# Fully Open Meditron: An Auditable Pipeline for Clinical LLMs

arXiv: https://arxiv.org/abs/2605.16215 · HTML: https://mlsanity.com/paper/2605.16215/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 33 of its 44 references that are in the map.
- First posted on arXiv 15 May 2026.

## Builds on (most cited first, 30 of 33)

- [Training Verifiers to Solve Math Word Problems](https://mlsanity.com/paper/2110.14168/) (2021)
- [Judging LLM-as-a-Judge with MT-Bench and Chatbot Arena](https://mlsanity.com/paper/2306.05685/) (2023)
- [Measuring Massive Multitask Language Understanding](https://mlsanity.com/paper/2009.03300/) (2020)
- [Think you have Solved Question Answering? Try ARC, the AI2 Reasoning Challenge](https://mlsanity.com/paper/1803.05457/) (2018)
- [HellaSwag: Can a Machine Really Finish Your Sentence?](https://mlsanity.com/paper/1905.07830/) (2019)
- [TruthfulQA: Measuring How Models Mimic Human Falsehoods](https://mlsanity.com/paper/2109.07958/) (2021)
- [Can a Suit of Armor Conduct Electricity? A New Dataset for Open Book Question Answering](https://mlsanity.com/paper/1809.02789/) (2018)
- [MMLU-Pro: A More Robust and Challenging Multi-Task Language Understanding Benchmark](https://mlsanity.com/paper/2406.01574/) (2024)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [gpt-oss-120b & gpt-oss-20b Model Card](https://mlsanity.com/paper/2508.10925/) (2025)
- [What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams](https://mlsanity.com/paper/2009.13081/) (2020)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [Instruction-Following Evaluation for Large Language Models](https://mlsanity.com/paper/2311.07911/) (2023)
- [Tulu 3: Pushing Frontiers in Open Language Model Post-Training](https://mlsanity.com/paper/2411.15124/) (2024)
- [MedGemma Technical Report](https://mlsanity.com/paper/2507.05201/) (2025)
- [HealthBench: Evaluating Large Language Models Towards Improved Human Health](https://mlsanity.com/paper/2505.08775/) (2025)
- [2 OLMo 2 Furious](https://mlsanity.com/paper/2501.00656/) (2024)
- [BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains](https://mlsanity.com/paper/2402.10373/) (2024)
- [MEDITRON-70B: Scaling Medical Pretraining for Large Language Models](https://mlsanity.com/paper/2311.16079/) (2023)
- [Capabilities of Gemini Models in Medicine](https://mlsanity.com/paper/2404.18416/) (2024)
- [MedXpertQA: Benchmarking Expert-Level Medical Reasoning and Understanding](https://mlsanity.com/paper/2501.18362/) (2025)
- [Judging the Judges: Evaluating Alignment and Vulnerabilities in LLMs-as-Judges](https://mlsanity.com/paper/2406.12624/) (2024)
- [Time Travel in LLMs: Tracing Data Contamination in Large Language Models](https://mlsanity.com/paper/2308.08493/) (2023)
- [Emergent Misalignment: Narrow finetuning can produce broadly misaligned LLMs](https://mlsanity.com/paper/2502.17424/) (2025)
- [Investigating Data Contamination in Modern Benchmarks for Large Language Models](https://mlsanity.com/paper/2311.09783/) (2023)
- [HuatuoGPT-II, One-stage Training for Medical Adaption of LLMs](https://mlsanity.com/paper/2311.09774/) (2023)
- [MedExpQA: Multilingual Benchmarking of Large Language Models for Medical Question Answering](https://mlsanity.com/paper/2404.05590/) (2024)
- [AfriMed-QA: A Pan-African, Multi-Specialty, Medical Question-Answering Benchmark Dataset](https://mlsanity.com/paper/2411.15640/) (2024)
- [Judge's Verdict: A Comprehensive Analysis of LLM Judge Capability Through Human Agreement](https://mlsanity.com/paper/2510.09738/) (2025)
- [The Model Openness Framework: Promoting Completeness and Openness for Reproducibility, Transparency, and Usability in Artificial Intelligence](https://mlsanity.com/paper/2403.13784/) (2024)

## Abstract (arXiv)

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.