TY - JOUR
T1 - A convolutional route to abbreviation disambiguation in clinical text
AU - Joopudi, Venkata
AU - Dandala, Bharath
AU - Devarakonda, Murthy
N1 - Publisher Copyright:
© 2018 Elsevier Inc.
PY - 2018/10
Y1 - 2018/10
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85052861729&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85052861729&partnerID=8YFLogxK
U2 - 10.1016/j.jbi.2018.07.025
DO - 10.1016/j.jbi.2018.07.025
M3 - Article
C2 - 30118854
AN - SCOPUS:85052861729
SN - 1532-0464
VL - 86
SP - 71
EP - 78
JO - Journal of Biomedical Informatics
JF - Journal of Biomedical Informatics
ER -