Przemyslaw Szostak

Gustav Bredell, Marcel Fischer, Przemyslaw Szostak et al.

Digital pathology has significantly advanced disease detection and pathologist efficiency through the analysis of gigapixel whole-slide images (WSI). In this process, WSIs are first divided into patches, for which a feature extractor model is applied to obtain feature vectors, which are subsequently processed by an aggregation model to predict the respective WSI label. With the rapid evolution of representation learning, numerous new feature extractor models, often termed foundational models, have emerged. Traditional evaluation methods rely on a static downstream aggregation model setup, encompassing a fixed architecture and hyperparameters, a practice we identify as potentially biasing the results. Our study uncovers a sensitivity of feature extractor models towards aggregation model configurations, indicating that performance comparability can be skewed based on the chosen configurations. By accounting for this sensitivity, we find that the performance of many current feature extractor models is notably similar. We support this insight by evaluating seven feature extractor models across three different datasets with 162 different aggregation model configurations. This comprehensive approach provides a more nuanced understanding of the feature extractors' sensitivity to various aggregation model configurations, leading to a fairer and more accurate assessment of new foundation models in digital pathology.

Victor Ibañez, Przemyslaw Szostak, Quincy Wong et al.

Graph convolutional networks (GCNs) have emerged as a powerful alternative to multiple instance learning with convolutional neural networks in digital pathology, offering superior handling of structural information across various spatial ranges - a crucial aspect of learning from gigapixel H&E-stained whole slide images (WSI). However, graph message-passing algorithms often suffer from oversmoothing when aggregating a large neighborhood. Hence, effective modeling of multi-range interactions relies on the careful construction of the graph. Our proposed multi-scale GCN (MS-GCN) tackles this issue by leveraging information across multiple magnification levels in WSIs. MS-GCN enables the simultaneous modeling of long-range structural dependencies at lower magnifications and high-resolution cellular details at higher magnifications, akin to analysis pipelines usually conducted by pathologists. The architecture's unique configuration allows for the concurrent modeling of structural patterns at lower magnifications and detailed cellular features at higher ones, while also quantifying the contribution of each magnification level to the prediction. Through testing on different datasets, MS-GCN demonstrates superior performance over existing single-magnification GCN methods. The enhancement in performance and interpretability afforded by our method holds promise for advancing computational pathology models, especially in tasks requiring extensive spatial context.