A Lesion-Aware Patch Sampling Approach with EfficientNet3D-UNet for Robust Multiple Sclerosis Lesion Segmentation

Accurate segmentation of multiple sclerosis (MS) lesions from 3D MRI scans is essential for diagnosis, disease monitoring, and treatment planning. However, this task remains challenging due to the sparsity, heterogeneity, and subtle appearance of lesions, as well as the difficulty in obtaining high-quality annotations. In this study, we propose Efficient-Net3D-UNet, a deep learning framework that combines compound-scaled MBConv3D blocks with a lesion-aware patch sampling strategy to improve volumetric segmentation performance across multi-modal MRI sequences (FLAIR, T1, and T2). The model was evaluated against a conventional 3D U-Net baseline using standard metrics including Dice similarity coefficient, precision, recall, accuracy, and specificity. On a held-out test set, EfficientNet3D-UNet achieved a Dice score of 48.39%, precision of 49.76%, and recall of 55.41%, outperforming the baseline 3D U-Net, which obtained a Dice score of 31.28%, precision of 32.48%, and recall of 43.04%. Both models reached an overall accuracy of 99.14%. Notably, EfficientNet3D-UNet also demonstrated faster convergence and reduced overfitting during training. These results highlight the potential of EfficientNet3D-UNet as a robust and computationally efficient solution for automated MS lesion segmentation, offering promising applicability in real-world clinical settings.