Molecular-driven Foundation Model for Oncologic Pathology

Authors: Vaidya, Anurag, Zhang, Andrew, Jaume, Guillaume, Song, Andrew H., Ding, Tong, Wagner, Sophia J., Lu, Ming Y., Doucet, Paul, Robertson, Harry, Almagro-Perez, Cristina, Chen, Richard J., ElHarouni, Dina, Ayoub, Georges, Bossi, Connor, Ligon, Keith L., Gerber, Georg, Le, Long Phi, Mahmood, Faisal

Subject Terms: Computer Science - Computer Vision and Pattern Recognition, Computer Science - Artificial Intelligence

Access URL: http://arxiv.org/abs/2501.16652

Multimodal Whole Slide Foundation Model for Pathology

Authors: Ding, Tong, Wagner, Sophia J., Song, Andrew H., Chen, Richard J., Lu, Ming Y., Zhang, Andrew, Vaidya, Anurag J., Jaume, Guillaume, Shaban, Muhammad, Kim, Ahrong, Williamson, Drew F. K., Chen, Bowen, Almagro-Perez, Cristina, Doucet, Paul, Sahai, Sharifa, Chen, Chengkuan, Komura, Daisuke, Kawabe, Akihiro, Ishikawa, Shumpei, Gerber, Georg, Peng, Tingying, Le, Long Phi, Mahmood, Faisal

Subject Terms: Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Artificial Intelligence, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Statistics - Applications

Access URL: http://arxiv.org/abs/2411.19666

Low-Resource Finetuning of Foundation Models Beats State-of-the-Art in Histopathology

Authors: Roth, Benedikt, Koch, Valentin, Wagner, Sophia J., Schnabel, Julia A., Marr, Carsten, Peng, Tingying

Source: 2024 IEEE International Symposium on Biomedical Imaging (ISBI) Biomedical Imaging (ISBI), 2024 IEEE International Symposium on. :1-5 May, 2024

Relation: 2024 IEEE International Symposium on Biomedical Imaging (ISBI)

HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis

Authors: 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

Subject Terms: Computer Science - Computer Vision and Pattern Recognition

Access URL: http://arxiv.org/abs/2406.16192

DinoBloom: A Foundation Model for Generalizable Cell Embeddings in Hematology

Authors: Koch, Valentin, Wagner, Sophia J., Kazeminia, Salome, Sancar, Ece, Hehr, Matthias, Schnabel, Julia, Peng, Tingying, Marr, Carsten

Subject Terms: Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2404.05022

Approaching Peak Ground Truth

Authors: 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

Source: 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI) Biomedical Imaging (ISBI), 2023 IEEE 20th International Symposium on. :1-6 Apr, 2023

Relation: 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI)

From Whole-slide Image to Biomarker Prediction: A Protocol for End-to-End Deep Learning in Computational Pathology

Authors: 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

Subject Terms: Computer Science - Computer Vision and Pattern Recognition

Access URL: http://arxiv.org/abs/2312.10944

Fully transformer-based biomarker prediction from colorectal cancer histology: a large-scale multicentric study

Authors: Wagner, Sophia J., Reisenbüchler, Daniel, West, Nicholas P., Niehues, Jan Moritz, Veldhuizen, Gregory Patrick, Quirke, Philip, Grabsch, Heike I., Brandt, Piet A. van den, Hutchins, Gordon G. A., Richman, Susan D., Yuan, Tanwei, Langer, Rupert, Jenniskens, Josien Christina Anna, Offermans, Kelly, Mueller, Wolfram, Gray, Richard, Gruber, Stephen B., Greenson, Joel K., Rennert, Gad, Bonner, Joseph D., Schmolze, Daniel, 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

Subject Terms: Computer Science - Computer Vision and Pattern Recognition

Access URL: http://arxiv.org/abs/2301.09617

Local Attention Graph-based Transformer for Multi-target Genetic Alteration Prediction

Authors: Reisenbüchler, Daniel, Wagner, Sophia J., Boxberg, Melanie, Peng, Tingying

Subject Terms: Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2205.06672

S5CL: Unifying Fully-Supervised, Self-Supervised, and Semi-Supervised Learning Through Hierarchical Contrastive Learning

Authors: Tran, Manuel, Wagner, Sophia J., Boxberg, Melanie, Peng, Tingying

Subject Terms: Computer Science - Computer Vision and Pattern Recognition, Statistics - Machine Learning

Access URL: http://arxiv.org/abs/2203.07307

Multi-Modality Microscopy Image Style Transfer for Nuclei Segmentation

Authors: Liu, Ye, Wagner, Sophia J., Peng, Tingying

Subject Terms: Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2111.12138

Structure-Preserving Multi-Domain Stain Color Augmentation using Style-Transfer with Disentangled Representations

Authors: Wagner, Sophia J., Khalili, Nadieh, Sharma, Raghav, Boxberg, Melanie, Marr, Carsten, de Back, Walter, Peng, Tingying

Subject Terms: Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition

Access URL: http://arxiv.org/abs/2107.12357

Built to Last? Reproducibility and Reusability of Deep Learning Algorithms in Computational Pathology

Authors: Wagner, Sophia J., Matek, Christian, Shetab Boushehri, Sayedali, Boxberg, Melanie, Lamm, Lorenz, Sadafi, Ario, Winter, Dominik J.E., Marr, Carsten, Peng, Tingying

Source: In Modern Pathology January 2024 37(1)

Transformer-based biomarker prediction from colorectal cancer histology: A large-scale multicentric study

Authors: 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, 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., 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

Source: In Cancer Cell 11 September 2023 41(9):1650-1661

From whole-slide image to biomarker prediction: end-to-end weakly supervised deep learning in computational pathology.

Authors: 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

Source: Nature Protocols; Jan2025, Vol. 20 Issue 1, p293-316, 24p

Die kommende Entwicklung großer Sprachmodelle in der Medizin. (German)

Authors: Clusmann, Jan, Kolbinger, Fiona R., Muti, Hannah Sophie, Carrero, Zunamys I., Eckardt, Jan-Niklas, Laleh, Narmin Ghaffari, Lavinia Loffler, Chiara Maria, Schwarzkopf, Sophie-Caroline, Unger, Michaela, Veldhuizen, Gregory P., Wagner, Sophia J., Kather, Jakob Nikolas

Source: Kompass Onkologie; 2024, Vol. 11 Issue 1, p3-10, 8p

Multi-Modality Microscopy Image Style Augmentation for Nuclei Segmentation.

Authors: Liu, Ye¹, yeliu0724@hotmail.com, Wagner, Sophia J.^1,2, sophia.wagner@helmholtz-muenchen.de, Peng, Tingying², tingying.peng@helmholtz-muenchen.de

Source: Journal of Imaging; Mar2022, Vol. 8 Issue 3, p71-N.PAG, 9p

Make deep learning algorithms in computational pathology more reproducible and reusable

Authors: Wagner, Sophia J., Matek, Christian, Shetab Boushehri, Sayedali, Boxberg, Melanie, Lamm, Lorenz, Sadafi, Ario, Waibel, Dominik J. E., Marr, Carsten, Peng, Tingying

Source: Nature Medicine; 20220101, Issue: Preprints p1-3, 3p

Built to last? Reproducibility and Reusability of Deep Learning Algorithms in Computational Pathology

Authors: Wagner, Sophia J., Matek, Christian, Boushehri, Sayedali Shetab, Boxberg, Melanie, Lamm, Lorenz, Sadafi, Ario, Waibel, Dominik J.E., Marr, Carsten, Peng, Tingying

Source: Modern Pathology; 20230101, Issue: Preprints