Papers › Representation Learning of Lab Values via Masked AutoEncoder
Representation Learning of Lab Values via Masked AutoEncoder
David Restrepo, Chenwei Wu, Yueran Jia, Jaden K. Sun, Jack Gallifant, Catherine G. Bielick, Yugang Jia, Leo A. Celi
Accurate imputation of missing laboratory values in electronic health records (EHRs) is critical to enable robust clinical predictions and reduce biases in AI systems in healthcare. Existing methods, such as variational autoencoders (VAEs) and decision tree-based approaches such as XGBoost, struggle to model the complex temporal and contextual dependencies in EHR data, mainly in underrepresented groups. In this work, we propose Lab-MAE, a novel transformer-based masked autoencoder framework that leverages self-supervised learning for the imputation of continuous sequential lab values. Lab-MAE introduces a structured encoding scheme that jointly models laboratory test values and their corresponding timestamps, enabling explicit capturing temporal dependencies. Empirical evaluation on the MIMIC-IV dataset demonstrates that Lab-MAE significantly outperforms the state-of-the-art baselines such as XGBoost across multiple metrics, including root mean square error (RMSE), R-squared (R2), and Wasserstein distance (WD). Notably, Lab-MAE achieves equitable performance across demographic groups of patients, advancing fairness in clinical predictions. We further investigate the role of follow-up laboratory values as potential shortcut features, revealing Lab-MAE's robustness in scenarios where such data is unavailable. The findings suggest that our transformer-based architecture, adapted to the characteristics of the EHR data, offers a foundation model for more accurate and fair clinical imputation models. In addition, we measure and compare the carbon footprint of Lab-MAE with the baseline XGBoost model, highlighting its environmental requirements.
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Tasks
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections