Automated data extraction from unstructured text using LLMs: A scalable workflow for Stata users

Loreta Isaraj
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Loreta Isaraj: IRCrES-CNR

Italian Stata Users' Group Meetings 2025 from Stata Users Group

Abstract: In several data-rich domains such as finance, medicine, law, and scientific publishing, most of the valuable information is embedded in unstructured textual formats, from clinical notes and legal briefs to financial statements and research papers. These sources are rarely available in structured formats suitable for immediate quantitative analysis. This presentation introduces a scalable and fully integrated workflow that employs large language models (LLMs), specifically ChatGPT 4.0 via API, in conjunction with Python and Stata to extract structured variables from unstructured documents and make them ready for further statistical processing in Stata. As a representative use case, I demonstrate the extraction of information from a SOAP clinical note, treated as a typical example of unstructured medical documentation. The process begins with a single PDF and extends to an automated pipeline capable of batch-processing multiple documents, highlighting the scalability of this approach. The workflow involves PDF parsing and text preprocessing using Python, followed by prompt engineering designed to optimize the performance of the LLM. In particular, the temperature parameter is tuned to a low value (for example, 0.0–0.3) to promote deterministic and concise extraction, minimizing variation across similar documents and ensuring consistency in output structure. Once the LLM returns structured data, typically in JSON or CSV format, it is seamlessly imported into Stata using custom.do scripts that handle parsing (insheet), transformation (split, reshape), and data cleaning. The final dataset is used for exploratory or inferential analysis, with visualization and summary statistics executed entirely within Stata. The presentation also addresses critical considerations including the computationala cost of using commercial LLM APIs (token-based billing), privacy and compliance risks when processing sensitive data (such as patient records), and the potential for bias or hallucination inherent to generative models. To assess the reliability of the extraction process, I report evaluation metrics such as cosine similarity (for text alignment and summarization accuracy) and F1-score (for evaluating named entity and numerical field extraction). By bridging the capabilities of LLMs with Stata’s powerful analysis tools, this workflow equips researchers and analysts with an accessible method to unlock structured insights from complex unstructured sources, extending the reach of empirical research into previously inaccessible text-heavy datasets.

Date: 2025-10-01
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