Exploratory electronic health record analysis with ehrapy

With progressive digitalization of healthcare systems worldwide, large-scale collection of electronic health records (EHRs) has become commonplace. However, an extensible framework for comprehensive exploratory analysis that accounts for data heterogeneity is missing. Here, we introduce ehrapy, a modular open-source Python framework designed for exploratory end-to-end analysis of heterogeneous epidemiology and electronic health record data. Ehrapy incorporates a series of analytical steps, from data extraction and quality control to the generation of low-dimensional representations. Complemented by rich statistical modules, ehrapy facilitates associating patients with disease states, differential comparison between patient clusters, survival analysis, trajectory inference, causal inference, and more. Leveraging ontologies, ehrapy further enables data sharing and training EHR deep learning models paving the way for foundational models in biomedical research. We demonstrated ehrapy’s features in five distinct examples: We first applied ehrapy to stratify patients affected by unspecified pneumonia into finer-grained phenotypes. Furthermore, we revealed biomarkers for significant differences in survival among these groups. Additionally, we quantify medication-class effects of pneumonia medications on length of stay. We further leveraged ehrapy to analyze cardiovascular risks across different data modalities. Finally, we reconstructed disease state trajectories in SARS-CoV-2 patients based on imaging data. Ehrapy thus provides a framework that we envision will standardize analysis pipelines on EHR data and serve as a cornerstone for the community.