transformers pytorch longformer fill-mask spanish biomedical clinical longformer-base-4096-biomedical-clinical-es es arxiv:2004.05150 license:apache-2.0 autotrain_compatible endpoints_compatible region:us
---
language:
- es
license: apache-2.0
tags:
- longformer
- spanish
- biomedical
- clinical
- longformer-base-4096-biomedical-clinical-es
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.
- text: 'Insuficiencia aórtica significativa, sin otras valvulopatías. Ventrículo
    derecho de tamaño y función normales. Raíz aórtica de diámetros aumentados (45
    mm), sin apreciarse clara imagen de flap. Vena cava inferior (VCI) normal. Derrame
    pericárdico ligero. Angio-TAC de aorta: disección aórtica tipo A con afectación
    de raíz aórtica que se extiende por la vertiente ant erior de la pared aórtica
    próxima al tronco coronario izquierdo (TCI) desde el plano valvular hasta el origen
    de arteria mesentérica inferior con afectación del origen proximal de TSA. Dilatación
    de raíz aórtica y de porción tubular de aorta ascendente (47 mm). Cayado 37 mm.
    Aorta descendente 31 mm. A nivel de aorta toraco-abdominal la luz verdadera presenta
    un calibre re ducido. Tronco celiaco, mesentérica superior y renal derecha tienen
    su origen en la luz verdadera. Renal izquierda se origina en una puerta de comunicación
    entre la luz verdadera y la falsa luz con buena perfusi ón renal. Aorta distal
    y sector iliofemoral normal. Conclusión: disección tipo A que se extiende desde
    raíz aórtica hasta el segmento aórtico proximal al origen de mesentérica inferior.
    EVOLUCIÓN CLÍNICA Ante un paciente con dolor torácico opresivo intenso, sin alteraciones
    significativas a nivel de ECG sugestivas de isquemia, se decidió realizar ETT
    urgente, objetivando una dilatación de raíz aórtica con insuficiencia signi ficativa.
    Ante estos hallazgos, se decidió solicitar angio-TAC que confirmó el diagnóstico
    de disección aórtica tipo A. Co n los resultados de las exploraciones complementarias
    y el diagnóstico, se contactó con el servicio de cirugía c ardiaca, realizándose
    intervención quirúrgica de forma emergente con técnica de Bono-Bentall mecánico
    (Carboseal 29 mm) (consiste en realizar en una misma intervención quirúrgica un
    reemplazo valvular aórtico, un reemplazo d e raíz aórtica y aorta ascendente,
    así como el reimplante de ostium coronarios), bajo circulación extracorpórea,
    parada electromecánica del corazón y parada circulatoria con perfusión cerebral
    selectiva bicarotídea. No se realizó recambio de arco <mask> ni aorta descendente
    dada la situación crítica del paciente, la complejid ad de la intervención y la
    mejoría tras eliminar el desgarro principal y reinstauración de flujo a luz verdadera.'
---

# Biomedical Longformer base for Spanish

## Table of contents
<details>
<summary>Click to expand</summary>

- [Model description](#model-description)
- [Intended uses and limitations](#intended-use)
- [How to use](#how-to-use)
- [Limitations and bias](#limitations-and-bias)
- [Training](#training)
- [Evaluation](#evaluation)
- [Additional information](#additional-information)
  - [Author](#author)
  - [Contact information](#contact-information)
  - [Copyright](#copyright)
  - [Licensing information](#licensing-information)
  - [Funding](#funding)
  - [Disclaimer](#disclaimer)
  
</details>

## Model description
The **longformer-base-4096-biomedical-clinical-es** is the [Longformer](https://huggingface.co/allenai/longformer-base-4096) version of the [roberta-base-biomedical-clinical-es](https://huggingface.co/PlanTL-GOB-ES/roberta-base-biomedical-clinical-es) model. The model started from the **roberta-base-biomedical-clinical-es** checkpoint and was pretrained for MLM on long documents from our biomedical and clinical corpora.

Longformer uses a combination of sliding window (local) attention and global attention. Global attention is user-configured based on the task to allow the model to learn task-specific representations. Please refer to the original [paper](https://arxiv.org/abs/2004.05150) for more details on how to set global attention.

For more details about the corpus, the pretraining, and the evaluation, check the official [repository](https://github.com/TeMU-BSC/longformer-es).


## Intended uses and limitations
The **longformer-base-4096-biomedical-clinical-es** model is ready-to-use only for masked language modeling to perform the Fill Mask task (try the inference API or read the next section). However, it is intended to be fine-tuned on non-generative downstream tasks such as Question Answering, Text Classification, or Named Entity Recognition.

## How to use
Here is how to use this model:

```python
from transformers import AutoModelForMaskedLM
from transformers import AutoTokenizer, FillMaskPipeline
from pprint import pprint
tokenizer_hf = AutoTokenizer.from_pretrained('PlanTL-GOB-ES/longformer-base-4096-biomedical-clinical-es')
model = AutoModelForMaskedLM.from_pretrained('PlanTL-GOB-ES/longformer-base-4096-biomedical-clinical-es')
model.eval()
pipeline = FillMaskPipeline(model, tokenizer_hf)
text = f"El único antecedente personal a reseñar era la <mask> arterial."
res_hf = pipeline(text)
pprint([r['token_str'] for r in res_hf])
```

## Limitations and bias
At the time of submission, no measures have been taken to estimate the bias embedded in the model. However, we are well aware that our models may be biased since the corpora have been collected using crawling techniques on multiple web sources. We intend to conduct research in these areas in the future, and if completed, this model card will be updated.

## Training
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:

  - data parsing in different formats
  - sentence splitting
  - language detection
  - filtering of ill-formed sentences 
  - deduplication of repetitive contents
  - keep the original document boundaries

Then, the biomedical corpora are concatenated and further global deduplication among the biomedical corpora have been applied.
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:

    
| Name                                                                                    | No. tokens  | Description                                                                                                                                                                                                                                          |
|-----------------------------------------------------------------------------------------|-------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| [Medical crawler](https://zenodo.org/record/4561970)                                    | 745,705,946 | Crawler of more than 3,000 URLs belonging to Spanish biomedical and health domains.                                                                                                                                                                                 |
| 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.                                                                                                                                                                                 |
| 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.                                                                                                                                                                                 |
| [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 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.                                                                                                                                                                    |
| 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.                                                                                                                                              |


For more details about the corpus, the pretraining, and the evaluation, check the official [repository](https://github.com/TeMU-BSC/longformer-es).

## Evaluation
The **longformer-base-4096-biomedical-clinical-es** was succesfully evaluated in a clinical coding task of discharge reports that do not fit in a standard 512 token sequence. The longformer version clearly outperformed the regular RoBERTa model. Currently, due to legal restrictions, we cannot distribute the evaluation corpus or the results.

## Additional information

### 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)

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

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

### Disclaimer

<details>
<summary>Click to expand</summary>

The models published in this repository are intended for a generalist purpose and are available to third parties. These models may have bias and/or any other undesirable distortions.

When third parties, deploy or provide systems and/or services to other parties using any of these models (or using systems based on these models) or become users of the models, they should note that it is their responsibility to mitigate the risks arising from their use and, in any event, to comply with applicable regulations, including regulations regarding the use of Artificial Intelligence.

In no event shall the owner of the models (SEDIA – State Secretariat for Digitalization and Artificial Intelligence) nor the creator (BSC – Barcelona Supercomputing Center) be liable for any results arising from the use made by third parties of these models.


Los modelos publicados en este repositorio tienen una finalidad generalista y están a disposición de terceros. Estos modelos pueden tener sesgos y/u otro tipo de distorsiones indeseables.

Cuando terceros desplieguen o proporcionen sistemas y/o servicios a otras partes usando alguno de estos modelos (o utilizando sistemas basados en estos modelos) o se conviertan en usuarios de los modelos, deben tener en cuenta que es su responsabilidad mitigar los riesgos derivados de su uso y, en todo caso, cumplir con la normativa aplicable, incluyendo la normativa en materia de uso de inteligencia artificial.

En ningún caso el propietario de los modelos (SEDIA – Secretaría de Estado de Digitalización e Inteligencia Artificial) ni el creador (BSC – Barcelona Supercomputing Center) serán responsables de los resultados derivados del uso que hagan terceros de estos modelos.
</details>