1 code implementation • 31 Aug 2024 • Jacqueline Lammert, Nicole Pfarr, Leonid Kuligin, Sonja Mathes, Tobias Dreyer, Luise Modersohn, Patrick Metzger, Dyke Ferber, Jakob Nikolas Kather, Daniel Truhn, Lisa Christine Adams, Keno Kyrill Bressem, Sebastian Lange, Kristina Schwamborn, Martin Boeker, Marion Kiechle, Ulrich A. Schatz, Holger Bronger, Maximilian Tschochohei
Rare gynecological tumors (RGTs) present major clinical challenges due to their low incidence and heterogeneity.
no code implementations • 28 Aug 2024 • 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
Advancements in artificial intelligence have driven the development of numerous pathology foundation models capable of extracting clinically relevant information.
no code implementations • 25 Aug 2024 • Felix J. Dorfner, Amin Dada, Felix Busch, Marcus R. Makowski, Tianyu Han, Daniel Truhn, Jens Kleesiek, Madhumita Sushil, Jacqueline Lammert, Lisa C. Adams, Keno K. Bressem
Large language models (LLMs) have shown potential in biomedical applications, leading to efforts to fine-tune them on domain-specific data.
no code implementations • 23 Jul 2024 • Jan Clusmann, Dyke Ferber, Isabella C. Wiest, Carolin V. Schneider, Titus J. Brinker, Sebastian Foersch, Daniel Truhn, Jakob N. Kather
Using a set of N=297 attacks, we show that all of these models are susceptible.
no code implementations • 22 Jul 2024 • Soroosh Tayebi Arasteh, Mahshad Lotfinia, Keno Bressem, Robert Siepmann, Dyke Ferber, Christiane Kuhl, Jakob Nikolas Kather, Sven Nebelung, Daniel Truhn
We evaluate the diagnostic accuracy of various LLMs when answering radiology-specific questions with and without access to additional online information via RAG.
no code implementations • 18 Jul 2024 • Dyke Ferber, Lars Hilgers, Isabella C. Wiest, Marie-Elisabeth Leßmann, Jan Clusmann, Peter Neidlinger, Jiefu Zhu, Georg Wölflein, Jacqueline Lammert, Maximilian Tschochohei, Heiko Böhme, Dirk Jäger, Mihaela Aldea, Daniel Truhn, Christiane Höper, Jakob Nikolas Kather
Matching cancer patients to clinical trials is essential for advancing treatment and patient care.
no code implementations • 23 Jun 2024 • Tianyu Han, Sven Nebelung, Firas Khader, Jakob Nikolas Kather, Daniel Truhn
Denoising diffusion models offer a promising approach to accelerating magnetic resonance imaging (MRI) and producing diagnostic-level images in an unsupervised manner.
no code implementations • 3 Jun 2024 • Firas Khader, Omar S. M. El Nahhas, Tianyu Han, Gustav Müller-Franzes, Sven Nebelung, Jakob Nikolas Kather, Daniel Truhn
The Transformer model has been pivotal in advancing fields such as natural language processing, speech recognition, and computer vision.
1 code implementation • 10 May 2024 • Hartmut Häntze, Lina Xu, Felix J. Dorfner, Leonhard Donle, Daniel Truhn, Hugo Aerts, Mathias Prokop, Bram van Ginneken, Alessa Hering, Lisa C. Adams, Keno K. Bressem
Results: The model showcased high accuracy in segmenting well-defined organs, achieving Dice Similarity Coefficient (DSC) scores of 0. 97 for the right and left lungs, and 0. 95 for the heart.
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.
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 • 8 Feb 2024 • Patrick Wienholt, Alexander Hermans, Firas Khader, Behrus Puladi, Bastian Leibe, Christiane Kuhl, Sven Nebelung, Daniel Truhn
This study investigates the application of ordinal regression methods for categorizing disease severity in chest radiographs.
1 code implementation • 1 Feb 2024 • Salman Ul Hassan Dar, Marvin Seyfarth, Jannik Kahmann, Isabelle Ayx, Theano Papavassiliu, Stefan O. Schoenberg, Norbert Frey, Bettina Baeßler, Sebastian Foersch, Daniel Truhn, Jakob Nikolas Kather, Sandy Engelhardt
Collectively, our results emphasize the importance of carefully training generative models on private medical imaging datasets, and examining the synthetic data to ensure patient privacy before sharing it for medical research and applications.
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
no code implementations • 24 Nov 2023 • Felix Busch, Tianyu Han, Marcus Makowski, Daniel Truhn, Keno Bressem, Lisa Adams
The study evaluates and compares GPT-4 and GPT-4Vision for radiological tasks, suggesting GPT-4Vision may recognize radiological features from images, thereby enhancing its diagnostic potential over text-based descriptions.
1 code implementation • 20 Nov 2023 • Georg Wölflein, Dyke Ferber, Asier R. Meneghetti, Omar S. M. El Nahhas, Daniel Truhn, Zunamys I. Carrero, David J. Harrison, Ognjen Arandjelović, Jakob Nikolas Kather
2) Which feature extractors are best for downstream slide-level classification?
no code implementations • 11 Oct 2023 • Amin Dada, Aokun Chen, Cheng Peng, Kaleb E Smith, Ahmad Idrissi-Yaghir, Constantin Marc Seibold, Jianning Li, Lars Heiliger, Xi Yang, Christoph M. Friedrich, Daniel Truhn, Jan Egger, Jiang Bian, Jens Kleesiek, Yonghui Wu
Traditionally, large language models have been either trained on general web crawls or domain-specific data.
1 code implementation • 1 Oct 2023 • Soroosh Tayebi Arasteh, Christiane Kuhl, Marwin-Jonathan Saehn, Peter Isfort, Daniel Truhn, Sven Nebelung
So far, the impact of training strategy, i. e., local versus collaborative, on the diagnostic on-domain and off-domain performance of AI models interpreting chest radiographs has not been assessed.
1 code implementation • 29 Sep 2023 • Tianyu Han, Laura Žigutytė, Luisa Huck, Marc Huppertz, Robert Siepmann, Yossi Gandelsman, Christian Blüthgen, Firas Khader, Christiane Kuhl, Sven Nebelung, Jakob Kather, Daniel Truhn
Current techniques for evaluating deep learning models cannot visualize confounding factors at a diagnostic level.
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.
1 code implementation • 10 Jun 2023 • Soroosh Tayebi Arasteh, Mahshad Lotfinia, Teresa Nolte, Marwin Saehn, Peter Isfort, Christiane Kuhl, Sven Nebelung, Georgios Kaissis, Daniel Truhn
We specifically investigate the performance of models trained with DP as compared to models trained without DP on data from institutions that the model had not seen during its training (i. e., external validation) - the situation that is reflective of the clinical use of AI models.
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.
no code implementations • 11 May 2023 • Firas Khader, Gustav Müller-Franzes, Tianyu Han, Sven Nebelung, Christiane Kuhl, Johannes Stegmaier, Daniel Truhn
X-rays are widely available and even if the CT reconstructed from these radiographs is not a replacement of a complete CT in the diagnostic setting, it might serve to spare the patients from radiation where a CT is only acquired for rough measurements such as determining organ size.
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.
no code implementations • 14 Apr 2023 • Tianyu Han, Lisa C. Adams, Jens-Michalis Papaioannou, Paul Grundmann, Tom Oberhauser, Alexander Löser, Daniel Truhn, Keno K. Bressem
As large language models (LLMs) like OpenAI's GPT series continue to make strides, we witness the emergence of artificial intelligence applications in an ever-expanding range of fields.
2 code implementations • 3 Feb 2023 • Soroosh Tayebi Arasteh, Alexander Ziller, Christiane Kuhl, Marcus Makowski, Sven Nebelung, Rickmer Braren, Daniel Rueckert, Daniel Truhn, Georgios Kaissis
In this work, we evaluated the effect of privacy-preserving training of AI models regarding accuracy and fairness compared to non-private training.
1 code implementation • 3 Feb 2023 • Coen de Vente, Koenraad A. Vermeer, Nicolas Jaccard, He Wang, Hongyi Sun, Firas Khader, Daniel Truhn, Temirgali Aimyshev, Yerkebulan Zhanibekuly, Tien-Dung Le, Adrian Galdran, Miguel Ángel González Ballester, Gustavo Carneiro, Devika R G, Hrishikesh P S, Densen Puthussery, Hong Liu, Zekang Yang, Satoshi Kondo, Satoshi Kasai, Edward Wang, Ashritha Durvasula, Jónathan Heras, Miguel Ángel Zapata, Teresa Araújo, Guilherme Aresta, Hrvoje Bogunović, Mustafa Arikan, Yeong Chan Lee, Hyun Bin Cho, Yoon Ho Choi, Abdul Qayyum, Imran Razzak, Bram van Ginneken, Hans G. Lemij, Clara I. Sánchez
Artificial intelligence (AI) can be used to analyze color fundus photographs (CFPs) in a cost-effective manner, making glaucoma screening more accessible.
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).
no code implementations • 27 Sep 2022 • Lisa C. Adams, Felix Busch, Daniel Truhn, Marcus R. Makowski, Hugo JWL. Aerts, Keno K. Bressem
Generative models such as DALL-E 2 could represent a promising future tool for image generation, augmentation, and manipulation for artificial intelligence research in radiology provided that these models have sufficient medical domain knowledge.
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.
1 code implementation • 25 Nov 2020 • Tianyu Han, Sven Nebelung, Federico Pedersoli, Markus Zimmermann, Maximilian Schulze-Hagen, Michael Ho, Christoph Haarburger, Fabian Kiessling, Christiane Kuhl, Volkmar Schulz, Daniel Truhn
Contrary to previous research on adversarially trained models, we found that the accuracy of such models was equal to standard models when sufficiently large datasets and dual batch norm training were used.
no code implementations • 23 Apr 2020 • Michael Gadermayr, Maximilian Tschuchnig, Laxmi Gupta, Dorit Merhof, Nils Krämer, Daniel Truhn, Burkhard Gess
Generative adversarial networks using a cycle-consistency loss facilitate unpaired training of image-translation models and thereby exhibit a very high potential in manifold medical applications.
no code implementations • 13 Oct 2019 • Christoph Haarburger, Justus Schock, Daniel Truhn, Philippe Weitz, Gustav Mueller-Franzes, Leon Weninger, Dorit Merhof
From these segmentations, we extract a high number of plausible feature vectors for each lung tumor and analyze feature variance with respect to the segmentations.
1 code implementation • 14 Jun 2019 • Christoph Haarburger, Michael Baumgartner, Daniel Truhn, Mirjam Broeckmann, Hannah Schneider, Simone Schrading, Christiane Kuhl, Dorit Merhof
Achieving an AUROC of 0. 89, we compare the performance of our approach to Mask R-CNN and Retina U-Net as well as a radiologist.