papers.bib

@article{pedersen2017cyvcf2,
  author  = {Pedersen, Brent S and Quinlan, Aaron R},
  title   = {cyvcf2: fast, flexible variant analysis with Python},
  year    = {2017},
  month   = {02},
  journal = {Bioinformatics},
  volume  = {33},
  number  = {12},
  pages   = {1867-1869},
  issn    = {1367-4803},
}

@article{isensee2020nnunet,
  author    = {Isensee,  Fabian and Jaeger,  Paul F. and Kohl,  Simon A. A. and Petersen,  Jens and Maier-Hein,  Klaus H.},
  title     = {nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation},
  year      = {2020},
  journal   = {Nature Methods},
  volume    = {18},
  number    = {2},
  pages     = {203--211},
  publisher = {Springer Science and Business Media LLC},
}

@misc{hie2022esm2,
  author        = {Hie, Brian and Candido, Salvatore and Lin, Zeming and Kabeli, Ori and Rao, Roshan and Smetanin, Nikita and Sercu, Tom and Rives, Alexander},
  title         = {A high-level programming language for generative protein design},
  year          = {2022},
  archiveprefix = {bioRxiv},
  eprint        = {2022.12.21.521526},
}

@article{pocock2022tiatoolbox,
  author    = {Pocock, Johnathan and Graham, Simon and Vu, Quoc Dang and Jahanifar, Mostafa and Deshpande, Srijay and Hadjigeorghiou, Giorgos and Shephard, Adam and Bashir, Raja Muhammad Saad and Bilal, Mohsin and Lu, Wenqi and others},
  title     = {TIAToolbox as an end-to-end library for advanced tissue image analytics},
  year      = {2022},
  journal   = {Communications medicine},
  volume    = {2},
  number    = {1},
  pages     = {120},
  publisher = {Nature Publishing Group UK London},
}

@misc{verkuil2022esm1,
  author        = {Verkuil, Robert and Kabeli, Ori and Du, Yilun and Wicky, Basile I. M. and Milles, Lukas F. and Dauparas, Justas and Baker, David and Ovchinnikov, Sergey and Sercu, Tom and Rives, Alexander},
  title         = {Language models generalize beyond natural proteins},
  year          = {2022},
  archiveprefix = {bioRxiv},
  eprint        = {2022.12.21.521521},
}

@article{kunes2023cytopus,
  author    = {Kunes,  Russell Z. and Walle,  Thomas and Land,  Max and Nawy,  Tal and Pe’er,  Dana},
  title     = {Supervised discovery of interpretable gene programs from single-cell data},
  year      = {2023},
  journal   = {Nature Biotechnology},
  volume    = {42},
  number    = {7},
  pages     = {1084--1095},
  publisher = {Springer Science and Business Media LLC},
}

@article{liang2023pathfinder,
  author    = {Liang,  Junhao and Zhang,  Weisheng and Yang,  Jianghui and Wu,  Meilong and Dai,  Qionghai and Yin,  Hongfang and Xiao,  Ying and Kong,  Lingjie},
  title     = {Deep learning supported discovery of biomarkers for clinical prognosis of liver cancer},
  year      = {2023},
  journal   = {Nature Machine Intelligence},
  volume    = {5},
  number    = {4},
  pages     = {408--420},
  publisher = {Springer Science and Business Media LLC},
}

@article{wasserthal2023totalsegmentator,
  author    = {Wasserthal, Jakob and Breit, Hanns-Christian and Meyer, Manfred T and Pradella, Maurice and Hinck, Daniel and Sauter, Alexander W and Heye, Tobias and Boll, Daniel T and Cyriac, Joshy and Yang, Shan and others},
  title     = {TotalSegmentator: robust segmentation of 104 anatomic structures in CT images},
  year      = {2023},
  journal   = {Radiology: Artificial Intelligence},
  volume    = {5},
  number    = {5},
  pages     = {e230024},
  publisher = {Radiological Society of North America},
}

@article{zhou2023retfound,
  author    = {Zhou,  Yukun and Chia,  Mark A. and Wagner,  Siegfried K. and Ayhan,  Murat S. and Williamson,  Dominic J. and Struyven,  Robbert R. and Liu,  Timing and Xu,  Moucheng and Lozano,  Mateo G. and Woodward-Court,  Peter and Kihara,  Yuka and Allen,  Naomi and Gallacher,  John E. J. and Littlejohns,  Thomas and Aslam,  Tariq and Bishop,  Paul and Black,  Graeme and Sergouniotis,  Panagiotis and Atan,  Denize and Dick,  Andrew D. and Williams,  Cathy and Barman,  Sarah and Barrett,  Jenny H. and Mackie,  Sarah and Braithwaite,  Tasanee and Carare,  Roxana O. and Ennis,  Sarah and Gibson,  Jane and Lotery,  Andrew J. and Self,  Jay and Chakravarthy,  Usha and Hogg,  Ruth E. and Paterson,  Euan and Woodside,  Jayne and Peto,  Tunde and Mckay,  Gareth and Mcguinness,  Bernadette and Foster,  Paul J. and Balaskas,  Konstantinos and Khawaja,  Anthony P. and Pontikos,  Nikolas and Rahi,  Jugnoo S. and Lascaratos,  Gerassimos and Patel,  Praveen J. and Chan,  Michelle and Chua,  Sharon Y. L. and Day,  Alexander and Desai,  Parul and Egan,  Cathy and Fruttiger,  Marcus and Garway-Heath,  David F. and Hardcastle,  Alison and Khaw,  Sir Peng T. and Moore,  Tony and Sivaprasad,  Sobha and Strouthidis,  Nicholas and Thomas,  Dhanes and Tufail,  Adnan and Viswanathan,  Ananth C. and Dhillon,  Bal and Macgillivray,  Tom and Sudlow,  Cathie and Vitart,  Veronique and Doney,  Alexander and Trucco,  Emanuele and Guggeinheim,  Jeremy A. and Morgan,  James E. and Hammond,  Chris J. and Williams,  Katie and Hysi,  Pirro and Harding,  Simon P. and Zheng,  Yalin and Luben,  Robert and Luthert,  Phil and Sun,  Zihan and McKibbin,  Martin and O’Sullivan,  Eoin and Oram,  Richard and Weedon,  Mike and Owen,  Chris G. and Rudnicka,  Alicja R. and Sattar,  Naveed and Steel,  David and Stratton,  Irene and Tapp,  Robyn and Yates,  Max M. and Petzold,  Axel and Madhusudhan,  Savita and Altmann,  Andre and Lee,  Aaron Y. and Topol,  Eric J. and Denniston,  Alastair K. and Alexander,  Daniel C. and Keane,  Pearse A.},
  title     = {A foundation model for generalizable disease detection from retinal images},
  year      = {2023},
  journal   = {Nature},
  volume    = {622},
  number    = {7981},
  pages     = {156--163},
  publisher = {Springer Science and Business Media LLC},
}

@article{zhou2023foundation,
  author    = {Zhou, Yukun and Chia, Mark A and Wagner, Siegfried K and Ayhan, Murat S and Williamson, Dominic J and Struyven, Robbert R and Liu, Timing and Xu, Moucheng and Lozano, Mateo G and Woodward-Court, Peter and others},
  title     = {A foundation model for generalizable disease detection from retinal images},
  year      = {2023},
  journal   = {Nature},
  volume    = {622},
  number    = {7981},
  pages     = {156--163},
  publisher = {Nature Publishing Group UK London},
}

@article{zeng2023abrsp,
  author    = {Zeng, Qinghe
               and Klein, Christophe
               and Caruso, Stefano
               and Maille, Pascale
               and Allende, Daniela S.
               and M{\'i}nguez, Beatriz
               and Iavarone, Massimo
               and Ningarhari, Massih
               and Casadei-Gardini, Andrea
               and Pedica, Federica
               and Rimini, Margherita
               and Perbellini, Riccardo
               and Boulagnon-Rombi, Camille
               and Heurgu{\'e}, Alexandra
               and Maggioni, Marco
               and Rela, Mohamed
               and Vij, Mukul
               and Baulande, Sylvain
               and Legoix, Patricia
               and Lameiras, Sonia
               and Amaddeo, Giuliana
               and Argemi, Josepmaria
               and Beaufr{\`e}re, Aur{\'e}lie
               and Berm{\'u}dez-Ramos, Mar{\'i}a
               and Boursier, J{\'e}r{\^o}me
               and Bruges, L{\'e}a
               and Calderaro, Julien
               and Campani, Claudia
               and Castano Garcia, Andres
               and Chan, Stephen Lam
               and D'Alessio, Antonio
               and Di Tommaso, Luca
               and Diaz, Alba
               and Digklia, Antonia
               and Dufour, Jean-Fran{\c{c}}ois
               and Garcia-Porrero, Guillermo
               and Ghaffari Laleh, Narmin
               and Gnemmi, Viviane
               and Gopal, Purva
               and Graham, Rondell P.
               and I{\~{n}}arrairaegui, Mercedes
               and Kather, Jakob Nikolas
               and Labgaa, Ismail
               and Lequoy, Marie
               and Leung, Howard Ho-Wai
               and Lom{\'e}nie, Nicolas
               and Mar{\'i}n-Zuluaga, Juan Ignacio
               and Mendoza-Pacas, Guillermo
               and Michalak, Sophie
               and El Nahhas, Omar S. M.
               and Nault, Jean-Charles
               and Navale, Pooja
               and Paradis, Val{\'e}rie
               and Park, Young Nyun
               and Pawlotsky, Jean-Michel
               and Peter, Simon
               and Pinato, David James
               and Pinter, Matthias
               and Radu, Pompilia
               and Regnault, H{\'e}l{\`e}ne
               and Reig, Maria
               and Rhee, Hyungjin
               and Rimassa, Lorenza
               and Salcedo, Mar{\'i}a Teresa
               and Sangro, Bruno
               and Scheiner, Bernhard
               and Sempoux, Christine
               and Su, Tung-Hung
               and Torres, Callie
               and Tran, Nguyen H.
               and Tr{\'e}po, Eric
               and Varela, Maria
               and Verset, Gontran
               and Vogel, Arndt
               and Wendum, Dominique
               and Ziol, Marianne},
  title     = {Artificial intelligence-based pathology as a biomarker of sensitivity to atezolizumab{\&}{\#}x2013;bevacizumab in patients with hepatocellular carcinoma: a multicentre retrospective study},
  year      = {2023},
  month     = {Dec},
  day       = {01},
  journal   = {The Lancet Oncology},
  volume    = {24},
  number    = {12},
  pages     = {1411-1422},
  publisher = {Elsevier},
  issn      = {1470-2045},
}

@article{abramson2024alphafold3,
  author    = {Abramson,  Josh and Adler,  Jonas and Dunger,  Jack and Evans,  Richard and Green,  Tim and Pritzel,  Alexander and Ronneberger,  Olaf and Willmore,  Lindsay and Ballard,  Andrew J. and Bambrick,  Joshua and Bodenstein,  Sebastian W. and Evans,  David A. and Hung,  Chia-Chun and O’Neill,  Michael and Reiman,  David and Tunyasuvunakool,  Kathryn and Wu,  Zachary and Žemgulytė,  Akvilė and Arvaniti,  Eirini and Beattie,  Charles and Bertolli,  Ottavia and Bridgland,  Alex and Cherepanov,  Alexey and Congreve,  Miles and Cowen-Rivers,  Alexander I. and Cowie,  Andrew and Figurnov,  Michael and Fuchs,  Fabian B. and Gladman,  Hannah and Jain,  Rishub and Khan,  Yousuf A. and Low,  Caroline M. R. and Perlin,  Kuba and Potapenko,  Anna and Savy,  Pascal and Singh,  Sukhdeep and Stecula,  Adrian and Thillaisundaram,  Ashok and Tong,  Catherine and Yakneen,  Sergei and Zhong,  Ellen D. and Zielinski,  Michal and Žídek,  Augustin and Bapst,  Victor and Kohli,  Pushmeet and Jaderberg,  Max and Hassabis,  Demis and Jumper,  John M.},
  title     = {Accurate structure prediction of biomolecular interactions with AlphaFold 3},
  year      = {2024},
  journal   = {Nature},
  volume    = {630},
  number    = {8016},
  pages     = {493--500},
  publisher = {Springer Science and Business Media LLC},
}

@misc{warner2024modernbert,
  author        = {Benjamin Warner and Antoine Chaffin and Benjamin Clavié and Orion Weller and Oskar Hallström and Said Taghadouini and Alexis Gallagher and Raja Biswas and Faisal Ladhak and Tom Aarsen and Nathan Cooper and Griffin Adams and Jeremy Howard and Iacopo Poli},
  title         = {Smarter, Better, Faster, Longer: A Modern Bidirectional Encoder for Fast, Memory Efficient, and Long Context Finetuning and Inference},
  year          = {2024},
  archiveprefix = {arXiv},
  eprint        = {2412.13663},
}

@misc{smith2024flowmap,
  author        = {Cameron Smith and David Charatan and Ayush Tewari and Vincent Sitzmann},
  title         = {FlowMap: High-Quality Camera Poses, Intrinsics, and Depth via Gradient Descent},
  year          = {2024},
  archiveprefix = {arXiv},
  eprint        = {2404.15259},
}

@article{chen2024uni,
  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},
  title     = {Towards a general-purpose foundation model for computational pathology},
  year      = {2024},
  journal   = {Nature Medicine},
  volume    = {30},
  number    = {3},
  pages     = {850--862},
  publisher = {Springer Science and Business Media LLC},
}

@article{elnahhas2024stamp,
  author    = {El Nahhas,  Omar S. M. and van Treeck,  Marko and W\"{o}lflein,  Georg and Unger,  Michaela and Ligero,  Marta and Lenz,  Tim and Wagner,  Sophia J. and Hewitt,  Katherine J. and Khader,  Firas and Foersch,  Sebastian and Truhn,  Daniel and Kather,  Jakob Nikolas},
  title     = {From whole-slide image to biomarker prediction: end-to-end weakly supervised deep learning in computational pathology},
  year      = {2024},
  journal   = {Nature Protocols},
  publisher = {Springer Science and Business Media LLC},
}

@misc{zigutyte2024mopadi,
  author        = {Laura Žigutytė and Tim Lenz and Tianyu Han and Katherine Jane Hewitt and Nic Gabriel Reitsam and Sebastian Foersch and Zunamys I Carrero and Michaela Unger and Alexander T Pearson and Daniel Truhn and Jakob Nikolas Kather},
  title         = {ounterfactual Diffusion Models for Mechanistic Explainability of Artificial Intelligence Models in Pathology},
  year          = {2024},
  url           = {https://www.biorxiv.org/content/10.1101/2024.10.29.620913v1},
  archiveprefix = {bioRxiv},
  eprint        = {2024.10.29.620913},
}

@article{lu2024conch,
  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},
  title     = {A visual-language foundation model for computational pathology},
  year      = {2024},
  journal   = {Nature Medicine},
  volume    = {30},
  number    = {3},
  pages     = {863--874},
  publisher = {Springer Science and Business Media LLC},
}

@article{ma2024medsam,
  author    = {Ma,  Jun and He,  Yuting and Li,  Feifei and Han,  Lin and You,  Chenyu and Wang,  Bo},
  title     = {Segment anything in medical images},
  year      = {2024},
  journal   = {Nature Communications},
  volume    = {15},
  number    = {1},
  publisher = {Springer Science and Business Media LLC},
}

@article{wiest2024llm,
  author  = {Wiest, Isabella Catharina and Wolf, Fabian and Le{\ss}mann, Marie-Elisabeth and van Treeck, Marko and Ferber, Dyke and Zhu, Jiefu and Boehme, Heiko and Bressem, Keno K and Ulrich, Hannes and Ebert, Matthias P and others},
  title   = {LLM-AIx: An open source pipeline for Information Extraction from unstructured medical text based on privacy preserving Large Language Models},
  year    = {2024},
  journal = {medRxiv},
}

@misc{yuksekgonul2024textgrad,
  author        = {Yuksekgonul, Mert and Bianchi, Federico and Boen, Joseph and Liu, Sheng and Huang, Zhi and Guestrin, Carlos and Zou, James},
  title         = {{TextGrad}: Automatic "differentiation" via text},
  year          = {2024},
  archiveprefix = {arXiv},
  eprint        = {2406.07496},
}

@article{hollmann2025tabpfn,
  author    = {Hollmann,  Noah and M\"{u}ller,  Samuel and Purucker,  Lennart and Krishnakumar,  Arjun and K\"{o}rfer,  Max and Hoo,  Shi Bin and Schirrmeister,  Robin Tibor and Hutter,  Frank},
  title     = {Accurate predictions on small data with a tabular foundation model},
  year      = {2025},
  journal   = {Nature},
  volume    = {637},
  number    = {8045},
  pages     = {319--326},
  publisher = {Springer Science and Business Media LLC},
}

@misc{neidlinger2025eagle,
  author        = {Peter Neidlinger and Tim Lenz and Sebastian Foersch and Chiara M. L. Loeffler and Jan Clusmann and Marco Gustav and Lawrence A. Shaktah and Rupert Langer and Bastian Dislich and Lisa A. Boardman and Amy J. French and Ellen L. Goode and Andrea Gsur and Stefanie Brezina and Marc J. Gunter and Robert Steinfelder and Hans-Michael Behrens and Christoph Röcken and Tabitha Harrison and Ulrike Peters and Amanda I. Phipps and Giuseppe Curigliano and Nicola Fusco and Antonio Marra and Michael Hoffmeister and Hermann Brenner and Jakob Nikolas Kather},
  title         = {A deep learning framework for efficient pathology image analysis},
  year          = {2025},
  url           = {https://arxiv.org/abs/2502.13027},
  archiveprefix = {arXiv},
  eprint        = {2502.13027},
  primaryclass  = {cs.CV},
}

@misc{jiang2025medsss,
  author        = {Shuyang Jiang and Yusheng Liao and Zhe Chen and Ya Zhang and Yanfeng Wang and Yu Wang},
  title         = {MedS$^3$: Towards Medical Small Language Models with Self-Evolved Slow Thinking},
  year          = {2025},
  archiveprefix = {arXiv},
  eprint        = {2501.12051},
}

@inproceedings{lenz2025cobra,
  author    = {T. Lenz* and Peter Neidlinger* and Marta Ligero and Georg Wölflein and Marko van Treeck and Jakob Nikolas Kather},
  title     = {Unsupervised Foundation Model-Agnostic Slide-Level Representation Learning},
  year      = {2025},
  booktitle = {Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
}

@article{xiang2025musk,
  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},
  title     = {A vision-language foundation model for precision oncology},
  year      = {2025},
  journal   = {Nature},
  publisher = {Springer Science and Business Media LLC},
}