Hi! đź‘‹
My name is Sean
I'm a PhD student in Natural Language Processing (NLP) at Durham University specialising in AI for public health research.
I'm a PhD student in Natural Language Processing (NLP) at Durham University specialising in AI for public health research.
Expert in transformer models, Retrieval Augmented Generation (RAG) systems, topic modelling, explainability, and multi-modal architectures using PyTorch and Huggingface. Specialised in low-resource training and domain adaptation.
Proficient in Python, R, SQL. Experienced in scalable pipeline design for low-resource environments, analysing datasets of 16M+ records, Git-based version control, and advanced statistical modeling.
Adept at creating clear, informative, and publication-quality visualisations. Skilled in website creation for serving models and presenting visualisations interactively.
Experienced in teaching NLP to master's-level students, adapting methods for varied skill levels. Mentoring a master’s student on an epidemiology-based project. Awarded with Associate Fellowship in Higher Education.
Experienced in delivering technical presentations to limited prior knowledge audiences. Capable of tailoring complex concepts to both expert and lay audiences, ensuring clarity and engagement. Won several best talk awards.
Published in peer-reviewed journals, skilled at structuring clear and concise papers, emphasising reproducibility and scientific rigor. Experience in writing ethics proposals.
Funded by the Biotechnology and Biological Sciences Research Council (BBSRC) to explore Natural Language Processing and deep learning methods for analysing over 16 million first-opinion veterinary electronic health records (EHRs) across the UK. The research addresses critical public health challenges by applying computational innovation to real-world data.
Thesis: Natural Language Processing for Early Detection and Mitigation of Critical Public Health Threats
Impact: Bridging computational innovation with real-world public health applications, advocating open science and standardised data sharing within veterinary research.
Developed interdisciplinary expertise across biology and healthcare to address complex public health challenges. Experienced in laboratory methods spanning Genetics, Microbiology, Biochemistry, and Immunology.
Thesis: Antimicrobial Usage in Hospitalised SARS-CoV-2 Patients and Its Impact on the Gut Microbiome
| Title | Authors | Venue | Date | Link | Download |
|---|---|---|---|---|---|
| PetEVAL: A veterinary free text electronic health records benchmark. | Farrell, S., Radford, A.D., Al Moubayed, N., Noble, P.-J.M. | Proceedings of the 24th Workshop on Biomedical Language Processing | 01/08/2025 | Link | |
| Premature mortality analysis of 52,000 deceased cats and dogs exposes socioeconomic disparities. | Farrell, S., Anderson, K., Noble, P.-J.M. and Al Moubayed, N. | Scientific Reports | 20/09/2024 | Link | |
| Explainable text-tabular models for predicting mortality risk in companion animals. | Farrell, S.*, Burton, J.*, Noble, P.-J.M. and Al Moubayed, N. | Scientific Reports | 20/06/2024 | Link | |
| PetBERT: automated ICD-11 syndromic disease coding for outbreak detection in first opinion veterinary electronic health records. | Farrell, S., Appleton, C., Noble, P.-J.M. and Al Moubayed, N. | Scientific Reports | 21/10/2023 | Link | |
| A multinational survey of companion animal veterinary clinicians: How can antimicrobial stewardship guidelines be optimised for the target stakeholder? | Farrell, S., Bagcigil, A.F., Chaintoutis, S.C., et al. | The Veterinary Journal | 23/09/2023 | Link | |
| Seasonality and other risk factors for fleas infestations in domestic dogs and cats. | Farrell, S., McGarry, J., Noble, P.-J.M., Pinchbeck, G.J., et al. | Medical and Veterinary Entomology | 09/01/2023 | Link | |
| Seasonality and risk factors for myxomatosis in pet rabbits in Great Britain. | Farrell, S., Noble, P.-J.M., Pinchbeck, G.L., et al. | Preventive Veterinary Medicine | 08/02/2020 | Link |
| Title | Authors | Venue | Date | Link | Download |
|---|---|---|---|---|---|
| Text mining for disease surveillance in veterinary clinical data: part two, training computers to identify features in clinical text. | Davies, H., Nenadic, G., Alfattni, G., et al., Farrell, S., Radford, A.D. and Noble, P.-J.M. | Frontiers in Veterinary Science | 22/08/2024 | Link | |
| Text mining for disease surveillance in veterinary clinical data: part one, rule-based extraction. | Davies, H., Nenadic, G., Alfattni, G., et al., Farrell, S., Radford, A.D. and Noble, P.-J.M. | Frontiers in Veterinary Science | 23/01/2024 | Link | |
| Evaluating ChatGPT text mining of clinical records for companion animal obesity monitoring. | Fins, I.S., Davies, H., Farrell, S., Torres, J.R., Pinchbeck, G., et al. | The Veterinary Record | 06/12/2023 | Link | |
| SARS-CoV-2 neutralising antibodies in dogs and cats in the United Kingdom. | Smith, S.L., Anderson, E.R., Cansado-Utrilla, C., Farrell, S., et al. | Current Research in Virological Science | 04/08/2021 | Link |
| Title | Authors | Venue | Date | Link | Download |
|---|---|---|---|---|---|
| In absence of vino, in machina discenti, veritas: Hierarchical semantic search in Ancient Greek texts. | Farrell, S., Cannatella, P. | In Review | - | - | |
| PetHarbor: A Standardised Framework for Sharing Veterinary Electronic Health Records. | Farrell, S., Radford, A.D., Al Moubayed, N., Noble, P.-J.M. | In Review | - | - | |
| Automated Disease Classification of Veterinary Clinical Narratives for Antimicrobial Stewardship Guideline Monitoring. | Farrell, S., Singleton, D.A., Radford, A.D., Pinchbeck G., Noble, P.-J.M. & Al Moubayed, N. | In Review | - | - | |
| Generalizable multilingual medical text de-identification using generative instruction tuning. | Chenghao, X., Hudson, T., Jones, B., Watson, M., Farrell, S., Harmsworth-King, J., & Al Moubayed, N. | In Review | - | - | |
| Comprehensive representation of health-related phenotypes in one million dogs using topic modelling of electronic health records. | Noble, P.-J.M., Farrell, S., Al Moubayed, N. & Radford, A.D. | In Review | - | - | |
| Quantifying and contextualising antimicrobial usage using automated disease classification tools. | Lawson, A., Farrell, S., Noble, P.-J., Mair, T., Smith, J., Pinchbeck, G. | In Review | - | - |
*Equal Contribution
| Title | Venue | Location | Date | Type | Link |
|---|---|---|---|---|---|
| 🏆 Best Talk Award Democratising Veterinary EHRs: Balancing Privacy & Open Science for the future of LLM Research in Veterinary Science | Symposium on Artificial Intelligence in Veterinary Medicine | Cornell University, USA | 17/05/2025 | Oral | |
| Unravelling HPCIA prescription trends in veterinary healthcare: LLM approach towards antimicrobial stewardship surveillance in the UKÂ | Association for Veterinary Informatics Talbot Veterinary Informatics Symposium | Virginia-Tech University, USA | 13/09/2024 | Oral | ppt |
| Can PetBERT help prevent the next apocalypse? | Symposium on Artificial Intelligence in Veterinary Medicine | Cornell University, USA | 19/04/2024 | Oral | ppt |
| 🏆 Best Talk Award Can CatGPT Help Prevent the Next Apocalypse? | Annual BBSRC NLD DTP Conference | Durham University, UK | 22/07/2024 | Oral | ppt |
| Where are all the antimicrobials being used? LLM’s for monitoring adherence to antimicrobial stewardship guidelines in veterinary practices | HealTAC Annual Conference | Lancaster University, UK | 13/06/2024 | Poster | |
| Survey Results on what do clinicians want from their antimicrobial stewardship guidelines | European Network for the Optimisation of Veterinary Antimicrobial Therapy (ENOVAT) Meeting | University of Copenhagen, Netherlands | 07/03/2024 | Oral | ppt |
| Syndromic Disease Classification of Veterinary EHR Notes for Disease Outbreak Detection | HealTAC Annual Conference | University of Manchester, UK | 15/06/2023 | Poster | |
| Syndromic Surveillance for Understanding Antimicrobial Usage in the veterinary community | Medical Research Foundation National PhD Conference | University of Bristol, UK | 07/08/2022 | Poster | |
| 🏆 Best Talk Award Can AI tell you when your pet will die? | Annual BBSRC NLD DTP Conference | Durham University, UK | 21/07/2022 | Oral | ppt |
| Current Status of multinational survey of companion animal veterinary clinicians: How can antimicrobial stewardship guidelines be optimised for the target stakeholder? | European Network for the Optimisation of Veterinary Antimicrobial Therapy (ENOVAT) Meeting | Aristotle University of Thessaloniki, Greece | 13/05/2022 | Oral | ppt |
Impact: Contextual antimicrobial usage in the UK equine population and automated disease coding in veterinary EHRs
Impact: Work integrated into a healthcare app serving over 1 million NHS patients.
Impact: Highest departmental module evaluations from students.
Impact: Published in the Journal of Medical and Veterinary Entomology.
Impact: Published in the Journal of Preventive Veterinary Medicine.
