Cohen and Hersh Briefings in Bioinformatics 2005

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Citation

Aaron M. Cohen and William R. Hersh. 2005. A Survey of Current Work in Biomedical Text Mining. Briefings in Bioinformatics. Vol 6. No 1. 57-71.

Online version

oxfordjournals

Summary

The paper presents a MEDical Information Extraction (MedIE) system, which extracts patient information from free-text clinical records.

They divided their extraction job into three tasks below.

  • extraction of medical terms
  • relation extraction
    • extraction of associated medical concepts
    • e.g. Blood pressure & 144/90 in the sentence, "Blood pressure is 144/90"
  • text classification
    • e.g. a patient can be classified as a former smoker, a current smoker, or a non-smoker

Their approaches are:

  • An ontology-based approach for extracting medical terms of interest
    • they used Unified Medical Language System (UMLS)
    • About terms that are not defined in UMLS, they predicted categories of some terms using sentence structures.
  • A graph-based approach which uses the parsing result of link-grammar parser for relation-extraction
    • They included the processing of negation.
    • When the parser fails, they used a pattern-based approach.
    • Because the parser did not process multi-word terms, they replaced the terms with placeholders.
  • an NLP-based feature extraction method coupled with an ID3-based decision tree for text classification


This approach was fairly successful mostly showing over 80% of precision and recall. However, the system was tested on the data written by only a clinician, which means that the style of free-text records was consistent. Nevertheless, the research is worth in that they applied various IE techniques to the free-text clinical records, explain about the problems they encountered.

Related papers

The widely cited Pang et al EMNLP 2002 paper was influenced by this paper - but considers supervised learning techniques. The choice of movie reviews as the domain was suggested by the (relatively) poor performance of Turney's method on movies.

An interesting follow-up paper is Turney and Littman, TOIS 2003 which focuses on evaluation of the technique of using PMI for predicting the semantic orientation of words.