Customize Deep Learning-based De-Identification Systems Using Local Clinical Notes - A Study of Sample Size

Abstract

ABSTRACTElectronic Health Records (EHRs) are a valuable resource for both clinical and translational research. However, much detailed patient information is embedded in clinical narratives, including a large number of patients’ identifiable information. De-identification of clinical notes is a critical technology to protect the privacy and confidentiality of patients. Previous studies presented many automated de-identification systems to capture and remove protected health information from clinical text. However, most of them were tested only in one institute setting where training and test data were from the same institution. Directly adapting these systems without customization could lead to a dramatic performance drop. Recent studies have shown that fine-tuning is a promising method to customize deep learning-based NLP systems across different institutes. However, it’s still not clear how much local data is required. In this study, we examined the customizing of a deep learning-based de-identification system using different sizes of local notes from UF Health. Our results showed that the fine-tuning could significantly improve the model performance even on a small local dataset. Yet, when the local data exceeded a threshold (e.g., 700 notes in this study), the performance improvement became marginal.