# Do ECG Foundation Models Transfer to Rare Cardiac Diseases? Evidence from Brugada Syndrome Detection

arXiv: https://arxiv.org/abs/2607.03009 · HTML: https://mlsanity.com/paper/2607.03009/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 30 of its 49 references that are in the map.
- First posted on arXiv 3 Jul 2026.

## Builds on (most cited first, 30 of 30)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
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- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [Training data-efficient image transformers & distillation through attention](https://mlsanity.com/paper/2012.12877/) (2020)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [wav2vec 2.0: A Framework for Self-Supervised Learning of Speech Representations](https://mlsanity.com/paper/2006.11477/) (2020)
- [Axiomatic Attribution for Deep Networks](https://mlsanity.com/paper/1703.01365/) (2017)
- [Training Compute-Optimal Large Language Models](https://mlsanity.com/paper/2203.15556/) (2022)
- [Efficiently Modeling Long Sequences with Structured State Spaces](https://mlsanity.com/paper/2111.00396/) (2021)
- [BEiT: BERT Pre-Training of Image Transformers](https://mlsanity.com/paper/2106.08254/) (2021)
- [HuBERT: Self-Supervised Speech Representation Learning by Masked Prediction of Hidden Units](https://mlsanity.com/paper/2106.07447/) (2021)
- [Designing Network Design Spaces](https://mlsanity.com/paper/2003.13678/) (2020)
- [ConViT: Improving Vision Transformers with Soft Convolutional Inductive Biases](https://mlsanity.com/paper/2103.10697/) (2021)
- [CLOCS: Contrastive Learning of Cardiac Signals Across Space, Time, and Patients](https://mlsanity.com/paper/2005.13249/) (2020)
- [Deep Learning for ECG Analysis: Benchmarks and Insights from PTB-XL](https://mlsanity.com/paper/2004.13701/) (2020)
- [ECG-FM: An Open Electrocardiogram Foundation Model](https://mlsanity.com/paper/2408.05178/) (2024)
- [Guiding Masked Representation Learning to Capture Spatio-Temporal Relationship of Electrocardiogram](https://mlsanity.com/paper/2402.09450/) (2024)
- [Zero-Shot ECG Classification with Multimodal Learning and Test-time Clinical Knowledge Enhancement](https://mlsanity.com/paper/2403.06659/) (2024)
- [HOLMES: Health OnLine Model Ensemble Serving for Deep Learning Models in Intensive Care Units](https://mlsanity.com/paper/2008.04063/) (2020)
- [Dist-PU: Positive-Unlabeled Learning from a Label Distribution Perspective](https://mlsanity.com/paper/2212.02801/) (2022)
- [An Electrocardiogram Foundation Model Built on over 10 Million Recordings with External Evaluation across Multiple Domains](https://mlsanity.com/paper/2410.04133/) (2024)
- [Learning General Representation of 12-Lead Electrocardiogram with a Joint-Embedding Predictive Architecture](https://mlsanity.com/paper/2410.08559/) (2024)
- [Inflation of test accuracy due to data leakage in deep learning-based classification of OCT images](https://mlsanity.com/paper/2202.12267/) (2022)
- [OpenECG: Benchmarking ECG Foundation Models with Public 1.2 Million Records](https://mlsanity.com/paper/2503.00711/) (2025)
- [BenchECG and xECG: a benchmark and baseline for ECG foundation models](https://mlsanity.com/paper/2509.10151/) (2025)
- [Benchmarking ECG FMs: A Reality Check Across Clinical Tasks](https://mlsanity.com/paper/2509.25095/) (2025)
- [An Electrocardiogram Multi-task Benchmark with Comprehensive Evaluations and Insightful Findings](https://mlsanity.com/paper/2512.08954/) (2025)

## Abstract (arXiv)

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.