Automated Thematic Analysis for Clinical Qualitative Data: Iterative Codebook Refinement with Full Provenance

Thematic analysis (TA) is widely used in health research to extract patterns from patient interviews, yet manual TA faces challenges in scalability and reproducibility. LLM-based automation can help, but existing approaches produce codebooks with limited generalizability and lack analytic auditability. We present an automated TA framework combining iterative codebook refinement with full provenance tracking. Evaluated on five corpora spanning clinical interviews, social media, and public transcripts, the framework achieves the highest composite quality score on four of five datasets compared to six baselines. Iterative refinement yields statistically significant improvements on four datasets with large effect sizes, driven by gains in code reusability and distributional consistency while preserving descriptive quality. On two clinical corpora (pediatric cardiology), generated themes align with expert-annotated themes.