Dynamic categorization of clinical research eligibility criteria by hierarchical clustering

Objective: To semi-automatically induce semantic categories of eligibility criteria from text and to automatically classify eligibility criteria based on their semantic similarity. Design: The UMLS semantic types and a set of previously developed semantic preference rules were utilized to create an unambiguous semantic feature representation to induce eligibility criteria categories through hierarchical clustering and to train supervised classifiers. Measurements: We induced 27 categories and measured the prevalence of the categories in 27,278 eligibility criteria from 1578 clinical trials and compared the classification performance (i.e., precision, recall, and F1-score) between the UMLS-based feature representation and the "bag of words" feature representation among five common classifiers in Weka, including J48, Bayesian Network, Naive Bayesian, Nearest Neighbor, and instance-based learning classifier. Results: The UMLS semantic feature representation outperforms the "bag of words" feature representation in 89% of the criteria categories. Using the semantically induced categories, machine-learning classifiers required only 2000 instances to stabilize classification performance. The J48 classifier yielded the best F1-score and the Bayesian Network classifier achieved the best learning efficiency. Conclusion: The UMLS is an effective knowledge source and can enable an efficient feature representation for semi-automated semantic category induction and automatic categorization for clinical research eligibility criteria and possibly other clinical text. (C) 2011 Elsevier Inc. All rights reserved.