PEHRT: A Common Pipeline for Harmonizing Electronic Health Record data for Translational Research
Jessica Gronsbell, Vidul Ayakulangara Panickan, Chris Lin, Thomas Charlon, Chuan Hong, Doudou Zhou, Linshanshan Wang, Jianhui Gao, Shirley Zhou, Yuan Tian, Yaqi Shi, Ziming Gan, Tianxi Cai
Published: 2025/9/10
Abstract
Integrative analysis of multi-institutional Electronic Health Record (EHR) data enhances the reliability and generalizability of translational research by leveraging larger, more diverse patient cohorts and incorporating multiple data modalities. However, harmonizing EHR data across institutions poses major challenges due to data heterogeneity, semantic differences, and privacy concerns. To address these challenges, we introduce $\textit{PEHRT}$, a standardized pipeline for efficient EHR data harmonization consisting of two core modules: (1) data pre-processing and (2) representation learning. PEHRT maps EHR data to standard coding systems and uses advanced machine learning to generate research-ready datasets without requiring individual-level data sharing. Our pipeline is also data model agnostic and designed for streamlined execution across institutions based on our extensive real-world experience. We provide a complete suite of open source software, accompanied by a user-friendly tutorial, and demonstrate the utility of PEHRT in a variety of tasks using data from diverse healthcare systems.