Related Experiment Video
Updated: Aug 6, 2026
Machine Learning Algorithms for Early Detection of Bone Metastases in an Experimental Rat Model
Published on: August 16, 2020
Strategies for Deploying Large Language Models for Ascertaining Clinical Outcomes and Sites of Metastases From
Syed Arsalan Ahmed Naqvi1, Irbaz Bin Riaz1,2, Amir Saeidi1,3
1Division of Hematology and Oncology, Department of Medicine, Mayo Clinic, Phoenix, AZ.
Purpose:
To evaluate open-source large language models (LLMs) for extracting cancer-specific phenotypic data, benchmark their performance against GPT4 models, and assess the impact of fine-tuning with training data sizes.
Methods:
Open-source LLMs (Mistral, LLaMa, MAMBA, BioMistral) were evaluated in zero-/one-shot and fine-tuned setups against GPT4-turbo/GPT4o to extract the cancer presence, progression, response, and metastatic sites from radiology impressions of patients with solid tumors treated at Dana-Farber Cancer Institute. Performance metrics (accuracy, precision, recall, F1-score) were computed. McNemar's odds ratio (OR), measuring which model is more likely to be correct when they disagree, was computed with 95% CI. Statistical significance was assessed using the alpha of .000139.
Results:
This study included 2,623 patients (25,273 radiology impressions). In zero-/one-shot settings, GPT4-turbo/GPT4o outperformed open-source LLMs. However, fine-tuned open-source LLMs achieved higher F1-scores than GPT4 models. Compared with the best-performing GPT4 model, fine-tuned Mistral0.2-7.3B (OR, 0.27 [95% CI, 0.20 to 0.36]; P < .00001), Mistral0.3-7.3B (OR, 0.26 [95% CI, 0.19 to 0.36]; P < .00001), LLaMa2-6.7B (OR, 0.30 [95% CI, 0.22 to 0.40]; P < .00001), LLaMa3.1-8B (OR, 0.37 [95% CI, 0.28 to 0.48]; P < .00001), and MAMBA-2.8B (OR, 0.32 [95% CI, 0.24 to 0.42]; P < .00001) showed significantly better performance in ascertaining disease progression. Performance was consistently better for inferring overall response, any evidence of cancer, and sites of metastases, with no significant differences among fine-tuned open-source LLMs. Fine-tuning gains plateaued at 25% of training data (5,718 impressions) and remained comparable at 5% (1,144 impressions).
Conclusion:
Open-source LLMs, when fine-tuned using labeled data, can effectively automate the ascertainment of key radiophenotypic variables using only the impression section of radiology reports, without the full report text. Their consistent performance in small training sets suggests that these models may provide a scalable approach for phenotypic characterization of patients with cancer in real-world clinical settings.
