Rapidly Retargetable Approaches to De-identification in Medical Records

Abstract

Objective: This paper describes a successful approach to de-identification that was developed to participate in a recent AMIA-sponsored challenge evaluation. Method: Our approach focused on rapid adaptation of existing toolkits for named entity recognition using two existing toolkits, Carafe and LingPipe. Results: The “out of the box” Carafe system achieved a very good score (phrase F-measure of 0.9664) with only four hours of work to adapt it to the de-identification task. With further tuning, we were able to reduce the token-level error term by over 36% through task-specific feature engineering and the introduction of a lexicon, achieving a phrase F-measure of 0.9736. Conclusions: We were able to achieve good performance on the de-identification task by the rapid retargeting of existing toolkits. For the Carafe system, we developed a method for tuning the balance of recall vs. precision, as well as a confidence score that correlated well with the measured F-score.