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 • 25 Jan 2024 • Lisa Adams, Felix Busch, Tianyu Han, Jean-Baptiste Excoffier, Matthieu Ortala, Alexander Löser, Hugo JWL. Aerts, Jakob Nikolas Kather, Daniel Truhn, Keno Bressem
However, all models struggled significantly in tasks requiring the identification of missing information, highlighting a critical area for improvement in clinical data interpretation.
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 • 29 Sep 2023 • Tianyu Han, Sven Nebelung, Firas Khader, Tianci Wang, Gustav Mueller-Franzes, Christiane Kuhl, Sebastian Försch, Jens Kleesiek, Christoph Haarburger, Keno K. Bressem, Jakob Nikolas Kather, Daniel Truhn
We validate our findings in a set of 1, 038 incorrect biomedical facts.
1 code implementation • 27 Aug 2023 • Soroosh Tayebi Arasteh, Tianyu Han, Mahshad Lotfinia, Christiane Kuhl, Jakob Nikolas Kather, Daniel Truhn, Sven Nebelung
A knowledge gap persists between machine learning (ML) developers (e. g., data scientists) and practitioners (e. g., clinicians), hampering the full utilization of ML for clinical data analysis.
2 code implementations • 15 Aug 2023 • Soroosh Tayebi Arasteh, Leo Misera, Jakob Nikolas Kather, Daniel Truhn, Sven Nebelung
In this study, we explored if SSL for pre-training on non-medical images can be applied to chest radiographs and how it compares to supervised pre-training on non-medical images and on medical images.
no code implementations • 11 May 2023 • Firas Khader, Jakob Nikolas Kather, Tianyu Han, Sven Nebelung, Christiane Kuhl, Johannes Stegmaier, Daniel Truhn
However, while the conventional transformer allows for a simultaneous processing of a large set of input tokens, the computational demand scales quadratically with the number of input tokens and thus quadratically with the number of image patches.
1 code implementation • 18 Apr 2023 • Gustav Müller-Franzes, Fritz Müller-Franzes, Luisa Huck, Vanessa Raaff, Eva Kemmer, Firas Khader, Soroosh Tayebi Arasteh, Teresa Nolte, Jakob Nikolas Kather, Sven Nebelung, Christiane Kuhl, Daniel Truhn
Accurate and automatic segmentation of fibroglandular tissue in breast MRI screening is essential for the quantification of breast density and background parenchymal enhancement.
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.
2 code implementations • 23 Jan 2023 • Sophia J. Wagner, Daniel Reisenbüchler, Nicholas P. West, Jan Moritz Niehues, Gregory Patrick Veldhuizen, Philip Quirke, Heike I. Grabsch, Piet A. van den Brandt, Gordon G. A. Hutchins, Susan D. Richman, Tanwei Yuan, Rupert Langer, Josien Christina Anna Jenniskens, Kelly Offermans, Wolfram Mueller, Richard Gray, Stephen B. Gruber, Joel K. Greenson, Gad Rennert, Joseph D. Bonner, Daniel Schmolze, Jacqueline A. James, Maurice B. Loughrey, Manuel Salto-Tellez, Hermann Brenner, Michael Hoffmeister, Daniel Truhn, Julia A. Schnabel, Melanie Boxberg, Tingying Peng, Jakob Nikolas Kather
Methods: In this study, we developed a new fully transformer-based pipeline for end-to-end biomarker prediction from pathology slides.
1 code implementation • 18 Dec 2022 • Firas Khader, Gustav Mueller-Franzes, Tianci Wang, Tianyu Han, Soroosh Tayebi Arasteh, Christoph Haarburger, Johannes Stegmaier, Keno Bressem, Christiane Kuhl, Sven Nebelung, Jakob Nikolas Kather, Daniel Truhn
Multimodal deep learning has been used to predict clinical endpoints and diagnoses from clinical routine data.
1 code implementation • 14 Dec 2022 • Gustav Müller-Franzes, Jan Moritz Niehues, Firas Khader, Soroosh Tayebi Arasteh, Christoph Haarburger, Christiane Kuhl, Tianci Wang, Tianyu Han, Sven Nebelung, Jakob Nikolas Kather, Daniel Truhn
The success of Deep Learning applications critically depends on the quality and scale of the underlying training data.
1 code implementation • 24 Nov 2022 • Soroosh Tayebi Arasteh, Peter Isfort, Marwin Saehn, Gustav Mueller-Franzes, Firas Khader, Jakob Nikolas Kather, Christiane Kuhl, Sven Nebelung, Daniel Truhn
Due to the rapid advancements in recent years, medical image analysis is largely dominated by deep learning (DL).
1 code implementation • 7 Nov 2022 • Firas Khader, Gustav Mueller-Franzes, Soroosh Tayebi Arasteh, Tianyu Han, Christoph Haarburger, Maximilian Schulze-Hagen, Philipp Schad, Sandy Engelhardt, Bettina Baessler, Sebastian Foersch, Johannes Stegmaier, Christiane Kuhl, Sven Nebelung, Jakob Nikolas Kather, Daniel Truhn
Furthermore, we demonstrate that synthetic images can be used in a self-supervised pre-training and improve the performance of breast segmentation models when data is scarce (dice score 0. 91 vs. 0. 95 without vs. with synthetic data).
1 code implementation • 22 Nov 2021 • Tianyu Han, Jakob Nikolas Kather, Federico Pedersoli, Markus Zimmermann, Sebastian Keil, Maximilian Schulze-Hagen, Marc Terwoelbeck, Peter Isfort, Christoph Haarburger, Fabian Kiessling, Volkmar Schulz, Christiane Kuhl, Sven Nebelung, Daniel Truhn
We present a generic solution for this problem by a methodology that allows the prediction of progression risk and morphology in individuals using a latent extrapolation optimization approach.
no code implementations • MICCAI Workshop COMPAY 2021 • Narmin Ghaffari Laleh, Amelie Echle, Hannah Sophie Muti, Katherine Jane Hewitt, Volkmar Schulz, Jakob Nikolas Kather
Digitized histopathology slides contain a wealth of information, only a fraction of which is being used in clinical routine.