A flexible framework for deriving assertions from electronic medical records

OBJECTIVE: This paper describes natural-language-processing techniques for two tasks: identification of medical concepts in clinical text, and classification of assertions, which indicate the existence, absence, or uncertainty of a medical problem. Because so many resources are available for processing clinical texts, there is interest in developing a framework in which features derived from these resources can be optimally selected for the two tasks of interest. MATERIALS AND METHODS: The authors used two machine-learning (ML) classifiers: support vector machines (SVMs) and conditional random fields (CRFs). Because SVMs and CRFs can operate on a large set of features extracted from both clinical texts and external resources, the authors address the following research question: Which features need to be selected for obtaining optimal results? To this end, the authors devise feature-selection techniques which greatly reduce the amount of manual experimentation and improve performance. RESULTS: The authors evaluated their approaches on the 2010 i2b2/VA challenge data. Concept extraction achieves 79.59 micro F-measure. Assertion classification achieves 93.94 micro F-measure. DISCUSSION: Approaching medical concept extraction and assertion classification through ML-based techniques has the advantage of easily adapting to new data sets and new medical informatics tasks. However, ML-based techniques perform best when optimal features are selected. By devising promising feature-selection techniques, the authors obtain results that outperform the current state of the art. CONCLUSION: This paper presents two ML-based approaches for processing language in the clinical texts evaluated in the 2010 i2b2/VA challenge. By using novel feature-selection methods, the techniques presented in this paper are unique among the i2b2 participants.