Domain Generalization of Histopathology Foundation Models in Multicenter, Multi-Scanner Cohorts: A Comparative Benchmark
TL;DR
These findings show that standard source-mixed CV can overestimate domain generalization across centers and scanners, and that FM choice matters in multi-source cohorts, especially for more challenging CPath tasks, where cross-domain failures are more visible.
Abstract
Histopathology foundation models (FMs) have become widely used as patch-level feature extractors in computational pathology (CPath), where domain shift is a central challenge, yet their generalization ability across acquisition centers and scanning platforms remains insufficiently studied. In this work, we evaluate the domain generalization of ten state-of-the-art FMs on two multi-source datasets with different supervision settings: SemiCOL, a colorectal cancer cohort of 499 whole-slide images (WSIs) for weakly labeled slide-level binary tumor classification, and BEETLE, a breast cancer cohort of 583 WSIs for patch-level four-class tissue classification. In an ablation-style setting, FMs are used as patch-level feature extractors, with patch embeddings mean-pooled into slide-level representations for SemiCOL, and a lightweight multi-layer perceptron trained for slide-level and patch-level classification on SemiCOL and BEETLE, respectively. To test FM domain generalization, we use three evaluation protocols: a Baseline source-mixed 5-fold cross-validation (CV) and two leave-source-out CV settings that assess cross-center and cross-scanner performance. On SemiCOL, all FMs achieve near-saturated performance, indicating stable performance under acquisition-source domain shift for slide-level Tumor vs. Benign classification. In contrast, BEETLE reveals clear generalization gaps, with scanner-induced domain shift more challenging than center-induced domain shift, and class-wise results showing that performance losses concentrate in epithelial discrimination. Overall, Virchow2 shows the strongest robustness across all evaluated protocols. These findings show that standard source-mixed CV can overestimate domain generalization across centers and scanners, and that FM choice matters in multi-source cohorts, especially for more challenging CPath tasks, where cross-domain failures are more visible.