Apertus-8B-MeditronFO/README.md

license, language, library_name, pipeline_tag, tags, base_model, base_model_relation, datasets

license	language	library_name	pipeline_tag	tags	base_model	base_model_relation	datasets
apache-2.0	en	transformers	text-generation	medical clinical healthcare meditron fully-open medical-llm	swiss-ai/Apertus-8B-Instruct-2509	finetune	EPFLiGHT/fully-open-meditron

Apertus-8B-MeditronFO

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📖 Check out the MeditronFO blog and MeditronFO preprint.
🔜 If you are a clinician join the MOOVE initiative here.

[Hugging Face] [Preprint] [GitHub] [Dataset]
License: Apache 2.0 | Authors: LiGHT

Note

We're introducing Apertus-8B-MeditronFO, our small fully open medical specialist LLM, medical specialization of Apertus-8B-Instruct on the Fully Open Meditron Corpus. This model is part of the Fully Open Meditron family — the first end-to-end auditable pipeline for clinical LLMs, with open weights, open data, open training recipe, and clinician-vetted corpus construction.

• Part of the Fully Open Meditron family: End to end fully open clinical LLMs
• Establishes a new state of the art: Best medical accuracy on medical benchmarks among small fully open medical LLMs
• Is prefered over Apertus-70B in 86.9% of comparisons: Comparison on the clinician validated LM judge evaluation AutoMOOVE.
• Apertus-8B-MeditronFO improves +13.35 points over its base on aggregate medical benchmarks: the largest gain in the MeditronFO family.

Benchmark

Accuracy (%) on standard medical benchmarks. See the paper for full evaluation details, confidence intervals, and open-ended Auto-MOOVE results.

Benchmark	Apertus-8B-Instruct	Apertus-8B-MeditronFO	Δ
MedMCQA	45.80	48.74	+2.94
MedQA	51.14	58.44	+7.30
PubMedQA	37.60	75.60	+38.00
MedXpertQA	11.71	13.67	+1.96
HealthBench Hard	21.55	38.11	+16.56
Average	33.56	46.91	+13.35

Usage

from transformers import AutoModelForCausalLM, AutoTokenizer
import torch

model_id = "EPFLiGHT/Apertus-8B-MeditronFO"
tokenizer = AutoTokenizer.from_pretrained(model_id)
model = AutoModelForCausalLM.from_pretrained(
    model_id,
    torch_dtype=torch.bfloat16,
    device_map="auto",
)

messages = [
    {"role": "user", "content": "A 62-year-old woman presents with a three-day history of dyspnea on exertion and a productive cough. What is the differential diagnosis?"},
]
inputs = tokenizer.apply_chat_template(
    messages,
    add_generation_prompt=True,
    tokenize=True,
    return_dict=True,
    return_tensors="pt",
).to(model.device)

outputs = model.generate(**inputs, max_new_tokens=512, do_sample=False)
print(tokenizer.decode(outputs[0][inputs["input_ids"].shape[-1]:], skip_special_tokens=True))

Training

• Base model: Apertus-8B-Instruct
• Corpus: Fully Open Meditron 601k examples (~150M tokens), aggregating eight public medical QA datasets with three clinician-vetted synthetic components: exam-style QA, guideline-grounded QA from 46,469 clinical practice guidelines, and open-ended clinical vignettes
• Hardware: 8 NVIDIA GH200 nodes
• Framework: Axolotl with FSDP v2 / DeepSpeed ZeRO-3, Flash Attention 2, bf16 mixed precision
• Decontamination: System-wide two-stage n-gram and token-alignment decontamination against all evaluation benchmarks

Full hyperparameters are in Appendix I of the paper.

Compute & footprint

The training was done on 8 nodes of 4 NVIDIA GH200 GPUs for approximately 6 hours on the CSCS Swiss National Supercomputing Centre. Our trainings have a carbon neutral footprint as the CSCS data center is carbon neutral (CSCS energy efficiency).

Limitations & intended use

MeditronFO can produce text on a variety of topics, but the generated content may not always be factually accurate, logically consistent, or free from biases present in the training data. MeditronFO has been trained to be specialised for Medicine and is intended to be used for Medicine related tasks evaluation. These models should be used as assistive tools rather than definitive sources of information. Users should always verify important information and critically evaluate any generated content.

Citation

If you find MeditronFO useful in your research, please cite our preprint:

@misc{theimerlienhard2026fullyopenmeditronauditable,
  title         = {Fully Open Meditron: An Auditable Pipeline for Clinical LLMs},
  author        = {Xavier Theimer-Lienhard and Mushtaha El-Amin and Fay Elhassan and Sahaj Vaidya and Victor Cartier-Negadi and David Sasu and Lars Klein and Mary-Anne Hartley},
  year          = {2026},
  eprint        = {2605.16215},
  archivePrefix = {arXiv},
  primaryClass  = {cs.AI},
  url           = {https://arxiv.org/abs/2605.16215}
}

Contact

Please use the community tab for any discussions or issue related to this model. Questions related to the project can be sent to xavier.theimer-lienhard@epfl.ch or mary-anne.hartley@epfl.ch.