README.md

---
license: mit
language:
- en
tags:
- life-sciences
- clinical
- biomedical
- bio
- medical
- biology
- synthetic
pretty_name: TransCorpus-bio
size_categories:
- 10M<n<100M
---
# TransCorpus-bio
**TransCorpus-bio** is a large-scale, parallel biomedical corpus consisting of PubMed abstracts. This dataset is used in the [TransCorpus Toolkit](https://github.com/jknafou/TransCorpus) and is designed to enable high-quality multi-lingual biomedical language modeling and downstream NLP research.

# Currently Translated with [TransCorpus Toolkit](https://github.com/jknafou/TransCorpus)
- In French : [TransCorpus-bio-fr 🤗](https://huggingface.co/datasets/jknafou/TransCorpus-bio-fr)
- In Spanish : [TransCorpus-bio-es 🤗](https://huggingface.co/datasets/jknafou/TransCorpus-bio-es)

# Dataset Details
- **Source**: PubMed abstracts (English)
- **Size**: 22 million abstracts, 30.2GB of text
- **Domain**: Biomedical, clinical, life sciences
- **Format**: one abstract per line

# Motivation
Non-English languages are low-resource languages for biomedical NLP, with limited availability of large, high-quality corpora. **TransCorpus-bio** bridges this gap by leveraging state-of-the-art neural machine translation to generate a massive, high-quality synthetic corpus, enabling robust pretraining and evaluation of Spanish biomedical language models.

```python
from datasets import load_dataset

dataset = load_dataset("jknafou/TransCorpus-bio", split="train")

print(dataset)
# Output:
# Dataset({
#    features: ['text'],
#    num_rows: 21567136
# })

print(dataset[0])
```

# Benchmark Results in our French Experiment
[TransBERT-bio-fr](https://huggingface.co/jknafou/TransBERT-bio-fr) pretrained on TransCorpus-bio-fr achieve state-of-the-art results on the French biomedical benchmark DrBenchmark, outperforming both general-domain and previous domain-specific models on classification, NER, POS, and STS tasks. See TransBERT-bio-fr for details.

# Why Synthetic Translation?
- **Scalable**: Enables creation of large-scale corpora for any language with a strong MT system.
- **Effective**: Supports state-of-the-art performance in downstream tasks.
- **Accessible**: Makes domain-specific NLP feasible for any languages.

# Citation
If you use this corpus, please cite:
```text
  @inproceedings{knafou-etal-2025-transbert,
      title = "{T}rans{BERT}: A Framework for Synthetic Translation in Domain-Specific Language Modeling",
      author = {Knafou, Julien  and
        Mottin, Luc  and
        Mottaz, Ana{\"i}s  and
        Flament, Alexandre  and
        Ruch, Patrick},
      editor = "Christodoulopoulos, Christos  and
        Chakraborty, Tanmoy  and
        Rose, Carolyn  and
        Peng, Violet",
      booktitle = "Findings of the Association for Computational Linguistics: EMNLP 2025",
      month = nov,
      year = "2025",
      address = "Suzhou, China",
      publisher = "Association for Computational Linguistics",
      url = "https://aclanthology.org/2025.findings-emnlp.1053/",
      doi = "10.18653/v1/2025.findings-emnlp.1053",
      pages = "19338--19354",
      ISBN = "979-8-89176-335-7",
      abstract = "The scarcity of non-English language data in specialized domains significantly limits the development of effective Natural Language Processing (NLP) tools. We present TransBERT, a novel framework for pre-training language models using exclusively synthetically translated text, and introduce TransCorpus, a scalable translation toolkit. Focusing on the life sciences domain in French, our approach demonstrates that state-of-the-art performance on various downstream tasks can be achieved solely by leveraging synthetically translated data. We release the TransCorpus toolkit, the TransCorpus-bio-fr corpus (36.4GB of French life sciences text), TransBERT-bio-fr, its associated pre-trained language model and reproducible code for both pre-training and fine-tuning. Our results highlight the viability of synthetic translation in a high-resource translation direction for building high-quality NLP resources in low-resource language/domain pairs."
  }
```