Exploring the limits of LLMs in low-resource information extraction: Case study in brain MRI reports for Epilepsy

Information extraction (IE) from specialized clinical texts such as brain MRI reports is important for various clinical and population health contexts. However, this topic is under-explored due to privacy concerns limiting data availability and the inherent complexity and domain-specificity of clinical language. Common methods relying on substantial amounts of training data fail. The recent advances in large language model (LLM) research provide a promising solution to bridge the data scarcity gap, with improved ability to adapt to novel tasks with little supervision. We introduce a new, challenging dataset of 100 expert-annotated brain MRI reports, featuring 152 fine-grained entity types and 4 relation types, characterised by low inter-annotator agreement. This task reflects the inherent complexity and real-world ambiguity of medical text.

We evaluate a small, open-weight LLM across span detection, named entity recognition, and relation extraction tasks. We compare few-shot prompting and parameter-efficient fine-tuning against specialized off-the-shelf biomedical IE systems. Our results demonstrate that both few-shot and fine-tuned LLM approaches substantially outperform off-the-shelf baselines. While LLMs show superiority, absolute performance, particularly for complex relations and fine-grained entities, remains modest, correlating with the dataset’s inherent difficulty and the extreme low-resource setting.