Cancer Type, Stage and Prognosis Assessment from Pathology Reports using LLMs

Rachit Saluja; Jacob Rosenthal; Yoav Artzi; David J. Pisapia; Benjamin L. Liechty; Mert R. Sabuncu

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arXiv · 2503.01194

Cancer Type, Stage and Prognosis Assessment from Pathology Reports using LLMs

Rachit Saluja·Jacob Rosenthal·Yoav Artzi·David J. Pisapia·Benjamin L. Liechty·Mert R. Sabuncu

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Abstract

Large Language Models (LLMs) have shown significant promise across various natural language processing tasks. However, their application in the field of pathology, particularly for extracting meaningful insights from unstructured medical texts such as pathology reports, remains underexplored and not well quantified. In this project, we leverage state-of-the-art language models, including the GPT family, Mistral models, and the open-source Llama models, to evaluate their performance in comprehensively analyzing pathology reports. Specifically, we assess their performance in cancer type identification, AJCC stage determination, and prognosis assessment, encompassing both information extraction and higher-order reasoning tasks. Based on a detailed analysis of their performance metrics in a zero-shot setting, we developed two instruction-tuned models: Path-llama3.1-8B and Path-GPT-4o-mini-FT. These models demonstrated superior performance in zero-shot cancer type identification, staging, and prognosis assessment compared to the other models evaluated.

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Rachit Saluja, Jacob Rosenthal, Yoav Artzi, David J. Pisapia, Benjamin L. Liechty, Mert R. Sabuncu. 2025-03-03. Cancer Type, Stage and Prognosis Assessment from Pathology Reports using LLMs. https://arxiv.org/abs/2503.01194

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