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J Am Med Inform Assoc 16:247-255 doi:10.1197/jamia.M2844
  • Original Investigation

BioTagger-GM: A Gene/Protein Name Recognition System

Table 4

Recognition Performance over the Test Corpus of the Modified JNLPBA Corpus, N = 6,241

System Notes Precision Recall F-Measure
ABNER Without post-processing 0.6491 0.7505 0.6961
LingPipe 36-gram without post-processing 0.6079 0.7166 0.6577
MEMM 2nd-order without post-processing 0.6668 0.7375 0.7004
CRF Configured for BioCreAtIvE 0.7083 0.7702 0.7379
BioTagger-GM Combination of four systems 0.7058 0.8247 0.7607

  • GM = gene mention; CRF = conditional random field.

  • The JNLPBA corpus is different from the BioCreAtIvE II GM corpus in several ways. The corpus and modules were adjusted for these differences, but the taggers were not tuned to the corpus.

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