision)},
     year = {2026},
     publisher = {IEEE},
   }

7. MedIA

   

   ARTNet: An Artifact-Robust Transfer Learning Model for Endoluminal Navigation

   Junyang Wu, Fangfang Xie, Minghui Zhang, Hanxiao Zhang, Jiayuan Sun, Yun Gu, and Guang-Zhong Yang

   Medical Image Analysis (Revision), 2026

   Bib

   @article{wu2025ARTNet,
     title = {ARTNet: An Artifact-Robust Transfer Learning Model for Endoluminal Navigation},
     author = {Wu, Junyang and Xie, Fangfang and Zhang, Minghui and Zhang, Hanxiao and Sun, Jiayuan and Gu, Yun and Yang, Guang-Zhong},
     journal = {Medical Image Analysis (Revision)},
     year = {2026},
   }

8. npj Digital Medicine

   

   Reconstruction from Multi-Planar MRI with Foundation Models for Uterine Fibroid Analysis

   Junhao Wang^*, Jinbo Wang^*, Hanxiao Zhang, Minghui Zhang, Yun Gu, Jin Qiu, and Guang-Zhong Yang

   npj Digital Medicine, Accepted, 2026

   Bib

   @article{wang2025Recon,
     title = {Reconstruction from Multi-Planar MRI with Foundation Models
     for Uterine Fibroid Analysis},
     author = {Wang, Junhao and Wang, Jinbo and Zhang, Hanxiao and Zhang, Minghui and Gu, Yun and Qiu, Jin and Yang, Guang-Zhong},
     journal = {npj Digital Medicine, Accepted},
     year = {2026},
     publisher = {Springer},
   }

2025

1. Arxiv

   

   AirwayNet: Constructing Fine-Grained Airway Atlases

   Minghui Zhang, Chenyu Li, Fangfang Xie, Yaoyu Liu, Hanxiao Zhang, Junyang Wu, Chunxi Zhang, Jie Yang, Jiayuan Sun^✉, Guang-Zhong Yang^✉, and Yun Gu^✉

   Under Review, 2025

   arXiv Bib HTML Code

   @article{zhang2024digitalized,
     title = {AirwayNet: Constructing Fine-Grained Airway Atlases},
     author = {Zhang, Minghui and Li, Chenyu and Xie, Fangfang and Liu, Yaoyu and Zhang, Hanxiao and Wu, Junyang and Zhang, Chunxi and Yang, Jie and Sun<sup>✉</sup>, Jiayuan and Yang<sup>✉</sup>, Guang-Zhong and Gu<sup>✉</sup>, Yun},
     journal = {Under Review},
     year = {2025},
   }

2. IJCARS

   

   ReshapeIT: Reliable Shape Interaction with Implicit Template for Anatomical Structure Reconstruction

   Minghui Zhang and Yun Gu

   International Journal of Computer Assisted Radiology and Surgery, 2025

   arXiv Bib HTML Code

   @article{zhang2023reshapeit,
     title = {ReshapeIT: Reliable Shape Interaction with Implicit Template for Anatomical Structure Reconstruction},
     author = {Zhang, Minghui and Gu, Yun},
     journal = {International Journal of Computer Assisted Radiology and Surgery},
     year = {2025},
   }

3. Arxiv

   

   TopoSculpt: Betti-Steered Topological Sculpting of 3D Fine-grained Tubular Shapes

   Minghui Zhang, Yaoyu Liu, Junyang Wu, Xin You, Hanxiao Zhang, Junjun He, and Yun Gu

   Under Review, 2025

   arXiv Bib Code

   @article{zhang2025toposculpt,
     title = {TopoSculpt: Betti-Steered Topological Sculpting of 3D Fine-grained Tubular Shapes},
     author = {Zhang, Minghui and Liu, Yaoyu and Wu, Junyang and You, Xin and Zhang, Hanxiao and He, Junjun and Gu, Yun},
     journal = {Under Review},
     year = {2025},
   }

4. Arxiv

   

   Shape-aware Sampling Matters in the Modeling of Multi-Class Tubular Structures

   Minghui Zhang, Yaoyu Liu, Xin You, Hanxiao Zhang, and Yun Gu

   Under review, 2025

   arXiv Bib HTML

   @article{zhang2025shape,
     title = {Shape-aware Sampling Matters in the Modeling of Multi-Class Tubular Structures},
     author = {Zhang, Minghui and Liu, Yaoyu and You, Xin and Zhang, Hanxiao and Gu, Yun},
     journal = {Under review},
     year = {2025},
   }

5. MedIA

   

   Pnpnet: Pull-and-push networks for volumetric segmentation with boundary confusion

   Xin You, Ming Ding, Minghui Zhang, Hanxiao Zhang, Yi Yu, Jie Yang, and Yun Gu

   Medical Image Analysis, 2025

   arXiv Bib HTML

   @article{you2023pnpnet,
     title = {Pnpnet: Pull-and-push networks for volumetric segmentation with boundary confusion},
     author = {You, Xin and Ding, Ming and Zhang, Minghui and Zhang, Hanxiao and Yu, Yi and Yang, Jie and Gu, Yun},
     journal = {Medical Image Analysis},
     year = {2025},
   }

6. IEEE TMI

   

   TopoVST: Toward Topology-fidelitous Vessel Skeleton Tracking

   Yaoyu Liu, Minghui Zhang, Junjun He, and Yun Gu

   IEEE transactions on medical imaging (Revision), 2025

   arXiv Bib

   @article{liu2025TopoVST,
     title = {TopoVST: Toward Topology-fidelitous Vessel Skeleton Tracking},
     author = {Liu, Yaoyu and Zhang, Minghui and He, Junjun and Gu, Yun},
     journal = {IEEE transactions on medical imaging (Revision)},
     year = {2025},
     publisher = {IEEE},
   }

7. IEEE JBHI

   

   SLoRD: Structural Low-Rank Descriptors for Shape Consistency in Vertebrae Segmentation

   Xin You, Yixin Lou, Minghui Zhang, Jie Yang, and Yun Gu

   IEEE Journal of Biomedical and Health Informatics, 2025

   Bib HTML

   @article{you2025slord,
     title = {SLoRD: Structural Low-Rank Descriptors for Shape Consistency in Vertebrae Segmentation},
     author = {You, Xin and Lou, Yixin and Zhang, Minghui and Yang, Jie and Gu, Yun},
     journal = {IEEE Journal of Biomedical and Health Informatics},
     year = {2025},
     publisher = {IEEE},
   }

8. MICCAI

   

   Temporal Differential Fields for 4D Motion Modeling via Image-to-Video Synthesis

   Xin You, Minghui Zhang, Hanxiao Zhang, Jie Yang, and Nassir Navab

   In International Conference on Medical Image Computing and Computer-Assisted Intervention, 2025

   Bib HTML

   @inproceedings{you2025temporal,
     title = {Temporal Differential Fields for 4D Motion Modeling via Image-to-Video Synthesis},
     author = {You, Xin and Zhang, Minghui and Zhang, Hanxiao and Yang, Jie and Navab, Nassir},
     booktitle = {International Conference on Medical Image Computing and Computer-Assisted Intervention},
     year = {2025},
     organization = {Springer},
   }

9. IJCARS

   

   Reflecting topology consistency and abnormality via learnable attentions for airway labeling

   Chenyu Li, Minghui Zhang, Chuyan Zhang, and Yun Gu

   International Journal of Computer Assisted Radiology and Surgery, 2025

   Bib HTML

   @article{li2025reflecting,
     title = {Reflecting topology consistency and abnormality via learnable attentions for airway labeling},
     author = {Li, Chenyu and Zhang, Minghui and Zhang, Chuyan and Gu, Yun},
     journal = {International Journal of Computer Assisted Radiology and Surgery},
     pages = {1--9},
     year = {2025},
     publisher = {Springer},
   }

2024

1. IEEE JBHI

   

   Towards connectivity-aware pulmonary airway segmentation

   Minghui Zhang and Yun Gu

   IEEE Journal of Biomedical and Health Informatics, 2024

   arXiv Bib HTML Code

   @article{zhang2023towards,
     title = {Towards connectivity-aware pulmonary airway segmentation},
     author = {Zhang, Minghui and Gu, Yun},
     journal = {IEEE Journal of Biomedical and Health Informatics},
     volume = {28},
     number = {1},
     pages = {321--332},
     year = {2024},
     publisher = {IEEE},
   }

2. MICCAI

   

   Implicit Representation Embraces Challenging Attributes of Pulmonary Airway Tree Structures

   Minghui Zhang, Hanxiao Zhang, Xin You, Guang-Zhong Yang, and Yun Gu

   In International Conference on Medical Image Computing and Computer-Assisted Intervention, 2024

   Bib HTML Code

   @inproceedings{zhang2024implicit,
     title = {Implicit Representation Embraces Challenging Attributes of Pulmonary Airway Tree Structures},
     author = {Zhang, Minghui and Zhang, Hanxiao and You, Xin and Yang, Guang-Zhong and Gu, Yun},
     booktitle = {International Conference on Medical Image Computing and Computer-Assisted Intervention},
     pages = {546--556},
     year = {2024},
     organization = {Springer},
   }

3. MedIA

   

   Hunting imaging biomarkers in pulmonary fibrosis: Benchmarks of the AIIB23 challenge

   Yang Nan, Xiaodan Xing, Shiyi Wang, Zeyu Tang, Federico N Felder, Sheng Zhang, others, Minghui Zhang, Yun Gu, Hanxiao Zhang, others, Athol Wells, Simon LF Walsh, and Guang Yang

   Medical Image Analysis, 2024

   Awarded Bib HTML Website

   We ranked the 2nd place in this challenge, hosted in MICCAI 2023.

   @article{nan2024hunting,
     title = {Hunting imaging biomarkers in pulmonary fibrosis: Benchmarks of the AIIB23 challenge},
     author = {Nan, Yang and Xing, Xiaodan and Wang, Shiyi and Tang, Zeyu and Felder, Federico N and Zhang, Sheng and others and Zhang, Minghui and Gu, Yun and Zhang, Hanxiao and others and Wells, Athol and Walsh, Simon LF and Yang, Guang},
     journal = {Medical Image Analysis},
     volume = {97},
     pages = {103253},
     year = {2024},
     publisher = {Elsevier},
   }

4. IEEE TMI

   

   Accurate airway tree segmentation in ct scans via anatomy-aware multi-class segmentation and topology-guided iterative learning

   Puyang Wang, Dazhou Guo, Dandan Zheng, Minghui Zhang, Haogang Yu, Xin Sun, Jia Ge, Yun Gu, Le Lu, Xianghua Ye, and Dakai Jin

   IEEE transactions on medical imaging, 2024

   Bib HTML

   @article{wang2024accurate,
     title = {Accurate airway tree segmentation in ct scans via anatomy-aware multi-class segmentation and topology-guided iterative learning},
     author = {Wang, Puyang and Guo, Dazhou and Zheng, Dandan and Zhang, Minghui and Yu, Haogang and Sun, Xin and Ge, Jia and Gu, Yun and Lu, Le and Ye, Xianghua and Jin, Dakai},
     journal = {IEEE transactions on medical imaging},
     year = {2024},
     publisher = {IEEE},
   }

5. MEBLA

   

   LNQ 2023 challenge: Benchmark of weakly-supervised techniques for mediastinal lymph node quantification

   Reuben Dorent, Roya Khajavi, Tagwa Idris, Erik Ziegler, Bhanusupriya Somarouthu, Heather Jacene, Ann LaCasce, others, Hanxiao Zhang, Minghui Zhang, Yun Gu, Guang-Zhong Yang, Gordon Harris, Ron Kikinis, and Tina Kapur

   Machine Learning for Biomedical Imaging, 2024

   Awarded Bib HTML Website

   We ranked the 2nd place in this challenge, hosted in MICCAI 2023.

   @article{dorent2024lnq,
     title = {LNQ 2023 challenge: Benchmark of weakly-supervised techniques for mediastinal lymph node quantification},
     author = {Dorent, Reuben and Khajavi, Roya and Idris, Tagwa and Ziegler, Erik and Somarouthu, Bhanusupriya and Jacene, Heather and LaCasce, Ann and others and Zhang, Hanxiao and Zhang, Minghui and Gu, Yun and Yang, Guang-Zhong and Harris, Gordon and Kikinis, Ron and Kapur, Tina},
     journal = {Machine Learning for Biomedical Imaging},
     year = {2024},
   }

2023

1. MedIA

   

   Multi-site, multi-domain airway tree modeling

   Minghui Zhang, Yangqian Wu, Hanxiao Zhang, Yulei Qin, Hao Zheng, others, Jiayuan Sun, Guang-Zhong Yang, and Yun Gu

   Medical image analysis, 2023

   arXiv Bib HTML Code Website

   @article{zhang2023multi,
     title = {Multi-site, multi-domain airway tree modeling},
     author = {Zhang, Minghui and Wu, Yangqian and Zhang, Hanxiao and Qin, Yulei and Zheng, Hao and others and Sun, Jiayuan and Yang, Guang-Zhong and Gu, Yun},
     journal = {Medical image analysis},
     volume = {90},
     pages = {102957},
     year = {2023},
     publisher = {Elsevier},
   }

2. MedIA

   

   Trustworthy learning with (un) sure annotation for lung nodule diagnosis with CT

   Hanxiao Zhang, Liang Chen, Xiao Gu, Minghui Zhang, Yulei Qin, Feng Yao, Zhexin Wang, Yun Gu, and Guang-Zhong Yang

   Medical Image Analysis, 2023

   Bib HTML

   @article{zhang2023trustworthy,
     title = {Trustworthy learning with (un) sure annotation for lung nodule diagnosis with CT},
     author = {Zhang, Hanxiao and Chen, Liang and Gu, Xiao and Zhang, Minghui and Qin, Yulei and Yao, Feng and Wang, Zhexin and Gu, Yun and Yang, Guang-Zhong},
     journal = {Medical Image Analysis},
     volume = {83},
     pages = {102627},
     year = {2023},
     publisher = {Elsevier},
   }

3. MICCAI

   

   Semantic difference guidance for the uncertain boundary segmentation of CT left atrial appendage

   Xin You, Ming Ding, Minghui Zhang, Yangqian Wu, Yi Yu, Yun Gu, and Jie Yang

   In International Conference on Medical Image Computing and Computer-Assisted Intervention, 2023

   Bib HTML

   @inproceedings{you2023semantic,
     title = {Semantic difference guidance for the uncertain boundary segmentation of CT left atrial appendage},
     author = {You, Xin and Ding, Ming and Zhang, Minghui and Wu, Yangqian and Yu, Yi and Gu, Yun and Yang, Jie},
     booktitle = {International Conference on Medical Image Computing and Computer-Assisted Intervention},
     pages = {121--131},
     year = {2023},
     organization = {Springer},
   }

4. IJCARS

   

   Deep anatomy learning for lung airway and artery-vein modeling with contrast-enhanced CT synthesis

   Hanxiao Zhang, Minghui Zhang, Yun Gu, and Guang-Zhong Yang

   International Journal of Computer Assisted Radiology and Surgery, 2023

   Awarded Bib HTML

   Maching Learning for CAI Award @ Information Processing in Computer-Assisted Interventions (IPCAI) 2023

   @article{zhang2023deep,
     title = {Deep anatomy learning for lung airway and artery-vein modeling with contrast-enhanced CT synthesis},
     author = {Zhang, Hanxiao and Zhang, Minghui and Gu, Yun and Yang, Guang-Zhong},
     journal = {International Journal of Computer Assisted Radiology and Surgery},
     volume = {18},
     number = {7},
     pages = {1287--1294},
     year = {2023},
     publisher = {Springer},
   }

2022

1. Medical Physics

   

   Progressive attention module for segmentation of volumetric medical images

   Minghui Zhang, Hong Pan, Yaping Zhu, and Yun Gu

   Medical Physics, 2022

   Bib HTML Code

   @article{zhang2022progressive,
     title = {Progressive attention module for segmentation of volumetric medical images},
     author = {Zhang, Minghui and Pan, Hong and Zhu, Yaping and Gu, Yun},
     journal = {Medical Physics},
     volume = {49},
     number = {1},
     pages = {295--308},
     year = {2022},
     publisher = {Wiley Online Library},
   }

2. MICCAI

   

   CFDA: collaborative feature disentanglement and augmentation for pulmonary airway tree modeling of COVID-19 CTs

   Minghui Zhang, Hanxiao Zhang, Guang-Zhong Yang, and Yun Gu

   In International conference on medical image computing and computer-assisted intervention, 2022

   Awarded Bib HTML PDF Code

   Early Accepted, Student Travel Award, [Top 4%]

   @inproceedings{zhang2022cfda,
     title = {CFDA: collaborative feature disentanglement and augmentation for pulmonary airway tree modeling of COVID-19 CTs},
     author = {Zhang, Minghui and Zhang, Hanxiao and Yang, Guang-Zhong and Gu, Yun},
     booktitle = {International conference on medical image computing and computer-assisted intervention},
     pages = {506--516},
     year = {2022},
     organization = {Springer},
     url = {https://link.springer.com/chapter/10.1007/978-3-031-16431-6_48},
   }

3. IJCARS

   

   LTSP: long-term slice propagation for accurate airway segmentation

   Yangqian Wu, Minghui Zhang, Weihao Yu, Hao Zheng, Jiasheng Xu, and Yun Gu

   International Journal of Computer Assisted Radiology and Surgery, 2022

   Awarded Bib HTML

   Bench-to-Bedside Award: 1st Place @ Information Processing in Computer-Assisted Interventions (IPCAI) 2022

   @article{wu2022ltsp,
     title = {LTSP: long-term slice propagation for accurate airway segmentation},
     author = {Wu, Yangqian and Zhang, Minghui and Yu, Weihao and Zheng, Hao and Xu, Jiasheng and Gu, Yun},
     journal = {International Journal of Computer Assisted Radiology and Surgery},
     volume = {17},
     number = {5},
     pages = {857--865},
     year = {2022},
     publisher = {Springer},
   }

2021

1. MICCAI Workshop

   

   Fda: Feature decomposition and aggregation for robust airway segmentation

   Minghui Zhang, Xin Yu, Hanxiao Zhang, Hao Zheng, Weihao Yu, Hong Pan, Xiangran Cai, and Yun Gu

   In Domain Adaptation and Representation Transfer @ MICCAI, MICCAI Workshop, 2021

   Bib HTML

   @inproceedings{zhang2021fda,
     title = {Fda: Feature decomposition and aggregation for robust airway segmentation},
     author = {Zhang, Minghui and Yu, Xin and Zhang, Hanxiao and Zheng, Hao and Yu, Weihao and Pan, Hong and Cai, Xiangran and Gu, Yun},
     booktitle = {Domain Adaptation and Representation Transfer @ MICCAI, MICCAI Workshop},
     pages = {25--34},
     year = {2021},
     organization = {Springer},
   }