Exploring the Privacy-Preserving Properties of Word Embeddings: Algorithmic Validation Study (Preprint)

BACKGROUND Word embeddings are dense numeric vectors used to represent language in neural networks. Until recently, there had been no publicly released embeddings trained on clinical data. Our work is the first to study the privacy implications of releasing these models. OBJECTIVE This paper aims to demonstrate that traditional word embeddings created on clinical corpora that have been deidentified by removing personal health information (PHI) can nonetheless be exploited to reveal sensitive patient information. METHODS We used embeddings created from 400,000 doctor-written consultation notes and experimented with 3 common word embedding methods to explore the privacy-preserving properties of each. RESULTS We found that if publicly released embeddings are trained from a corpus anonymized by PHI removal, it is possible to reconstruct up to 68.5% (n=411/600) of the full names that remain in the deidentified corpus and associated sensitive information to specific patients in the corpus from which the embeddings were created. We also found that the distance between the word vector representation of a patient’s name and a diagnostic billing code is informative and differs significantly from the distance between the name and a code not billed for that patient. CONCLUSIONS Special care must be taken when sharing word embeddings created from clinical texts, as current approaches may compromise patient privacy. If PHI removal is used for anonymization before traditional word embeddings are trained, it is possible to attribute sensitive information to patients who have not been fully deidentified by the (necessarily imperfect) removal algorithms. A promising alternative (ie, anonymization by PHI replacement) may avoid these flaws. Our results are timely and critical, as an increasing number of researchers are pushing for publicly available health data.