A Multi-Layered GRU Model for COVID-19 Patient Representation and Phenotyping from Large-Scale EHR Data

The unprecedented scale of the COVID-19 pandemic created an alarming shortage of healthcare resources. To enable a more efficient resource allocation and targeted treatment, in this manuscript, we conducted a data-driven study of COVID-19 patients to predict patient outcomes and identify patient phenotypes. Specifically, we developed a multi-layered gated recurrent units-based model, referred to as mGRU-CP, to learn patient embeddings and estimate patient survival probabilities by leveraging their electronic health record (EHR) data in the COVID-19 Research Data Commons. We empirically compared mGRU-CP against four state-of-the-art baseline methods on three sets of patient features. The experimental results demonstrate that mGRU-CP could achieve competitive or superior performance over the baseline methods in all the settings. Our analysis also shows that the learned patient embeddings in mGRU-CP could enable meaningful patient phenotyping to better understand patient mortalities. Our study is significant in understanding patients in the past COVID-19 pandemic, and provides computational tools to predict patient outcomes and inform associated healthcare resource allocation for the future pandemics proactively.