ECG Latent Feature Extraction with Autoencoders for Downstream Prediction Tasks

TL;DR

This paper explores novel autoencoder-based methods for extracting meaningful features from ECG signals, improving prediction accuracy while reducing computational complexity, especially useful for small datasets.

Contribution

Introduces three new Variational Autoencoder variants for ECG feature extraction and demonstrates their effectiveness in downstream prediction tasks with limited data.

Findings

A beta-VAE achieved near-noise level signal reconstruction.

SAE encodings improved LVEF prediction with high AUROC.

The pipeline reduces overfitting and performs well with less training data.

Abstract

The electrocardiogram (ECG) is an inexpensive and widely available tool for cardiac assessment. Despite its standardized format and small file size, the high complexity and inter-individual variability of ECG signals (typically a 60,000-size vector with 12 leads at 500 Hz) make it challenging to use in deep learning models, especially when only small training datasets are available. This study addresses these challenges by exploring feature generation methods from representative beat ECGs, focusing on Principal Component Analysis (PCA) and Autoencoders to reduce data complexity. We introduce three novel Variational Autoencoder (VAE) variants-Stochastic Autoencoder (SAE), Annealed beta-VAE (A beta-VAE), and Cyclical beta VAE (C beta-VAE)-and compare their effectiveness in maintaining signal fidelity and enhancing downstream prediction tasks using a Light Gradient Boost Machine (LGBM). The A beta-VAE achieved superior signal reconstruction, reducing the mean absolute error (MAE) to 15.7+/-3.2 muV, which is at the level of signal noise. Moreover, the SAE encodings, when combined with traditional ECG summary features, improved the prediction of reduced Left Ventricular Ejection Fraction (LVEF), achieving an holdout test set area under the receiver operating characteristic curve (AUROC) of 0.901 with a LGBM classifier. This performance nearly matches the 0.909 AUROC of state-of-the-art CNN model but requires significantly less computational resources. Further, the ECG feature extraction-LGBM pipeline avoids overfitting and retains predictive performance when trained with less data. Our findings demonstrate that these VAE encodings are not only effective in simplifying ECG data but also provide a practical solution for applying deep learning in contexts with limited-scale labeled training data.