{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/leveraging-large-language-models-for-25","title":"Leveraging large language models for structured information extraction from pathology reports","arxiv_id":"2502.12183","date":"2025-02-14","proceeding":null,"authors":["Jeya Balaji Balasubramanian","Daniel Adams","Ioannis Roxanis","Amy Berrington de Gonzalez","Penny Coulson","Jonas S. Almeida","Montserrat García-Closas"],"abstract":"Background: Structured information extraction from unstructured histopathology reports facilitates data accessibility for clinical research. Manual extraction by experts is time-consuming and expensive, limiting scalability. Large language models (LLMs) offer efficient automated extraction through zero-shot prompting, requiring only natural language instructions without labeled data or training. We evaluate LLMs' accuracy in extracting structured information from breast cancer histopathology reports, compared to manual extraction by a trained human annotator. Methods: We developed the Medical Report Information Extractor, a web application leveraging LLMs for automated extraction. We developed a gold standard extraction dataset to evaluate the human annotator alongside five LLMs including GPT-4o, a leading proprietary model, and the Llama 3 model family, which allows self-hosting for data privacy. Our assessment involved 111 histopathology reports from the Breast Cancer Now (BCN) Generations Study, extracting 51 pathology features specified in the study's data dictionary. Results: Evaluation against the gold standard dataset showed that both Llama 3.1 405B (94.7% accuracy) and GPT-4o (96.1%) achieved extraction accuracy comparable to the human annotator (95.4%; p = 0.146 and p = 0.106, respectively). While Llama 3.1 70B (91.6%) performed below human accuracy (p <0.001), its reduced computational requirements make it a viable option for self-hosting. Conclusion: We developed an open-source tool for structured information extraction that can be customized by non-programmers using natural language. Its modular design enables reuse for various extraction tasks, producing standardized, structured data from unstructured text reports to facilitate analytics through improved accessibility and interoperability.","url_abs":"https://arxiv.org/abs/2502.12183v1","url_pdf":"https://arxiv.org/pdf/2502.12183v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"leveraging-large-language-models-for-25","repo_url":"https://github.com/jeyabbalas/medical-report-information-extractor","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[{"method_slug":"llama","method_name":"LLaMA"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":"https://app.syntology.ai/?focus=2502.12183","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}