SCALE: Synthetic Calibration via Agreement Labeling in Embedding Space

arXiv:2609.38705v1 Announce Type: new Abstract: Foundation models for computational pathology are usually evaluated using AUC and accuracy, while calibration is often left untested. This matters because a model can be accurate on average but still assign overly confident probabilities to cases that are difficult even for pathologists. We study calibration across eight pathology foundation models. Using pathologist agreement as a measure of diagnostic difficulty, we find that calibration error is consistently higher on low-agreement cases than on high-agreement cases. This pattern is not apparent from aggregate expected calibration error (ECE) alone. We then propose synthetic agreement calibration, a method for improving calibration without collecting multi-annotator labels. Given a trained linear probe, we select high-confidence embeddings as class anchors and interpolate between anchors from opposite classes. The interpolation weights encode a continuous notion of diagnostic ambiguity, which we use as a synthetic agreement signal to retrain the probe with agreement-aware label smoothing. On MHIST, which includes annotations from seven pathologists, synthetic agreement calibration recovers most of the calibration improvement obtained by label smoothing based on real pathologist agreement, while substantially reducing low-agreement ECE relative to the uncalibrated baseline. Discrimination metrics are preserved. On PatchCamelyon and BreakHis, public histopathology datasets without multi-annotator labels, the method improves calibration across the evaluated foundation models, whereas annotator-dependent approaches cannot be used without additional expert annotation.