Developing a named entity framework for thyroid cancer staging and risk level classification using large language models

Abstract

We developed a named entity (NE) framework for information extraction from semi-structured clinical notes retrieved from The Cancer Genome Atlas—Thyroid Cancer (TCGA-THCA) database and examined Large Language Models (LLMs) strategies to classify the 8^th edition of American Joint Committee on Cancer (AJCC) staging and American Thyroid Association (ATA) risk category for patients with well-differentiated thyroid cancer. The NE framework consisted of annotation guidelines development, ground truth labelling, prompting approaches, and evaluation codes. Four LLMs (Mistral-7B-Instruct, Llama-3.1-8B-Instruct, Gemma-2-9B-Instruct, and Qwen2.5-7B-Instruct) were offline utilised for information extraction, comparing with expert-curated ground truth. Our framework was developed using 50 TCGA-THCA pathology notes. 289 TCGA-THCA notes and 35 pseudo-clinical cases were used for validation. Taking an ensemble-like majority-vote strategy achieved satisfactory performance for AJCC and ATA in both development and validation sets. Our framework and ensemble classifier optimised efficiency and accuracy of classifying stage and risk category in thyroid cancer patients.