Model Card for Cardioner.Cz 128 Paragraph
This a ufal/robeczech-base base model finetuned for span classification. For this model we used IOB-tagging. Using the IOB-tagging schema facilitates the aggregation of predictions over sequences. This specific model is trained on a batch of about 500 span-labeled documents.
This is version was trained with context windows of 128 tokens. For the chunking we used a paragraph-based splitter.
The training was performed with 10 fold CV, with weight averaging of the best epochs per fold.
Expected input and output
The input should be a string with Czech cardio clinical text.
CardioNER.cz_128_paragraph is a muticlass span classification model. The classes that can be predicted are ['procedure,medication,disease,symptom'].
Extracting span classification from CardioNER.cz_128_paragraph
The following script converts a string of <512 tokens to a list of span predictions.
from transformers import pipeline
le_pipe = pipeline('ner',
model=model,
tokenizer=model, aggregation_strategy="simple",
device=-1)
named_ents = le_pipe(SOME_TEXT)
To process a string of arbitrary length you can split the string into sentences or paragraphs using e.g. pysbd or spacy(sentencizer) and iteratively parse the list of with the span-classification pipe. You can also use the strider built in the transformer pipeline, although this is limited to non-overlapping strides plus it requires a FastTokenizer and it does not work for aggregation_strategy=None;
named_ents = le_pipe(SOME_TEXT, stride=256)
Data description
CardioCCC; manually labeled cardiology discharge letters; procedure, medication, disease, symptom
Acknowledgement
This is part of the DT4H project.
Doi and reference
For more details about training/eval and other scripts, see CardioNER github repo. and for more information on the background, see Datatools4Heart Huggingface/Website
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Model tree for UMCU/cardioner.cz_128_paragraph
Base model
ufal/robeczech-base