Domain-Adapted Fine-Tuning of ECG Foundation Models for Multi-Label Structural Heart Disease Screening
Authors: Duc N. Do, Minh N. Do, Dang Nguyen, Khanh T. Q. Le, Khoa D. Pham, Hung N. Huynh, Phi Pham-Van-Hoang, Quan K. Huynh, +9 more
Organizations: 1PASSIO Laboratory, North Carolina A&T State University, Greensboro, NC, USA · Department of Computer Science, University of Manitoba, Winnipeg, MB, Canada · 3Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA · Department of Medicine, Jordan University of Science and Technology, Irbid, Jordan · Department of Biomedical Engineering, Duke University, Durham, NC, USA · 6Harvard Medical School, Boston, MA, USA · 7Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
Abstract
Transthoracic echocardiography is the reference standard for confirming structural heart disease (SHD), but first-line screening is limited by cost, workflow burden, and specialist availability. We evaluated whether open pretrained electrocardiogram (ECG) foundation models can support echo-confirmed multi-label SHD detection using the public EchoNext Mini-Model benchmark. Six echocardiography-derived abnormalities were targeted: reduced left ventricular ejection fraction, increased left ventricular wall thickness, aortic stenosis, mitral regurgitation, tricuspid regurgitation, and right ventricular systolic dysfunction. Under a common pipeline, we compared engineered ECG features with gradient boosting, end-to-end waveform learning from scratch, and transfer from open ECG foundation models. We then applied in-domain self-supervised adaptation of an ECG foundation model (ECG-FM) on EchoNext waveforms followed by selective supervised fine-tuning, and evaluated trade-offs between discrimination and adaptation cost. Adapted ECG-FM models achieved the best overall performance: peak macro-AUROC 0.8509 and macro-AUPRC 0.4297, while a parameter-efficient operating point preserved AUROC (0.8501) and attained the highest fixed-threshold macro-F1 0.3691. Late fusion with covariates did not improve threshold-independent discrimination, and evaluated LoRA, alternative backbones, and mixture-of-foundations strategies did not surpass the best adapted single-backbone models. These results indicate that for ECG-based case finding and echocardiography triage, combining target-domain self-supervised adaptation with selective supervised updating of a pretrained ECG backbone is the most effective transfer strategy.
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.
Beatrice Zanchi, Giuliana Monachino, Alvise Dei Rossi +4
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.
Standardized echocardiography conclusions provide meaningful supervision for learning ECG representations of echocardiography-derived cardiac findings. Global ECG--text alignment may entangle modality-specific factors, while long-tailed finding distributions provide sparse positive supervision for low-prevalence conditions. We propose EchoBridge with Complementary Shared--Private Projection (CSPP) and Adaptive Prototype Boundary Calibration (APBC). CSPP maps each modality into shared and auxiliary private projections, reduces directional redundancy via within-modality orthogonality, and bidirectionally aligns normalized shared projections. APBC organizes the shared hypersphere with class-specific prototypes, training-frequency-adaptive angular margins, and spherical Riesz repulsion. We evaluate EchoBridge on EchoNext-Mini and independent PKUPH and SHTMU cohorts under four protocols: prompt-based inference without downstream classifier training, in-domain frozen linear probing, target-domain cross-center frozen linear probing, and source-only cross-center transfer, supplemented by finding-specific analyses. EchoBridge improves classifier-free AUROC, AUPRC, and F1 over the strongest baselines by 7.88, 5.61, and 4.54 points, respectively, and achieves the highest point estimates across all in-domain and target-domain probing budgets and both source-only transfer cohorts. Finding-specific analyses show gains for most conditions, including several low-prevalence valvular findings.