Integrating linguistic knowledge into a conditional random fieldframework to identify biomedical named entities

Tzong Han Tsai, Wen Chi Chou, Shih Hung Wu, Ting Yi Sung, Jieh Hsiang, Wen Lian Hsu

Research output: Contribution to journalArticlepeer-review

41 Scopus citations


As new high-throughput technologies have created an explosion of biomedical literature, there arises a pressing need for automatic information extraction from the literature bank. To this end, biomedical named entity recognition (NER) from natural language text is indispensable. Current NER approaches include: dictionary based, rule based, or machine learning based. Since, there is no consolidated nomenclature for most biomedical NEs, any NER system relying on limited dictionaries or rules does not seem to perform satisfactorily. In this paper, we consider a machine learning model, CRF, for the construction of our NER framework. CRF is a well-known model for solving other sequence tagging problems. In our framework, we do our best to utilize available resources including dictionaries, web corpora, and lexical analyzers, and represent them as linguistic features in the CRF model. In the experiment on the JNLPBA 2004 data, with minimal post-processing, our system achieves an F-score of 70.2%, which is better than most state-of-the-art systems. On the GENIA 3.02 corpus, our system achieves an F-score of 78.4% for protein names, which is 2.8% higher than the next-best system. In addition, we also examine the usefulness of each feature in our CRF model. Our experience could be valuable to other researchers working on machine learning based NER.

Original languageEnglish
Pages (from-to)117-128
Number of pages12
JournalExpert Systems with Applications
Issue number1
StatePublished - Jan 2006


  • Biomedical named entity recognition
  • Conditional random fields
  • Linguistic features
  • Literature mining


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