English BertForTokenClassification Cased model (from ncats)

Description

Pretrained BertForTokenClassification model, adapted from Hugging Face and curated to provide scalability and production-readiness using Spark NLP. EpiExtract4GARD-v2 is a English model originally trained by ncats.

Predicted Entities

ETHN, LOC, SEX, DATE, STAT, EPI

Live Demo Open in Colab Download Copy S3 URI

How to use

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

sentenceDetector = SentenceDetectorDLModel.pretrained("sentence_detector_dl", "xx")\
       .setInputCols(["document"])\
       .setOutputCol("sentence")

tokenizer = Tokenizer() \
    .setInputCols("sentence") \
    .setOutputCol("token")

tokenClassifier = BertForTokenClassification.pretrained("bert_ner_EpiExtract4GARD_v2","en") \
    .setInputCols(["sentence", "token"]) \
    .setOutputCol("ner")

pipeline = Pipeline(stages=[documentAssembler, sentenceDetector, tokenizer, tokenClassifier])

data = spark.createDataFrame([["PUT YOUR STRING HERE"]]).toDF("text")

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

val documentAssembler = new DocumentAssembler() 
          .setInputCol("text") 
          .setOutputCol("document")

val sentenceDetector = SentenceDetectorDLModel.pretrained("sentence_detector_dl", "xx")
       .setInputCols(Array("document"))
       .setOutputCol("sentence")

val tokenizer = new Tokenizer() 
    .setInputCols(Array("sentence"))
    .setOutputCol("token")

val tokenClassifier = BertForTokenClassification.pretrained("bert_ner_EpiExtract4GARD_v2","en") 
    .setInputCols(Array("sentence", "token")) 
    .setOutputCol("ner")

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

val data = Seq("PUT YOUR STRING HERE").toDF("text")

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

Model Information

References

• https://huggingface.co/ncats/EpiExtract4GARD-v2
• https://github.com/ncats/epi4GARD/blob/master/EpiExtract4GARD/extract_abs.py
• https://github.com/ncats/epi4GARD/blob/master/EpiExtract4GARD/gard-id-name-synonyms.json
• https://github.com/ncats/epi4GARD/tree/master/EpiExtract4GARD#epiextract4gard
• https://aws.amazon.com/ec2/instance-types/
• https://pubmed.ncbi.nlm.nih.gov/21659675/
• https://github.com/ncats/epi4GARD/blob/master/EpiExtract4GARD/Case%20Study.ipynb
• https://github.com/wzkariampuzha
• https://github.com/ncats/epi4GARD/blob/master/EpiExtract4GARD/classify_abs.py