Extraction and classification of structured data from unstructured hepatobiliary pathology reports using large
Ruben Geevarghese1, Carlie Sigel2, John Cadley3
1Division of Interventional Radiology, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
Aims:
Structured reporting in pathology is not universally adopted and extracting elements essential to research often requires expensive and time-intensive manual curation. The accuracy and feasibility of using large language models (LLMs) to extract essential pathology elements, for cancer research is examined here.
Methods:
Retrospective study of patients who underwent pathology sampling for suspected hepatocellular carcinoma and underwent Ytrrium-90 embolisation. Five pathology report elements of interest were included for evaluation. LLMs (Generative Pre-trained Transformer (GPT) 3.5 turbo and GPT-4) were used to extract elements of interest. For comparison, a rules-based, regular expressions (REGEX) approach was devised for extraction. Accuracy for each approach was calculated.
Results:
88 pathology reports were identified. LLMs and REGEX were both able to extract research elements with high accuracy (average 84.1%-94.8%).
Conclusions:
LLMs have significant potential to simplify the extraction of research elements from pathology reporting, and therefore, accelerate the pace of cancer research.
