Abstract: De-identification is the task of detecting protected health information (PHI) in medical text. It is a critical step in sanitizing electronic health records (EHR) to be shared for research. Automatic de-identification classifiers can significantly speed up the sanitization process. However, obtaining a large and diverse dataset to train such a classifier that works well across many types of medical text poses a challenge as privacy laws prohibit the sharing of raw medical records. We introduce a method to create privacy-preserving shareable representations of medical text (i.e. they contain no PHI) that does not require expensive manual pseudonymization. These representations can be shared between organizations to create unified datasets for training de-identification models. Our representation allows training a simple LSTM-CRF de-identification model to an F1 score of 97.4%, which is comparable to a strong baseline that exposes private information in its representation. A robust, widely available de-identification classifier based on our representation could potentially enable studies for which de-identification would otherwise be too costly.
Authors: Max Friedrich, Arne Köhn, Gregor Wiedemann, Chris Biemann (Universitat Hamburg, Saarland University)