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1.  Combining an Expert-Based Medical Entity Recognizer to a Machine-Learning System: Methods and a Case Study 
Biomedical Informatics Insights  2013;6(Suppl 1):51-62.
Medical entity recognition is currently generally performed by data-driven methods based on supervised machine learning. Expert-based systems, where linguistic and domain expertise are directly provided to the system are often combined with data-driven systems. We present here a case study where an existing expert-based medical entity recognition system, Ogmios, is combined with a data-driven system, Caramba, based on a linear-chain Conditional Random Field (CRF) classifier. Our case study specifically highlights the risk of overfitting incurred by an expert-based system. We observe that it prevents the combination of the 2 systems from obtaining improvements in precision, recall, or F-measure, and analyze the underlying mechanisms through a post-hoc feature-level analysis. Wrapping the expert-based system alone as attributes input to a CRF classifier does boost its F-measure from 0.603 to 0.710, bringing it on par with the data-driven system. The generalization of this method remains to be further investigated.
PMCID: PMC3776026  PMID: 24052691
natural language processing; information extraction; medical records; machine learning; hybrid methods; overfitting

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