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Life sciences · Preprint
arXiv · October 24, 2026
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Photoplethysmography (PPG) plays a central role in wearable health monitoring and clinical decision support. However, existing approaches to universal PPG representation learning are predominantly trained on high-quality large-scale datasets obtained from oximeters in hospital settings and often struggle to adapt to sparse and low-quality real-world datasets, thereby limiting their generalization to clinically relevant tasks on prevalent PPG data such as collected from wearable devices. Surprisingly, even after full fine-tuning, PPG foundation models cannot consistently outperform general-purpose time-series models. Therefore, a key question is how to effectively adapt PPG foundation models to target prediction tasks. Through empirical studies on various PPG foundation models, we find that pretrained models often exhibit inherent sparsity and computational redundancy, suggesting that PPG foundation models have learned to activate task-relevant network substructures for different prediction tasks. To preserve this valuable prior knowledge, we propose a structured pruning-and-fine-tuning framework, SPAFT, which regularizes the adaptive fine-tuning process by constraining it to a more relevant and compact parameter space based on parameter importance and structural redundancy. Extensive experiments across four PPG foundation models, five benchmark datasets, and ten downstream tasks demonstrate that SPAFT achieves win rates of 82.8% and 87.5% on regression and classification tasks, respectively. This prune-then-finetune paradigm often enables PPG foundation models to achieve state-of-the-art performance, laying a promising foundation for the real-world clinical deployment of PPG foundation models and the development of personalized PPG foundation models.