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---
language:
- es
tags:
- biomedical
- spanish
license: apache-2.0
metrics:
- ppl
widget:
- text: "El único antecedente personal a reseñar era la <mask> arterial."
- text: "Las radiologías óseas de cuerpo entero no detectan alteraciones <mask>, ni alteraciones vertebrales."
- text: "En el <mask> toraco-abdómino-pélvico no se encontraron hallazgos patológicos de interés."
---
# Biomedical language model for Spanish
## BibTeX citation
If you use any of these resources (datasets or models) in your work, please cite our latest paper:
```bibtex
@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}
}
```
## Model and tokenization
This model is a [RoBERTa-based](https://github.com/pytorch/fairseq/tree/master/examples/roberta) model trained on a
biomedical corpus collected from several sources (see next section).
## Training corpora and preprocessing
The training corpus is composed of several biomedical corpora in Spanish, collected from publicly available corpora and crawlers:
| Name | No. tokens | Description |
|-----------------------------------------------------------------------------------------|-------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| [Medical crawler](https://zenodo.org/record/4561971#.YTtwM32xXbQ) | 745,705,946 | Crawler of more than 3,000 URLs belonging to Spanish biomedical and health domains. |
| [Scielo](https://github.com/PlanTL-SANIDAD/SciELO-Spain-Crawler) | 60,007,289 | Publications written in Spanish crawled from the Spanish SciELO server in 2017. |
| [BARR2_background](https://temu.bsc.es/BARR2/downloads/background_set.raw_text.tar.bz2) | 24,516,442 | Biomedical Abbreviation Recognition and Resolution (BARR2) containing Spanish clinical case study sections from a variety of clinical disciplines. |
| Wikipedia_life_sciences | 13,890,501 | Wikipedia articles belonging to the Life Sciences category crawled on 04/01/2021 |
| Patents | 13,463,387 | Google Patent in Medical Domain for Spain (Spanish). The accepted codes (Medical Domain) for Json files of patents are: "A61B", "A61C","A61F", "A61H", "A61K", "A61L","A61M", "A61B", "A61P". |
| [EMEA](http://opus.nlpl.eu/download.php?f=EMEA/v3/moses/en-es.txt.zip) | 5,377,448 | Spanish-side documents extracted from parallel corpora made out of PDF documents from the European Medicines Agency. |
| [mespen_Medline](https://zenodo.org/record/3562536#.YTt1fH2xXbR) | 4,166,077 | Spanish-side articles extracted from a collection of Spanish-English parallel corpus consisting of biomedical scientific literature. The collection of parallel resources are aggregated from the MedlinePlus source. |
| PubMed | 1,858,966 | Open-access articles from the PubMed repository crawled in 2017. |
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 860M tokens.
## Evaluation and results
The model has been evaluated on the Named Entity Recognition (NER) using the following datasets:
- [PharmaCoNER](https://zenodo.org/record/4270158): is a track on chemical and drug mention recognition from Spanish medical texts (for more info see: https://temu.bsc.es/pharmaconer/).
- [CANTEMIST](https://zenodo.org/record/3978041#.YTt5qH2xXbQ): 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:
| F1 - Precision - Recall | roberta-base-biomedical-es | mBERT | BETO |
|---------------------------|----------------------------|-------------------------------|-------------------------|
| PharmaCoNER | **89.48** - **87.85** - **91.18** | 87.46 - 86.50 - 88.46 | 88.18 - 87.12 - 89.28 |
| CANTEMIST | **83.87** - **81.70** - **86.17** | 82.61 - 81.12 - 84.15 | 82.42 - 80.91 - 84.00 |
| ICTUSnet | **88.12** - **85.56** - **90.83** | 86.75 - 83.53 - 90.23 | 85.95 - 83.10 - 89.02 |
## Intended uses & limitations
The model is ready-to-use only for masked language modelling to perform the Fill Mask task (try the inference API or read the next section)
However, the is intended to be fine-tuned on downstream tasks such as Named Entity Recognition or Text Classification.
---
## How to use
```python
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"
}
]
``` |