Abstract
Existing pipelines for clinical timeline extraction from case reports are evaluated using an expert reference and are limited by imperfect reference annotations and imprecise event alignment. We developed GAVEL, an LLM judge protocol that compares two timelines with the case report and returns a discrepancy type, verdict, and report passage for each difference. We evaluated the event matcher, reviewed 2,738 findings from GPT5.6sol and DeepSeek V3.2, ranked six LLM extractors and two human annotators, and tested GAVEL guided merging. True match rates were 60% immediately below and 48% immediately above the 0.10 cutoff. Manual review confirmed 89.4% and 88.6% of findings. Across 126 reports, merged timelines were preferred in 77.0% of comparisons (95% CI, 69.8 to 84.1%) and reduced discrepancies attributed to the evaluated timeline from 7.63 to 0.85 per report. GAVEL supports report-based comparison and revision without treating either timeline as ground truth.
Abstract (translated)
URL
https://arxiv.org/abs/2609.13475
