Nanne Aben

kaiko. ai, Nanne Aben, Edwin D. de Jong et al. · eth-zurich

Driven by the recent advances in deep learning methods and, in particular, by the development of modern self-supervised learning algorithms, increased interest and efforts have been devoted to build foundation models (FMs) for medical images. In this work, we present our scalable training pipeline for large pathology imaging data, and a comprehensive analysis of various hyperparameter choices and training techniques for building pathology FMs. We release and make publicly available the first batch of our pathology FMs (https://github.com/kaiko-ai/towards_large_pathology_fms) trained on open-access TCGA whole slide images, a commonly used collection of pathology images. The experimental evaluation shows that our models reach state-of-the-art performance on various patch-level downstream tasks, ranging from breast cancer subtyping to colorectal nuclear segmentation. Finally, to unify the evaluation approaches used in the field and to simplify future comparisons of different FMs, we present an open-source framework (https://github.com/kaiko-ai/eva) designed for the consistent evaluation of pathology FMs across various downstream tasks.

Samantha Biegel, Rafah El-Khatib, Luiz Otavio Vilas Boas Oliveira et al.

The availability of labelled data is one of the main limitations in machine learning. We can alleviate this using weak supervision: a framework that uses expert-defined rules $\boldsymbolλ$ to estimate probabilistic labels $p(y|\boldsymbolλ)$ for the entire data set. These rules, however, are dependent on what experts know about the problem, and hence may be inaccurate or may fail to capture important parts of the problem-space. To mitigate this, we propose Active WeaSuL: an approach that incorporates active learning into weak supervision. In Active WeaSuL, experts do not only define rules, but they also iteratively provide the true label for a small set of points where the weak supervision model is most likely to be mistaken, which are then used to better estimate the probabilistic labels. In this way, the weak labels provide a warm start, which active learning then improves upon. We make two contributions: 1) a modification of the weak supervision loss function, such that the expert-labelled data inform and improve the combination of weak labels; and 2) the maxKL divergence sampling strategy, which determines for which data points expert labelling is most beneficial. Our experiments show that when the budget for labelling data is limited (e.g. $\leq 60$ data points), Active WeaSuL outperforms weak supervision, active learning, and competing strategies, with only a handful of labelled data points. This makes Active WeaSuL ideal for situations where obtaining labelled data is difficult.