De-identification of clinical data: A systematic review of free text, image and tabular data approaches

The digitisation of healthcare has generated vast amounts of data in various formats, including free-text notes, tabular records and medical images. This data is critical for research and innovation, but often contains sensitive information that must be de-identified to ensure patient privacy and regulatory compliance. Natural Language Processing (NLP) enables automated de-identification of sensitive information to safely share medical datasets.

This study aims to systematically review the literature on NLP-based de-identification techniques applied to free-text medical reports, tabular data, and burned-in text within medical images over the past decade. It seeks to identify state-of-the-art methods, analyse how de-identification tasks are assessed, and find existing gaps for future research.

We systematically searched five important databases (PubMed, Web of Science, DBLP, ACM and IEEE) for articles published from January 2015 to December 2024 (10 years) about de-identification of medical data in free text, tabular data and burned-in pixels in images. We filtered the articles based on their titles and abstracts against inclusion and exclusion criteria, followed by a quality filter.

From a set of 734 papers, 83 articles were deemed relevant. Most studies de-identify free text, with a few working with tabular data and a much scarcer number dealing with text embedded in the pixels of the images.

De-identification techniques have evolved, with increased use of Language Models and a decline in recurrence-based neural networks. Off-the-shelf tools often require customisation for optimal performance. Most studies de-identify English content, supported by the prevalence of English datasets. Key challenges include the phenomenon of code-mixing (i.e., more than one language used in the same sentence) and the scarcity of available datasets for reproducibility.