doctomodernbert-fr-large

DoctoModernBERT-fr-large

<center> <img src="assets/logo_doctomodernbert.png" width="100%" alt="DoctoModernBERT"> </center> <p align="center"> <a href="https://huggingface.co/blog/bofenghuang/doctobert-fr-release">🤗 Blog</a> | <a href="https://arxiv.org/abs/2606.22079">📄 Paper</a> | <a href="https://github.com/doctolib-lab/doctobert">💻 Code</a> | <a href="https://huggingface.co/collections/doctolib-lab/finemed-fr">🌐 FineMed</a> | <a href="https://huggingface.co/collections/doctolib-lab/doctobert-fr">🩺 DoctoBERT</a> </p>

📚 Introduction

DoctoModernBERT-fr-large is the large-size French medical encoder in the DoctoBERT family, for biomedical and clinical NLP. It uses the ModernBERT architecture (395M parameters, up to 8192-token context) and is pretrained from scratch on FineMed-fr and FineMed-rephrased-fr.

Its training data is curated from heterogeneous open web corpora (FineWeb-2, FinePDFs, FineWiki), which bring scale, source and stylistic diversity, and inherited quality control. Each document is annotated along three axes: subdomain, educational quality, and medical-term density. DoctoModernBERT then trains on a mix of two parts: the filtered high-quality, entity-rich documents, and LLM-rephrased variants that raise medical-term density and vary the contexts around medical terms across many genres, audiences, and registers. This breadth and density build robustness to real-world clinical text, which is often noisy and inconsistent in style.

For the base-size version, see DoctoModernBERT-fr-base. For a classic RoBERTa encoder, see DoctoBERT-fr-base.

🚀 How to Use

Requires a recent transformers with ModernBERT support.

Fill-mask

Using AutoModelForMaskedLM:

from transformers import AutoTokenizer, AutoModelForMaskedLM

model_id = "doctolib-lab/doctomodernbert-fr-large"
tokenizer = AutoTokenizer.from_pretrained(model_id)
model = AutoModelForMaskedLM.from_pretrained(model_id)

text = f"Le patient souffre d'une {tokenizer.mask_token} aiguë."
inputs = tokenizer(text, return_tensors="pt")
logits = model(**inputs).logits

masked_index = inputs["input_ids"][0].tolist().index(tokenizer.mask_token_id)
print(tokenizer.decode(logits[0, masked_index].argmax(-1)))

Using a pipeline:

from transformers import pipeline

fill = pipeline("fill-mask", model="doctolib-lab/doctomodernbert-fr-large")
print(fill(f"Le patient souffre d'une {fill.tokenizer.mask_token} aiguë."))

For long inputs, load with attn_implementation="flash_attention_2" for faster, more memory-efficient attention.

Fine-tuning

DoctoModernBERT fine-tunes like any BERT/ModernBERT encoder, with the appropriate task head or framework:

• For sequence classification, load it with AutoModelForSequenceClassification (see the text-classification guide).
• For token classification (NER), use AutoModelForTokenClassification (see the token-classification guide).
• For embeddings / retrieval, use Sentence Transformers or PyLate.

📐 Model Overview

🔧 Training

The tokenizer is a SentencePiece BPE model of 50,368 tokens, trained on the entity-rich FineMed-filtered subset (educational quality >= 4 and medical-term density >= 0.1) for efficient tokenization of dense medical vocabulary. It splits digits into single tokens and uses byte fallback for unseen characters.

DoctoModernBERT-fr-large is pretrained from scratch on a mix of FineMed-filtered (FineMed-fr under the same educational-quality and medical-term-density filter) and FineMed-rephrased-fr, over three phases totaling 140B tokens:

1. Pretraining (100B tokens). Masked-language-modeling at 1024-token context on the full mix (long documents are hierarchically chunked to fit the context window rather than truncated), building broad medical-language representations.
2. Context extension (20B tokens). Extends the context window from 1024 to 8192 tokens, training on a subset upsampled toward long documents.
3. Annealing (20B tokens). Continued training on the biomedical & clinical subdomains of the mix, focusing the final updates on content closest to downstream medical use.

⚠️ Intended Use & Limitations

DoctoModernBERT is an encoder for French biomedical and clinical NLP (NER, classification, retrieval, long-document tasks), used by fine-tuning on a downstream task. It is not generative and not a medical device; its outputs must not drive clinical decisions. It was pretrained on public web, PDF, and encyclopedic medical text and reflects the biases and gaps of those sources.

<!-- ## 📖 Citation ```bibtex @misc{doctobert2026, title = {Where Does the Signal Live? A Web Data Recipe for Medical Encoder Pretraining}, author = {Huang, Bofeng and Sun, Jacques and Bouchacourt, Diane and Barascud, Nicolas and Fogel, Fajwel}, year = {2026}, eprint = {2606.XXXXX}, archivePrefix = {arXiv}, primaryClass = {cs.CL} } ``` -->

⚖️ License

Released under Apache-2.0. DoctoModernBERT was trained on FineMed-fr and FineMed-rephrased-fr, which derive from FineWeb-2 / FinePDFs (ODC-BY 1.0) and FineWiki (CC BY-SA 4.0); please attribute those upstream sources.

🏛️ Acknowledgments

This work was granted access to the HPC resources of IDRIS (Jean Zay) under the allocations 2025-AD011016291 and 2026-A0200617487 made by GENCI.