Publications

A Multi-pass Sieve for Clinical Concept Normalization

Published in Traitement Automatique des Langues, 2021

We present a rule-based multipass sieve approach incorporating both exact and approximate matching based on dictionaries, and experiment with back-translation as a means of data augmentation.

Recommended citation: Wang, Yuxia, Brian Hur, Karin Verspoor and Timothy Baldwin (2021) A Multi-pass Sieve for Clinical Concept Normalization, Traitement Automatique des Langues 2020 Volume 61 Numéro 2. https://www.atala.org/sites/default/files/TAL-61-2-2_Wang.pdf

Use of cefovecin in dogs and cats attending first-opinion veterinary practices in Australia

Published in Veterinary Record, 2020

The authors describe the common indications for cefovecin use in dogs and cats, and the frequency of culture and susceptibility testing

Recommended citation: Hardefeldt, Laura Y, Brian Hur, Karin Verspoor, Timothy Baldwin, Kirsten E Bailey, Riata Scarborough, Suzanna Richards, Helen Bilman-Jacobe, Glenn F Browning and James R Gilkerson (2020) Use of cefovecin in dogs and cats attending first-opinion veterinary practices in Australia, Veterinary Record. https://pubmed.ncbi.nlm.nih.gov/32826347/

Domain Adaptation and Instance Selection for Disease Syndrome Classification over Veterinary Clinical Notes

Published in 19th SIGBioMed Workshop on Biomedical Language Processing (BioNLP 2020) @ ACL 2020, 2020

We propose a document classification approach to determine the reason for administration of a given drug, with particular focus on domain adaptation from one drug to another, and instance selection to minimize annotation effort.

Recommended citation: Hur, Brian, Timothy Baldwin, Karin Verspoor, Laura Hardefeldt and James Gilkerson (2020) Domain Adaptation and Instance Selection for Disease Syndrome Classification over Veterinary Clinical Notes, In Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing (BioNLP 2020), pp. 156—166. https://www.aclweb.org/anthology/2020.bionlp-1.17/

Describing the Antimicrobial Usage Patterns of Companion Animal Veterinary Practices; Free Text Analysis of more than 4.4 Million Consultation Records

Published in PLOS ONE, 2020

The aim of this study is to describe how frequently antimicrobials were used in veterinary consultations and identify the most frequently used antimicrobials.

Recommended citation: Hur, Brian A., Laura Y. Hardefeldt, Karin M. Verspoor, Timothy Baldwin, and James R Gilkerson (2020) Describing the Antimicrobial Usage Patterns of Companion Animal Veterinary Practices; Free Text Analysis of more than 4.4 Million Consultation Records, PLoS ONE 15(3): e0230049. https://doi.org/10.1371/journal.pone.0230049

Using natural language processing and VetCompass to understand antimicrobial usage patterns in Australia

Published in Australian veterinary journal, 2019

In this paper we develop and test machine learning and rules-based methods in extracting antimicrobials used in clinical records stored within VetCompass from over 180 clinics accross Australia.

Recommended citation: Brian Hur, Laura Y. Hardefeldt, Karin Verspoor, Timothy Baldwin and James R Gilkerson (2019) Using Natural Language Processing and VetCompass to understand antimicrobial usage patterns in Australia, Australian Veterinary Journal 97(8), pp. 298—300. https://pubmed.ncbi.nlm.nih.gov/31209869/