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J Am Med Inform Assoc 16:580-584 doi:10.1197/jamia.M3087
  • Focus on i2b2 Obesity NLP Challenge

Semantic Classification of Diseases in Discharge Summaries Using a Context-aware Rule-based Classifier

Table 3

Performance of Assertion Classification on the BioNLP2009 Corpus

Semantic Class System Precision Recall F1-Measure
Negation NegEx 0.4070 0.5152 0.4548
Negation Our original system 0.5015 0.4626 0.4813
Negation Our adapted system 0.7662 0.7460 0.7561
Speculation NegEx 0.0000 0.0000 0.0000
Speculation Our original system 0.1340 0.0236 0.0402
Speculation Our adapted system 0.6049 0.5472 0.5746

  • We compared NegEx (v1.01 of Imre Solti's implementation, code.google.com/p/negex/), our system developed for the i2b2 Obesity Challenge, and the adaptation of our system towards the BioNLP2009 Shared Task (for comparison only).

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