Morphology-aware deep learning predicts colorectal cancer survival from whole-slide images

Abstract

Background: Five-year survival prediction from hematoxylin-and-eosin whole-slide images could support risk stratification, but the task is weakly supervised, and the tissue morphologies carrying prognostic information remain incompletely characterized. Methods: We conducted a retrospective secondary analysis using TCGA-COAD/READ (n=562) for morphology-specific analysis, Alliance/ CALGB 89803 (n=424) for model development, and SurGen (n=218) for external evaluation. We propose MorphContrast, a morphology-aware contrastive multiple-instance learning framework that uses tissue labels as structural supervision for five-year survival prediction. MorphContrast combines gated-attention pooling with three auxiliary objectives: patch-level morphology labels define within-patient contrasts, outcome concordance or discordance defines cross-patient contrasts within matched morphologies, and diversity regularization discourages representational collapse. Morphology-matched patches from patients with discordant outcomes serve as hard negatives, encouraging prognostic discrimination within comparable histologic contexts. Results: Morphology-specific models show weak but distributed prognostic discrimination: adipose tissue achieves an area under the receiver operating characteristic curve (AUC) of 0.622, stroma achieves 0.604, and both perform comparably to tumor epithelium (0.601-0.605). On Alliance/CALGB 89803, the single model achieves an AUC of 0.642, while the post hoc ensemble reaches a pooled out-of-fold AUC of 0.70 and a risk-group hazard ratio of 3.79 (95% confidence interval: 2.55-5.63). On the external SurGen colon cancer cohort (n=218), the single model and ensemble achieve AUCs of 0.669 and 0.678, respectively. Conclusions: These findings support tissue morphology as structural supervision for outcome-aware representation learning in colorectal cancer prognosis.