title: DNorm: disease name normalization with pairwise learning to rank.
abstract: BACKGROUND
  Despite the central role of diseases in biomedical research, there have been much fewer attempts to automatically determine which diseases are mentioned in a text-the task of disease name normalization (DNorm)-compared with other normalization tasks in biomedical text mining research.
  
  
  METHODS
  In this article we introduce the first machine learning approach for DNorm, using the NCBI disease corpus and the MEDIC vocabulary, which combines MeSH® and OMIM. Our method is a high-performing and mathematically principled framework for learning similarities between mentions and concept names directly from training data. The technique is based on pairwise learning to rank, which has not previously been applied to the normalization task but has proven successful in large optimization problems for information retrieval.
  
  
  RESULTS
  We compare our method with several techniques based on lexical normalization and matching, MetaMap and Lucene. Our algorithm achieves 0.782 micro-averaged F-measure and 0.809 macro-averaged F-measure, an increase over the highest performing baseline method of 0.121 and 0.098, respectively.
  
  
  BACKGROUND
  The source code for DNorm is available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/DNorm, along with a web-based demonstration and links to the NCBI disease corpus. Results on PubMed abstracts are available in PubTator: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator .
authors: National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, MD 20894, USA and Department of Biomedical Informatics, Arizona State University, 13212 East Shea Blvd, Scottsdale, AZ 85259, USA.
authors: Robert
authors: R
authors: Leaman
authors: Rezarta
authors: R
authors: Islamaj Dogan
authors: Zhiyong
authors: Z
authors: Lu
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D057225:Data Mining; D004194:Disease; D006801:Humans; D020407:Internet; D039781:PubMed; D009626:Terminology as Topic; D018875:Vocabulary, Controlled
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