A convolutional route to abbreviation disambiguation in clinical text

Venkata Joopudi, Bharath Dandala, Murthy Devarakonda

    Research output: Contribution to journalArticlepeer-review

    26 Scopus citations


    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
    StatePublished - Oct 2018

    ASJC Scopus subject areas

    • Computer Science Applications
    • Health Informatics


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