Description
Detect Drug, Dosage and administration instructions in text using pretraiend NER model.
Predicted Entities
DOSAGE
, DRUG
, STRENGTH
, FORM
, DURATION
, FREQUENCY
, ROUTE
Live Demo Open in Colab Copy S3 URI
How to use
document_assembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
sentence_detector = SentenceDetector()\
.setInputCols(["document"])\
.setOutputCol("sentence")
embeddings_clinical = BertEmbeddings.pretrained("biobert_pubmed_base_cased")\
.setInputCols(["sentence", "token"])\
.setOutputCol("embeddings")
clinical_ner = MedicalNerModel.pretrained("ner_posology_large_biobert", "en", "clinical/models")\
.setInputCols(["sentence", "token", "embeddings"])\
.setOutputCol("ner")
ner_converter = NerConverter()\
.setInputCols(["sentence", "token", "ner"])\
.setOutputCol("ner_chunk")
nlpPipeline = Pipeline(stages=[document_assembler, sentence_detector, tokenizer, embeddings_clinical, clinical_ner, ner_converter])
model = nlpPipeline.fit(spark.createDataFrame([[""]]).toDF("text"))
results = model.transform(spark.createDataFrame([["EXAMPLE_TEXT"]]).toDF("text"))
val document_assembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val sentence_detector = new SentenceDetector()
.setInputCols("document")
.setOutputCol("sentence")
val tokenizer = new Tokenizer()
.setInputCols("sentence")
.setOutputCol("token")
val embeddings_clinical = BertEmbeddings.pretrained("biobert_pubmed_base_cased")
.setInputCols(Array("sentence", "token"))
.setOutputCol("embeddings")
val ner = MedicalNerModel.pretrained("ner_posology_large_biobert", "en", "clinical/models")
.setInputCols(Array("sentence", "token", "embeddings"))
.setOutputCol("ner")
val ner_converter = new NerConverter()
.setInputCols(Array("sentence", "token", "ner"))
.setOutputCol("ner_chunk")
val pipeline = new Pipeline().setStages(Array(document_assembler, sentence_detector, tokenizer, embeddings_clinical, ner, ner_converter))
val result = pipeline.fit(data).transform(data)
import nlu
nlu.load("en.med_ner.posology.large_biobert").predict("""Put your text here.""")
Model Information
Model Name: | ner_posology_large_biobert |
Compatibility: | Healthcare NLP 3.0.0+ |
License: | Licensed |
Edition: | Official |
Input Labels: | [sentence, token, embeddings] |
Output Labels: | [ner] |
Language: | en |