Leveraging Fine-Tuned Large Language Models for Interpretable Pancreatic Cystic Lesion Feature Extraction and Risk Categorization

TL;DR

This study develops and evaluates fine-tuned large language models that automatically extract pancreatic cystic lesion features and categorize risk from radiology reports, matching GPT-4o performance and enabling scalable research.

Contribution

It introduces a method for fine-tuning open-source LLMs with chain-of-thought prompting to accurately extract PCL features and risk categories from reports.

Findings

Fine-tuned models achieved over 97% feature extraction accuracy.

Risk categorization F1 scores exceeded 0.94, comparable to GPT-4o.

Radiologist agreement levels were maintained, demonstrating clinical reliability.

Abstract

Background: Manual extraction of pancreatic cystic lesion (PCL) features from radiology reports is labor-intensive, limiting large-scale studies needed to advance PCL research. Purpose: To develop and evaluate large language models (LLMs) that automatically extract PCL features from MRI/CT reports and assign risk categories based on guidelines. Materials and Methods: We curated a training dataset of 6,000 abdominal MRI/CT reports (2005-2024) from 5,134 patients that described PCLs. Labels were generated by GPT-4o using chain-of-thought (CoT) prompting to extract PCL and main pancreatic duct features. Two open-source LLMs were fine-tuned using QLoRA on GPT-4o-generated CoT data. Features were mapped to risk categories per institutional guideline based on the 2017 ACR White Paper. Evaluation was performed on 285 held-out human-annotated reports. Model outputs for 100 cases were independently reviewed by three radiologists. Feature extraction was evaluated using exact match accuracy, risk categorization with macro-averaged F1 score, and radiologist-model agreement with Fleiss' Kappa. Results: CoT fine-tuning improved feature extraction accuracy for LLaMA (80% to 97%) and DeepSeek (79% to 98%), matching GPT-4o (97%). Risk categorization F1 scores also improved (LLaMA: 0.95; DeepSeek: 0.94), closely matching GPT-4o (0.97), with no statistically significant differences. Radiologist inter-reader agreement was high (Fleiss' Kappa = 0.888) and showed no statistically significant difference with the addition of DeepSeek-FT-CoT (Fleiss' Kappa = 0.893) or GPT-CoT (Fleiss' Kappa = 0.897), indicating that both models achieved agreement levels on par with radiologists. Conclusion: Fine-tuned open-source LLMs with CoT supervision enable accurate, interpretable, and efficient phenotyping for large-scale PCL research, achieving performance comparable to GPT-4o.