ClinAgent: AI-Assisted Methodology for Clinical Trial Data Processing and Statistical Programming

Abstract Clinical trial statistical programming requires 12 to 24 full-time-equivalent months per Phase 3 study and remains a bottleneck in pharmaceutical research. Modern artificial intelligence coding agents reason capably but lack domain-specific tools: they cannot read proprietary statistical software datasets, parse analysis specifications, or generate standards-compliant code without extensive guidance. We present ClinAgent, a skill and tool layer that augments any artificial intelligence coding agent with clinical programming capabilities through Model Context Protocol tools. Its design separates minimal data access from rich domain logic: skills package prompts, rule engines, and decision trees encoding expert knowledge, while tools provide stateless input-output for statistical software datasets, spreadsheet specifications, and log files. In this single-study proof-of-concept evaluation, we validate ClinAgent’s nine skills on artifacts from a production Phase 2 cardiovascular study, with synthetic datasets spanning 13 analysis domains and 102,109 observations. All skills pass functional validation. On this small sample, deterministic components identify one error and seven warnings without false positives and match all 56 subject-level variables; corresponding confidence intervals are wide, so these point estimates should be read as upper bounds pending replication. Prompt-based specification generation, dependent on the underlying language model, reaches 72.1 percent derivation accuracy overall, above 96 percent in simple domains and below 55 percent in complex ones, indicating that generated specifications require expert review. Our contributions include an agent-augmentation architecture, nine validated skills, tool implementations for clinical data formats, and a validation methodology distinguishing deterministic tool correctness from language-model-dependent output.