arXiv:2510.09649v1 Announce Type: cross Abstract: Batten disease (neuronal ceroid lipofuscinosis) is a rare pediatric neurodegenerative disorder whose early MRI signs are subtle and often missed. We propose TinyViT-Batten, a few-shot Vision Transformer (ViT) framework to detect early Batten disease from pediatric brain MRI with limited training cases. We distill a large teacher ViT into a 5 M-parameter TinyViT and fine-tune it using metric-based few-shot learning (prototypical loss with 5-shot episodes). Our model achieves high accuracy (approximately 91%) and area under ROC of at least 0.95 on a multi-site dataset of 79 genetically confirmed Batten-disease MRIs (27 CLN3 from the Hochstein natural-history study, 32 CLN2 from an international longitudinal cohort, 12 early-manifestation CLN2 cases reported by Cokal et al., and 8 public Radiopaedia scans) together with 90 age-matched controls, outperforming a 3D-ResNet and Swin-Tiny baseline. We further integrate Gradient-weighted Class Activation Mapping (Grad-CAM) to highlight disease-relevant brain regions, enabling explainable predictions. The model's small size and strong performance (sensitivity greater than 90%, specificity approximately 90%) demonstrates a practical AI solution for early Batten disease detection.