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. 2013 Nov 15;29(22):2909-17.
doi: 10.1093/bioinformatics/btt474. Epub 2013 Aug 21.

DNorm: disease name normalization with pairwise learning to rank

Robert Leaman  1 , Rezarta Islamaj Dogan, Zhiyong Lu
Affiliations

DNorm: disease name normalization with pairwise learning to rank

Robert Leaman et al. Bioinformatics. .

Abstract

Motivation: 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.

Availability: 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 .

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Figures

Fig. 1.
Fig. 1.
The DNorm disease normalization pipeline, with examples, as described in Section 2.1
Fig. 2.
Fig. 2.
Comparison between BANNER + Lucene, BANNER + cosine similarity and DNorm (BANNER + pLTR) of the micro-averaged recall when considering a concept to be found if it appears in the top n ranked results
Fig. 3.
Fig. 3.
Summary of error analysis. Errors in the NER and ranking components contributed >95% of the total errors
See this image and copyright information in PMC

References

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