Description

This model is a spaCy SpanCategorizer model trained from scratch on Dutch echocardiogram reports sourced from Electronic Health Records. The publication associated with the span classification task can be found at https://arxiv.org/abs/2408.06930. The config file for training the model can be found at https://github.com/umcu/echolabeler.

Minimum working example

!pip install https://huggingface.co/baukearends/Echocardiogram-SpanCategorizer-pericardial-effusion/resolve/main/nl_Echocardiogram_SpanCategorizer_pericardial_efuusion-any-py3-none-any.whl

import spacy
nlp = spacy.load("nl_Echocardiogram_SpanCategorizer_pericardial_effusion")

prediction = nlp("Op dit echo geen duidelijke WMA te zien, goede systolische L.V. functie, wel L.V.H., diastolische dysfunctie graad 1A tot 2. Geringe aortastenose en - matige -insufficientie. Geringe M.I. Geen PE.")
for span, score in zip(prediction.spans['sc'], prediction.spans['sc'].attrs['scores']):
    print(f"Span: {span}, label: {span.label_}, score: {score[0]:.3f}")

Label Scheme

View label scheme (5 labels for 1 components)

Component	Labels
`spancat`	`pe_not_present`, `pe_moderate`, `pe_mild`, `pe_severe`, `pe`

Intended use

The model is developed for span classification on Dutch clinical text. Since it is a domain-specific model trained on medical data, it is meant to be used on medical NLP tasks for Dutch.

Data

The model was trained on approximately 4,000 manually annotated echocardiogram reports from the University Medical Centre Utrecht. The training data was anonymized before starting the training procedure.

Feature	Description
Name	`Echocardiogram_SpanCategorizer_pericardial_effusion`
Version	`1.0.0`
spaCy	`>=3.7.4,<3.8.0`
Default Pipeline	`tok2vec`, `spancat`
Components	`tok2vec`, `spancat`
License	`cc-by-sa-4.0`
Author	Bauke Arends

Contact

If you are having problems with this model please add an issue on our git: https://github.com/umcu/echolabeler/issues

Usage

If you use the model in your work please use the following referral; https://doi.org/10.48550/arXiv.2408.06930

References

Paper: Bauke Arends, Melle Vessies, Dirk van Osch, Arco Teske, Pim van der Harst, René van Es, Bram van Es (2024): Diagnosis extraction from unstructured Dutch echocardiogram reports using span- and document-level characteristic classification, Arxiv https://arxiv.org/abs/2408.06930

baukearends
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Echocardiogram-SpanCategorizer-pericardial-effusion