A calibration-aware hierarchical CNN-SWIN fusion framework for robust Cross-Dataset brain MRI analysis.

Introduction: Deep learning approaches have become central to brain MRI analysis; however, their reliability under dataset shift remains a critical barrier to safe and scalable deployment in neuroscience and clinical research. While convolutional neural networks (CNNs) provide strong locality-driven inductive biases for robust feature extraction, they lack global contextual awareness. Conversely, transformer-based architectures capture long-range dependencies but often exhibit reduced robustness and miscalibrated confidence when applied to heterogeneous medical imaging data, particularly in Cross-Dataset settings. Methods: In this work, we propose a Results: Experimental results demonstrate that the proposed fusion model achieves competitive classification performance while substantially improving probabilistic calibration relative to both CNN-only and transformer-only baselines. Specifically, the model attains an average accuracy of 99.20% and achieves lower Expected Calibration Error (ECE = 0.0041), Brier score (0.0028), and Negative Log-Likelihood (NLL = 0.0277) compared to a standalone Swin Transformer and a strong ResNet50 baseline. Discussion: These findings demonstrate that calibration-aware hierarchical CNN-Transformer fusion enhances both predictive reliability and robustness under Cross-Dataset evaluation. By improving the alignment between predictive confidence and empirical correctness, the proposed method supports safer large-scale analysis of heterogeneous brain MRI data, with important implications for multi-center neuroscience studies and trustworthy clinical decision support.