The increasing volume and complexity of clinical documentation in Electronic Medical Records systems pose significant challenges for clinical coders, who must mentally process and summarise vast amounts of clinical text to extract essential information needed for coding tasks. While large language models have been successfully applied to shorter summarisation tasks in recent years, the challenge of summarising a hospital course remains an open area for further research and development. In this study, we adapted three pre trained LLMs, Llama 3, BioMistral, Mistral Instruct v0.1 for the hospital course summarisation task, using Quantized Low Rank Adaptation fine tuning. We created a free text clinical dataset from MIMIC III data by concatenating various clinical notes as the input clinical text, paired with ground truth Brief Hospital Course sections extracted from the discharge summaries for model training. The fine tuned models were evaluated using BERTScore and ROUGE metrics to assess the effectiveness of clinical domain fine tuning. Additionally, we validated their practical utility using a novel hospital course summary assessment metric specifically tailored for clinical coding. Our findings indicate that fine tuning pre trained LLMs for the clinical domain can significantly enhance their performance in hospital course summarisation and suggest their potential as assistive tools for clinical coding. Future work should focus on refining data curation methods to create higher quality clinical datasets tailored for hospital course summary tasks and adapting more advanced open source LLMs comparable to proprietary models to further advance this research.

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.