ExBEHRT: Extended Transformer for Electronic Health Records

Maurice Rupp, Oriane Peter, Thirupathi Pattipaka

Keywords: BERT, EHR, RWE, RWD, Transformers, Patient subtyping, explainability, interpretability, risk assessment, Deep learning, personalized medecine, NLP, multi-modal data, temporal data

TL;DR: Modification of BEHRT with new features, better performance and deeper explainability for more robust event predictions and patient subtyping.

Abstract: In this study, we introduce ExBEHRT, an extended version of BEHRT (BERT applied to electronic health record data) and applied various algorithms to interpret its results. While BEHRT only considers diagnoses and patient age, we extend the feature space to several multi-modal records, namely demographics, clinical characteristics, vital signs, smoking status, diagnoses, procedures, medications and lab tests by applying a novel method to unify the frequencies and temporal dimensions of the different features. We show that additional features significantly improve model performance for various down-stream tasks in different diseases. To ensure robustness, we interpret the model predictions using an adaption of expected gradients, which has not been applied to transformers with EHR data so far and provides more granular interpretations than previous approaches such as feature and token importances. Furthermore, by clustering the models' representations of oncology patients, we show that the model has implicit understanding of the disease and is able to classify patients with same cancer type into different risk groups. Given the additional features and interpretability, ExBEHRT can help making informed decisions about disease progressions, diagnoses and risk factors of various diseases.