Sophia J. Wagner

According to our database, Sophia J. Wagner authored at least 21 papers between 2021 and 2026.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2026

A multimodal and temporal foundation model for virtual patient representations at healthcare system scale.

Andrew Zhang, Tong Ding, Sophia J. Wagner, Caiwei Tian, Ming Y. Lu, Rowland Pettit, Joshua E. Lewis, Alexandre Misrahi, Dandan Mo, Long Phi Le, Faisal Mahmood

CoRR, April, 2026

Towards Spatial Transcriptomics-driven Pathology Foundation Models.

Konstantin Hemker, Andrew H. Song, Cristina Almagro-Pérez, Guillaume Jaume, Sophia J. Wagner, Anurag Vaidya, Nikola Simidjievski, Mateja Jamnik, Faisal Mahmood

CoRR, February, 2026

Hierarchical supervision in DINOv2 training improves generalizability on white blood cell images.

Manon Chossegros, Sophia J. Wagner, Christian Matek, Daniel Stockholm, Xavier Tannier, Carsten Marr

Expert Syst. Appl., 2026

2025

A Foundation Model for Spatial Proteomics.

Muhammad Shaban, Yuzhou Chang, Huaying Qiu, Yao Yu Yeo, Andrew H. Song, Guillaume Jaume, Yuchen Wang, Luca L. Weishaupt, Tong Ding, Anurag Vaidya, Abdallah Lamane, Daniel Shao, Mohammed Zidane, Yunhao Bai, Paige McCallum, Shuli Luo, Wenrui Wu, Yang Wang, Precious Cramer, Chi Ngai Chan, Pierre Stéphan, Johanna Schaffenrath, Jia Le Lee, Hendrik A. Michel, Caiwei Tian, Cristina Almagro-Pérez, Sophia J. Wagner, Sharifa Sahai, Ming Y. Lu, Richard J. Chen, Andrew Zhang, Mark Edward M. Gonzales, Ahmad Makky, Jia-Ying Joey Lee, Hao Cheng, Nourhan El Ahmar, Sayed Matar, Maximilian Haist, Darci Phillips, Yuqi Tan, Garry P. Nolan, W. Richard Burack, Jacob D. Estes, Jonathan T. C. Liu, Toni K. Choueiri, Neeraj Agarwal, Marc Barry, Scott J. Rodig, Long Phi Le, Georg Gerber, Christian M. Schürch, Fabian J. Theis, Youn H. Kim, Joe Yeong, Sabina Signoretti, Brooke E. Howitt, Lit-Hsin Loo, Qin Ma, Sizun Jiang, Faisal Mahmood

CoRR, June, 2025

Navigating Through Whole Slide Images With Hierarchy, Multi-Object, and Multi-Scale Data.

Manuel Tran, Sophia J. Wagner, Wilko Weichert, Christian Matek, Melanie Boxberg, Tingying Peng

IEEE Trans. Medical Imaging, May, 2025

Molecular-driven Foundation Model for Oncologic Pathology.

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

CoRR, January, 2025

A Large-Scale Benchmark of Cross-Modal Learning for Histology and Gene Expression in Spatial Transcriptomics.

Rushin H. Gindra, Giovanni Palla, Mathias Nguyen, Sophia J. Wagner, Manuel Tran, Fabian J. Theis, Dieter Saur, Lorin Crawford, Tingying Peng

Proceedings of the IEEE/CVF International Conference on Computer Vision, ICCV 2025, 2025

2024

Multimodal Whole Slide Foundation Model for Pathology.

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

CoRR, 2024

Using histopathology latent diffusion models as privacy-preserving dataset augmenters improves downstream classification performance.

Jan Moritz Niehues, Gustav Müller-Franzes, Yoni Schirris, Sophia J. Wagner, Michael Jendrusch, Matthias Kloor, Alexander T. Pearson, Hannah Sophie Muti, Katherine Jane Hewitt, Gregory Patrick Veldhuizen, Laura Zigutyte, Daniel Truhn, Jakob Nikolas Kather

Comput. Biol. Medicine, 2024

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

Guillaume Jaume, Paul Doucet, Andrew H. Song, Ming Yang Lu, Cristina Almagro-Pérez, Sophia J. Wagner, Anurag Vaidya, Richard J. Chen, Drew F. K. Williamson, Ahrong Kim, Faisal Mahmood

Proceedings of the Advances in Neural Information Processing Systems 37: Annual Conference on Neural Information Processing Systems 2024, 2024

DinoBloom: A Foundation Model for Generalizable Cell Embeddings in Hematology.

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

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2024, 2024

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

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

Proceedings of the IEEE International Symposium on Biomedical Imaging, 2024

2023

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

Omar S. M. El Nahhas, Marko van Treeck, Georg Wölflein, Michaela Unger, Marta Ligero, Tim Lenz, Sophia J. Wagner, Katherine Jane Hewitt, Firas Khader, Sebastian Foersch, Daniel Truhn, Jakob Nikolas Kather

CoRR, 2023

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

Sophia J. Wagner, Daniel Reisenbüchler, Nicholas P. West, Jan Moritz Niehues, Gregory Patrick Veldhuizen, Philip Quirke, Heike Irmgard Grabsch, Piet A. van den Brandt, Gordon G. A. Hutchins, Susan D. Richman, Tanwei Yuan, Rupert Langer, Josien Christina Anna Jenniskens, Kelly Offermans, Wolfram Müller, 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

CoRR, 2023

B-Cos Aligned Transformers Learn Human-Interpretable Features.

Manuel Tran, Amal Lahiani, Yashin Dicente Cid, Melanie Boxberg, Peter Lienemann, Christian Matek, Sophia J. Wagner, Fabian J. Theis, Eldad Klaiman, Tingying Peng

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2023, 2023

Approaching Peak Ground Truth.

Florian Kofler, Johannes Wahle, Ivan Ezhov, Sophia J. Wagner, Rami Al-Maskari, Emilia Gryska, Mihail I. Todorov, Christina Bukas, Felix Meissen, Tingying Peng, Ali Ertürk, Daniel Rueckert, Rolf A. Heckemann, Jan Kirschke, Claus Zimmer, Benedikt Wiestler, Bjoern H. Menze, Marie Piraud

Proceedings of the 20th IEEE International Symposium on Biomedical Imaging, 2023

2022

Multi-Modality Microscopy Image Style Augmentation for Nuclei Segmentation.

Ye Liu, Sophia J. Wagner, Tingying Peng

J. Imaging, 2022

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

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

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2022, 2022

Local Attention Graph-Based Transformer for Multi-target Genetic Alteration Prediction.

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

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2022, 2022

2021

Multi-Modality Microscopy Image Style Transfer for Nuclei Segmentation.

Ye Liu, Sophia J. Wagner, Tingying Peng

CoRR, 2021

Structure-Preserving Multi-domain Stain Color Augmentation Using Style-Transfer with Disentangled Representations.

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

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2021 - 24th International Conference, Strasbourg, France, September 27, 2021