The future landscape of large language models in medicine
Clusmann, Jan, Kolbinger, Fiona R., Muti, Hannah Sophie, Carrero, Zunamys I., Eckardt, Jan-Niklas, Laleh, Narmin Ghaffari, Löffler, Chiara Maria Lavinia, Schwarzkopf, Sophie-Caroline, Unger, Michaela, Veldhuizen, Gregory P., Wagner, Sophia J., Kather, Jakob Nikolas
Published in Communications medicine (10.10.2023)
Published in Communications medicine (10.10.2023)
Get full text
Journal Article
Transformer-based biomarker prediction from colorectal cancer histology: A large-scale multicentric study
Wagner, Sophia J., Reisenbüchler, Daniel, West, Nicholas P., Niehues, Jan Moritz, Zhu, Jiefu, Foersch, Sebastian, Veldhuizen, Gregory Patrick, Quirke, Philip, Grabsch, Heike I., van den Brandt, Piet A., Hutchins, Gordon G.A., Richman, Susan D., Yuan, Tanwei, Langer, Rupert, Jenniskens, Josien C.A., Offermans, Kelly, Mueller, Wolfram, Gray, Richard, Gruber, Stephen B., Greenson, Joel K., Rennert, Gad, Bonner, Joseph D., Schmolze, Daniel, Jonnagaddala, Jitendra, Hawkins, Nicholas J., Ward, Robyn L., Morton, Dion, Seymour, Matthew, Magill, Laura, Nowak, Marta, Hay, Jennifer, Koelzer, Viktor H., Church, David N., Church, David, Domingo, Enric, Edwards, Joanne, Glimelius, Bengt, Gogenur, Ismail, Harkin, Andrea, Hay, Jen, Iveson, Timothy, Jaeger, Emma, Kelly, Caroline, Kerr, Rachel, Maka, Noori, Morgan, Hannah, Oien, Karin, Orange, Clare, Palles, Claire, Roxburgh, Campbell, Sansom, Owen, Saunders, Mark, Tomlinson, Ian, Matek, Christian, Geppert, Carol, Peng, Chaolong, Zhi, Cheng, Ouyang, Xiaoming, James, Jacqueline A., Loughrey, Maurice B., Salto-Tellez, Manuel, Brenner, Hermann, Hoffmeister, Michael, Truhn, Daniel, Schnabel, Julia A., Boxberg, Melanie, Peng, Tingying, Kather, Jakob Nikolas
Published in Cancer cell (11.09.2023)
Published in Cancer cell (11.09.2023)
Get full text
Journal Article
Make deep learning algorithms in computational pathology more reproducible and reusable
Wagner, Sophia J., Matek, Christian, Shetab Boushehri, Sayedali, Boxberg, Melanie, Lamm, Lorenz, Sadafi, Ario, Waibel, Dominik J. E., Marr, Carsten, Peng, Tingying
Published in Nature medicine (01.09.2022)
Published in Nature medicine (01.09.2022)
Get full text
Journal Article
Built to Last? Reproducibility and Reusability of Deep Learning Algorithms in Computational Pathology
Wagner, Sophia J, Matek, Christian, Shetab Boushehri, Sayedali, Boxberg, Melanie, Lamm, Lorenz, Sadafi, Ario, Winter, Dominik J E, Marr, Carsten, Peng, Tingying
Published in Modern pathology (01.01.2024)
Published in Modern pathology (01.01.2024)
Get full text
Journal Article
From whole-slide image to biomarker prediction: end-to-end weakly supervised deep learning in computational pathology
El Nahhas, Omar S M, van Treeck, Marko, Wölflein, Georg, Unger, Michaela, Ligero, Marta, Lenz, Tim, Wagner, Sophia J, Hewitt, Katherine J, Khader, Firas, Foersch, Sebastian, Truhn, Daniel, Kather, Jakob Nikolas
Published in Nature protocols (16.09.2024)
Published in Nature protocols (16.09.2024)
Get full text
Journal Article
Approaching Peak Ground Truth
Kofler, Florian, Wahle, Johannes, Ezhov, Ivan, Wagner, Sophia J., Al-Maskari, Rami, Gryska, Emilia, Todorov, Mihail, Bukas, Christina, Meissen, Felix, Peng, Tingying, Erturk, Ali, Rueckert, Daniel, Heckemann, Rolf, Kirschke, Jan, Zimmer, Claus, Wiestler, Benedikt, Menze, Bjoern, Piraud, Marie
Published in 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI) (18.04.2023)
Published in 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI) (18.04.2023)
Get full text
Conference Proceeding
Low-Resource Finetuning of Foundation Models Beats State-of-the-Art in Histopathology
Roth, Benedikt, Koch, Valentin, Wagner, Sophia J., Schnabel, Julia A., Marr, Carsten, Peng, Tingying
Published in 2024 IEEE International Symposium on Biomedical Imaging (ISBI) (27.05.2024)
Published in 2024 IEEE International Symposium on Biomedical Imaging (ISBI) (27.05.2024)
Get full text
Conference Proceeding
Structure-Preserving Multi-domain Stain Color Augmentation Using Style-Transfer with Disentangled Representations
Wagner, Sophia J., Khalili, Nadieh, Sharma, Raghav, Boxberg, Melanie, Marr, Carsten, de Back, Walter, Peng, Tingying
Published in Medical Image Computing and Computer Assisted Intervention - MICCAI 2021 (2021)
Published in Medical Image Computing and Computer Assisted Intervention - MICCAI 2021 (2021)
Get full text
Book Chapter
S5CL: Unifying Fully-Supervised, Self-supervised, and Semi-supervised Learning Through Hierarchical Contrastive Learning
Tran, Manuel, Wagner, Sophia J., Boxberg, Melanie, Peng, Tingying
Published in Medical Image Computing and Computer Assisted Intervention - MICCAI 2022 (2022)
Published in Medical Image Computing and Computer Assisted Intervention - MICCAI 2022 (2022)
Get full text
Book Chapter
Local Attention Graph-based Transformer for Multi-target Genetic Alteration Prediction
Reisenbüchler, Daniel, Wagner, Sophia J, Boxberg, Melanie, Peng, Tingying
Year of Publication 13.05.2022
Year of Publication 13.05.2022
Get full text
Journal Article
Low-resource finetuning of foundation models beats state-of-the-art in histopathology
Roth, Benedikt, Koch, Valentin, Wagner, Sophia J, Schnabel, Julia A, Marr, Carsten, Peng, Tingying
Year of Publication 09.01.2024
Year of Publication 09.01.2024
Get full text
Journal Article
DinoBloom: A Foundation Model for Generalizable Cell Embeddings in Hematology
Koch, Valentin, Wagner, Sophia J, Kazeminia, Salome, Sancar, Ece, Hehr, Matthias, Schnabel, Julia, Peng, Tingying, Marr, Carsten
Year of Publication 07.04.2024
Year of Publication 07.04.2024
Get full text
Journal Article
B-Cos Aligned Transformers Learn Human-Interpretable Features
Tran, Manuel, Lahiani, Amal, Cid, Yashin Dicente, Boxberg, Melanie, Lienemann, Peter, Matek, Christian, Wagner, Sophia J, Theis, Fabian J, Klaiman, Eldad, Peng, Tingying
Year of Publication 16.01.2024
Year of Publication 16.01.2024
Get full text
Journal Article
HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis
Jaume, Guillaume, Doucet, Paul, Song, Andrew H, Lu, Ming Y, Almagro-Pérez, Cristina, Wagner, Sophia J, Vaidya, Anurag J, Chen, Richard J, Williamson, Drew F. K, Kim, Ahrong, Mahmood, Faisal
Year of Publication 23.06.2024
Year of Publication 23.06.2024
Get full text
Journal Article
Structure-Preserving Multi-Domain Stain Color Augmentation using Style-Transfer with Disentangled Representations
Wagner, Sophia J, Khalili, Nadieh, Sharma, Raghav, Boxberg, Melanie, Marr, Carsten, de Back, Walter, Peng, Tingying
Year of Publication 26.07.2021
Year of Publication 26.07.2021
Get full text
Journal Article
From Whole-slide Image to Biomarker Prediction: A Protocol for End-to-End Deep Learning in Computational Pathology
Nahhas, Omar S. M. El, van Treeck, Marko, Wölflein, Georg, Unger, Michaela, Ligero, Marta, Lenz, Tim, Wagner, Sophia J, Hewitt, Katherine J, Khader, Firas, Foersch, Sebastian, Truhn, Daniel, Kather, Jakob Nikolas
Year of Publication 18.12.2023
Year of Publication 18.12.2023
Get full text
Journal Article