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arXiv · 2608.30367

Beat-Synchronous Tokenization for ECG Transformers

Ahmed Sameh·Nolan Wilson·Max Enderlein·Yogatheesan Varatharajah
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Abstract

Transformer-based electrocardiogram (ECG) models commonly tokenize waveforms into fixed temporal patches. Though convenient, fixed patching can split heartbeat structures across token boundaries. We study beat-synchronous tokenization as a physiologically grounded alternative, comparing fixed patches with three beat-aligned strategies: resampled beats, adaptive pooled beats, and resampled beats augmented with R--R interval information. Experiments span two settings: 10-second 12-lead diagnostic classification on PTB-XL after MIMIC-IV-ECG masked pretraining, and 60-second single-lead rhythm classification on Icentia11k after patient-level contrastive pretraining. On PTB-XL, resampled beat tokens achieve the highest mean macro Area Under the ROC Curve (AUROC; 0.8945) and nearly match the best fixed-patch macro Area Under the Precision-Recall Curve (AUPRC; 0.7414), reducing average sequence length from 100 to 11.2 tokens. On Icentia11k, beat-synchronous tokenizers obtain comparable AUPRC to fixed patching with better stability across runs. These results suggest morphology-preserving beat tokenization is a compact, competitive alternative to fixed temporal patching.

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Ahmed Sameh, Nolan Wilson, Max Enderlein, Yogatheesan Varatharajah. 2026-08-31. Beat-Synchronous Tokenization for ECG Transformers. https://arxiv.org/abs/2608.30367

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