Reliable medical image classification demands two things from deep learning models: high diagnostic accuracy and confidence scores that reflect true uncertainty. Poorly calibrated predictions mislead clinical decision support systems even when accuracy looks acceptable. Hybrid CNN–Transformer architectures capture both local texture and global structural features, but their fusion strategies treat every input identically—a critical limitation, because texture detail and global morphology carry different diagnostic weight across conditions and patients. This work introduces Dual-granularity Adaptive Calibration (DAC), which reframes branch fusion as a per-sample reliability calibration problem. Instead of fixed weights or spatial attention, DAC estimates the reliability of each branch for every input using three complementary signals: predictive entropy, Jensen–Shannon divergence between branch distributions, and exponential moving average feature consistency. A lightweight reliability estimator converts these signals into per-sample fusion weights over branch representations projected to a common feature space. An Adaptive Prototype Classifier (APC) with a dedicated reliability calibration loss then ensures that confidence scores faithfully reflect empirical accuracy. All baselines are reimplemented on identical lesion-disjoint data splits under five independent random seeds to ensure fair comparison; ECE improvements are measured against temperature-scaled post hoc calibration. On HAM10000 (7-class skin lesion, (n = 9015) deduplicated, lesion-disjoint split) and the Kermany Retinal OCT dataset (4-class, (n = 92{,}484)), DAC achieves (93.74 pm 0.29%) and (98.30 pm 0.14%) accuracy whilst reducing Expected Calibration Error (ECE) to (0.031 pm 0.003) and (0.018 pm 0.002)—improvements of 0.031 and 0.030 ECE over the strongest reimplemented baselines (McNemar’s test, (p < 0.001) for both accuracy comparisons, per-seed). A ten-row ablation study confirms each component contributes independently and consistently, and the learned fusion weights show that DAC autonomously prefers local texture on skin data and global structure on retinal data without explicit supervision.


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