FOUND-AF: Benchmarking ECG Foundation Models for Atrial Fibrillation Detection

Objective: Atrial fibrillation (AF) is the most common cardiac arrhythmia experienced by intensive care unit (ICU) patients and can cause adverse health effects. In this study, we publish a labelled ICU dataset and benchmarks for AF detection. Methods: We compared machine learning models across three data-driven artificial intelligence (AI) approaches: feature-based classifiers, deep learning (DL), and ECG foundation models (FMs). This comparison addresses a critical gap in the literature and aims to pinpoint which AI approach is best for accurate AF detection. Electrocardiograms (ECGs) from a Canadian ICU and the 2021 PhysioNet/Computing in Cardiology Challenge were used to conduct the experiments. Multiple training configurations were tested, ranging from zero-shot inference to transfer learning. Results: On average and across both datasets, ECG FMs performed best, followed by DL, then feature-based classifiers. The model that achieved the top F1 score on our ICU test set was ECG-FM through a transfer learning strategy (F1=0.89). Conclusion: This study demonstrates promising potential for using AI to build an automatic patient monitoring system. Significance: By publishing our labelled ICU dataset (LinkToBeAdded) and performance benchmarks, this work enables the research community to continue advancing the state-of-the-art in AF detection in the ICU. https://physionet.org/content/kingston-icu-af/

Background: Foundation models (FMs) trained on large-scale unlabeled physiological data have emerged as a promising paradigm for medical artificial intelligence. Their ability to capture clinically meaningful, transferable representations for rare diseases remains largely unproven. This study investigates whether FM pre-training provides genuine clinical generalization benefits beyond improved optimization for rare electrocardiographic (ECG) phenotypes. Methods: We systematically evaluated nine publicly available ECG FMs for Brugada syndrome detection on the BrSwiss cohort (294 patients, 87 cases) and the independent external HUCA cohort (363 patients, 76 cases), under three strategies (from-scratch training, linear probing, full fine-tuning) across several configurations, including a 3% data ablation and zero-shot cross-site transfers. Results: Pre-training was necessary for high-capacity architectures unable to converge from scratch (AUC gain up to 0.411, p < 0.05), but gave no significant gain for compact architectures already converged on labeled data alone. On full BrSwiss, the best fine-tuned FM (ECG-CPC, AUC = 0.962) only marginally exceeded the strongest supervised baseline (ECG-CPC from scratch, AUC = 0.932; p = 0.091). At matched training-set size, the data-efficiency advantage on BrSwiss-3% (AUC gain = 0.055, p < 0.01) did not replicate on HUCA. Under zero-shot cross-site transfer, FM-based pipelines did not generalize better than supervised baselines, all approaching chance-level performance. Conclusion: For Brugada syndrome detection, FM pre-training is mechanical rather than semantic, providing optimization stability rather than transferable clinical knowledge. These findings challenge the assumption that large-scale pre-training inherently encodes clinically meaningful representations, highlighting the central role of model architecture and data-domain alignment.

Specialized foundation models are beginning to emerge in various medical subdomains, but pretraining methodologies and parametric scaling with the size of the pretraining dataset are rarely assessed systematically and in a like-for-like manner. This work focuses on foundation models for electrocardiography (ECG) data, one of the most widely captured physiological time series world-wide. We present a comprehensive assessment of pretraining methodologies, covering five different contrastive and non-contrastive self-supervised learning objectives for ECG foundation models, and investigate their scaling behavior with pretraining dataset sizes up to 11M input samples, exclusively from publicly available sources. Pretraining strategy has a meaningful and consistent impact on downstream performance, with contrastive predictive coding (slightly ahead of JEPA) yielding the most transferable representations across diverse clinical tasks. Scaling pretraining data continues to yield meaningful improvements up to 11M samples for most objectives. We also compare model architectures across all pretraining methodologies and find evidence for a clear superiority of structured state space models compared to transformers and CNN models. We hypothesize that the strong inductive biases of structured state space models, rather than pretraining scale alone, are the primary driver of effective ECG representation learning, with important implications for future foundation model development in this and potentially other physiological signal domains.