Label-Space Mismatch Distorts Cross-Cohort Evaluation in Breast Cancer Molecular Subtyping
Cross-cohort evaluation of breast cancer subtype classifiers is unreliable when source and target cohorts use different annotation standards: METABRIC labels six classes, PAM50 defines five, and a claudin-low prediction cannot be correct under a five-class standard. A classifier transferred from 1,369 METABRIC patients (train n=958) to TCGA-BRCA (n=987) and GSE21653 (n=266) separates three evaluation operations routinely conflated in cross-site comparisons. (1) Label-space restriction - an evaluation-rule change, not a retraining gain - is the dominant correction (73.76%->79.74% on TCGA-BRCA; 63.16%->68.42% on GSE21653); (2) EM prior correction on the reconciled space is an optional calib...
| Authors | Suxing Liu, Byungwon Min, Zhijian Zheng et al. |
|---|---|
| Primary category | cs.LG |
| Published | 18 October 2026 |
| Last updated at source | 18 October 2026 |
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