From study design to executable code: automating target trial emulation with large language models

Implementing target trial emulation (TTE) studies as standardized, reproducible analytic workflows is technically demanding. We developed Text-guided Health-study Estimation and Specification Engine Using Strategus (THESEUS), which uses large language models (LLMs) to translate free-text study descriptions into structured analytic specifications and Strategus R scripts within the Observational Health Data Sciences and Informatics (OHDSI) ecosystem.

THESEUS executes 2 steps: an LLM maps study descriptions to a JavaScript Object Notation (JSON) schema, and validated specifications are converted into Strategus R scripts through rule-based logic. For standardization evaluation, we compared specifications generated by 8 LLMs using 15 OHDSI-based TTE studies and 15 non-OHDSI studies under primary-analysis and full-analyses settings.

Under the primary-analysis setting, overall standardization accuracy ranged from 0.93 to 0.97 across models in OHDSI studies and from 0.82 to 0.95 in non-OHDSI studies. Gemini-3.1-Pro achieved the highest overall accuracy in OHDSI studies, while Gemini-3.1-Pro and Gpt-5.5 jointly achieved the highest overall accuracy in non-OHDSI studies. Under the full-analyses setting, field-level sensitivity ranged from 0.83 to 0.97 in OHDSI studies, with 0.07-0.80 false positives (FPs) per study, and from 0.77 to 0.89 in non-OHDSI studies, with 0.53-1.20 FPs per study. Gpt-5.5 performed best at the field level. THESEUS was implemented as a web application and coding-agent tools.

Pairing a standardized data model with a structured analysis framework enables reliable LLM-assisted interpretation of study descriptions and deterministic workflow construction in observational research.

THESEUS supports translation of natural language study descriptions into executable, shareable code in standardized observational research settings.