Medical university automates patient data processing

Semmelweis University’s clinical database stores medical data transformed to the OMOP standard. However, much of this data is in free-text documents (e.g., discharge summaries, histories, physical status), making analysis ineffective.

Manual standardization is labor-intensive. There are examples of applying Large Language Models for data extraction; however, there is no out-of-the-box solution for extracting specific medical data.

With a limited scope of only a few parameters, our pilot focused on validating the methodology.

In preparation to use the source data with LLMs, we created specific prompts for efficient parameter extraction and structurization. Working with subject matter medical experts, we created a golden set for data validation, containing about 730 documents. In each case, the targeted parameters were hand-labelled.

The pilot achieved a 95% accuracy, and LLMs even recognized parameter instances that manual labeling missed. After post-processing and mapping the acquired data to the OMOP standard, it was ready for integration into the data warehouse.