New directions for deep learning in cancer research through concept explainability and virtual experimentation.

Project Information

NADIR

Grant agreement ID: 101114631

DOI

10.3030/101114631

EC signature date 15 December 2023

Start date 1 January 2024

End date 31 December 2028

Funded under

• European Research Council (ERC)

Total cost

€ 1 498 750,00

EU contribution

€ 1 498 750,00

Coordinated by

TECHNISCHE UNIVERSITAET DRESDEN
Germany

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (29)

Weakly Supervised Deep Learning Can Analyze Focal Liver Lesions in Contrast-Enhanced Ultrasound

Author(s): Adil Oezsoy, James Alexander Brooks, Marko van Treeck, Yvonne Doerffel, Ulrike Morgera, Jens Berger, Marco Gustav, Oliver Lester Saldanha, Tom Luedde, Jakob Nikolas Kather, Tobias Paul Seraphin, Michael Kallenbach
Published in: Digestion, Issue 106, 2025, ISSN 0012-2823
Publisher: S. Karger AG
DOI: 10.1159/000545098

Artificial intelligence predicts outcome-related molecular profiles and vascular invasion in hepatocellular carcinoma

Author(s): Tobias Paul Seraphin, Agavni Mesropian, Laura Žigutytė, James Brooks, Ezequiel Mauro, Albert Gris-Oliver, Roser Pinyol, Carla Montironi, Ugne Balaseviciute, Marta Piqué-Gili, Júlia Huguet-Pradell, Marko van Treeck, Michael Kallenbach, Anne Theres Schneider, Christoph Roderburg, Jakob Nikolas Kather, Tom Luedde, Josep M. Llovet
Published in: JHEP Reports, Issue 7, 2025, ISSN 2589-5559
Publisher: Elsevier BV
DOI: 10.1016/J.JHEPR.2025.101592

HIBRID: histology-based risk-stratification with deep learning and ctDNA in colorectal cancer

Author(s): Chiara M. L. Loeffler, Hideaki Bando, Srividhya Sainath, Hannah Sophie Muti, Xiaofeng Jiang, Marko van Treeck, Nic Gabriel Reitsam, Zunamys I. Carrero, Asier Rabasco Meneghetti, Tomomi Nishikawa, Toshihiro Misumi, Saori Mishima, Daisuke Kotani, Hiroya Taniguchi, Ichiro Takemasa, Takeshi Kato, Eiji Oki, Yuan Tanwei, Wankhede Durgesh, Sebastian Foersch, Hermann Brenner, Michael Hoffmeister, Yoshiaki Nakamura, Takayuki Yoshino, Jakob Nikolas Kather
Published in: Nature Communications, Issue 16, 2025, ISSN 2041-1723
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41467-025-62910-8

Histopathological evaluation of abdominal aortic aneurysms with deep learning

Author(s): Fiona R. Kolbinger, Omar S. M. El Nahhas, Maja Carina Nackenhorst, Christine Brostjan, Wolf Eilenberg, Albert Busch, Jakob Nikolas Kather
Published in: Diagnostic Pathology, Issue 20, 2025, ISSN 1746-1596
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/S13000-025-01684-5

If a therapy bot walks like a duck and talks like a duck then it is a medically regulated duck

Author(s): Max Ostermann, Oscar Freyer, F. Gerrik Verhees, Jakob Nikolas Kather, Stephen Gilbert
Published in: npj Digital Medicine, Issue 8, 2025, ISSN 2398-6352
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41746-025-02175-Z

Use of artificial intelligence for liver diseases: A survey from the EASL congress 2024

Author(s): Laura Žigutytė, Thomas Sorz-Nechay, Jan Clusmann, Jakob Nikolas Kather
Published in: JHEP Reports, Issue 6, 2024, ISSN 2589-5559
Publisher: Elsevier BV
DOI: 10.1016/J.JHEPR.2024.101209

Examining human-AI interaction in real-world healthcare beyond the laboratory

Author(s): Magdalena Katharina Wekenborg, Stephen Gilbert, Jakob Nikolas Kather
Published in: npj Digital Medicine, Issue 8, 2025, ISSN 2398-6352
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41746-025-01559-5

Prompt injection attacks on vision language models in oncology

Author(s): Jan Clusmann, Dyke Ferber, Isabella C. Wiest, Carolin V. Schneider, Titus J. Brinker, Sebastian Foersch, Daniel Truhn, Jakob Nikolas Kather
Published in: Nature Communications, Issue 16, 2025, ISSN 2041-1723
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41467-024-55631-X

Medical large language models are susceptible to targeted misinformation attacks

Author(s): Tianyu Han, Sven Nebelung, Firas Khader, Tianci Wang, Gustav Müller-Franzes, Christiane Kuhl, Sebastian Försch, Jens Kleesiek, Christoph Haarburger, Keno K. Bressem, Jakob Nikolas Kather, Daniel Truhn
Published in: npj Digital Medicine, Issue 7, 2024, ISSN 2398-6352
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41746-024-01282-7

Artificial Intelligence for Contrast-Enhanced Ultrasound of the Liver: A Systematic Review

Author(s): James A. Brooks, Michael Kallenbach, Iuliana-Pompilia Radu, Annalisa Berzigotti, Christoph F. Dietrich, Jakob N. Kather, Tom Luedde, Tobias P. Seraphin
Published in: Digestion, Issue 106, 2024, ISSN 0012-2823
Publisher: S. Karger AG
DOI: 10.1159/000541540

The age of foundation models

Author(s): Jana Lipkova, Jakob Nikolas Kather
Published in: Nature Reviews Clinical Oncology, Issue 21, 2024, ISSN 1759-4774
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41571-024-00941-8

Multimodal histopathologic models stratify hormone receptor-positive early breast cancer

Author(s): Kevin M. Boehm, Omar S. M. El Nahhas, Antonio Marra, Michele Waters, Justin Jee, Lior Braunstein, Nikolaus Schultz, Pier Selenica, Hannah Y. Wen, Britta Weigelt, Evan D. Paul, Pavol Cekan, Ramona Erber, Chiara M. L. Loeffler, Elena Guerini-Rocco, Nicola Fusco, Chiara Frascarelli, Eltjona Mane, Elisabetta Munzone, Silvia Dellapasqua, Paola Zagami, Giuseppe Curigliano, Pedram Razavi, Jorge S. Reis-Filho, Fresia Pareja, Sarat Chandarlapaty, Sohrab P. Shah, Jakob Nikolas Kather
Published in: Nature Communications, Issue 16, 2025, ISSN 2041-1723
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41467-025-57283-X

Pathologist-like explainable AI for interpretable Gleason grading in prostate cancer

Author(s): Gesa Mittmann, Sara Laiouar-Pedari, Hendrik A. Mehrtens, Sarah Haggenmüller, Tabea-Clara Bucher, Tirtha Chanda, Nadine T. Gaisa, Mathias Wagner, Gilbert Georg Klamminger, Tilman T. Rau, Christina Neppl, Eva Maria Compérat, Andreas Gocht, Monika Haemmerle, Niels J. Rupp, Jula Westhoff, Irene Krücken, Maximilian Seidl, Christian M. Schürch, Marcus Bauer, Wiebke Solass, Yu Chun Tam, Florian Weber, Rainer Grobholz, Jaroslaw Augustyniak, Thomas Kalinski, Christian Hörner, Kirsten D. Mertz, Constanze Döring, Andreas Erbersdobler, Gabriele Deubler, Felix Bremmer, Ulrich Sommer, Michael Brodhun, Jon Griffin, Maria Sarah L. Lenon, Kiril Trpkov, Liang Cheng, Fei Chen, Angelique Levi, Guoping Cai, Tri Q. Nguyen, Ali Amin, Alessia Cimadamore, Ahmed Shabaik, Varsha Manucha, Nazeel Ahmad, Nidia Messias, Francesca Sanguedolce, Diana Taheri, Ezra Baraban, Liwei Jia, Rajal B. Shah, Farshid Siadat, Nicole Swarbrick, Kyung Park, Oudai Hassan, Siamak Sakhaie, Michelle R. Downes, Hiroshi Miyamoto, Sean R. Williamson, Tim Holland-Letz, Christoph Wies, Carolin V. Schneider, Jakob Nikolas Kather, Yuri Tolkach, Titus J. Brinker
Published in: Nature Communications, Issue 16, 2025, ISSN 2041-1723
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41467-025-64712-4

Artificial intelligence-based biomarkers for treatment decisions in oncology

Author(s): Marta Ligero, Omar S.M. El Nahhas, Mihaela Aldea, Jakob Nikolas Kather
Published in: Trends in Cancer, Issue 11, 2025, ISSN 2405-8033
Publisher: Elsevier BV
DOI: 10.1016/J.TRECAN.2024.12.001

Privacy-preserving large language models for structured medical information retrieval

Author(s): Isabella Catharina Wiest, Dyke Ferber, Jiefu Zhu, Marko van Treeck, Sonja K. Meyer, Radhika Juglan, Zunamys I. Carrero, Daniel Paech, Jens Kleesiek, Matthias P. Ebert, Daniel Truhn, Jakob Nikolas Kather
Published in: npj Digital Medicine, Issue 7, 2024, ISSN 2398-6352
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41746-024-01233-2

Deep learning in cancer genomics and histopathology

Author(s): Michaela Unger, Jakob Nikolas Kather
Published in: Genome Medicine, Issue 16, 2024, ISSN 1756-994X
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/S13073-024-01315-6

Detection of suicidality from medical text using privacy-preserving large language models

Author(s): Isabella Catharina Wiest, Falk Gerrik Verhees, Dyke Ferber, Jiefu Zhu, Michael Bauer, Ute Lewitzka, Andrea Pfennig, Pavol Mikolas, Jakob Nikolas Kather
Published in: The British Journal of Psychiatry, Issue 225, 2024, ISSN 0007-1250
Publisher: Royal College of Psychiatrists
DOI: 10.1192/BJP.2024.134

End-to-end prediction of clinical outcomes in head and neck squamous cell carcinoma with foundation model-based multiple instance learning

Author(s): Asier Rabasco Meneghetti, Marta Ligero Hernández, Jens-Peter Kühn, Steffen Löck, Zunamys Itzell Carrero, Raquel Perez-Lopez, Keno K. Bressem, Titus J. Brinker, Alexander T. Pearson, Daniel Truhn, Sven Nebelung, Jakob Nikolas Kather
Published in: BMC Artificial Intelligence, Issue 1, 2025, ISSN 3005-1924
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/S44398-025-00003-8

The barriers to uptake of artificial intelligence in hepatology and how to overcome them

Author(s): Jan Clusmann, Maria Balaguer-Montero, Octavi Bassegoda, Carolin V. Schneider, Tobias Seraphin, Ellis Paintsil, Tom Luedde, Raquel Perez Lopez, Julien Calderaro, Stephen Gilbert, Thomas Marjot, Ashley Spann, Debbie L. Shawcross, Sabela Lens, Eric Trépo, Jakob Nikolas Kather
Published in: Journal of Hepatology, Issue 83, 2025, ISSN 0168-8278
Publisher: Elsevier BV
DOI: 10.1016/J.JHEP.2025.07.003

Artificial intelligence-based biomarkers for treatment decisions in oncology

Author(s): Marta Ligero, Omar S.M. El Nahhas, Mihaela Aldea, Jakob Nikolas Kather
Published in: Trends in Cancer, Issue 11, 2025, ISSN 2405-8033
Publisher: Elsevier BV
DOI: 10.1016/J.TRECAN.2024.12.001

Deep learning can predict cardiovascular events from liver imaging

Author(s): Gregory Patrick Veldhuizen, Tim Lenz, Didem Cifci, Marko van Treeck, Jan Clusmann, Yazhou Chen, Carolin V. Schneider, Tom Luedde, Peter W. de Leeuw, Ali El-Armouche, Daniel Truhn, Jakob Nikolas Kather
Published in: JHEP Reports, Issue 7, 2025, ISSN 2589-5559
Publisher: Elsevier BV
DOI: 10.1016/J.JHEPR.2025.101427

Benchmarking foundation models as feature extractors for weakly supervised computational pathology

Author(s): Peter Neidlinger, Omar S. M. El Nahhas, Hannah Sophie Muti, Tim Lenz, Michael Hoffmeister, Hermann Brenner, Marko van Treeck, Rupert Langer, Bastian Dislich, Hans Michael Behrens, Christoph Röcken, Sebastian Foersch, Daniel Truhn, Antonio Marra, Oliver Lester Saldanha, Jakob Nikolas Kather
Published in: Nature Biomedical Engineering, 2025, ISSN 2157-846X
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41551-025-01516-3

Deep Learning Reveals Liver MRI Features Associated With <i>PNPLA3</i> I148M in Steatotic Liver Disease

Author(s): Yazhou Chen, Benjamin P. M. Laevens, Teresa Lemainque, Gustav Anton Müller‐Franzes, Tobias Seibel, Carola Dlugosch, Jan Clusmann, Paul‐Henry Koop, Rongpeng Gong, Yuanyuan Liu, Niharika Jakhar, Feng Cao, Simon Schophaus, Thriveni Basavanapura Raju, Anastasia Artemis Raptis, Felix van Haag, Joel Joy, Rohit Loomba, Luca Valenti, Jakob Nikolas Kather, Titus J. Brinker, Moritz Herzog, Ivan G. Costa, Diego Hernando, Kai Markus Schneider, Daniel Truhn, Carolin V. Schneider
Published in: Liver International, Issue 45, 2025, ISSN 1478-3223
Publisher: Wiley
DOI: 10.1111/LIV.70164

A software pipeline for medical information extraction with large language models, open source and suitable for oncology

Author(s): Isabella Catharina Wiest, Fabian Wolf, Marie-Elisabeth Leßmann, Marko van Treeck, Dyke Ferber, Jiefu Zhu, Heiko Boehme, Keno K. Bressem, Hannes Ulrich, Matthias P. Ebert, Jakob Nikolas Kather
Published in: npj Precision Oncology, Issue 9, 2025, ISSN 2397-768X
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41698-025-01103-4

Multimodal analysis of whole slide images in colorectal cancer

Author(s): Jitendra Jonnagaddala, Miljana Shulajkovska, Anton Gradišek, Toni Rose Jue, Qifeng Zhou, Yuzhi Guo, Jamil Mahmoud El Chayeb, Ruijiang Li, Jana Lipkova, Jakob Nikolas Kather, Junzhou Huang
Published in: npj Digital Medicine, Issue 8, 2025, ISSN 2398-6352
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41746-025-02095-Y

Large language models as a diagnostic support tool in neuropathology

Author(s): Katherine J Hewitt, Isabella C Wiest, Zunamys I Carrero, Laura Bejan, Thomas O Millner, Sebastian Brandner, Jakob Nikolas Kather
Published in: The Journal of Pathology: Clinical Research, Issue 10, 2024, ISSN 2056-4538
Publisher: Wiley
DOI: 10.1002/2056-4538.70009

Reducing manual workload in CT and MRI annotation with the Segment Anything Model 2

Author(s): Leo Misera, Sven Nebelung, Zunamys I. Carrero, Keno Bressem, Marta Ligero, Jens-Peter Kühn, Ralf-Thorsten Hoffmann, Daniel Truhn, Jakob Nikolas Kather
Published in: BMC Medical Imaging, Issue 26, 2026, ISSN 1471-2342
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/S12880-025-02075-4

Benchmarking Vision Capabilities of Large Language Models in Surgical Examination Questions

Author(s): Jean-Paul Bereuter, Mark Enrik Geissler, Anna Klimova, Robert-Patrick Steiner, Kevin Pfeiffer, Fiona R. Kolbinger, Isabella C. Wiest, Hannah Sophie Muti, Jakob Nikolas Kather
Published in: Journal of Surgical Education, Issue 82, 2025, ISSN 1931-7204
Publisher: Elsevier BV
DOI: 10.1016/J.JSURG.2025.103442

Large language models could make natural language again the universal interface of healthcare

Author(s): Jakob Nikolas Kather, Dyke Ferber, Isabella C. Wiest, Stephen Gilbert, Daniel Truhn
Published in: Nature Medicine, Issue 30, 2024, ISSN 1078-8956
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41591-024-03199-W