In domains where both predictive performance and interpretability are essential, deep neural networks achieve strong results but provide limited insight into how their predictions are made. Projection-based prototype networks address this limitation by grounding predictions in similarity to representative training examples, enabling case-based explanations and global prototype inspection. However, existing approaches rely on label supervision, tying prototypes to a specific task and requiring large labeled datasets. We introduce ProtoSSL, a framework for pretraining a foundational latent prototype bank on unlabeled data and transferring it to downstream tasks to create interpretable, projection-based prototype models. Our key idea is to separate motif discovery from label alignment. ProtoSSL first learns a transferrable prototype bank using a self-supervised objective applied directly to prototype activations, and then aligns these prototypes to downstream tasks through a novel efficient assignment procedure. Across six electrocardiography (ECG) datasets, ProtoSSL improves label efficiency, outperforming supervised prototype baselines in low-data regimes with as few as 256 labeled examples; with fine-tuning, ProtoSSL outperforms supervised prototype baselines at full dataset scale. In a human evaluation study, ProtoSSL produces prototypes and prototype-based explanations that are judged more favorably than those learned with direct label supervision. We further show that the framework extends to audio classification. Thus, ProtoSSL enables both learning foundational prototypes from unlabeled data before the downstream label space is known, and subsequent assignment to new tasks to create interpretable, projection-grounded prototypes.

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