ECG-Nest-FM: A Frequency-Focused ECG Foundation Model with Nested Embeddings

Electrocardiograms (ECGs) are fundamental to cardiac diagnostics, providing noninvasive insights into cardiovascular conditions. Recent advancements in deep learning have led to foundation models (FMs) capable of learning powerful representations of ECG signals. However, these models often fail to fully exploit the periodic nature and diagnostic frequency bands of ECGs, leading to inefficiencies in computational cost and interpretability. We propose a novel ECG foundation model that learns nested embeddings, where each subset of dimensions encodes progressively higher-frequency information. By explicitly modeling frequency structures and applying a correlation penalty, the method achieves compact, high-rank representations that reduce model size without sacrificing performance.We evaluate our approach on two large-scale datasets for embedding redundancy and prediction performance on downstream clinical tasks such as arrhythmia classification, and cardiac condition detection. We observe similar prediction performance AUROC scores and lower embedding redundancy, offering a computationally efficient and interpretable framework for ECG analysis. Finally, the representations obtained from our model in UK Biobank data capture known cardiovascular variants and detect novel loci, which can be applied to drug discovery.