Real-time classifiers from free-text for continuous surveillance of small animal disease



Newman, J
(2018) Real-time classifiers from free-text for continuous surveillance of small animal disease. PhD thesis, University of Liverpool.

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Abstract

A wealth of information of epidemiological importance is held within unstructured narrative clinical records. Text mining provides computational techniques for extracting usable information from the language used to communicate between humans, including the spoken and written word. The aim of this work was to develop text-mining methodologies capable of rendering the large volume of information within veterinary clinical narratives accessible for research and surveillance purposes. The free-text records collated within the dataset of the Small Animal Veterinary Surveillance Network formed the development material and target of this work. The efficacy of pre-existent clinician-assigned coding applied to the dataset was evaluated and the nature of notation and vocabulary used in documenting consultations was explored and described. Consultation records were pre-processed to improve human and software readability, and software was developed to redact incidental identifiers present within the free-text. An automated system able to classify for the presence of clinical signs, utilising only information present within the free-text record, was developed with the aim that it would facilitate timely detection of spatio-temporal trends in clinical signs. Clinician-assigned main reason for visit coding provided a poor summary of the large quantity of information exchanged during a veterinary consultation and the nature of the coding and questionnaire triggering further obfuscated information. Delineation of the previously undocumented veterinary clinical sublanguage identified common themes and their manner of documentation, this was key to the development of programmatic methods. A rule-based classifier using logically-chosen dictionaries, sequential processing and data-masking redacted identifiers while maintaining research usability of records. Highly sensitive and specific free-text classification was achieved by applying classifiers for individual clinical signs within a context-sensitive scaffold, this permitted or prohibited matching dependent on the clinical context in which a clinical sign was documented. The mean sensitivity achieved within an unseen test dataset was 98.17 (74.47, 99.9)% and mean specificity 99.94 (77.1, 100.0)%. When used in combination to identify animals with any of a combination of gastrointestinal clinical signs, the sensitivity achieved was 99.44% (95% CI: 98.57, 99.78)% and specificity 99.74 (95% CI: 99.62, 99.83). This work illustrates the importance, utility and promise of free-text classification of clinical records and provides a framework within which this is possible whilst respecting the confidentiality of client and clinician.

Item Type: Thesis (PhD)
Uncontrolled Keywords: electronic health record, ehr, text-mining, syndromic surveillance, de-identification, context-sensitive
Divisions: Faculty of Health and Life Sciences
Depositing User: Symplectic Admin
Date Deposited: 21 Nov 2018 12:12
Last Modified: 02 Apr 2021 08:12
DOI: 10.17638/03023953
Supervisors:
  • Jones, Philip Hywel
  • Noble, Peter John Mantalya
  • Nenadic, Goran
URI: https://livrepository.liverpool.ac.uk/id/eprint/3023953