A Multi-Analyst LLM Pipeline for Auditable Rule Discovery Across 68 Public Physiological Corpora

Synthetic perturbations appear to offer inexpensive calibration data for LLM evaluators in biomedical ML, where expert review is scarce. Yet a planted mutation key is neither a detector output nor automatically human ground truth. We formalize four distinct ledgers: planted perturbations, independent detector outputs, source-linked human dispositions, and human-added discoveries. We then audit the evaluation design, scoring code, read paths, and current human records of a private synthetic Japanese care-handoff workflow. The factory stored 69 planted error cards across 47 targets. Final review covers 22 targets and contains 22 confirmed imported proposals, 9 rejected proposals, and 79 human-added cards; only 3 reviewed targets are double annotated. Passing imported plant keys to a generic detector scorer yields 22/(22+9)=0.710 and 22/(22+79)=0.218. A direct audit identity shows that these values are proposal-confirmation yield and submitted-ledger composition, not judge precision and recall, because no independent detector realization was preserved for the audited proposals in the available records. The audit also finds source-name collisions, row shadowing, forced severity, vacuous ratio defaults, and unsupported zero-support field weights. We contribute a provenance-aware claim audit, a storage contract, and a minimum calibration gate for responsibly communicating biomedical ML capability claims. This single-workflow forensic case is an existence proof of a failure mode, not an estimate of its prevalence: existing human work supports an exploratory audit of synthetic proposals, but not LLM-judge operating characteristics, clinical validity, corpus prevalence, or robust inter-annotator agreement.

Clinical decision support systems (CDSS) require scrutable, auditable pipelines that enable rigorous, reproducible validation. Yet current LLM-based CDSS remain largely opaque. Most "open" models are open-weight only, releasing parameters while withholding the data provenance, curation procedures, and generation pipelines that determine model behavior. Fully Open (FO) models, which expose the complete training stack end-to-end, do not currently exist in medicine. We introduce Fully Open Meditron, the first fully open pipeline for building LLM-CDSS, comprising a clinician-audited training corpus, a reproducible data construction and training framework, and a use-aligned evaluation protocol. The corpus unifies eight public medical QA datasets into a normalized conversational format and expands coverage with three clinician-vetted synthetic extensions: exam-style QA, guideline-grounded QA derived from 46,469 clinical practice guidelines, and clinical vignettes. The pipeline enforces system-wide decontamination, gold-label resampling of teacher generations, and end-to-end validation by a four-physician panel. We evaluate using an LLM-as-a-judge protocol over expert-written clinical vignettes, calibrated against 204 human raters. We apply the recipe to five FO base models (Apertus-70B/8B-Instruct, OLMo-2-32B-SFT, EuroLLM-22B/9B-Instruct). All MeditronFO variants are preferred over their bases. Apertus-70B-MeditronFO improves +6.6 points over its base (47.2% to 53.8%) on aggregate medical benchmarks, establishing a new FO SoTA. Gemma-3-27B-MeditronFO is preferred over MedGemma in 58.6% of LLM-as-a-judge comparisons and outperforms it on HealthBench (58% vs 55.9%). These results show that fully open pipelines can achieve state-of-the-art domain-specific performance without sacrificing auditability or reproducibility.

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).