Combining knowledge- and data-driven methods for de-identification of clinical narratives

Azad Dehghan, Aleksandar Kovacevic, George Karystianis, John A. Keane, Goran Nenadic*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

42 Citations (Scopus)


A recent promise to access unstructured clinical data from electronic health records on large-scale has revitalized the interest in automated de-identification of clinical notes, which includes the identification of mentions of Protected Health Information (PHI). We describe the methods developed and evaluated as part of the i2b2/UTHealth 2014 challenge to identify PHI defined by 25 entity types in longitudinal clinical narratives. Our approach combines knowledge-driven (dictionaries and rules) and data-driven (machine learning) methods with a large range of features to address de-identification of specific named entities. In addition, we have devised a two-pass recognition approach that creates a patient-specific run-time dictionary from the PHI entities identified in the first step with high confidence, which is then used in the second pass to identify mentions that lack specific clues. The proposed method achieved the overall micro F1-measures of 91% on strict and 95% on token-level evaluation on the test dataset (514 narratives). Whilst most PHI entities can be reliably identified, particularly challenging were mentions of Organizations and Professions. Still, the overall results suggest that automated text mining methods can be used to reliably process clinical notes to identify personal information and thus providing a crucial step in large-scale de-identification of unstructured data for further clinical and epidemiological studies.

Original languageEnglish
Pages (from-to)S53-S59
Number of pages7
JournalJournal of Biomedical Informatics
Volume58 Suppl
Publication statusPublished - 1 Dec 2015
Externally publishedYes


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