A System For Identifying Named Entities in Biomedical Text: How Results From Two Evaluations Reﬂect on Both the System and the Evaluations
David Bourget (Western Ontario)
David Chalmers (ANU, NYU)
Rafael De Clercq
Ezio Di Nucci
Jack Alan Reynolds
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We present a maximum-entropy based system for identifying Named Entities (NEs) in biomedical abstracts and present its performance in the only two biomedical Named Entity Recognition (NER) comparative evaluations that have been held to date, namely BioCreative and Coling BioNLP. Our system obtained an exact match f-score of 83.2% in the BioCreative evaluation and 70.1% in the BioNLP evaluation. We discuss our system in detail including its rich use of local features, attention to correct boundary identiﬁcation, innovative use of external knowledge resources including parsing and web searches, and rapid adaptation to new NE sets. We also discuss in depth problems with data annotation in the evaluations which caused the ﬁnal performance to be lower than the optimal.
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