A Text Mining Approach to the Prediction of Disease Status from Clinical Discharge Summaries

Objective: The authors present a system developed for the Challenge in Natural Language Processing for Clinical Data-the i2b2 obesity challenge, whose aim was to automatically identify the status of obesity and 15 related co-morbidities in patients using their clinical discharge summaries. The challenge consisted of two tasks, textual and intuitive. The textual task was to identify explicit references to the diseases, whereas the intuitive task focused on the prediction of the disease status when the evidence was not explicitly asserted. Design: The authors assembled a set of resources to lexically and semantically profile the diseases and their associated symptoms, treatments, etc. These features were explored in a hybrid text mining approach, which combined dictionary look-up, rule-based, and machine-learning methods. Measurements: The methods were applied on a set of 507 previously unseen discharge summaries, and the predictions were evaluated against a manually prepared gold standard. The overall ranking of the participating teams was primarily based on the macro-averaged F-measure. Results: The implemented method achieved the macro-averaged F-measure of 81% for the textual task (which was the highest achieved in the challenge) and 63% for the intuitive task (ranked 7th out of 28 teams-the highest was 66%). The micro-averaged F-measure showed an average accuracy of 97% for textual and 96% for intuitive annotations. Conclusions: The performance achieved was in line with the agreement between human annotators, indicating the potential of text mining for accurate and efficient prediction of disease statuses from clinical discharge summaries. © 2009 J Am Med Inform Assoc.