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Comparison of rule-based and neural network models for negation detection in radiology reports

Published online by Cambridge University Press:  18 November 2020

D. Sykes ,
A. Grivas ,
C. Grover ,
R. Tobin ,
C. Sudlow ,
W. Whiteley ,
A. Mcintosh ,
H. Whalley  and
B. Alex
D. Sykes*
Affiliation:
Division of Psychiatry, Centre for Clinical Brain Sciences
A. Grivas
Affiliation:
Institute for Language, Cognition and Computation, School of Informatics
C. Grover
Affiliation:
Institute for Language, Cognition and Computation, School of Informatics
R. Tobin
Affiliation:
Institute for Language, Cognition and Computation, School of Informatics
C. Sudlow
Affiliation:
Usher Institute of Population Health Sciences and Informatics
W. Whiteley
Affiliation:
Centre for Clinical Brain Sciences, Edinburgh Medical School
A. Mcintosh
Affiliation:
Division of Psychiatry, Centre for Clinical Brain Sciences
H. Whalley
Affiliation:
Division of Psychiatry, Centre for Clinical Brain Sciences
B. Alex
Affiliation:
Institute for Language, Cognition and Computation, School of Informatics Edinburgh Futures Institute, School of Literatures, Languages and Cultures, University of Edinburgh, Edinburgh, UK
*
*Corresponding author. E-mail: dominic.sykes@ed.ac.uk
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Abstract

Using natural language processing, it is possible to extract structured information from raw text in the electronic health record (EHR) at reasonably high accuracy. However, the accurate distinction between negated and non-negated mentions of clinical terms remains a challenge. EHR text includes cases where diseases are stated not to be present or only hypothesised, meaning a disease can be mentioned in a report when it is not being reported as present. This makes tasks such as document classification and summarisation more difficult. We have developed the rule-based EdIE-R-Neg, part of an existing text mining pipeline called EdIE-R (Edinburgh Information Extraction for Radiology reports), developed to process brain imaging reports, (https://www.ltg.ed.ac.uk/software/edie-r/) and two machine learning approaches; one using a bidirectional long short-term memory network and another using a feedforward neural network. These were developed on data from the Edinburgh Stroke Study (ESS) and tested on data from routine reports from NHS Tayside (Tayside). Both datasets consist of written reports from medical scans. These models are compared with two existing rule-based models: pyConText (Harkema et al. 2009. Journal of Biomedical Informatics42(5), 839–851), a python implementation of a generalisation of NegEx, and NegBio (Peng et al. 2017. NegBio: A high-performance tool for negation and uncertainty detection in radiology reports. arXiv e-prints, p. arXiv:1712.05898), which identifies negation scopes through patterns applied to a syntactic representation of the sentence. On both the test set of the dataset from which our models were developed, as well as the largely similar Tayside test set, the neural network models and our custom-built rule-based system outperformed the existing methods. EdIE-R-Neg scored highest on F1 score, particularly on the test set of the Tayside dataset, from which no development data were used in these experiments, showing the power of custom-built rule-based systems for negation detection on datasets of this size. The performance gap of the machine learning models to EdIE-R-Neg on the Tayside test set was reduced through adding development Tayside data into the ESS training set, demonstrating the adaptability of the neural network models.

Keywords

Machine learningNatural language processing for biomedical textsCorpus annotationInformation extractionText data mining
Type
Article
Information
Natural Language Engineering , Volume 27 , Issue 2 , March 2021 , pp. 203 - 224
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Copyright
© The Author(s), 2020. Published by Cambridge University Press

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