Joseph S. Boyle

Joseph S. Boyle, Antanas Kascenas, Pat Lok et al.

The task of assigning diagnostic ICD codes to patient hospital admissions is typically performed by expert human coders. Efforts towards automated ICD coding are dominated by supervised deep learning models. However, difficulties in learning to predict the large number of rare codes remain a barrier to adoption in clinical practice. In this work, we leverage off-the-shelf pre-trained generative large language models (LLMs) to develop a practical solution that is suitable for zero-shot and few-shot code assignment, with no need for further task-specific training. Unsupervised pre-training alone does not guarantee precise knowledge of the ICD ontology and specialist clinical coding task, therefore we frame the task as information extraction, providing a description of each coded concept and asking the model to retrieve related mentions. For efficiency, rather than iterating over all codes, we leverage the hierarchical nature of the ICD ontology to sparsely search for relevant codes.

Joseph S. Boyle, Anthony Dranfield, Mike O'Neil et al.

In this paper we introduce ClinQueryAgent, a system for translating natural language population health questions into executable database queries using agents with access to both local and external knowledge bases. Our novel architecture enables the use of powerful cloud-based language models whilst ensuring that no patient data leaves the secure environment. To combat inaccuracies over the course of longer dialogues due to context rot, information retrieval is delegated to a sub-agent. We deploy the system via a chat window embedded within an existing population health management platform where it has been used by 128 staff from 15 healthcare practices covering a total of 148,319 patients in the UK's National Health Service (NHS). We evaluate the system's capacity to autonomously handle a range of health informatics tasks on a constructed dataset and via a beta-testing phase. Our results show that both analysts and clinicians are able to easily generate actionable information from patient health records using natural language requests requiring no programming expertise to verify. We make a public demo of the system available at: https://demo-899965260288.europe-west1.run.app/