publications

2026

1. IEEE TBME

   

   Segment anything model 2: an application to 2d and 3d medical images

   Haoyu Dong, Hanxue Gu, Yaqian Chen, and 3 more authors

   IEEE Transactions on Biomedical Engineering, 2026

   DOI Bib HTML

   @article{dong2026segment,
     title = {Segment anything model 2: an application to 2d and 3d medical images},
     author = {Dong, Haoyu and Gu, Hanxue and Chen, Yaqian and Yang, Jichen and Chen, Yuwen and Mazurowski, Maciej A},
     journal = {IEEE Transactions on Biomedical Engineering},
     year = {2026},
     doi = {10.1109/TBME.2026.3653267},
     publisher = {IEEE},
   }

2. MedIA

   

   Fréchet Radiomic Distance (FRD): A Versatile Metric for Comparing Medical Imaging Datasets

   Nicholas Konz, Richard Osuala, Preeti Verma, and 16 more authors

   Medical Image Analysis, 2026

   DOI Bib HTML

   @article{konz2026frechet,
     title = {Fréchet Radiomic Distance (FRD): A Versatile Metric for Comparing Medical Imaging Datasets},
     author = {Konz, Nicholas and Osuala, Richard and Verma, Preeti and Chen, Yuwen and Gu, Hanxue and Dong, Haoyu and Chen, Yaqian and Marshall, Andrew and Garrucho, Lidia and Kushibar, Kaisar and Lang, Daniel M. and Kim, Gene S. and Grimm, Lars J. and Lewin, John M. and Duncan, James S. and Schnabel, Julia A. and Diaz, Oliver and Lekadir, Karim and Mazurowski, Maciej A.},
     journal = {Medical Image Analysis},
     pages = {103943},
     year = {2026},
     issn = {1361-8415},
     doi = {10.1016/j.media.2026.103943},
   }

2025

1. MedIA

   

   SegmentAnyBone: A universal model that segments any bone at any location on MRI

   Hanxue Gu, Roy Colglazier, Haoyu Dong, and 8 more authors

   Medical Image Analysis, 2025

   DOI Bib HTML

   @article{gu2025segmentanybone,
     title = {SegmentAnyBone: A universal model that segments any bone at any location on MRI},
     author = {Gu, Hanxue and Colglazier, Roy and Dong, Haoyu and Zhang, Jikai and Chen, Yaqian and Yildiz, Zafer and Chen, Yuwen and Li, Lin and Yang, Jichen and Willhite, Jay and others},
     journal = {Medical Image Analysis},
     volume = {101},
     pages = {103469},
     doi = {10.1016/j.media.2025.103469},
     year = {2025},
     publisher = {Elsevier},
   }

2. IEEE TMI

   

   Accelerating Volumetric Medical Image Annotation via Short-Long Memory SAM 2

   Yuwen Chen, Zafer Yildiz, Qihang Li, and 5 more authors

   IEEE Transactions on Medical Imaging, 2025

   DOI Bib HTML

   @article{chen2025accelerating,
     title = {Accelerating Volumetric Medical Image Annotation via Short-Long Memory SAM 2},
     author = {Chen, Yuwen and Yildiz, Zafer and Li, Qihang and Chen, Yaqian and Dong, Haoyu and Gu, Hanxue and Konz, Nicholas and Mazurowski, Maciej A},
     journal = {IEEE Transactions on Medical Imaging},
     year = {2025},
     doi = {10.1109/TMI.2025.3627954},
   }

3. MELBA

   

   ContourDiff: Unpaired Medical Image Translation with Structural Consistency

   Yuwen Chen, Nicholas Konz, Hanxue Gu, and 5 more authors

   Machine Learning for Biomedical Imaging, 2025

   DOI Bib HTML

   @article{chen2025contourdiff,
     title = {ContourDiff: Unpaired Medical Image Translation with Structural Consistency},
     author = {Chen, Yuwen and Konz, Nicholas and Gu, Hanxue and Dong, Haoyu and Chen, Yaqian and Li, Lin and Lee, Jisoo and Mazurowski, Maciej A},
     journal = {Machine Learning for Biomedical Imaging},
     volume = {3},
     pages = {711--727},
     year = {2025},
     doi = {10.59275/j.melba.2025-79a2},
   }

4. MELBA

   

   Automated Muscle and Fat Segmentation in Computed Tomography for Comprehensive Body Composition Analysis

   Yaqian Chen, Hanxue Gu, Yuwen Chen, and 7 more authors

   Machine Learning for Biomedical Imaging, 2025

   DOI Bib HTML

   @article{chen2025bodycomp,
     title = {Automated Muscle and Fat Segmentation in Computed Tomography for Comprehensive Body Composition Analysis},
     author = {Chen, Yaqian and Gu, Hanxue and Chen, Yuwen and Yang, Jicheng and Dong, Haoyu and Cao, Joseph Y. and Camarena, Adrian and Mantyh, Christopher and Colglazier, Roy and Mazurowski, Maciej A.},
     journal = {Machine Learning for Biomedical Imaging},
     volume = {3},
     issue = {November 2025 issue},
     pages = {581--618},
     year = {2025},
     issn = {2766-905X},
     doi = {10.59275/j.melba.2025-ag5g},
   }

5. arXiv

   

   MRI-CORE: A Foundation Model for Magnetic Resonance Imaging

   Haoyu Dong, Yuwen Chen, Hanxue Gu, and 4 more authors

   arXiv preprint arXiv:2506.12186, 2025

   DOI Bib HTML

   @article{dong2025mri,
     title = {MRI-CORE: A Foundation Model for Magnetic Resonance Imaging},
     author = {Dong, Haoyu and Chen, Yuwen and Gu, Hanxue and Konz, Nicholas and Chen, Yaqian and Li, Qihang and Mazurowski, Maciej A},
     journal = {arXiv preprint arXiv:2506.12186},
     year = {2025},
     doi = {10.48550/arXiv.2506.12186},
   }

6. IEEE JBHI

   

   GuidedMorph: Two-Stage Deformable Registration for Breast MRI

   Yaqian Chen, Hanxue Gu, Haoyu Dong, and 5 more authors

   IEEE Journal of Biomedical and Health Informatics, 2025

   DOI Bib HTML

   @article{chen2025guidedmorph,
     title = {GuidedMorph: Two-Stage Deformable Registration for Breast MRI},
     author = {Chen, Yaqian and Gu, Hanxue and Dong, Haoyu and Li, Qihang and Chen, Yuwen and Konz, Nicholas and Li, Lin and Mazurowski, Maciej A.},
     journal = {IEEE Journal of Biomedical and Health Informatics},
     pages = {1--14},
     year = {2025},
     doi = {10.1109/JBHI.2025.3647349},
   }

7. MICCAI DEEP-BREA3TH

   

   BreastSegNet: Multi-label Segmentation of Breast MRI

   Qihang Li, Jichen Yang, Yaqian Chen, and 4 more authors

   In Deep Breast Workshop on AI and Imaging for Diagnostic and Treatment Challenges in Breast Care, 2025

   DOI Bib HTML

   @inproceedings{li2025breastsegnet,
     title = {BreastSegNet: Multi-label Segmentation of Breast MRI},
     author = {Li, Qihang and Yang, Jichen and Chen, Yaqian and Chen, Yuwen and Gu, Hanxue and Grimm, Lars J and Mazurowski, Maciej A},
     booktitle = {Deep Breast Workshop on AI and Imaging for Diagnostic and Treatment Challenges in Breast Care},
     pages = {196--205},
     year = {2025},
     doi = {10.1007/978-3-032-05559-0_20},
     organization = {Springer},
   }

8. arXiv

   

   Transplant-Ready? Evaluating AI Lung Segmentation Models in Candidates with Severe Lung Disease

   Jisoo Lee, Michael R Harowicz, Yuwen Chen, and 5 more authors

   arXiv preprint arXiv:2509.15083, 2025

   DOI Bib HTML

   @article{lee2025transplant,
     title = {Transplant-Ready? Evaluating AI Lung Segmentation Models in Candidates with Severe Lung Disease},
     author = {Lee, Jisoo and Harowicz, Michael R and Chen, Yuwen and Gu, Hanxue and Alderete, Isaac S and Li, Lin and Mazurowski, Maciej A and Hartwig, Matthew G},
     journal = {arXiv preprint arXiv:2509.15083},
     year = {2025},
     doi = {10.48550/arXiv.2509.15083},
   }

9. arXiv

   

   SegmentAnyMuscle: A universal muscle segmentation model across different locations in MRI

   Roy Colglazier, Jisoo Lee, Haoyu Dong, and 8 more authors

   arXiv preprint arXiv:2506.22467, 2025

   DOI Bib HTML

   @article{colglazier2025segmentanymuscle,
     title = {SegmentAnyMuscle: A universal muscle segmentation model across different locations in MRI},
     author = {Colglazier, Roy and Lee, Jisoo and Dong, Haoyu and Gu, Hanxue and Chen, Yaqian and Cao, Joseph and Yildiz, Zafer and Liu, Zhonghao and Konz, Nicholas and Yang, Jichen and others},
     journal = {arXiv preprint arXiv:2506.22467},
     year = {2025},
     doi = {10.48550/arXiv.2506.22467},
   }

2024

1. MICCAI

   

   Anatomically-controllable medical image generation with segmentation-guided diffusion models

   Nicholas Konz, Yuwen Chen, Haoyu Dong, and 1 more author

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

   DOI Bib HTML

   @inproceedings{konz2024anatomically,
     title = {Anatomically-controllable medical image generation with segmentation-guided diffusion models},
     author = {Konz, Nicholas and Chen, Yuwen and Dong, Haoyu and Mazurowski, Maciej A},
     booktitle = {International Conference on Medical Image Computing and Computer-Assisted Intervention},
     pages = {88--98},
     year = {2024},
     organization = {Springer},
     doi = {10.1007/978-3-031-72104-5_9},
   }

2. arXiv

   

   Sam & sam 2 in 3d slicer: Segmentwithsam extension for annotating medical images

   Zafer Yildiz, Yuwen Chen, and Maciej A Mazurowski

   arXiv preprint arXiv:2408.15224, 2024

   DOI Bib HTML

   @article{yildiz2024sam,
     title = {Sam \& sam 2 in 3d slicer: Segmentwithsam extension for annotating medical images},
     author = {Yildiz, Zafer and Chen, Yuwen and Mazurowski, Maciej A},
     journal = {arXiv preprint arXiv:2408.15224},
     year = {2024},
     doi = {10.48550/arXiv.2408.15224},
   }

3. MIDL

   

   Rethinking perceptual metrics for medical image translation

   Nicholas Konz, Yuwen Chen, Hanxue Gu, and 2 more authors

   2024

   DOI Bib HTML

   @article{konz2024rethinking,
     title = {Rethinking perceptual metrics for medical image translation},
     author = {Konz, Nicholas and Chen, Yuwen and Gu, Hanxue and Dong, Haoyu and Mazurowski, Maciej A},
     booktitle = {Medical Imaging with Deep Learning (MIDL) 2024: Short Paper Track},
     year = {2024},
     doi = {10.48550/arXiv.2404.07318},
   }

2023

1. Commun. Biol.

   

   Smart-Plexer: A breakthrough workflow for hybrid development of multiplex PCR assays

   Luca Miglietta, Yuwen Chen, Zhi Luo, and 8 more authors

   Communications Biology, 2023

   DOI Bib HTML

   @article{miglietta2023smart,
     title = {Smart-Plexer: A breakthrough workflow for hybrid development of multiplex PCR assays},
     author = {Miglietta, Luca and Chen, Yuwen and Luo, Zhi and Xu, Ke and Ding, Ning and Peng, Tianyi and Moniri, Ahmad and Kreitmann, Louis and Cacho-Soblechero, Miguel and Holmes, Alison and others},
     journal = {Communications Biology},
     volume = {6},
     number = {1},
     pages = {922},
     year = {2023},
     doi = {10.1038/s42003-023-05235-w},
     publisher = {Nature Publishing Group UK London},
   }

2. CHIL

   

   Evaluating model performance in medical datasets over time

   Helen Zhou, Yuwen Chen, and Zachary Lipton

   In Conference on Health, Inference, and Learning, 2023

   Bib HTML

   @inproceedings{zhou2023evaluating,
     title = {Evaluating model performance in medical datasets over time},
     author = {Zhou, Helen and Chen, Yuwen and Lipton, Zachary},
     booktitle = {Conference on Health, Inference, and Learning},
     pages = {498--508},
     year = {2023},
     organization = {PMLR},
   }

3. Med-Neurips

   

   Moco-transfer: Investigating out-of-distribution contrastive learning for limited-data domains

   Yuwen Chen, Helen Zhou, and Zachary C Lipton

   2023

   DOI Bib HTML

   @article{chen2023moco,
     title = {Moco-transfer: Investigating out-of-distribution contrastive learning for limited-data domains},
     author = {Chen, Yuwen and Zhou, Helen and Lipton, Zachary C},
     booktitle = {Neurips Meets Medical Imaging},
     year = {2023},
     doi = {10.48550/arXiv.2311.09401},
   }

2020

1. IEEE ICITM

   

   Blockchain in enterprise: An innovative management scheme utilizing smart contract

   Yuwen Chen

   In 2020 9th International Conference on Industrial Technology and Management (ICITM), 2020

   DOI Bib HTML

   @inproceedings{chen2020blockchain,
     title = {Blockchain in enterprise: An innovative management scheme utilizing smart contract},
     author = {Chen, Yuwen},
     booktitle = {2020 9th International Conference on Industrial Technology and Management (ICITM)},
     pages = {21--24},
     year = {2020},
     organization = {IEEE},
     doi = {10.1109/ICITM48982.2020.9080356},
   }