Publications
2025
Papers in international journals
- M. Tran, P. Schmidle, R. Guo, S. Wagner, V. Koch, V. Lupperger, B. Novotny, D. Murphree, H. Hardway, M. D'Amato, J. Lefkes, D. Geijs, A. Feuchtinger, A. Böhner, R. Kaczmarczyk, T. Biedermann, A. Amir, A. Mooyaart, F. Ciompi, G. Litjens, C. Wang, N. Comfere, K. Eyerich, S. Braun, C. Marr and T. Peng, "Generating dermatopathology reports from gigapixel whole slide images with HistoGPT", Nature Communications, 2025;16.
- M. Schuurmans, A. Saha, N. Alves, P. Vendittelli, D. Yakar, S. Sabroso-Lasa, N. Xue, N. Malats, H. Huisman, J. Hermans and G. Litjens, "End-to-end prognostication in pancreatic cancer by multimodal deep learning: a retrospective, multicenter study", European Radiology, 2025.
- J.S. Bosma, K. Dercksen, L. Builtjes, R. André, C. Roest, S. Fransen, C. Noordman, M. Navarro-Padilla, J. Lefkes, N. Alves, M. de Grauw, L. van Eekelen, J. Spronck, M. Schuurmans, B. de Wilde, W. Hendrix, W. Aswolinskiy, A. Saha, J. Twilt, D. Geijs, J. Veltman, D. Yakar, M. de Rooij, F. Ciompi, A. Hering, J. Geerdink, H. Huisman, O. behalf of the consortium, M. de Grauw, L. van Eekelen, B. de Wilde, Q. van Lohuizen, M. Stegeman, K. Rutten, I. Smit, G. Stultiens, C. Overduin, M. Rutten, E. Scholten, R. van der Post, K. Grünberg, S. Vos, E. Taken, I. Nagtegaal, A. Mickan, M. Groeneveld, P. Gerke, J. Meakin, M. Looijen-Salamon, T. de Haas, F. Hoitsma, M. D'Amato and M. de Rooij, "The DRAGON benchmark for clinical NLP", npj Digital Medicine, 2025;8.
- T. Haddad, J. Bokhorst, L. van den Dobbelsteen, S. Öztürk, E. Baumann, S. van Vliet, K. Verrijp, N. Jamieson, C. Wood, M. Berger, R. Kirsch, M. Aben, N. Rutgers, H. Ueno, F. Ciompi, F. Simmer, J. van der Laak, A. Lugli, I. Zlobec and I. Nagtegaal, "Tumor budding and poorly differentiated clusters as a biological continuum in colorectal cancer invasion and prognosis", Scientific Reports, 2025;15.
- A. Farris, J. van der Laak and D. van Midden, "Artificial intelligence-enhanced interpretation of kidney transplant biopsy: focus on rejection", Current Opinion in Organ Transplantation, 2025.
- D. van Midden, L. Studer, M. Hermsen, E. Steenbergen, J. Kers, N. Kozakowski, Z. Kikic, L. Hilbrands and J. van der Laak, "Deep learning-based histopathologic segmentation of peritubular capillaries in kidney transplant biopsies", Computers in biology and medicine, 2025;193:110395.
Preprints
- M. D'Amato, J. van der Laak and F. Ciompi, ""No negatives needed": weakly-supervised regression for interpretable tumor detection in whole-slide histopathology images", arXiv:2502.21109, 2025.
- M. van Rijthoven, W. Aswolinskiy, L. Tessier, M. Balkenhol, J. Bogaerts, D. Drubay, L. Blesa, D. Peeters, E. Stovgaard, A. L\aenkholm , H. Haynes, L. Craciun, D. Larsimont, M. Amgad, L. Cooper, C. de Kock, V. Dechering, J. Lotz, N. Weiss, M. van Bockstal, C. Galant, E. Lips, H. Horlings, J. Wesseling, L. Mulder, S. van den Belt, K. Weber, P. Jank, C. Denkert, E. Munari, G. Bogina, C. Russ, A. Lemm, S. Loi, J. Douglas, S. Michiels, H. Joensuu, M. Fan, D. Lee, J. Ye, K. Byun, J. Kim, S. Xu, Z. Ji, F. Xie, J. Kuang, X. Chen, L. Chen, A. Tsakiroglou, R. Byers, M. Fergie, V. Ramanathan, A. Martel, A. Shephard, S. Ahmed Raza, M. Jahanifar, N. Rajpoot, S. Cho, D. Kim, H. Jang, C. Park, K. Kim, R. Donders, S. Maurits, M. Groeneveld, A. Mickan, J. Meakin, B. van Ginneken, R. Salgado, J. van der Laak and F. Ciompi, "Tumor-infiltrating lymphocytes in breast cancer through artificial intelligence: biomarker analysis from the results of the TIGER challenge", medRxiv, 2025.
- S. Sun, D. van Midden, G. Litjens and C. Baumgartner, "Prototype-Based Multiple Instance Learning for Gigapixel Whole Slide Image Classification", arXiv:2503.08384, 2025.
- S. Sun, L. Tessier, F. Meeuwsen, C. Grisi, D. van Midden, G. Litjens and C. Baumgartner, "Label-free Concept Based Multiple Instance Learning for Gigapixel Histopathology", arXiv:2501.02922, 2025.
Papers in conference proceedings
- J. Lefkes, M. D'Amato, S. Sun, G. Litjens and F. Ciompi, "Large Language Models Automate Diagnostic Conclusions Generation from Microscopic Descriptions in Multiple Cancer Types", Laboratory Investigation, 2025;105:103608.
- C. Lems, N. Klubíčková, B. Brattoli, T. Lee, S. Kim, V. Besler, P. Fernandez, L. Pons, A. Laurinavicius, J. Drachneris, D. Montezuma, D. Oliveira, S. Vos, M. Balkenhol, J. van Ipenburg, A. Vos, M. Poceviciute, N. Khalili and F. Ciompi, "Towards a multicentric open DigitAL PatHology assIstant beNchmark: Initial Results from the DALPHIN Study", Laboratory Investigation, 2025;105:103609.
- J. Lefkes, C. Grisi and G. Litjens, "A Balancing Act: Optimizing Classification and Retrieval in Cross-Modal Vision Models", Medical Imaging with Deep Learning, 2025.
- N. Khalili, J. Spronck, F. Ciompi, J. der Van Laak and G. Litjens, "A human-in-the-loop framework for refining deep learning models in pathology segmentation", Medical Imaging 2025: Digital and Computational Pathology, 2025:21.
PhD theses
- H. Pinckaers, "Prognostic modeling for prostate cancer patients using gigapixel-sized images", PhD thesis, 2025.
- E. Markus-Smeets, "Build bridges to break barriers: Using quantitative imaging to understand pancreas tumor biology", PhD thesis, 2025.
- J. Linmans, "Uncertainty estimation in digital pathology: Towards applying artificial intelligence in an uncertain clinical world", PhD thesis, 2025.