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J Am Med Inform Assoc. 2011 Sep-Oct;18(5):557-62. doi: 10.1136/amiajnl-2011-000150. Epub 2011 May 12.

Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010.

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Institute for Information Technology, National Research Council, Ottawa, Ontario, Canada.



As clinical text mining continues to mature, its potential as an enabling technology for innovations in patient care and clinical research is becoming a reality. A critical part of that process is rigid benchmark testing of natural language processing methods on realistic clinical narrative. In this paper, the authors describe the design and performance of three state-of-the-art text-mining applications from the National Research Council of Canada on evaluations within the 2010 i2b2 challenge.


The three systems perform three key steps in clinical information extraction: (1) extraction of medical problems, tests, and treatments, from discharge summaries and progress notes; (2) classification of assertions made on the medical problems; (3) classification of relations between medical concepts. Machine learning systems performed these tasks using large-dimensional bags of features, as derived from both the text itself and from external sources: UMLS, cTAKES, and Medline.


Performance was measured per subtask, using micro-averaged F-scores, as calculated by comparing system annotations with ground-truth annotations on a test set.


The systems ranked high among all submitted systems in the competition, with the following F-scores: concept extraction 0.8523 (ranked first); assertion detection 0.9362 (ranked first); relationship detection 0.7313 (ranked second).


For all tasks, we found that the introduction of a wide range of features was crucial to success. Importantly, our choice of machine learning algorithms allowed us to be versatile in our feature design, and to introduce a large number of features without overfitting and without encountering computing-resource bottlenecks.

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