Foundation models (FMs) are transforming computational pathology by offering new ways to analyze histopathology images. However, FMs typically require weeks of training on large databases, making their creation a resource-intensive process. In this paper, we present a training for foundation models from whole slide images using supervised, end-to-end, multitask learning on slide-level labels. Notably, it is the first model to incorporate cancer subtyping, risk estimation, and genetic mutation prediction into one model. The presented model outperforms self-supervised models on seven benchmark tasks while the training only required 5% of the computational resources. The results not only show that supervised training can outperform self-supervision with less data, but also offer a solution to annotation problems, as patient-based labels are widely available through routine clinical processes. Furthermore, an attention module provides a layer of explainability across different tasks and serves as a tumor detector for unseen cancer types. To address the issue of closed-source datasets, the model was fully trained on openly available data. The code and model weights are made available under https://github.com/FraunhoferMEVIS/MedicalMultitaskModeling.
@article{arxiv.2507.05742,
title = {Whole Slide Concepts: A Supervised Foundation Model For Pathological Images},
author = {Till Nicke and Daniela Schacherer and Jan Raphael Schäfer and Natalia Artysh and Antje Prasse and André Homeyer and Andrea Schenk and Henning Höfener and Johannes Lotz},
journal= {arXiv preprint arXiv:2507.05742},
year = {2026}
}