# Fine-tuning foundational models to code diagnoses from veterinary health records

arXiv: https://arxiv.org/abs/2410.15186 · HTML: https://mlsanity.com/paper/2410.15186/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 66 references that are in the map.
- First posted on arXiv 19 Oct 2024.

## Builds on (most cited first, 18 of 18)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [Longformer: The Long-Document Transformer](https://mlsanity.com/paper/2004.05150/) (2020)
- [Axiomatic Attribution for Deep Networks](https://mlsanity.com/paper/1703.01365/) (2017)
- [DeBERTaV3: Improving DeBERTa using ELECTRA-Style Pre-Training with Gradient-Disentangled Embedding Sharing](https://mlsanity.com/paper/2111.09543/) (2021)
- [Aligning Books and Movies: Towards Story-like Visual Explanations by Watching Movies and Reading Books](https://mlsanity.com/paper/1506.06724/) (2015)
- [ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmission](https://mlsanity.com/paper/1904.05342/) (2019)
- [MedAlpaca -- An Open-Source Collection of Medical Conversational AI Models and Training Data](https://mlsanity.com/paper/2304.08247/) (2023)
- [MEDITRON-70B: Scaling Medical Pretraining for Large Language Models](https://mlsanity.com/paper/2311.16079/) (2023)
- [GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Records](https://mlsanity.com/paper/2203.03540/) (2022)
- [Explainable Prediction of Medical Codes from Clinical Text](https://mlsanity.com/paper/1802.05695/) (2018)
- [A Simple Method for Commonsense Reasoning](https://mlsanity.com/paper/1806.02847/) (2018)
- [A Pretrainer's Guide to Training Data: Measuring the Effects of Data Age, Domain Coverage, Quality, & Toxicity](https://mlsanity.com/paper/2305.13169/) (2023)
- [Deep Representation Learning of Patient Data from Electronic Health Records (EHR): A Systematic Review](https://mlsanity.com/paper/2010.02809/) (2020)
- [Automated Clinical Coding: What, Why, and Where We Are?](https://mlsanity.com/paper/2203.11092/) (2022)
- [Parameter-Efficient Fine-Tuning of Large Language Models using Semantic Knowledge Tuning](https://mlsanity.com/paper/2410.08598/) (2024)

## Built on by (most cited first, 3 of 3)

- [Synthetic Data for Veterinary EHR De-identification: Benefits, Limits, and Safety Trade-offs Under Fixed Compute](https://mlsanity.com/paper/2601.09756/) (2026)
- [MorphologyFM: A Foundation Model for Morphology-Aware Representation Learning from ECG and Pulse Oximetry Waveforms](https://mlsanity.com/paper/2607.09749/) (2026)
- [VetScore: Risk-Weighted Fact Verification for Veterinary Long-Form QA with Citations](https://mlsanity.com/paper/2608.03675/) (2026)

## Abstract (arXiv)

Veterinary medical records represent a large data resource for application to veterinary and One Health clinical research efforts. Use of the data is limited by interoperability challenges including inconsistent data formats and data siloing. Clinical coding using standardized medical terminologies enhances the quality of medical records and facilitates their interoperability with veterinary and human health records from other sites. Previous studies, such as DeepTag and VetTag, evaluated the application of Natural Language Processing (NLP) to automate veterinary diagnosis coding, employing long short-term memory (LSTM) and transformer models to infer a subset of Systemized Nomenclature of Medicine - Clinical Terms (SNOMED-CT) diagnosis codes from free-text clinical notes. This study expands on these efforts by incorporating all 7,739 distinct SNOMED-CT diagnosis codes recognized by the Colorado State University (CSU) Veterinary Teaching Hospital (VTH) and by leveraging the increasing availability of pre-trained language models (LMs). 13 freely-available pre-trained LMs were fine-tuned on the free-text notes from 246,473 manually-coded veterinary patient visits included in the CSU VTH's electronic health records (EHRs), which resulted in superior performance relative to previous efforts. The most accurate results were obtained when expansive labeled data were used to fine-tune relatively large clinical LMs, but the study also showed that comparable results can be obtained using more limited resources and non-clinical LMs. The results of this study contribute to the improvement of the quality of veterinary EHRs by investigating accessible methods for automated coding and support both animal and human health research by paving the way for more integrated and comprehensive health databases that span species and institutions.