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@misc{Hinton:arXiv:2015:Distilling,
 title={Distilling the knowledge in a neural network},
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@misc{gal2021stylegannada,
      title={{StyleGAN-NADA}: {CLIP}-Guided Domain Adaptation of Image Generators},
      author={Rinon Gal and Or Patashnik and Haggai Maron and Gal Chechik and Daniel Cohen-Or},
      year={2021},
      eprint={2108.00946},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      howpublished={Eprint \href{http://arxiv.org/abs/2108.00946}{arXiv:2108.00946}},
}
@inproceedings{supcon,
author = {Prannay Khosla and Piotr Teterwak and Chen Wang and Aaron Sarna and Yonglong Tian and Phillip Isola and Aaron Maschinot and Ce Liu and Dilip Krishnan},
title = {Supervised contrastive learning},
year = {2020},
publisher = {Curran Associates Inc.},
address = {Red Hook, NY, USA},
booktitle = {Proceedings of the 34th International Conference on Neural Information Processing Systems},
articleno = {1567},
numpages = {13},
location = {Vancouver, BC, Canada},
series = {NIPS '20}
}
@software{open_clip,
  author       = {Ilharco, Gabriel and
                  Wortsman, Mitchell and
                  Wightman, Ross and
                  Gordon, Cade and
                  Carlini, Nicholas and
                  Taori, Rohan and
                  Dave, Achal and
                  Shankar, Vaishaal and
                  Namkoong, Hongseok and
                  Miller, John and
                  Hajishirzi, Hannaneh and
                  Farhadi, Ali and
                  Schmidt, Ludwig},
  title        = {{OpenCLIP}},
  month        = jul,
  year         = {2021},
  publisher    = {Zenodo},
  version      = {0.1},
}

@inproceedings{wang2022medclip,
  title={{MedCLIP}: Contrastive learning from unpaired medical images and text},
  author={Wang, Haoran and Liu, Ke and Ng, Nathan and others},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  year={2022}
}
@inproceedings{wu2023pmcclip,
  title={{PMC-CLIP}: Contrastive vision-language pretraining on biomedical literature},
  author={Wu, Junde and Zhang, Yusheng and Xie, Yuanpu and Ma, Tao and et al.},
  booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
  year={2023}
}
@article{biomedclip,
  title={A Multimodal Biomedical Foundation Model Trained from Fifteen Million Image–Text Pairs},
  author={Sheng Zhang and Yanbo Xu and Naoto Usuyama and Hanwen Xu and Jaspreet Bagga and Robert Tinn and Sam Preston and Rajesh Rao and Mu Wei and Naveen Valluri and Cliff Wong and Andrea Tupini and Yu Wang and Matt Mazzola and Swadheen Shukla and Lars Liden and Jianfeng Gao and Angela Crabtree and Brian Piening and Carlo Bifulco and Matthew P. Lungren and Tristan Naumann and Sheng Wang and Hoifung Poon},
  journal={{NEJM AI}},
  year={2024},
  volume={2},
  number={1},

}
@article{radford2021learning,
  title={Learning Transferable Visual Models From Natural Language Supervision},
  author={Radford, Alec and Kim, Jong Wook and Hallacy, Christopher and Ramesh, Aditya and Goh, Gabriel and Agarwal, Sandhini and Sastry, Girish and Askell, Amanda and Mishkin, Pamela and Clark, Jack and Krueger, Gretchen and Sutskever, Ilya},
  booktitle={Proceedings of the International Conference on Machine Learning},
  year={2021},
  journal={Proceedings of the International Conference on Machine Learning}
}
@article{tumsyn,
  title={Toward general text-guided multimodal brain {MRI} synthesis for diagnosis and medical image analysis},
  author={Wang, Yulin and Xiong, Honglin and Sun, Kaicong and Bai, Shuwei and Dai, Ling and Ding, Zhongxiang and Liu, Jiameng and Wang, Qian and Liu, Qian and Shen, Dinggang},
  journal={{Cell Reports Medicine}},
  volume={6},
  number={6},
  pages={102182},
  year={2025},
}
@InProceedings{WanYul_Unisyn_MICCAI2025,
        author = { Wang, Yulin AND Xiong, Honglin AND Sun, Kaicong AND Liu, Jiameng AND Lin, Xin AND Chen, Ziyi AND He, Yuanzhe AND Wang, Qian AND Shen, Dinggang},
        title = {  Unisyn: A Generative Foundation Model for Universal Medical Image Synthesis across {MRI, CT and PET}  },
        booktitle = {Medical Image Computing and Computer Assisted Intervention – MICCAI 2025},
        year = {2025},
        pages = {673 -- 682}
}
@article{oct-clip,
title = {Metadata-enhanced contrastive learning from retinal optical coherence tomography images},
journal = {{Medical Image Analysis}},
volume = {97},
pages = {103296},
year = {2024},
author = {Robbie Holland and Oliver Leingang and Hrvoje Bogunović and Sophie Riedl and Lars Fritsche and Toby Prevost and Hendrik P.N. Scholl and Ursula Schmidt-Erfurth and Sobha Sivaprasad and Andrew J. Lotery and Daniel Rueckert and Martin J. Menten},

}

@misc{avci2025mrclipefficientmetadataguidedlearning,
      title={{MR-CLIP}: Efficient Metadata-Guided Learning of {MRI} Contrast Representations}, 
      author={Mehmet Yigit Avci and Pedro Borges and Paul Wright and Mehmet Yigitsoy and Sebastien Ourselin and Jorge Cardoso},
      year={2025},
      eprint={2507.00043},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
     howpublished={Eprint \href{http://arxiv.org/abs/2507.00043}{arXiv:2507.00043}},
}
@misc{avci2025metadataaligned3dmrirepresentations,
      title={Metadata-Aligned {3D MRI} Representations for Contrast Understanding and Quality Control}, 
      author={Mehmet Yigit Avci and Pedro Borges and Virginia Fernandez and Paul Wright and Mehmet Yigitsoy and Sebastien Ourselin and Jorge Cardoso},
      year={2025},
      eprint={2511.00681},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
     howpublished={Eprint \href{http://arxiv.org/abs/2511.00681}{arXiv:2511.00681}},
}
@article{contextmri,
  title={{ContextMRI}: Enhancing Compressed Sensing {MRI} through Metadata Conditioning},
  author={Chung, Hyungjin and Lee, Dohun and Wu, Zihui and Kim, Byung-Hoon and Bouman, Katherine L. and Ye, Jong Chul},
  journal={{arXiv preprint arXiv:2501.04284}},
  year={2025},
  eprint={2501.04284},
  archivePrefix={arXiv},
  primaryClass={cs.CV},
  howpublished={Eprint \href{http://arxiv.org/abs/2501.04284}{arXiv:2501.04284}},
}
@article{mcdaniel2022contrast,
  title={Improving the automatic classification of brain {MRI} acquisition contrast with machine learning},
  author={McDaniel, Jeff W and Moore, Anna Z and Mareci, Thomas H and Price, Stephen L and Conklin, Diane J and Wagle, Neal and Pinho, Marcelo C and Landman, Bennett A},
  journal={{Academic Radiology}},
  year={2022},
  publisher={Elsevier},
}
@article{gauriau2020dicom,
  title={Using {DICOM} Metadata for Radiological Image Series Categorization: A Feasibility Study on Large Clinical Brain {MRI} Datasets},
  author={Gauriau, Romain and Bridge, Catriona and Chen, Lu and Glocker, Ben and Hajnal, Joseph and Rueckert, Daniel and Bai, Wenjia},
  journal={{Journal of Digital Imaging}},
  volume={33},
  number={3},
  pages={747--762},
  year={2020},
  publisher={Springer}
}
@article{Denck_2021,
   title={{MR}-contrast-aware image-to-image translations with generative adversarial networks},
   volume={16},
   number={12},
   journal={{International Journal of Computer Assisted Radiology and Surgery}},
   publisher={Springer Science and Business Media LLC},
   author={Denck, Jonas and Guehring, Jens and Maier, Andreas and Rothgang, Eva},
   year={2021},
   month=jun, pages={2069–2078} }
@inproceedings{du2020radnet,
  title={{3D-RADNet}: Extracting labels from {DICOM} metadata for training general medical domain deep 3{D} convolution neural networks},
  author={Du, Ruixuan and Vardhanabhuti, Vin},
  booktitle={Proceedings of the Third Conference on Medical Imaging with Deep Learning},
  pages={174--192},
  year={2020},
  volume={121},
  organization={PMLR}
}
@article{synthstrip,
    title = {{SynthStrip}: skull-stripping for any brain image},
    journal = {{NeuroImage}},
    volume = {260},
    pages = {119474},
    year = {2022},
    author = {Andrew Hoopes and Jocelyn S. Mora and Adrian V. Dalca and Bruce Fischl and Malte Hoffmann},
}
@article{sinha2024mrqa,
  title={Solving the Pervasive Problem of Protocol Non-Compliance in {MRI} using an Open-Source tool {mrQA}},
  author={Sinha, Himanshu and Raamana, Pradeep Reddy},
  journal={{Neuroinformatics}},
  volume={22},
  pages={297--315},
  year={2024},
  publisher={Springer},
}
@article{liang2021mri,
  title = {Magnetic {R}esonance {I}maging Sequence Identification Using a Metadata Learning Approach},
  author = {Shuai Liang and Derek Beaton and Stephen R. Arnott and Tom Gee and Mojdeh Zamyadi and Robert Bartha and Sean Symons and Glenda M. MacQueen and Stefanie Hassel and Jason P. Lerch and Evdokia Anagnostou and Raymond W. Lam and Benicio N. Frey and Roumen Milev and Daniel J. Müller and Sidney H. Kennedy and Christopher J. M. Scott and {ONDRI Investigators} and Stephen C. Strother},
  journal = {{Frontiers in Neuroinformatics}},
  volume = {15},
  pages = {622951},
  year = {2021},
  pmid = {34867254},
  pmcid = {PMC8635782}
}
@article{haca3,
title = {{HACA3}: A unified approach for multi-site {MR} image harmonization},
journal = {{Computerized Medical Imaging and Graphics}},
volume = {109},
pages = {102285},
year = {2023},
author = {Lianrui Zuo and Yihao Liu and Yuan Xue and Blake E. Dewey and Samuel W. Remedios and Savannah P. Hays and Murat Bilgel and Ellen Mowry and Scott Newsome and Peter A. Calabresi and Susan M. Resnick and Jerry L. Prince and Aaron Carass},
keywords = {MRI, Harmonization, Standardization, Disentanglement, Attention, Contrastive learning, Synthesis},
}
@inproceedings{ouyang2021representation,
  title = {Representation Disentanglement for Multi-modal Brain {MRI} Analysis},
  author = {Ouyang, Jintang and Adeli, Ehsan and Pohl, Kilian M and Zhao, Qingyu and Zaharchuk, Gregory},
  booktitle = {Information Processing in Medical Imaging (IPMI)},
  series = {Lecture Notes in Computer Science},
  volume = {12729},
  pages = {321--333},
  year = {2021},
  publisher = {Springer},
  pmid = {35173402},
  pmcid = {PMC8844656}
}
@misc{DICOMStandard,
  title        = {Digital Imaging and Communications in Medicine ({DICOM}) Standard},
  author       = {{National Electrical Manufacturers Association}},
  howpublished = {\url{https://www.dicomstandard.org/}},
  note         = {{NEMA PS3 / ISO 12052}},
  year         = {2025},
  month        = {May}
}
@article {oasis,
	author = {LaMontagne, Pamela J. and Benzinger, Tammie LS. and Morris, John C. and Keefe, Sarah and Hornbeck, Russ and Xiong, Chengjie and Grant, Elizabeth and Hassenstab, Jason and Moulder, Krista and Vlassenko, Andrei G. and Raichle, Marcus E. and Cruchaga, Carlos and Marcus, Daniel},
	title = {{OASIS-3}: Longitudinal Neuroimaging, Clinical, and Cognitive Dataset for Normal Aging and {Alzheimer Disease}},
	elocation-id = {2019.12.13.19014902},
	year = {2019},
	publisher = {Cold Spring Harbor Laboratory Press},
	journal = {medRxiv}
}

@misc{infonce,
      title={Representation Learning with Contrastive Predictive Coding}, 
      author={Aaron van den Oord and Yazhe Li and Oriol Vinyals},
      year={2019},
  journal={{arXiv preprint arXiv:1807.03748}},
  eprint={1807.03748},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  howpublished={Eprint \href{http://arxiv.org/abs/1807.03748}{arXiv:1807.03748}},
}
@misc{kwon2021clipstyler,
  title={{CLIPStyler}: Image style transfer with a single text condition},
  author={Kwon, Gihyun and Ye, Jong Chul},
  journal={{arXiv preprint arXiv:2112.00374}},
  year={2021},
  eprint={2112.00374},
  archivePrefix={arXiv},
  primaryClass={cs.CV},
  howpublished={Eprint \href{http://arxiv.org/abs/2112.00374}{arXiv:2112.00374}},
}

@article{Litjens2017,
  title={A survey on deep learning in medical image analysis},
  author={Litjens, Geert and Kooi, Thijs and Bejnordi, Babak Ehteshami and Setio, Arnaud Arindra Adiyoso and Ciompi, Francesco and Ghafoorian, Mohsen and van der Laak, Jeroen AWM and van Ginneken, Bram and S{\'a}nchez, Clara I},
  journal={{Medical Image Analysis}},
  volume={42},
  pages={60--88},
  year={2017},
  publisher={Elsevier}
}
@article{Kelly2022,
  title={Key challenges for delivering clinical impact with artificial intelligence},
  author={Kelly, Christopher J and Karthikesalingam, Alan and Suleyman, Mustafa and Corrado, Greg and King, Dominic},
  journal={{BMC Medicine}},
  volume={20},
  number={1},
  pages={206},
  year={2022},
  publisher={Springer}
}
@misc{Guo2024,
  author    = {Brian Guo and Darui Lu and Gregory Szumel and Rongze Gui and Tingyu Wang and Nicholas Konz and Maciej A. Mazurowski},
  title     = {The Impact of Scanner Domain Shift on Deep Learning Performance in Medical Imaging: an Experimental Study},
  journal   = {{arXiv preprint arXiv:2409.04368}},
  year      = {2024},
  eprint={2409.04368},
  archivePrefix={arXiv},
  primaryClass={cs.CV},
  howpublished={Eprint \href{http://arxiv.org/abs/2409.04368}{arXiv:2409.04368}},
}
@article{SendraBalcells2022DomainGeneralization,
  author    = {Sendra{-}Balcells, Carla and Campello, V{\'{\i}}ctor M. and Mart{\'{\i}}n{-}Isla, Carlos and others},
  title     = {Domain Generalization in Deep Learning for Contrast-Enhanced Imaging},
  journal   = {{Computers in Biology and Medicine}},
  volume    = {149},
  pages     = {106052},
  year      = {2022},
}
@article{HU2023120125,
title = {Image harmonization: A review of statistical and deep learning methods for removing batch effects and evaluation metrics for effective harmonization},
journal = {{NeuroImage}},
volume = {274},
pages = {120125},
year = {2023},
author = {Fengling Hu and Andrew A. Chen and Hannah Horng and Vishnu Bashyam and Christos Davatzikos and Aaron Alexander-Bloch and Mingyao Li and Haochang Shou and Theodore D. Satterthwaite and Meichen Yu and Russell T. Shinohara},
}
@misc{zhu2020unpairedimagetoimagetranslationusing,
      title={Unpaired Image-to-Image Translation using {Cycle-Consistent Adversarial Networks}}, 
      author={Jun-Yan Zhu and Taesung Park and Phillip Isola and Alexei A. Efros},
      year={2020},
      eprint={1703.10593},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      howpublished={Eprint \href{http://arxiv.org/abs/1703.10593}{arXiv:1703.10593}},
}
@article{Abbasi2024,
  author    = {Soolmaz Abbasi and Haoyu Lan and Jeiran Choupan and Nasim Sheikh‑Bahaei and Gaurav Pandey and Bino Varghese},
  title     = {Deep learning for the harmonization of structural {MRI} scans: a survey},
  journal   = {{BioMedical Engineering OnLine}},
  volume    = {23},
  number    = {1},
  pages     = {90},
  year      = {2024},
}
@article{ROCA2025103388,
title = {{IGUANe}: A 3{D} generalizable {CycleGAN} for multicenter harmonization of brain {MR} images},
journal = {{Medical Image Analysis}},
volume = {99},
pages = {103388},
year = {2025},
author = {Vincent Roca and Grégory Kuchcinski and Jean-Pierre Pruvo and Dorian Manouvriez and Renaud Lopes},
keywords = {Brain MRI, Harmonization, Multisite, Brain age, Alzheimer, Image synthesis},
}
@misc{choi2020starganv2diverseimage,
      title={{StarGAN v2}: Diverse Image Synthesis for Multiple Domains}, 
      author={Yunjey Choi and Youngjung Uh and Jaejun Yoo and Jung-Woo Ha},
      year={2020},
      eprint={1912.01865},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      howpublished={Eprint \href{http://arxiv.org/abs/1912.01865}{arXiv:1912.01865}},
}
@misc{huang2017arbitrarystyletransferrealtime,
      title={Arbitrary Style Transfer in Real-time with Adaptive Instance Normalization}, 
      author={Xun Huang and Serge Belongie},
      year={2017},
      eprint={1703.06868},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      howpublished={Eprint \href{http://arxiv.org/abs/1703.06868}{arXiv:1703.06868}},
}
@misc{huang2018multimodalunsupervisedimagetoimagetranslation,
      title={Multimodal Unsupervised Image-to-Image Translation}, 
      author={Xun Huang and Ming-Yu Liu and Serge Belongie and Jan Kautz},
      year={2018},
      eprint={1804.04732},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      howpublished={Eprint \href{http://arxiv.org/abs/1804.04732}{arXiv:1804.04732}},
}
@inproceedings{dewey2020,
author = {Dewey, Blake E. and Zuo, Lianrui and Carass, Aaron and He, Yufan and Liu, Yihao and Mowry, Ellen M. and Newsome, Scott and Oh, Jiwon and Calabresi, Peter A. and Prince, Jerry L.},
title = {A Disentangled Latent Space for Cross-Site {MRI} Harmonization},
year = {2020},
booktitle = {Medical Image Computing and Computer Assisted Intervention – MICCAI 2020},
pages = {720–729},
numpages = {10},
}
@inproceedings{Modanwal2020,
  author    = {Modanwal, Gourav and Vellal, Adithya and Buda, Mateusz and Mazurowski, Maciej A.},
  title     = {{MRI} image harmonization using cycle-consistent generative adversarial network},
  booktitle = {Medical Imaging 2020: Computer-Aided Diagnosis},
  volume    = {11314},
  pages     = {1131413},
  year      = {2020},
  publisher = {SPIE},

}
@misc{Ouyang2021RepresentationDisentanglement,
  author    = {Ouyang, Jiahong and Adeli, Ehsan and Pohl, Kilian M. and Zhao, Qingyu and Zaharchuk, Greg},
  title     = {Representation Disentanglement for Multi-Modal Brain {MR} Analysis},
  journal   = {{arXiv preprint arXiv:2102.11456}},
  year      = {2021},
  month     = jun,
  eprint={2102.11456},
  archivePrefix={arXiv},
  primaryClass={cs.CV},
  howpublished={Eprint \href{http://arxiv.org/abs/2102.11456}{arXiv:2102.11456}},
}

@inproceedings{park2019SPADE,
  title={Semantic Image Synthesis with Spatially-Adaptive Normalization},
  author={Park, Taesung and Liu, Ming-Yu and Wang, Ting-Chun and Zhu, Jun-Yan},
  booktitle={Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
  year={2019}
}

@misc{kingma2017adammethodstochasticoptimization,
      title={Adam: A Method for Stochastic Optimization}, 
      author={Diederik P. Kingma and Jimmy Ba},
      year={2017},
      eprint={1412.6980},
      archivePrefix={arXiv},
      primaryClass={cs.LG},
  howpublished={Eprint \href{http://arxiv.org/abs/1412.6980}{arXiv:1412.6980}}, 
}