Development and Validation of a Natural Language Processing Algorithm to Pseudonymize Documents in the Context of a Clinical Data Warehouse

Abstract Objective The objective of this study is to address the critical issue of deidentification of clinical reports to allow access to data for research purposes, while ensuring patient privacy. The study highlights the difficulties faced in sharing tools and resources in this domain and presents the experience of the Greater Paris University Hospitals (AP-HP for Assistance Publique-Hôpitaux de Paris) in implementing a systematic pseudonymization of text documents from its Clinical Data Warehouse. Methods We annotated a corpus of clinical documents according to 12 types of identifying entities and built a hybrid system, merging the results of a deep learning model as well as manual rules. Results and Discussion Our results show an overall performance of 0.99 of F1-score. We discuss implementation choices and present experiments to better understand the effort involved in such a task, including dataset size, document types, language models, or rule addition. We share guidelines and code under a 3-Clause BSD license.