Portuguese BioBERT Embeddings (from pucpr)

Description

Pretrained BioBERT Embeddings model, uploaded to Hugging Face, adapted and imported into Spark NLP. biobertpt-clin is a Portuguese model orginally trained by pucpr.

Download

How to use

documentAssembler = DocumentAssembler() \    
    .setInputCol("text") \    
    .setOutputCol("document")

tokenizer = Tokenizer() \
    .setInputCols("document") \
    .setOutputCol("token")
  
embeddings = BertEmbeddings.pretrained("biobert_embeddings_clinical","pt") \
    .setInputCols(["document", "token"]) \
    .setOutputCol("embeddings")
    
pipeline = Pipeline(stages=[documentAssembler, tokenizer, embeddings])

data = spark.createDataFrame([["Odeio o cancro"]]).toDF("text")

result = pipeline.fit(data).transform(data)
val documentAssembler = new DocumentAssembler() 
      .setInputCol("text") 
      .setOutputCol("document")
 
val tokenizer = new Tokenizer() 
    .setInputCols(Array("document"))
    .setOutputCol("token")

val embeddings = BertEmbeddings.pretrained("biobert_embeddings_clinical","pt") 
    .setInputCols(Array("document", "token")) 
    .setOutputCol("embeddings")

val pipeline = new Pipeline().setStages(Array(documentAssembler, tokenizer, embeddings))

val data = Seq("Odeio o cancro").toDF("text")

val result = pipeline.fit(data).transform(data)

Model Information

Model Name: biobert_embeddings_clinical
Compatibility: Spark NLP 3.4.2+
License: Open Source
Edition: Official
Input Labels: [sentence, token]
Output Labels: [bert]
Language: pt
Size: 667.9 MB
Case sensitive: true

References

  • https://huggingface.co/pucpr/biobertpt-clin
  • https://aclanthology.org/2020.clinicalnlp-1.7/
  • https://github.com/HAILab-PUCPR/BioBERTpt