An Explainable Multi-Scale Deep Learning Framework for Multi-Class Brain MRI Classification

Background/Objectives: Brain magnetic resonance imaging (MRI) is an important imaging modality for assessing neurological disorders. However, automatic multi-class MRI classification remains challenging because of visual similarity between disease categories, heterogeneous pathological patterns, class imbalance, and the need for reliable confidence estimation. This study aims to develop a comprehensive and well-calibrated deep learning framework for image-level brain MRI classification across multiple neurological categories. Methods: This paper introduces a new deep learning framework, MCND-ComputeNet++, for brain MRI classification into eight image-level categories using the MCND dataset, which comprises 16,400 two-dimensional brain MRI images belonging to eight diagnostic categories: AD-MildDemented, AD-ModerateDemented, AD-VeryMildDemented, BT-glioma, BT-meningioma, BT-pituitary, MS, and Normal. The proposed model uses a single pretrained EfficientNetV2-S backbone to extract hierarchical feature maps from three intermediate stages. These multi-level features are projected into a common latent space, spatially aligned, adaptively fused through learnable gated multi-scale fusion, further refined using convolutional processing, and aggregated using spatial attention pooling before classification. The training strategy combines class-balanced focal loss with label smoothing, MixUp/CutMix regularization, exponential moving average weight smoothing, warmup cosine learning-rate scheduling, temperature scaling, and test-time augmentation to improve generalization and calibration. The framework was evaluated using accuracy, precision, recall, macro-F1, macro-AUC, macro-average precision, expected calibration error, Brier score, bootstrap confidence intervals, ablation analysis, McNemar testing, and comparisons against standard pretrained baseline models. Results: MCND-ComputeNet++ achieved mean accuracy, macro-F1, macro-AUC, and macro-average precision values of 0.9738, 0.9771, 0.9993, and 0.9971, respectively, with narrow bootstrap confidence intervals indicating stable image-level performance. These findings should be interpreted as image-level/slice-level performance on MCND, because patient-level identifiers and subject-wise splitting were not available. These results outperformed most evaluated baselines, including ResNet50, DenseNet121, EfficientNetB0, EfficientNetV2-S with a standard classifier, Swin-Tiny, and ConvNeXt-Tiny, across several discrimination and calibration metrics. Compared with ConvNeXt-Tiny, the proposed model achieved higher macro-AUC and macro-average precision, together with a lower ECE and Brier score, suggesting improved image-level discrimination and confidence reliability. Compared with the EfficientNetV2-S standard classifier, accuracy increased from 0.9308 to 0.9738, while the Brier score decreased from 0.1045 to 0.0400. Conclusions: The results suggest that MCND-ComputeNet++ is a promising image-level brain MRI classification framework for the eight MCND categories. The proposed model integrates hierarchical feature extraction, shared latent projection, gated multi-scale fusion, convolutional refinement, spatial attention pooling, and calibrated inference within a unified architecture. However, because the current evaluation was conducted at the image/slice level without available patient-level identifiers, the findings should not be interpreted as patient-level clinical diagnostic validation. Further studies using subject-wise splitting, external multi-center datasets, 3D volumetric modeling, and multimodal clinical information are required to assess generalizability and potential clinical decision-support applicability.