A convolutional route to abbreviation disambiguation in clinical text

Venkata Joopudi, Bharath Dandala, Murthy Devarakonda

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Objective: Abbreviations sense disambiguation is a special case of word sense disambiguation. Machine learning methods based on neural networks showed promising results for word sense disambiguation (Festag and Spreckelsen, 2017) [1] and, here we assess their effectiveness for abbreviation sense disambiguation. Methods: Convolutional Neural Network (CNN) models were trained, one for each abbreviation, to disambiguate abbreviation senses. A reverse substitution (of long forms with short forms) method from a previous study was used on clinical narratives from Cleveland Clinic, USA, to auto-generate training data. Accuracy of the CNN and traditional Support Vector Machine (SVM) models were studied using: (a) 5-fold cross validation on the auto-generated training data; (b) a manually created, set-aside gold standard; and (c) 10-fold cross validation on a publicly available dataset from a previous study. Results: CNN improved accuracy by 1–4 percentage points on all the three datasets compared to SVM, and the improvement was the most for the set-aside dataset. The improvement was statistically significant at p < 0.05 on the auto-generated dataset. We found that for some common abbreviations, sense distributions mismatch between the test and auto generated training data, and mitigating the mismatch significantly improved the model accuracy. Conclusion: The neural network models work well in disambiguating abbreviations in clinical narratives, and they are robust across datasets. This avoids feature-engineering for each dataset. Coupled with an enhanced auto-training data generation, neural networks can simplify development of a practical abbreviation disambiguation system.

Original languageEnglish (US)
Pages (from-to)71-78
Number of pages8
JournalJournal of Biomedical Informatics
Volume86
DOIs
StatePublished - Oct 1 2018

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Neural networks
Neural Networks (Computer)
Support vector machines
Learning systems
Datasets
Substitution reactions
Support Vector Machine

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics

Cite this

A convolutional route to abbreviation disambiguation in clinical text. / Joopudi, Venkata; Dandala, Bharath; Devarakonda, Murthy.

In: Journal of Biomedical Informatics, Vol. 86, 01.10.2018, p. 71-78.

Research output: Contribution to journalArticle

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