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--- |
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language: |
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- es |
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tags: |
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- biomedical |
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- clinical |
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- spanish |
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license: apache-2.0 |
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metrics: |
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- ppl |
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widget: |
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- text: "El único antecedente personal a reseñar era la <mask> arterial." |
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- text: "Las radiologías óseas de cuerpo entero no detectan alteraciones <mask>, ni alteraciones vertebrales." |
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- text: "En el <mask> toraco-abdómino-pélvico no se encontraron hallazgos patológicos de interés." |
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--- |
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**⚠️NOTICE⚠️: THIS MODEL HAS BEEN MOVED TO THE FOLLOWING URL AND WILL SOON BE REMOVED:** https://huggingface.co/PlanTL-GOB-ES/roberta-base-biomedical-clinical-es |
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# Biomedical-clinical language model for Spanish |
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Biomedical pretrained language model for Spanish. For more details about the corpus, the pretraining and the evaluation, check the official [repository](https://github.com/PlanTL-SANIDAD/lm-biomedical-clinical-es) and read our [preprint](https://arxiv.org/abs/2109.03570) "_Carrino, C. P., Armengol-Estapé, J., Gutiérrez-Fandiño, A., Llop-Palao, J., Pàmies, M., Gonzalez-Agirre, A., & Villegas, M. (2021). Biomedical and Clinical Language Models for Spanish: On the Benefits of Domain-Specific Pretraining in a Mid-Resource Scenario._". |
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## Tokenization and model pretraining |
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This model is a [RoBERTa-based](https://github.com/pytorch/fairseq/tree/master/examples/roberta) model trained on a |
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**biomedical-clinical** corpus in Spanish collected from several sources (see next section). |
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The training corpus has been tokenized using a byte version of [Byte-Pair Encoding (BPE)](https://github.com/openai/gpt-2) |
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used in the original [RoBERTA](https://github.com/pytorch/fairseq/tree/master/examples/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. |
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## Training corpora and preprocessing |
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The training corpus is composed of several biomedical corpora in Spanish, collected from publicly available corpora and crawlers, and a real-world clinical corpus collected from more than 278K clinical documents and notes. To obtain a high-quality training corpus while retaining the idiosyncrasies of the clinical language, a cleaning pipeline has been applied only to the biomedical corpora, keeping the clinical corpus uncleaned. Essentially, the cleaning operations used are: |
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- data parsing in different formats |
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- sentence splitting |
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- language detection |
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- filtering of ill-formed sentences |
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- deduplication of repetitive contents |
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- keep the original document boundaries |
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Then, the biomedical corpora are concatenated and further global deduplication among the biomedical corpora have been applied. |
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Eventually, the clinical corpus is concatenated to the cleaned biomedical corpus resulting in a medium-size biomedical-clinical corpus for Spanish composed of more than 1B tokens. The table below shows some basic statistics of the individual cleaned corpora: |
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| Name | No. tokens | Description | |
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|-----------------------------------------------------------------------------------------|-------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| |
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| [Medical crawler](https://zenodo.org/record/4561970) | 745,705,946 | Crawler of more than 3,000 URLs belonging to Spanish biomedical and health domains. | |
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| Clinical cases misc. | 102,855,267 | A miscellany of medical content, essentially clinical cases. Note that a clinical case report is a scientific publication where medical practitioners share patient cases and it is different from a clinical note or document. | |
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| Clinical notes/documents | 91,250,080 | Collection of more than 278K clinical documents, including discharge reports, clinical course notes and X-ray reports, for a total of 91M tokens. | |
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| [Scielo](https://github.com/PlanTL-SANIDAD/SciELO-Spain-Crawler) | 60,007,289 | Publications written in Spanish crawled from the Spanish SciELO server in 2017. | |
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| [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. | |
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| Wikipedia_life_sciences | 13,890,501 | Wikipedia articles crawled 04/01/2021 with the [Wikipedia API python library](https://pypi.org/project/Wikipedia-API/) starting from the "Ciencias\_de\_la\_vida" category up to a maximum of 5 subcategories. Multiple links to the same articles are then discarded to avoid repeating content. | |
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| 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". | |
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| [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. | |
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| [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. | |
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| PubMed | 1,858,966 | Open-access articles from the PubMed repository crawled in 2017. | |
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## Evaluation and results |
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The model has been evaluated on the Named Entity Recognition (NER) using the following datasets: |
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- [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/). |
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- [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). |
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- 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. |
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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: |
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| F1 - Precision - Recall | roberta-base-biomedical-clinical-es | mBERT | BETO | |
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|---------------------------|----------------------------|-------------------------------|-------------------------| |
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| PharmaCoNER | **90.04** - **88.92** - **91.18** | 87.46 - 86.50 - 88.46 | 88.18 - 87.12 - 89.28 | |
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| CANTEMIST | **83.34** - **81.48** - **85.30** | 82.61 - 81.12 - 84.15 | 82.42 - 80.91 - 84.00 | |
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| ICTUSnet | **88.08** - **84.92** - **91.50** | 86.75 - 83.53 - 90.23 | 85.95 - 83.10 - 89.02 | |
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## Intended uses & limitations |
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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) |
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However, the is intended to be fine-tuned on downstream tasks such as Named Entity Recognition or Text Classification. |
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## Cite |
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If you use our models, please cite our latest preprint: |
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```bibtex |
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@misc{carrino2021biomedical, |
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title={Biomedical and Clinical Language Models for Spanish: On the Benefits of Domain-Specific Pretraining in a Mid-Resource Scenario}, |
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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}, |
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year={2021}, |
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eprint={2109.03570}, |
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archivePrefix={arXiv}, |
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primaryClass={cs.CL} |
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} |
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``` |
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If you use our Medical Crawler corpus, please cite the preprint: |
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```bibtex |
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@misc{carrino2021spanish, |
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title={Spanish Biomedical Crawled Corpus: A Large, Diverse Dataset for Spanish Biomedical Language Models}, |
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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}, |
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year={2021}, |
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eprint={2109.07765}, |
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archivePrefix={arXiv}, |
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primaryClass={cs.CL} |
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} |
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``` |
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--- |
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--- |
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## How to use |
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```python |
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from transformers import AutoTokenizer, AutoModelForMaskedLM |
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tokenizer = AutoTokenizer.from_pretrained("BSC-TeMU/roberta-base-biomedical-es") |
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model = AutoModelForMaskedLM.from_pretrained("BSC-TeMU/roberta-base-biomedical-es") |
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from transformers import pipeline |
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unmasker = pipeline('fill-mask', model="BSC-TeMU/roberta-base-biomedical-es") |
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unmasker("El único antecedente personal a reseñar era la <mask> arterial.") |
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``` |
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``` |
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# Output |
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[ |
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{ |
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"sequence": " El único antecedente personal a reseñar era la hipertensión arterial.", |
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"score": 0.9855039715766907, |
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"token": 3529, |
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"token_str": " hipertensión" |
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}, |
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{ |
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"sequence": " El único antecedente personal a reseñar era la diabetes arterial.", |
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"score": 0.0039140828885138035, |
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"token": 1945, |
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"token_str": " diabetes" |
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}, |
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{ |
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"sequence": " El único antecedente personal a reseñar era la hipotensión arterial.", |
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"score": 0.002484665485098958, |
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"token": 11483, |
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"token_str": " hipotensión" |
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}, |
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{ |
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"sequence": " El único antecedente personal a reseñar era la Hipertensión arterial.", |
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"score": 0.0023484621196985245, |
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"token": 12238, |
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"token_str": " Hipertensión" |
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}, |
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{ |
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"sequence": " El único antecedente personal a reseñar era la presión arterial.", |
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"score": 0.0008009297889657319, |
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"token": 2267, |
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"token_str": " presión" |
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} |
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] |
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``` |
