Text mining for the Vaccine Adverse Event Reporting System: medical text classification using informative feature selection

Taxiarchis Botsis, Michael D Nguyen, Emily Jane Woo, Marianthi Markatou, Robert Ball
2011 JAMIA Journal of the American Medical Informatics Association  
Objective The US Vaccine Adverse Event Reporting System (VAERS) collects spontaneous reports of adverse events following vaccination. Medical officers review the reports and often apply standardized case definitions, such as those developed by the Brighton Collaboration. Our objective was to demonstrate a multi-level text mining approach for automated text classification of VAERS reports that could potentially reduce human workload. Design We selected 6034 VAERS reports for H1N1 vaccine that
more » ... e classified by medical officers as potentially positive (N pos ¼237) or negative for anaphylaxis. We created a categorized corpus of text files that included the class label and the symptom text field of each report. A validation set of 1100 labeled text files was also used. Text mining techniques were applied to extract three feature sets for important keywords, low-and high-level patterns. A rule-based classifier processed the high-level feature representation, while several machine learning classifiers were trained for the remaining two feature representations. Measurements Classifiers' performance was evaluated by macro-averaging recall, precision, and F-measure, and Friedman's test; misclassification error rate analysis was also performed. Results Rule-based classifier, boosted trees, and weighted support vector machines performed well in terms of macro-recall, however at the expense of a higher mean misclassification error rate. The rule-based classifier performed very well in terms of average sensitivity and specificity (79.05% and 94.80%, respectively). Conclusion Our validated results showed the possibility of developing effective medical text classifiers for VAERS reports by combining text mining with informative feature selection; this strategy has the potential to reduce reviewer workload considerably. < Additional materials are published online only. To view these files please visit the journal online (www.jamia.org).
doi:10.1136/amiajnl-2010-000022 pmid:21709163 pmcid:PMC3168300 fatcat:dvomwl5ahza73eok2ogsmou4u4