Four Ledgers, Not One Score: Responsible Communication of LLM-Judge Calibration in Biomedical ML

LLM-as-a-Judge evaluation has become a standard tool for assessing base model performance. However, characterizing performance via the naive estimator, i.e., raw judge outputs, is systematically biased. Recent work has proposed estimators to correct this bias, but their reliability depends critically on judge quality and, for model comparisons, on calibration stability. Sharing calibration across compared models is practically attractive but can introduce severe bias, including cases where the comparison estimate points in the wrong direction with high apparent confidence. We study these failure modes through analytical results, simulations over judge quality ($J$) and cross-model calibration instability ($ΔJ$), and a real-data MMLU-Pro case study with sign reversal. We propose $J$ and $ΔJ$ as diagnostics for when corrected estimates, especially shared-calibration comparisons, are likely unreliable, and provide reporting guidance for LaaJ evaluation.

Ambient AI scribes draft clinical notes, and published audits find their dominant error is omission: information the encounter established that the note fails to record. The standard check is an LLM judge: a second model reads the note against the transcript and flags problems. We ask whether judges detect omissions. Public corpora cannot supply the answer key: their clinician reference notes and transcripts are materially discrepant. Our benchmark has 500 single-error note pairs from audited fact sheets, 298 with a named fact certainly absent and 202 added-or-altered controls. Across eight judge designs, paired discrimination (the flawed note below its clean twin, 0.5 a coin flip) reads 0.79-0.94 on added or altered content and 0.50-0.63 on omissions. On single notes, no design flags omissions reliably more often than perfect notes. Wording changes, voting and GEPA prompt optimisation move the operating point without creating usable detection. Restructuring the task recovers it: list the facts the transcript establishes, then check the note for each. Two methods reach it independently and trade off: a per-fact pipeline, and a GEPA-evolved prompt doing the same in one call. The pipeline's flags name the missing fact and its severity at 2.7% false alarms. The single call detects more (36.9% against 24.6%, p=0.002) at 6.2% false alarms and a tenth of the cost per note. A physician author validated 70 items and, where the two routes disagree, sided with the pipeline on 10 of 10 (p=0.002). A second clinician, not an author, graded the severity rubric blind and agrees to within a grade. On real vendor notes from a companion census no benchmark threshold transfers, but the re-calibrated single call detects more than the best of the eight at half its false-alarm rate. Omissions whose fact is restated elsewhere defeat both routes. We release the benchmark, prompts and judgements.

Open-response evaluation provides stronger clinical validity than multiple-choice benchmarks but creates a scoring bottleneck that motivates automated LLM-asa-Judge approaches. Whether such evaluators replicate clinical calibration and caution, however, remains untested. We introduce MedQADE, the first standardised open-response clinical benchmark for German, a major clinical language lacking native evaluation infrastructure, comprising 3,800 items annotated by ten practising physicians and nine Large Language Model (LLM) evaluators. The top-performing evaluator model, Gemini 3 Flash, reached alignment consistent with the physician ceiling (\k{appa} = 0.694 vs. \k{appa} = 0.709), though wide confidence intervals limit interpretation. Despite this statistical alignment, automated evaluators exhibited near-absent clinical metacognition: physicians scaled abstention with item difficulty, while frontier models assigned definitive scores in every case. We additionally quantified systematic lineage-dependent biases, where models preferentially scored architectural siblings, an effect independent of language. These results show that statistical alignment does not ensure clinical caution, and that evaluator independence requires explicit verification.