Making every stage of medical device document assessment with large language models deterministic

Incorporating large language models (LLMs) in medical question answering demands more than high average accuracy: a model that returns substantively different answers each time it is queried is not a reliable medical tool. Online health communities such as Reddit have become a primary source of medical information for millions of users, yet they remain highly susceptible to misinformation; deploying LLMs as assistants in these settings amplifies the need for output consistency alongside correctness. We present a practical, open-source evaluation framework for assessing small, locally-deployable open-weight LLMs on medical question answering, treating reproducibility as a first-class metric alongside lexical and semantic accuracy. Our pipeline computes eight quality metrics, including BERTScore, ROUGE-L, and an LLM-as-judge rubric, together with two within-model reproducibility metrics derived from repeated inference (N=10 runs per question). Evaluating three models (Llama 3.1 8B, Gemma 3 12B, MedGemma 1.5 4B) on 50 MedQuAD questions (N=1,500 total responses) reveals that despite low-temperature generation (T=0.2), self-agreement across runs reaches at most 0.20, while 87-97% of all outputs per model are unique -- a safety gap that single-pass benchmarks entirely miss. The clinically fine-tuned MedGemma 1.5 4B underperforms the larger general-purpose models on both quality and reproducibility; however, because MedGemma is also the smallest model, this comparison confounds domain fine-tuning with model scale. We describe the methodology in sufficient detail for practitioners to replicate or extend the evaluation for their own model-selection workflows. All code and data pipelines are available at https://github.com/aviad-buskila/llm_medical_reproducibility.

Language-model judges now gate training data, score generations, and drive leaderboards. The judge is then a measurement instrument, resting on one rarely stated assumption: the same request, sent to the same model name, reads the same tomorrow. We audited that assumption in two preregistered campaigns with every threshold fixed in advance; neither got past validating its instrument. Across 52,988 audited request attempts, same-window repeat rankings agreed at Spearman 0.400 against a required 0.90, and byte-identical next-day replays agreed at 0.78 against a required 0.99, each time with the execution record at ceiling. Three mechanisms explain the gap: a label-to-meaning mapping that biased readouts as strongly as the signal; candidate gaps seven orders of magnitude below the instrument's own noise floor; and byte-identical inputs returning different rankings, a noise that exact-permutation readouts compound. Neither metric substitution nor sampling repaired it on the tested grid. Preregistered follow-ups bound the problem: waiting did not help on the days sampled (0.805 versus 0.800, replicated over five further days); switching providers did not help (four providers share the floor, medians 0.74 to 0.88, predicted by none of the metadata fields they expose); self-hosting on batch-invariant kernels helped only while the server was quiet; and on constructed errors with known gaps, the readout's separation tracks error type, not size. We distill the evidence into a three-level snapshot-identity ladder, eight design rules, and a reporting checklist; a pilot at roughly 2% of the study's call volume would have exposed both unreachable gates in advance. All results concern externally measured behaviour on shared serving infrastructure. On a shared endpoint, a model name is not a frozen instrument; a preregistered evaluation must measure its instrument before freezing any gate on it.

As autonomous research agents and AI co-scientist systems push large language models (LLMs) from drafting toward end-to-end manuscript production, the bottleneck shifts from generation to verification. Fluent LLM output can hide fabricated citations, numbers that drift from source tables, and unmet reporting-guideline items; existing tools generate without verifying, and self-critique inherits the blind spots that produce confident fabrication. We describe an architecture pairing generation with verification, resting on three principles: decompose the workflow into self-contained skills, gate every stage transition with halt-on-failure, and resolve each integrity question with the cheapest sufficient mechanism, a deterministic, re-executable check where one suffices and a prose-level probe only where interpretation is unavoidable. This determinism-where-possible split, organized as an integrity-gate taxonomy, is the core contribution. It is realized as MedSci Skills, an open-source toolkit of 43 skills with a 21-detector deterministic tier, evaluated on three public-dataset pipelines (STARD, PRISMA, STROBE) and a seeded-defect ablation. Across the three pipelines every content-hash manifest verified clean and the gates surfaced real defects; on 27 identical injected defects the deterministic gates detected all 27 with no false positives on the matched clean fixtures, whereas a single-prompt LLM reviewer detected 11, its misses in code, bibliography, and style defects the prose hides. Determinism-where-possible verification yields an auditable, re-executable trail that exposes the evidence a human needs to check an LLM-assisted manuscript: feasibility and reproducibility evidence, not a claim of human-competitive quality, which a separate blinded study addresses. MedSci Skills is MIT-licensed and archived (v3.8.0).