@String(PAMI = {IEEE Trans. Pattern Anal. Mach. Intell.})
@String(IJCV = {Int. J. Comput. Vis.})
@String(CVPR= {IEEE Conf. Comput. Vis. Pattern Recog.})
@String(ICCV= {Int. Conf. Comput. Vis.})
@String(ECCV= {Eur. Conf. Comput. Vis.})
@String(NIPS= {Adv. Neural Inform. Process. Syst.})
@String(ICPR = {Int. Conf. Pattern Recog.})
@String(BMVC= {Brit. Mach. Vis. Conf.})
@String(TOG= {ACM Trans. Graph.})
@String(TIP  = {IEEE Trans. Image Process.})
@String(TVCG  = {IEEE Trans. Vis. Comput. Graph.})
@String(TMM  = {IEEE Trans. Multimedia})
@String(ACMMM= {ACM Int. Conf. Multimedia})
@String(ICME = {Int. Conf. Multimedia and Expo})
@String(ICASSP=	{ICASSP})
@String(ICIP = {IEEE Int. Conf. Image Process.})
@String(ACCV  = {ACCV})
@String(ICLR = {Int. Conf. Learn. Represent.})
@String(IJCAI = {IJCAI})
@String(PR   = {Pattern Recognition})
@String(AAAI = {AAAI})
@String(CVPRW= {IEEE Conf. Comput. Vis. Pattern Recog. Worksh.})
@String(CSVT = {IEEE Trans. Circuit Syst. Video Technol.})

@String(SPL	= {IEEE Sign. Process. Letters})
@String(VR   = {Vis. Res.})
@String(JOV	 = {J. Vis.})
@String(TVC  = {The Vis. Comput.})
@String(JCST  = {J. Comput. Sci. Tech.})
@String(CGF  = {Comput. Graph. Forum})
@String(CVM = {Computational Visual Media})


@String(PAMI  = {IEEE TPAMI})
@String(IJCV  = {IJCV})
@String(CVPR  = {CVPR})
@String(ICCV  = {ICCV})
@String(ECCV  = {ECCV})
@String(NIPS  = {NeurIPS})
@String(ICPR  = {ICPR})
@String(BMVC  =	{BMVC})
@String(TOG   = {ACM TOG})
@String(TIP   = {IEEE TIP})
@String(TVCG  = {IEEE TVCG})
@String(TCSVT = {IEEE TCSVT})
@String(TMM   =	{IEEE TMM})
@String(ACMMM = {ACM MM})
@String(ICME  =	{ICME})
@String(ICASSP=	{ICASSP})
@String(ICIP  = {ICIP})
@String(ACCV  = {ACCV})
@String(ICLR  = {ICLR})
@String(IJCAI = {IJCAI})
@String(PR = {PR})
@String(AAAI = {AAAI})
@String(CVPRW= {CVPRW})
@String(CSVT = {IEEE TCSVT})


% Motivation

@inproceedings{microsoftMotivationRadiology,
  title={Multimodal healthcare AI: identifying and designing clinically relevant vision-language applications for radiology},
  author={Yildirim, Nur and Richardson, Hannah and Wetscherek, Maria Teodora and Bajwa, Junaid and Jacob, Joseph and Pinnock, Mark Ames and Harris, Stephen and Coelho De Castro, Daniel and Bannur, Shruthi and Hyland, Stephanie and others},
  booktitle={Proceedings of the CHI Conference on Human Factors in Computing Systems},
  pages={1--22},
  year={2024}
}

@article{Finegraind_visual_prompting,
  title={Fine-grained visual prompting},
  author={Yang, Lingfeng and Wang, Yueze and Li, Xiang and Wang, Xinlong and Yang, Jian},
  journal={Advances in Neural Information Processing Systems},
  volume={36},
  year={2024}
}


@inproceedings{sam,
  title={Segment anything},
  author={Kirillov, Alexander and Mintun, Eric and Ravi, Nikhila and Mao, Hanzi and Rolland, Chloe and Gustafson, Laura and Xiao, Tete and Whitehead, Spencer and Berg, Alexander C and Lo, Wan-Yen and others},
  booktitle={Proceedings of the IEEE/CVF international conference on computer vision},
  pages={4015--4026},
  year={2023}
}

@inproceedings{sun2024alpha,
  title={Alpha-clip: A clip model focusing on wherever you want},
  author={Sun, Zeyi and Fang, Ye and Wu, Tong and Zhang, Pan and Zang, Yuhang and Kong, Shu and Xiong, Yuanjun and Lin, Dahua and Wang, Jiaqi},
  booktitle={Proceedings of the IEEE/CVF conference on computer vision and pattern recognition},
  pages={13019--13029},
  year={2024}
}

@article{macmahon2017guidelines,
  title={Guidelines for management of incidental pulmonary nodules detected on CT images: from the Fleischner Society 2017},
  author={MacMahon, Heber and Naidich, David P and Goo, Jin Mo and Lee, Kyung Soo and Leung, Ann NC and Mayo, John R and Mehta, Atul C and Ohno, Yoshiharu and Powell, Charles A and Prokop, Mathias and others},
  journal={Radiology},
  volume={284},
  number={1},
  pages={228--243},
  year={2017},
  publisher={Radiological Society of North America}
}

% Methods


@inproceedings{redCircle,
  title={What does clip know about a red circle? visual prompt engineering for vlms},
  author={Shtedritski, Aleksandar and Rupprecht, Christian and Vedaldi, Andrea},
  booktitle={Proceedings of the IEEE/CVF International Conference on Computer Vision},
  pages={11987--11997},
  year={2023}
}

@article{maier2024metrics,
  title={Metrics reloaded: recommendations for image analysis validation},
  author={Maier-Hein, Lena and Reinke, Annika and Godau, Patrick and Tizabi, Minu D and Buettner, Florian and Christodoulou, Evangelia and Glocker, Ben and Isensee, Fabian and Kleesiek, Jens and Kozubek, Michal and others},
  journal={Nature methods},
  volume={21},
  number={2},
  pages={195--212},
  year={2024},
  publisher={Nature Publishing Group US New York}
}


@article{hanley1982meaning,
  title={The meaning and use of the area under a receiver operating characteristic (ROC) curve.},
  author={Hanley, James A and McNeil, Barbara J},
  journal={Radiology},
  volume={143},
  number={1},
  pages={29--36},
  year={1982}
}

@article{tsne,
  title={Visualizing data using t-SNE.},
  author={Van der Maaten, Laurens and Hinton, Geoffrey},
  journal={Journal of machine learning research},
  volume={9},
  number={11},
  year={2008}
}

@article{lozano2025biomedica,
  title={BIOMEDICA: An Open Biomedical Image-Caption Archive, Dataset, and Vision-Language Models Derived from Scientific Literature},
  author={Lozano, Alejandro and Sun, Min Woo and Burgess, James and Chen, Liangyu and Nirschl, Jeffrey J and Gu, Jeffrey and Lopez, Ivan and Aklilu, Josiah and Katzer, Austin Wolfgang and Chiu, Collin and others},
  journal={arXiv preprint arXiv:2501.07171},
  year={2025}
}


@inproceedings{alphaCLIP,
  title={Alpha-clip: A clip model focusing on wherever you want},
  author={Sun, Zeyi and Fang, Ye and Wu, Tong and Zhang, Pan and Zang, Yuhang and Kong, Shu and Xiong, Yuanjun and Lin, Dahua and Wang, Jiaqi},
  booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
  pages={13019--13029},
  year={2024}
}

@article{LearnedvisualPromptingAshkan,
  title={Learning Visual Prompts for Guiding the Attention of Vision Transformers},
  author={Rezaei, Razieh and Sabet, Masoud Jalili and Gu, Jindong and Rueckert, Daniel and Torr, Philip and Khakzar, Ashkan},
  journal={arXiv preprint arXiv:2406.03303},
  year={2024}
}

@inproceedings{roco,
  title={Radiology objects in context (roco): a multimodal image dataset},
  author={Pelka, Obioma and Koitka, Sven and R{\"u}ckert, Johannes and Nensa, Felix and Friedrich, Christoph M},
  booktitle={Intravascular Imaging and Computer Assisted Stenting and Large-Scale Annotation of Biomedical Data and Expert Label Synthesis: 7th Joint International Workshop, CVII-STENT 2018 and Third International Workshop, LABELS 2018, Held in Conjunction with MICCAI 2018, Granada, Spain, September 16, 2018, Proceedings 3},
  pages={180--189},
  year={2018},
  organization={Springer}
}

@article{medicat,
  title={Medicat: A dataset of medical images, captions, and textual references},
  author={Subramanian, Sanjay and Wang, Lucy Lu and Mehta, Sachin and Bogin, Ben and van Zuylen, Madeleine and Parasa, Sravanthi and Singh, Sameer and Gardner, Matt and Hajishirzi, Hannaneh},
  journal={arXiv preprint arXiv:2010.06000},
  year={2020}
}

@article{padchest-gr,
  title={PadChest-GR: A Bilingual Chest X-ray Dataset for Grounded Radiology Report Generation},
  author={Castro, Daniel C and Bustos, Aurelia and Bannur, Shruthi and Hyland, Stephanie L and Bouzid, Kenza and Wetscherek, Maria Teodora and S{\'a}nchez-Valverde, Maria Dolores and Jaques-P{\'e}rez, Lara and P{\'e}rez-Rodr{\'\i}guez, Lourdes and Takeda, Kenji and others},
  journal={arXiv preprint arXiv:2411.05085},
  year={2024}
}


@inproceedings{nih14,
  title={Chestx-ray8: Hospital-scale chest x-ray database and benchmarks on weakly-supervised classification and localization of common thorax diseases},
  author={Wang, Xiaosong and Peng, Yifan and Lu, Le and Lu, Zhiyong and Bagheri, Mohammadhadi and Summers, Ronald M},
  booktitle={Proceedings of the IEEE conference on computer vision and pattern recognition},
  pages={2097--2106},
  year={2017}
}

@article{vindrcxr,
  title={VinDr-CXR: An open dataset of chest X-rays with radiologist’s annotations},
  author={Nguyen, Ha Q and Lam, Khanh and Le, Linh T and Pham, Hieu H and Tran, Dat Q and Nguyen, Dung B and Le, Dung D and Pham, Chi M and Tong, Hang TT and Dinh, Diep H and others},
  journal={Scientific Data},
  volume={9},
  number={1},
  pages={429},
  year={2022},
  publisher={Nature Publishing Group UK London}
}

@article{LeGrad,
  title={LeGrad: An Explainability Method for Vision Transformers via Feature Formation Sensitivity},
  author={Bousselham, Walid and Boggust, Angie and Chaybouti, Sofian and Strobelt, Hendrik and Kuehne, Hilde},
  journal={arXiv preprint arXiv:2404.03214},
  year={2024}
}

@inproceedings{pmc-clip,
  title={Pmc-clip: Contrastive language-image pre-training using biomedical documents},
  author={Lin, Weixiong and Zhao, Ziheng and Zhang, Xiaoman and Wu, Chaoyi and Zhang, Ya and Wang, Yanfeng and Xie, Weidi},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={525--536},
  year={2023},
  organization={Springer}
}

@inproceedings{CLIP,
  title={Learning transferable visual models from natural language supervision},
  author={Radford, Alec and Kim, Jong Wook and Hallacy, Chris and Ramesh, Aditya and Goh, Gabriel and Agarwal, Sandhini and Sastry, Girish and Askell, Amanda and Mishkin, Pamela and Clark, Jack and others},
  booktitle={International conference on machine learning},
  pages={8748--8763},
  year={2021},
  organization={PMLR}
}

@article{MaskInversion,
  title={MaskInversion: Localized Embeddings via Optimization of Explainability Maps},
  author={Bousselham, Walid and Chaybouti, Sofian and Rupprecht, Christian and Ferrari, Vittorio and Kuehne, Hilde},
  journal={arXiv preprint arXiv:2407.20034},
  year={2024}
}
@article{BiomedCLIP1,
  title={Large-scale domain-specific pretraining for biomedical vision-language processing},
  author={Zhang, Sheng and Xu, Yanbo and Usuyama, Naoto and Bagga, Jaspreet and Tinn, Robert and Preston, Sam and Rao, Rajesh and Wei, Mu and Valluri, Naveen and Wong, Cliff and others},
  journal={arXiv preprint arXiv:2303.00915},
  volume={2},
  number={3},
  pages={6},
  year={2023}
}

@article{BiomedCLIP2,
  title={BiomedCLIP: a multimodal biomedical foundation model pretrained from fifteen million scientific image-text pairs},
  author={Zhang, Sheng and Xu, Yanbo and Usuyama, Naoto and Xu, Hanwen and Bagga, Jaspreet and Tinn, Robert and Preston, Sam and Rao, Rajesh and Wei, Mu and Valluri, Naveen and others},
  journal={arXiv preprint arXiv:2303.00915},
  year={2023}
}

@article{huggingface,
  title={Huggingface's transformers: State-of-the-art natural language processing},
  author={Wolf, Thomas and Debut, Lysandre and Sanh, Victor and Chaumond, Julien and Delangue, Clement and Moi, Anthony and Cistac, Pierric and Rault, Tim and Louf, R{\'e}mi and Funtowicz, Morgan and others},
  journal={arXiv preprint arXiv:1910.03771},
  year={2019}
}
@article{MedSam,
  title={Segment anything in medical images},
  author={Ma, Jun and He, Yuting and Li, Feifei and Han, Lin and You, Chenyu and Wang, Bo},
  journal={Nature Communications},
  volume={15},
  number={1},
  pages={654},
  year={2024},
  publisher={Nature Publishing Group UK London}
}
@article{JSRT,
  title={Development of a digital image database for chest radiographs with and without a lung nodule: receiver operating characteristic analysis of radiologists' detection of pulmonary nodules},
  author={Shiraishi, Junji and Katsuragawa, Shigehiko and Ikezoe, Junpei and Matsumoto, Tsuneo and Kobayashi, Takeshi and Komatsu, Ken-ichi and Matsui, Mitate and Fujita, Hiroshi and Kodera, Yoshie and Doi, Kunio},
  journal={American journal of roentgenology},
  volume={174},
  number={1},
  pages={71--74},
  year={2000},
  publisher={Am Roentgen Ray Soc}
}

@article{holste2024towards,
  title={Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge},
  author={Holste, Gregory and Zhou, Yiliang and Wang, Song and Jaiswal, Ajay and Lin, Mingquan and Zhuge, Sherry and Yang, Yuzhe and Kim, Dongkyun and Nguyen-Mau, Trong-Hieu and Tran, Minh-Triet and others},
  journal={Medical Image Analysis},
  pages={103224},
  year={2024},
  publisher={Elsevier}
}

@inproceedings{pubmedclip,
  title={Pubmedclip: How much does clip benefit visual question answering in the medical domain?},
  author={Eslami, Sedigheh and Meinel, Christoph and De Melo, Gerard},
  booktitle={Findings of the Association for Computational Linguistics: EACL 2023},
  pages={1181--1193},
  year={2023}
}

@misc{langlotz2023future,
  title={The future of AI and informatics in radiology: 10 predictions},
  author={Langlotz, Curtis P},
  journal={Radiology},
  volume={309},
  number={1},
  pages={e231114},
  year={2023},
  publisher={Radiological Society of North America}
}

@article{taskDifficulty,
  title={The solitary pulmonary nodule},
  author={Ost, David and Fein, Alan M and Feinsilver, Steven H},
  journal={New England Journal of Medicine},
  volume={348},
  number={25},
  pages={2535--2542},
  year={2003},
  publisher={Mass Medical Soc}
}

@article{MCCoverF1,
  title={The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation},
  author={Chicco, Davide and Jurman, Giuseppe},
  journal={BMC genomics},
  volume={21},
  pages={1--13},
  year={2020},
  publisher={Springer}
}

@article{ViT,
  title={An image is worth 16x16 words: Transformers for image recognition at scale},
  author={Dosovitskiy, Alexey and Beyer, Lucas and Kolesnikov, Alexander and Weissenborn, Dirk and Zhai, Xiaohua and Unterthiner, Thomas and Dehghani, Mostafa and Minderer, Matthias and Heigold, Georg and Gelly, Sylvain and others},
  journal={arXiv preprint arXiv:2010.11929},
  year={2020}
}


@article{example_image_1_red_circle_xray,
  title={Management of persistent hyponatremia induced by long-acting injectable risperidone therapy},
  author={Chowdhury, Waliul and Lodhi, Muhammad Uzair and Kuzel, Aaron R and Johnson, Peter and Rahim, Umar and Rahim, Mustafa},
  journal={Cureus},
  volume={10},
  number={5},
  year={2018},
  publisher={Cureus Inc.}
}

@article{example_image_2_3_ct,
  title={Synchronous intussusception with primary neuroendocrine tumour in an adult},
  author={Turco, Jennifer},
  journal={Journal of Surgical Case Reports},
  volume={2024},
  number={3},
  pages={rjae128},
  year={2024},
  publisher={Oxford University Press}
}

@article{example_image_4_ct,
  title={A new fully automatic and robust algorithm for fast segmentation of liver tissue and tumors from CT scans},
  author={Massoptier, Laurent and Casciaro, Sergio},
  journal={European radiology},
  volume={18},
  number={8},
  pages={1658--1665},
  year={2008},
  publisher={Springer}
}


@misc{Authors14,
 author = {FirstName LastName},
 title = {The frobnicatable foo filter},
 note = {Face and Gesture submission ID 324. Supplied as supplemental material {\tt fg324.pdf}},
 year = 2014
}

@misc{Authors14b,
 author = {FirstName LastName},
 title = {Frobnication tutorial},
 note = {Supplied as supplemental material {\tt tr.pdf}},
 year = 2014
}

@article{Alpher02,
author = {FirstName Alpher},
title = {Frobnication},
journal = PAMI,
volume = 12,
number = 1,
pages = {234--778},
year = 2002
}

@article{Alpher03,
author = {FirstName Alpher and  FirstName Fotheringham-Smythe},
title = {Frobnication revisited},
journal = {Journal of Foo},
volume = 13,
number = 1,
pages = {234--778},
year = 2003
}

@article{Alpher04,
author = {FirstName Alpher and FirstName Fotheringham-Smythe and FirstName Gamow},
title = {Can a machine frobnicate?},
journal = {Journal of Foo},
volume = 14,
number = 1,
pages = {234--778},
year = 2004
}

@inproceedings{Alpher05,
author = {FirstName Alpher and FirstName Gamow},
title = {Can a computer frobnicate?},
booktitle = CVPR,
pages = {234--778},
year = 2005
}



