Generalizable clinical note section identification with large language models

Clinical note section identification helps locate relevant information and could be beneficial for downstream tasks such as named entity recognition. However, the traditional supervised methods suffer from transferability issues. This study proposes a new framework for using large language models (LLMs) for section identification to overcome the limitations.

We framed section identification as question-answering and provided the section definitions in free-text. We evaluated multiple LLMs off-the-shelf without any training. We also fine-tune our LLMs to investigate how the size and the specificity of the fine-tuning dataset impacts model performance.

GPT4 achieved the highest F1 score of 0.77. The best open-source model (Tulu2-70b) achieved 0.64 and is on par with GPT3.5 (ChatGPT). GPT4 is also found to obtain F1 scores greater than 0.9 for 9 out of the 27 (33%) section types and greater than 0.8 for 15 out of 27 (56%) section types. For our fine-tuned models, we found they plateaued with an increasing size of the general domain dataset. We also found that adding a reasonable amount of section identification examples is beneficial.

These results indicate that GPT4 is nearly production-ready for section identification, and seemingly contains both knowledge of note structure and the ability to follow complex instructions, and the best current open-source LLM is catching up.

Our study shows that LLMs are promising for generalizable clinical note section identification. They have the potential to be further improved by adding section identification examples to the fine-tuning dataset.