PySlyde: A Lightweight, Open-Source Toolkit for Pathology Preprocessing

The integration of artificial intelligence (AI) into pathology is advancing precision medicine by improving diagnosis, treatment planning, and patient outcomes. Digitised whole-slide images (WSIs) capture rich spatial and morphological information vital for understanding disease biology, yet their gigapixel scale and variability pose major challenges for standardisation and analysis. Robust preprocessing, covering tissue detection, tessellation, stain normalisation, and annotation parsing is critical but often limited by fragmented and inconsistent workflows. We present PySlyde, a lightweight, open-source Python toolkit built on OpenSlide to simplify and standardise WSI preprocessing. PySlyde provides an intuitive API for slide loading, annotation management, tissue detection, tiling, and feature extraction, compatible with modern pathology foundation models. By unifying these processes, it streamlines WSI preprocessing, enhances reproducibility, and accelerates the generation of AI-ready datasets, enabling researchers to focus on model development and downstream analysis.

Leakage and Interpretability in Concept-Based Models

Concept Bottleneck Models aim to improve interpretability by predicting high-level intermediate concepts, representing a promising approach for deployment in high-risk scenarios. However, they are known to suffer from information leakage, whereby models exploit unintended information encoded within the learned concepts. We introduce an information-theoretic framework to rigorously characterise and quantify leakage, and define two complementary measures: the concepts-task leakage (CTL) and interconcept leakage (ICL) scores. We show that these measures are strongly predictive of model behaviour under interventions and outperform existing alternatives in robustness and reliability. Using this framework, we identify the primary causes of leakage and provide strong evidence that Concept Embedding Models exhibit substantial leakage regardless of the hyperparameters choice. Finally, we propose practical guidelines for designing concept-based models to reduce leakage and ensure interpretability.