Roberta Base Biomedical Es

🚀 Biomedical language model for Spanish

This is a biomedical pretrained language model for Spanish, which can be used for masked language modelling and is expected to be fine - tuned on downstream tasks.

🚀 Quick Start

This biomedical language model for Spanish can be used for masked language modelling tasks. For more details about the corpus, the pretraining and the evaluation, check the official repository and read our preprint.

✨ Features

• Ready - to - use for masked language modelling to perform the Fill Mask task.
• Intended to be fine - tuned on downstream tasks such as Named Entity Recognition or Text Classification.

📦 Installation

The installation process is mainly about using the transformers library in Python. You can install it via pip install transformers if not already installed.

💻 Usage Examples

Basic Usage

from transformers import AutoTokenizer, AutoModelForMaskedLM
tokenizer = AutoTokenizer.from_pretrained("BSC-TeMU/roberta-base-biomedical-es")
model = AutoModelForMaskedLM.from_pretrained("BSC-TeMU/roberta-base-biomedical-es")
from transformers import pipeline
unmasker = pipeline('fill-mask', model="BSC-TeMU/roberta-base-biomedical-es")
unmasker("El único antecedente personal a reseñar era la <mask> arterial.")

# Output
[
  {
    "sequence": " El único antecedente personal a reseñar era la hipertensión arterial.",
    "score": 0.9855039715766907,
    "token": 3529,
    "token_str": " hipertensión"
  },
  {
    "sequence": " El único antecedente personal a reseñar era la diabetes arterial.",
    "score": 0.0039140828885138035,
    "token": 1945,
    "token_str": " diabetes"
  },
  {
    "sequence": " El único antecedente personal a reseñar era la hipotensión arterial.",
    "score": 0.002484665485098958,
    "token": 11483,
    "token_str": " hipotensión"
  },
  {
    "sequence": " El único antecedente personal a reseñar era la Hipertensión arterial.",
    "score": 0.0023484621196985245,
    "token": 12238,
    "token_str": " Hipertensión"
  },
  {
    "sequence": " El único antecedente personal a reseñar era la presión arterial.",
    "score": 0.0008009297889657319,
    "token": 2267,
    "token_str": " presión"
  }
]

🔧 Technical Details

Tokenization and model pretraining

This model is a RoBERTa - based model trained on a biomedical corpus in Spanish collected from several sources (see next section).

The training corpus has been tokenized using a byte version of [Byte - Pair Encoding (BPE)](https://github.com/openai/gpt - 2) used in the original RoBERTA model with a vocabulary size of 52,000 tokens. The pretraining consists of a masked language model training at the subword level following the approach employed for the RoBERTa base model with the same hyperparameters as in the original work. The training lasted a total of 48 hours with 16 NVIDIA V100 GPUs of 16GB DDRAM, using Adam optimizer with a peak learning rate of 0.0005 and an effective batch size of 2,048 sentences.

Training corpora and preprocessing

The training corpus is composed of several biomedical corpora in Spanish, collected from publicly available corpora and crawlers. To obtain a high - quality training corpus, a cleaning pipeline with the following operations has been applied:

• Data parsing in different formats
  • Sentence splitting
  • Language detection
  • Filtering of ill - formed sentences
  • Deduplication of repetitive contents
  • Keep the original document boundaries

Finally, the corpora are concatenated and further global deduplication among the corpora have been applied. The result is a medium - size biomedical corpus for Spanish composed of about 963M tokens. The table below shows some basic statistics of the individual cleaned corpora:

📚 Documentation

The model has been evaluated on the Named Entity Recognition (NER) using the following datasets:

• PharmaCoNER: is a track on chemical and drug mention recognition from Spanish medical texts (for more info see: https://temu.bsc.es/pharmaconer/).
• CANTEMIST: is a shared task specifically focusing on named entity recognition of tumor morphology, in Spanish (for more info see: https://zenodo.org/record/3978041#.YTt5qH2xXbQ).
• ICTUSnet: consists of 1,006 hospital discharge reports of patients admitted for stroke from 18 different Spanish hospitals. It contains more than 79,000 annotations for 51 different kinds of variables.

The evaluation results are compared against the [mBERT](https://huggingface.co/bert - base - multilingual - cased) and [BETO](https://huggingface.co/dccuchile/bert - base - spanish - wwm - cased) models:

📄 License

[Apache License, Version 2.0](https://www.apache.org/licenses/LICENSE - 2.0)

Author

Text Mining Unit (TeMU) at the Barcelona Supercomputing Center (bsc - temu@bsc.es)

Contact information

For further information, send an email to <plantl - gob - es@bsc.es>

Copyright

Copyright by the Spanish State Secretariat for Digitalization and Artificial Intelligence (SEDIA) (2022)

Funding

This work was funded by the Spanish State Secretariat for Digitalization and Artificial Intelligence (SEDIA) within the framework of the Plan - TL.

Citation information

If you use our models, please cite our latest preprint:

@misc{carrino2021biomedical,
      title={Biomedical and Clinical Language Models for Spanish: On the Benefits of Domain - Specific Pretraining in a Mid - Resource Scenario}, 
      author={Casimiro Pio Carrino and Jordi Armengol - Estapé and Asier Gutiérrez - Fandiño and Joan Llop - Palao and Marc Pàmies and Aitor Gonzalez - Agirre and Marta Villegas},
      year={2021},
      eprint={2109.03570},
      archivePrefix={arXiv},
      primaryClass={cs.CL}
}

If you use our Medical Crawler corpus, please cite the preprint:

@misc{carrino2021spanish,
      title={Spanish Biomedical Crawled Corpus: A Large, Diverse Dataset for Spanish Biomedical Language Models}, 
      author={Casimiro Pio Carrino and Jordi Armengol - Estapé and Ona de Gibert Bonet and Asier Gutiérrez - Fandiño and Aitor Gonzalez - Agirre and Martin Krallinger and Marta Villegas},
      year={2021},
      eprint={2109.07765},
      archivePrefix={arXiv},
      primaryClass={cs.CL}
}

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