From Basic to Extra Features: Hypergraph Transformer Pretrain-then-Finetuning for Balanced Clinical Predictions on EHR

Ran Xu, Yiwen Lu, Chang Liu, Yong Chen, Yan Sun, Xiao Hu, Joyce C. Ho, Carl Yang

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Abstract: Electronic Health Records (EHRs) contain rich patient information and are crucial for clinical research and practice. In recent years, deep learning models have been applied to EHRs, but they often rely on massive features, which may not be readily available for all patients. We propose HTP-Star, which leverages hypergraph structures with a pretrain-then-finetune framework for modeling EHR data, enabling seamless integration of additional features. Additionally, we design two techniques, namely (1) \emph{Smoothness-inducing Regularization} and (2) \emph{Group-balanced Reweighting}, to enhance the model's robustness during finetuning. Through experiments conducted on two real EHR datasets, we demonstrate that HTP-Star consistently outperforms various baselines while striking a balance between patients with basic and extra features.