TY - JOUR

T1 - PetBERT

T2 - automated ICD-11 syndromic disease coding for outbreak detection in first opinion veterinary electronic health records

AU - Farrell, Sean

AU - Appleton, Charlotte

AU - Noble, Peter-John Mäntylä

AU - Al Moubayed, Noura

PY - 2023/10/21

Y1 - 2023/10/21

N2 - Effective public health surveillance requires consistent monitoring of disease signals such that researchers and decision-makers can react dynamically to changes in disease occurrence. However, whilst surveillance initiatives exist in production animal veterinary medicine, comparable frameworks for companion animals are lacking. First-opinion veterinary electronic health records (EHRs) have the potential to reveal disease signals and often represent the initial reporting of clinical syndromes in animals presenting for medical attention, highlighting their possible significance in early disease detection. Yet despite their availability, there are limitations surrounding their free text-based nature, inhibiting the ability for national-level mortality and morbidity statistics to occur. This paper presents PetBERT, a large language model trained on over 500 million words from 5.1 million EHRs across the UK. PetBERT-ICD is the additional training of PetBERT as a multi-label classifier for the automated coding of veterinary clinical EHRs with the International Classification of Disease 11 framework, achieving F1 scores exceeding 83% across 20 disease codings with minimal annotations. PetBERT-ICD effectively identifies disease outbreaks, outperforming current clinician-assigned point-of-care labelling strategies up to 3 weeks earlier. The potential for PetBERT-ICD to enhance disease surveillance in veterinary medicine represents a promising avenue for advancing animal health and improving public health outcomes.

AB - Effective public health surveillance requires consistent monitoring of disease signals such that researchers and decision-makers can react dynamically to changes in disease occurrence. However, whilst surveillance initiatives exist in production animal veterinary medicine, comparable frameworks for companion animals are lacking. First-opinion veterinary electronic health records (EHRs) have the potential to reveal disease signals and often represent the initial reporting of clinical syndromes in animals presenting for medical attention, highlighting their possible significance in early disease detection. Yet despite their availability, there are limitations surrounding their free text-based nature, inhibiting the ability for national-level mortality and morbidity statistics to occur. This paper presents PetBERT, a large language model trained on over 500 million words from 5.1 million EHRs across the UK. PetBERT-ICD is the additional training of PetBERT as a multi-label classifier for the automated coding of veterinary clinical EHRs with the International Classification of Disease 11 framework, achieving F1 scores exceeding 83% across 20 disease codings with minimal annotations. PetBERT-ICD effectively identifies disease outbreaks, outperforming current clinician-assigned point-of-care labelling strategies up to 3 weeks earlier. The potential for PetBERT-ICD to enhance disease surveillance in veterinary medicine represents a promising avenue for advancing animal health and improving public health outcomes.

U2 - 10.1038/s41598-023-45155-7

DO - 10.1038/s41598-023-45155-7

M3 - Journal article

VL - 13

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

IS - 1

M1 - 18015

ER -