no code implementations • 6 Apr 2024 • Dyke Ferber, Omar S. M. El Nahhas, Georg Wölflein, Isabella C. Wiest, Jan Clusmann, Marie-Elisabeth Leßman, Sebastian Foersch, Jacqueline Lammert, Maximilian Tschochohei, Dirk Jäger, Manuel Salto-Tellez, Nikolaus Schultz, Daniel Truhn, Jakob Nikolas Kather
We believe, that our work can serve as a proof-of-concept for more advanced LLM-agents in the medical domain.
no code implementations • 12 Mar 2024 • Dyke Ferber, Georg Wölflein, Isabella C. Wiest, Marta Ligero, Srividhya Sainath, Narmin Ghaffari Laleh, Omar S. M. El Nahhas, Gustav Müller-Franzes, Dirk Jäger, Daniel Truhn, Jakob Nikolas Kather
Medical image classification requires labeled, task-specific datasets which are used to train deep learning networks de novo, or to fine-tune foundation models.
no code implementations • 7 Mar 2024 • Tim Lenz, Omar S. M. El Nahhas, Marta Ligero, Jakob Nikolas Kather
Specifically, we analyzed the effects of adaptations in data volume, architecture, and algorithms on downstream classification tasks, emphasizing their impact on computational resources.
1 code implementation • 6 Mar 2024 • Omar S. M. El Nahhas, Georg Wölflein, Marta Ligero, Tim Lenz, Marko van Treeck, Firas Khader, Daniel Truhn, Jakob Nikolas Kather
Deep Learning (DL) can predict biomarkers directly from digitized cancer histology in a weakly-supervised setting.
1 code implementation • 18 Dec 2023 • Omar S. M. El Nahhas, Marko van Treeck, Georg Wölflein, Michaela Unger, Marta Ligero, Tim Lenz, Sophia J. Wagner, Katherine J. Hewitt, Firas Khader, Sebastian Foersch, Daniel Truhn, Jakob Nikolas Kather
Hematoxylin- and eosin (H&E) stained whole-slide images (WSIs) are the foundation of diagnosis of cancer.
Ranked #1 on Classification on TCGA
1 code implementation • 20 Nov 2023 • Georg Wölflein, Dyke Ferber, Asier Rabasco Meneghetti, Omar S. M. El Nahhas, Daniel Truhn, Zunamys I. Carrero, David J. Harrison, Ognjen Arandjelović, Jakob N. Kather
We question this belief in the context of weakly supervised whole slide image classification, motivated by the emergence of powerful feature extractors trained using self-supervised learning on diverse pathology datasets.
1 code implementation • 11 Apr 2023 • Omar S. M. El Nahhas, Chiara M. L. Loeffler, Zunamys I. Carrero, Marko van Treeck, Fiona R. Kolbinger, Katherine J. Hewitt, Hannah S. Muti, Mara Graziani, Qinghe Zeng, Julien Calderaro, Nadina Ortiz-Brüchle, Tanwei Yuan, Michael Hoffmeister, Hermann Brenner, Alexander Brobeil, Jorge S. Reis-Filho, Jakob Nikolas Kather
We tested our method for multiple clinically and biologically relevant biomarkers: homologous repair deficiency (HRD) score, a clinically used pan-cancer biomarker, as well as markers of key biological processes in the tumor microenvironment.