Publications

2025

Papers in international journals

  1. 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.
    Abstract DOI PMID
  2. 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.
    Abstract DOI PMID
  3. 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.
    Abstract DOI PMID
  4. 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.
    Abstract DOI PMID
  5. 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.
    Abstract DOI PMID
  6. 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.
    Abstract DOI

Preprints

  1. 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.
    Abstract DOI arXiv
  2. 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.
    Abstract DOI
  3. 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.
    Abstract DOI arXiv
  4. 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.
    Abstract DOI arXiv

Papers in conference proceedings

  1. 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.
    Abstract DOI
  2. 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.
    Abstract DOI
  3. 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.
    Abstract Url
  4. 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.
    Abstract DOI

PhD theses

  1. H. Pinckaers, "Prognostic modeling for prostate cancer patients using gigapixel-sized images", PhD thesis, 2025.
    Abstract Url
  2. E. Markus-Smeets, "Build bridges to break barriers: Using quantitative imaging to understand pancreas tumor biology", PhD thesis, 2025.
    Abstract Url
  3. J. Linmans, "Uncertainty estimation in digital pathology: Towards applying artificial intelligence in an uncertain clinical world", PhD thesis, 2025.
    Abstract Url