alexa Eventual situations for timeline extraction from clinical reports.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Health & Medical Informatics

Author(s): Grouin C, Grabar N, Hamon T, Rosset S, Tannier X,

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Abstract OBJECTIVE: To identify the temporal relations between clinical events and temporal expressions in clinical reports, as defined in the i2b2/VA 2012 challenge. DESIGN: To detect clinical events, we used rules and Conditional Random Fields. We built Random Forest models to identify event modality and polarity. To identify temporal expressions we built on the HeidelTime system. To detect temporal relations, we systematically studied their breakdown into distinct situations; we designed an oracle method to determine the most prominent situations and the most suitable associated classifiers, and combined their results. RESULTS: We achieved F-measures of 0.8307 for event identification, based on rules, and 0.8385 for temporal expression identification. In the temporal relation task, we identified nine main situations in three groups, experimentally confirming shared intuitions: within-sentence relations, section-related time, and across-sentence relations. Logistic regression and Naïve Bayes performed best on the first and third groups, and decision trees on the second. We reached a 0.6231 global F-measure, improving by 7.5 points our official submission. CONCLUSIONS: Carefully hand-crafted rules obtained good results for the detection of events and temporal expressions, while a combination of classifiers improved temporal link prediction. The characterization of the oracle recall of situations allowed us to point at directions where further work would be most useful for temporal relation detection: within-sentence relations and linking History of Present Illness events to the admission date. We suggest that the systematic situation breakdown proposed in this paper could also help improve other systems addressing this task.
This article was published in J Am Med Inform Assoc and referenced in Journal of Health & Medical Informatics

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