A deep foundation model for electrocardiogram interpretation: enabling rare disease detection through transfer learning

In healthcare, scarcity of high-quality human-adjudicated labelled data may limit the potential of deep neural networks (DNNs). Foundation models provide an efficient starting point for deep learning that can facilitate effective DNN training with fewer labelled training examples. In this study, we leveraged cardiologist-confirmed labels from a large dataset of 1.6 million electrocardiograms (ECGs) acquired as part of routine clinical care at UCSF between 1986 and 2019 to pre-train a convolutional DNN to predict 68 common ECG diagnoses. To our knowledge, this model is one of the most comprehensive ECG DNN models to date, demonstrating high performance with a median area under the receiver operating curve (AUC) of 0.978, median sensitivity of 0.937, and median specificity of 0.923. We then demonstrate the model's utility as a foundation model by additionally training (fine-tuning) the DNN to detect three novel ECG diagnoses with relatively small datasets: carcinoid syndrome, pericardial constriction, and rheumatic doming of the mitral valve. Fine-tuning training of the foundation model achieved an AUC of 0.772 (95% CI 0.723-0.816) for carcinoid syndrome, 0.883 (0.863-0.906) for pericardial constriction, and 0.826 (95% CI 0.802-0.854) for rheumatic doming, compared to 0.492 (95% CI 0.434-0.558), 0.689 (95% CI 0.656-0.720), and 0.701 (95% CI 0.657-0.745), respectively, for DNNs trained from scratch on the same small datasets. Our results demonstrate that the ECG foundation model learned a flexible representation of ECG waveforms and can improve performance of fine-tuned downstream models, particularly in data-limited settings.