HEART: Learning better representation of EHR data with a heterogeneous relation-aware transformer

Abstract

Objective:

Pretrained language models have recently demonstrated their effectiveness in modeling Electronic Health Record (EHR) data by modeling the encounters of patients as sentences. However, existing methods fall short of utilizing the inherent heterogeneous correlations between medical entities—which include diagnoses, medications, procedures, and lab tests. Existing studies either focus merely on diagnosis entities or encode different entities in a homogeneous space, leading to suboptimal performance. Motivated by this, we aim to develop a foundational language model pre-trained on EHR data with explicitly incorporating the heterogeneous correlations among these entities.

Methods:

In this study, we propose HEART, a heterogeneous relation-aware transformer for EHR. Our model includes a range of heterogeneous entities within each input sequence and represents pairwise relationships between entities as a relation embedding. Such a higher-order representation allows the model to perform complex reasoning and derive attention weights in the heterogeneous context. Additionally, a multi-level attention scheme is employed to exploit the connection between different encounters while alleviating the high computational costs. For pretraining, HEART engages with two tasks, missing entity prediction and anomaly detection, which both effectively enhance the model’s performance on various downstream tasks.

Results:

Extensive experiments on two EHR datasets and five downstream tasks demonstrate HEART’s superior performance compared to four SOTA foundation models. For instance, HEART achieves improvements of 12.1% and 4.1% over Med-BERT in death and readmission prediction, respectively. Additionally, case studies show that HEART offers interpretable insights into the relationships between entities through the learned relation embeddings.

Conclusion:

We study the problem of EHR representation learning and propose HEART, a model that leverages the heterogeneous relationships between medical entities. Our approach includes a multi-level encoding scheme and two specialized pretrained objectives, designed to boost both the efficiency and effectiveness of the model. We have comprehensively evaluated HEART across five clinically significant downstream tasks using two EHR datasets. The experimental results verify the model’s great performance and validate its practical utility in healthcare applications. Code: https://github.com/Graph-and-Geometric-Learning/HEART.