%% resnet model
@inproceedings{heDeepResidualLearning2016,
  title = {Deep {{Residual Learning}} for {{Image Recognition}}},
  booktitle = {2016 {{IEEE Conference}} on {{Computer Vision}} and {{Pattern Recognition}} ({{CVPR}})},
  author = {He, Kaiming and Zhang, Xiangyu and Ren, Shaoqing and Sun, Jian},
  date = {2016-06},
  year = 2016,
  pages = {770--778},
  publisher = {IEEE},
  location = {Las Vegas, NV, USA},
  doi = {10.1109/CVPR.2016.90},
  url = {http://ieeexplore.ieee.org/document/7780459/},
  eventtitle = {2016 {{IEEE Conference}} on {{Computer Vision}} and {{Pattern Recognition}} ({{CVPR}})},
  isbn = {978-1-4673-8851-1},
  langid = {english}
}

%% vit model
@inproceedings{dosovitskiyImageWorth16x162021,
  title = {An {{Image}} Is {{Worth}} 16x16 {{Words}}: {{Transformers}} for {{Image Recognition}} at {{Scale}}},
  shorttitle = {{{ViT}}},
  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 Uszkoreit, Jakob and Houlsby, Neil},
  date = {2021-06-03},
  year = 2021,
  eprint = {2010.11929},
  eprinttype = {arXiv},
  eprintclass = {cs},
  publisher = {ICLR},
  url = {http://arxiv.org/abs/2010.11929},
  eventtitle = {{{ICLR}}}
}

%% plip model
@article{huangVisualLanguageFoundation2023,
  title = {A {{Visual}}–{{Language Foundation Model}} for {{Pathology Image Analysis Using Medical Twitter}}},
  author = {Huang, Zhi and Bianchi, Federico and Yuksekgonul, Mert and Montine, Thomas J. and Zou, James},
  date = {2023-09},
  year = 2023,
  journaltitle = {Nature Medicine},
  shortjournal = {Nat Med},
  volume = {29},
  number = {9},
  pages = {2307--2316},
  issn = {1078-8956, 1546-170X},
  doi = {10.1038/s41591-023-02504-3},
  url = {https://www.nature.com/articles/s41591-023-02504-3},
  langid = {english}
}

%% uni model
@article{chenGeneralPurposeFoundationModel2024,
  title = {Towards a {{General-Purpose Foundation Model}} for {{Computational Pathology}}},
  author = {Chen, Richard J. and Ding, Tong and Lu, Ming Y. and Williamson, Drew F. K. and Jaume, Guillaume and Song, Andrew H. and Chen, Bowen and Zhang, Andrew and Shao, Daniel and Shaban, Muhammad and Williams, Mane and Oldenburg, Lukas and Weishaupt, Luca L. and Wang, Judy J. and Vaidya, Anurag and Le, Long Phi and Gerber, Georg and Sahai, Sharifa and Williams, Walt and Mahmood, Faisal},
  date = {2024-03},
  year = 2024,
  journaltitle = {Nature Medicine},
  shortjournal = {Nat Med},
  volume = {30},
  number = {3},
  pages = {850--862},
  issn = {1078-8956, 1546-170X},
  doi = {10.1038/s41591-024-02857-3},
  url = {https://www.nature.com/articles/s41591-024-02857-3},
  langid = {english}
}

%% phikon model
@online{filiotScalingSelfSupervisedLearning2023,
  title = {Scaling {{Self-Supervised Learning}} for {{Histopathology}} with {{Masked Image Modeling}}},
  author = {Filiot, Alexandre and Ghermi, Ridouane and Olivier, Antoine and Jacob, Paul and Fidon, Lucas and Kain, Alice Mac and Saillard, Charlie and Schiratti, Jean-Baptiste},
  date = {2023-09-14},
  year = 2023,
  eprinttype = {medRxiv},
  pages = {2023.07.21.23292757},
  doi = {10.1101/2023.07.21.23292757},
  url = {https://www.medrxiv.org/content/10.1101/2023.07.21.23292757v2},
  langid = {english},
  pubstate = {prepublished}
}

%% demographic bias
@article{vaidyaDemographicBiasMisdiagnosis2024,
  title = {Demographic {{Bias}} in {{Misdiagnosis}} by {{Computational Pathology Models}}},
  author = {Vaidya, Anurag and Chen, Richard J. and Williamson, Drew F. K. and Song, Andrew H. and Jaume, Guillaume and Yang, Yuzhe and Hartvigsen, Thomas and Dyer, Emma C. and Lu, Ming Y. and Lipkova, Jana and Shaban, Muhammad and Chen, Tiffany Y. and Mahmood, Faisal},
  year = 2024,
  journaltitle = {Nature Medicine},
  shortjournal = {Nature Medicine},
  volume = {30},
  number = {4},
  pages = {1174--1190},
  issn = {1546-170X},
  doi = {10.1038/s41591-024-02885-z},
  url = {https://doi.org/10.1038/s41591-024-02885-z},
  langid = {american}
}

%% tsne model
@article{vandermaatenVisualizingDataUsing2008,
  title={{Visualizing Data using t-SNE}},
  author={Van der Maaten, Laurens and Hinton, Geoffrey},
  journal={Journal of Machine Learning Research},
  volume={9},
  pages={2579--2605},
  year={2008}
}

%% giga-path model
@article{xuWholeSlideFoundationModel2024,
  title = {A {{Whole-Slide Foundation Model}} for {{Digital Pathology}} from {{Real-World Data}}},
  author = {Xu, Hanwen and Usuyama, Naoto and Bagga, Jaspreet and Zhang, Sheng and Rao, Rajesh and Naumann, Tristan and Wong, Cliff and Gero, Zelalem and Gonz{\'a}lez, Javier and Gu, Yu and Xu, Yanbo and Wei, Mu and Wang, Wenhui and Ma, Shuming and Wei, Furu and Yang, Jianwei and Li, Chunyuan and Gao, Jianfeng and Rosemon, Jaylen and Bower, Tucker and Lee, Soohee and Weerasinghe, Roshanthi and Wright, Bill J. and Robicsek, Ari and Piening, Brian and Bifulco, Carlo and Wang, Sheng and Poon, Hoifung},
  year = 2024,
  month = jun,
  journal = {Nature},
  volume = {630},
  number = {8015},
  pages = {181--188},
  issn = {0028-0836, 1476-4687},
  doi = {10.1038/s41586-024-07441-w},
  langid = {english}
}

%% conch model
@article{luVisualLanguageFoundationModel2024,
  title = {A {{Visual-Language Foundation Model}} for {{Computational Pathology}}},
  author = {Lu, Ming Y. and Chen, Bowen and Williamson, Drew F. K. and Chen, Richard J. and Liang, Ivy and Ding, Tong and Jaume, Guillaume and Odintsov, Igor and Le, Long Phi and Gerber, Georg and Parwani, Anil V. and Zhang, Andrew and Mahmood, Faisal},
  year = 2024,
  month = mar,
  journal = {Nature Medicine},
  volume = {30},
  number = {3},
  pages = {863--874},
  issn = {1078-8956, 1546-170X},
  doi = {10.1038/s41591-024-02856-4},
  langid = {english}
}

%% titan model
@article{dingMultimodalWholeSlideFoundation2025,
  title = {A {{Multimodal Whole-Slide Foundation Model}} for {{Pathology}}},
  author = {Ding, Tong and Wagner, Sophia J. and Song, Andrew H. and Chen, Richard J. and Lu, Ming Y. and Zhang, Andrew and Vaidya, Anurag J. and Jaume, Guillaume and Shaban, Muhammad and Kim, Ahrong and Williamson, Drew F. K. and Robertson, Harry and Chen, Bowen and {Almagro-P{\'e}rez}, Cristina and Doucet, Paul and Sahai, Sharifa and Chen, Chengkuan and Chen, Christina S. and Komura, Daisuke and Kawabe, Akihiro and Ochi, Mieko and Sato, Shinya and Yokose, Tomoyuki and Miyagi, Yohei and Ishikawa, Shumpei and Gerber, Georg and Peng, Tingying and Le, Long Phi and Mahmood, Faisal},
  year = 2025,
  month = nov,
  journal = {Nature Medicine},
  volume = {31},
  number = {11},
  pages = {3749--3761},
  issn = {1546-170X},
  doi = {10.1038/s41591-025-03982-3}
}

%%% musk model
@article{xiangVisionLanguageFoundation2025,
  title = {A {{Vision}}--{{Language Foundation Model}} for {{Precision Oncology}}},
  author = {Xiang, Jinxi and Wang, Xiyue and Zhang, Xiaoming and Xi, Yinghua and Eweje, Feyisope and Chen, Yijiang and Li, Yuchen and Bergstrom, Colin and Gopaulchan, Matthew and Kim, Ted and Yu, Kun-Hsing and Willens, Sierra and Olguin, Francesca Maria and Nirschl, Jeffrey J. and Neal, Joel and Diehn, Maximilian and Yang, Sen and Li, Ruijiang},
  year = 2025,
  month = feb,
  journal = {Nature},
  volume = {638},
  number = {8051},
  pages = {769--778},
  issn = {1476-4687},
  doi = {10.1038/s41586-024-08378-w},
  langid = {american}
}

%% virchow model
@article{vorontsovFoundationModelClinicalGrade2024,
  title = {A {{Foundation Model}} for {{Clinical-Grade Computational Pathology}} and {{Rare Cancers Detection}}},
  author = {Vorontsov, Eugene and Bozkurt, Alican and Casson, Adam and Shaikovski, George and Zelechowski, Michal and Severson, Kristen and Zimmermann, Eric and Hall, James and Tenenholtz, Neil and Fusi, Nicolo and Yang, Ellen and Mathieu, Philippe and Van Eck, Alexander and Lee, Donghun and Viret, Julian and Robert, Eric and Wang, Yi Kan and Kunz, Jeremy D. and Lee, Matthew C. H. and Bernhard, Jan H. and Godrich, Ran A. and Oakley, Gerard and Millar, Ewan and Hanna, Matthew and Wen, Hannah and Retamero, Juan A. and Moye, William A. and Yousfi, Razik and Kanan, Christopher and Klimstra, David S. and Rothrock, Brandon and Liu, Siqi and Fuchs, Thomas J.},
  year = 2024,
  month = oct,
  journal = {Nature Medicine},
  volume = {30},
  number = {10},
  pages = {2924--2935},
  issn = {1078-8956, 1546-170X},
  doi = {10.1038/s41591-024-03141-0},
  langid = {english}
}

%% phikon 2 model
@misc{filiotPhikonV2LargePublic2024,
  title = {Phikon-{{V2}}, {{A Large}} and {{Public Feature Extractor}} for {{Biomarker Prediction}}},
  author = {Filiot, Alexandre and Jacob, Paul and Kain, Alice Mac and Saillard, Charlie},
  year = 2024,
  month = sep,
  number = {arXiv:2409.09173},
  eprint = {2409.09173},
  primaryclass = {eess},
  publisher = {arXiv},
  doi = {10.48550/arXiv.2409.09173},
  archiveprefix = {arXiv}
}


%% hoptimus-0 model
@misc{hoptimus0,
  title = {H-Optimus-0},
  author = {Saillard, Charlie and Jenatton, Rodolphe and {Llinares-L{\'o}pez}, Felipe and Mariet, Zelda and Cahan{\'e}, David and Durand, Eric and Vert, Jean-Philippe},
  year = 2024
}

%% clip model
@inproceedings{radfordLearningTransferableVisual2021,
  title = {Learning {{Transferable Visual Models}} from {{Natural Language Supervision}}},
  booktitle = {Proceedings of the 38th International Conference on Machine Learning},
  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 Krueger, Gretchen and Sutskever, Ilya},
  editor = {Meila, Marina and Zhang, Tong},
  year = 2021,
  month = jul,
  series = {Proceedings of Machine Learning Research},
  volume = {139},
  pages = {8748--8763},
  publisher = {PMLR}
}

%% dino model
@misc{caronEmergingPropertiesSelfSupervised2021,
  title = {Emerging {{Properties}} in {{Self-Supervised Vision Transformers}}},
  author = {Caron, Mathilde and Touvron, Hugo and Misra, Ishan and J{\'e}gou, Herv{\'e} and Mairal, Julien and Bojanowski, Piotr and Joulin, Armand},
  year = 2021,
  month = may,
  number = {arXiv:2104.14294},
  eprint = {2104.14294},
  primaryclass = {cs},
  publisher = {arXiv},
  doi = {10.48550/arXiv.2104.14294},
  archiveprefix = {arXiv},
  langid = {english}
}

%% clam model
@article{luDataEfficientWeaklySupervised2021,
  title = {Data-{{Efficient}} and {{Weakly Supervised Computational Pathology}} on {{Whole-Slide Images}}},
  author = {Lu, Ming Y. and Williamson, Drew F. K. and Chen, Tiffany Y. and Chen, Richard J. and Barbieri, Matteo and Mahmood, Faisal},
  year = 2021,
  month = jun,
  journal = {Nature Biomedical Engineering},
  volume = {5},
  number = {6},
  pages = {555--570},
  issn = {2157-846X},
  doi = {10.1038/s41551-020-00682-w},
  langid = {american}
}

%% pfm rubust
@misc{jongCurrentPathologyFoundation2025,
  title = {Current {{Pathology Foundation Models Are Unrobust}} to {{Medical Center Differences}}},
  author = {de Jong, Edwin D. and Marcus, Eric and Teuwen, Jonas},
  year = 2025,
  month = feb,
  number = {arXiv:2501.18055},
  eprint = {2501.18055},
  primaryclass = {cs},
  publisher = {arXiv},
  doi = {10.48550/arXiv.2501.18055},
  archiveprefix = {arXiv},
  langid = {english}
}

%% tcga-ut
@misc{daisuke_komura_2021_5889558,
  title = {Histology {{Images}} from {{Uniform Tumor Regions}} in {{TCGA Whole Slide Images}} ({{TCGA-UT}})},
  author = {Komura, Daisuke and Ishikawa, Shumpei},
  year = 2021,
  month = jan,
  publisher = {Zenodo},
  doi = {10.5281/zenodo.5889558}
}

%% tcga-brca
@article{cancergenomeatlasnetworkComprehensiveMolecularPortraits2012,
  title = {Comprehensive {{Molecular Portraits}} of {{Human Breast Tumours}}},
  author = {{The Cancer Genome Atlas Network}},
  year = 2012,
  month = oct,
  journal = {Nature},
  volume = {490},
  number = {7418},
  pages = {61--70},
  address = {England},
  issn = {1476-4687 0028-0836},
  doi = {10.1038/nature11412},
  langid = {english},
  pmcid = {PMC3465532},
  pmid = {23000897}
}

%% luad dataset
@article{collissonComprehensiveMolecularProfiling2014,
  title = {Comprehensive {{Molecular Profiling}} of {{Lung Adenocarcinoma}}},
  author = {{The Cancer Genome Atlas Research Network}},
  year = 2014,
  month = jul,
  journal = {Nature},
  volume = {511},
  number = {7511},
  pages = {543--550},
  issn = {1476-4687},
  doi = {10.1038/nature13385}
}

@article{hammermanComprehensiveGenomicCharacterization2012,
  title = {Comprehensive {{Genomic Characterization}} of {{Squamous Cell Lung Cancers}}},
  author = {{The Cancer Genome Atlas Research Network}},
  year = 2012,
  month = sep,
  journal = {Nature},
  volume = {489},
  number = {7417},
  pages = {519--525},
  issn = {1476-4687},
  doi = {10.1038/nature11404}
}


%%% macenko
@inproceedings{m.macenkoMethodNormalizingHistology2009,
  title = {A {{Method}} for {{Normalizing Histology Slides}} for {{Quantitative Analysis}}},
  booktitle = {2009 {{IEEE International Symposium}} on {{Biomedical Imaging}}: {{From Nano}} to {{Macro}}},
  author = {{M. Macenko} and {M. Niethammer} and {J. S. Marron} and {D. Borland} and {J. T. Woosley} and {Xiaojun Guan} and {C. Schmitt} and {N. E. Thomas}},
  year = 2009,
  month = jun,
  pages = {1107--1110},
  doi = {10.1109/ISBI.2009.5193250},
  isbn = {1945-8452}
}

%% lora
@misc{huLoRALowRankAdaptation2021,
  title = {{{LoRA}}: {{Low-Rank Adaptation}} of {{Large Language Models}}},
  shorttitle = {{{LoRA}}},
  author = {Hu, Edward J. and Shen, Yelong and Wallis, Phillip and {Allen-Zhu}, Zeyuan and Li, Yuanzhi and Wang, Shean and Wang, Lu and Chen, Weizhu},
  year = 2021,
  month = oct,
  number = {arXiv:2106.09685},
  eprint = {2106.09685},
  primaryclass = {cs},
  publisher = {arXiv},
  doi = {10.48550/arXiv.2106.09685},
  archiveprefix = {arXiv}
}

%% camelyon17
@article{p.bandiDetectionIndividualMetastases2019,
  title = {From {{Detection}} of {{Individual Metastases}} to {{Classification}} of {{Lymph Node Status}} at the {{Patient Level}}: {{The CAMELYON17 Challenge}}},
  author = {{P. B\'andi} and {O. Geessink} and {Q. Manson} and {M. Van Dijk} and {M. Balkenhol} and {M. Hermsen} and {B. Ehteshami Bejnordi} and {B. Lee} and {K. Paeng} and {A. Zhong} and {Q. Li} and {F. G. Zanjani} and {S. Zinger} and {K. Fukuta} and {D. Komura} and {V. Ovtcharov} and {S. Cheng} and {S. Zeng} and {J. Thagaard} and {A. B. Dahl} and {H. Lin} and {H. Chen} and {L. Jacobsson} and {M. Hedlund} and {M. \c Cetin} and {E. Hal\i c\i} and {H. Jackson} and {R. Chen} and {F. Both} and {J. Franke} and {H. K\"usters-Vandevelde} and {W. Vreuls} and {P. Bult} and {B. van Ginneken} and {J. van der Laak} and {G. Litjens}},
  year = 2019,
  month = feb,
  journal = {IEEE Transactions on Medical Imaging},
  volume = {38},
  number = {2},
  pages = {550--560},
  issn = {1558-254X},
  doi = {10.1109/TMI.2018.2867350}
}

%% vahadane
@article{a.vahadaneStructurePreservingColorNormalization2016,
  title = {Structure-{{Preserving Color Normalization}} and {{Sparse Stain Separation}} for {{Histological Images}}},
  author = {{A. Vahadane} and {T. Peng} and {A. Sethi} and {S. Albarqouni} and {L. Wang} and {M. Baust} and {K. Steiger} and {A. M. Schlitter} and {I. Esposito} and {N. Navab}},
  year = 2016,
  month = aug,
  journal = {IEEE Transactions on Medical Imaging},
  volume = {35},
  number = {8},
  pages = {1962--1971},
  issn = {1558-254X},
  doi = {10.1109/TMI.2016.2529665}
}

%% dann
@incollection{ganinDomainAdversarialTrainingNeural2017,
  title = {Domain-{{Adversarial Training}} of {{Neural Networks}}},
  booktitle = {Domain {{Adaptation}} in {{Computer Vision Applications}}},
  author = {Ganin, Yaroslav and Ustinova, Evgeniya and Ajakan, Hana and Germain, Pascal and Larochelle, Hugo and Laviolette, Fran{\c c}ois and Marchand, Mario and Lempitsky, Victor},
  editor = {Csurka, Gabriela},
  year = 2017,
  pages = {189--209},
  publisher = {Springer International Publishing},
  address = {Cham},
  doi = {10.1007/978-3-319-58347-1_10},
  isbn = {978-3-319-58346-4 978-3-319-58347-1},
  langid = {english}
}

%%% reviewer1
@article{asilianbidgoliBiasReductionRepresentation2022,
  title = {Bias {{Reduction}} in {{Representation}} of {{Histopathology Images Using Deep Feature Selection}}},
  author = {Asilian Bidgoli, Azam and Rahnamayan, Shahryar and Dehkharghanian, Taher and Grami, Ali and Tizhoosh, H.R.},
  date = {2022-11-21},
  year = 2022,
  journaltitle = {Scientific Reports},
  shortjournal = {Scientific Reports},
  volume = {12},
  number = {1},
  pages = {19994},
  issn = {2045-2322},
  doi = {10.1038/s41598-022-24317-z},
  url = {https://doi.org/10.1038/s41598-022-24317-z}
}

%% reviewer 2
@online{linUnveilingInstitutionSpecificBias2025,
  title = {Unveiling {{Institution-Specific Bias}} in {{Pathology Foundation Models}}: {{Detriments}}, {{Causes}}, and {{Potential Solutions}}},
  shorttitle = {Unveiling {{Institution-Specific Bias}} in {{Pathology Foundation Models}}},
  author = {Lin, Weiping and Liu, Shen and Zhu, Runchen and Wang, Liansheng},
  date = {2025-02-24},
  year = 2025,
  eprint = {2502.16889},
  eprinttype = {arXiv},
  eprintclass = {cs},
  doi = {10.48550/arXiv.2502.16889},
  url = {http://arxiv.org/abs/2502.16889},
  pubstate = {prepublished},
  version = {1}
}

%% reviewer 3
@article{kheiriInvestigationPotentialBias2025a,
  title = {Investigation on {{Potential Bias Factors}} in {{Histopathology Datasets}}},
  author = {Kheiri, Farnaz and Rahnamayan, Shahryar and Makrehchi, Masoud and Asilian Bidgoli, Azam},
  date = {2025-04-02},
  year = 2025,
  journaltitle = {Scientific Reports},
  shortjournal = {Scientific Reports},
  volume = {15},
  number = {1},
  pages = {11349},
  issn = {2045-2322},
  doi = {10.1038/s41598-025-89210-x},
  url = {https://doi.org/10.1038/s41598-025-89210-x}
}
