Large Language Models to Extract Cancer Staging Data From Clinical Documentation at Scale

To develop a large language model (LLM) (Truveta Language Model Oncology [TLM-Oncology]) to extract real-world oncology staging data across multiple cancer types from clinical documentation with high precision.

We selected patients from a large integrated health system with a bladder, cervical, colorectal, breast, or prostate cancer diagnosis in their structured data. We identified relevant notes using note metadata and keywords and annotated overall stage; T, N, and M; associated timeframe; and cancer diagnosis on a sample of 700 notes as ground truth. Of the 700 notes, 450 were divided equally between training, validation, and test sets for bladder, cervical, and colorectal cancers; 150 were used for targeted error-pattern training on these cancers; and the remaining 100 were split equally between breast and prostate cancer test sets. We started with a pretrained LLM and applied supervised fine-tuning to adapt the model to structured clinical information extraction. Model performance was measured using precision, recall, and F1 scores at the relation level and individual attribute level.

We extracted over 2.5 million staging records for 217,768 patients from over two million notes. Relation-level precision across the six attributes ranged from 0.77 to 1.0 for the first three cancers and, without further training, 0.83 to 1.0 for two additional cancers.

TLM-Oncology extracted detailed cancer staging information for five cancers from a variety of clinical documentation within a single integrated health system with high precision and turned data that were previously inaccessible into a valuable resource for downstream use. We are currently evaluating TLM-Oncology on other solid tumors within three additional health systems to assess its generalizability.