Automated Flow and local LLM-Driven clinical Context Engineering: Precision colorectal cancer recurrence registry

This study develops and validates a deployable, privacy-preserving automated tool to address the labor-intensive nature of colorectal cancer (CRC) recurrence registration. Our tool utilizes a reproducible, two-stage 'Clinical Context Engineering' workflow to mimic expert clinical reasoning and overcome the limitations of handling longitudinal clinical data ambiguity.

We retrospectively studied 3053 CRC patients (2010-2018). A local Large Language Model (LLM) (Qwen3:14B) analyzed ∼ 19,900 pathology and ∼ 43,900 imaging reports using iterative, patch-based analysis ("raw LLM"). Clinical validation rules were applied to generate "rule-based LLM" output, enhancing explainability and trustworthiness. Both automated methods and the manual Taiwan Cancer Registry (TCR) database were compared against a 20% manual reference standard (N = 602). Full prompts and validation code are provided for complete reproducibility.

Under a strict 60-day temporal tolerance, the Rule-Based LLM achieved 90.7% accuracy, comparable to standard TCR processes (92.0%), and 77.2% sensitivity. The application of clinical validation rules significantly improved specificity from 87.7% (Raw LLM) to 93.9% (Rule-Based LLM). In time window analysis, the Rule-Based LLM identified 87.1% of recurrences within 60 days of the reference date.

Our locally deployed, privacy-preserving, and explainable Clinical Context Engineering framework offers a viable, non-inferior alternative to standard TCR processes, reducing workload while maintaining data quality and fostering trust in AI-assisted cancer registry automation.