Description
Extract different types of chemical compounds mentioned in text using pretrained NER model. This model is trained with the BertForTokenClassification method from the transformers library and imported into Spark NLP.
Predicted Entities
CHEM
How to use
documentAssembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
tokenizer = Tokenizer()\
.setInputCols(["document"])\
.setOutputCol("token")
tokenClassifier = MedicalBertForTokenClassifier.pretrained("bert_token_classifier_ner_chemicals", "en", "clinical/models")\
.setInputCols("token", "document")\
.setOutputCol("ner")\
.setCaseSensitive(True)
ner_converter = NerConverter()\
.setInputCols(["document","token","ner"])\
.setOutputCol("ner_chunk")
pipeline = Pipeline(stages=[documentAssembler, tokenizer, tokenClassifier, ner_converter])
data = spark.createDataFrame([["""The results have shown that the product p - choloroaniline is not a significant factor in chlorhexidine - digluconate associated erosive cystitis. "A high percentage of kanamycin - colistin and povidone - iodine irrigations were associated with erosive cystitis."""]]).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 tokenClassifier = MedicalBertForTokenClassifier.pretrained("bert_token_classifier_ner_chemicals", "en", "clinical/models")
.setInputCols(Array("document","token"))
.setOutputCol("ner")
.setCaseSensitive(True)
val ner_converter = NerConverter()
.setInputCols(Array("document","token","ner"))
.setOutputCol("ner_chunk")
val pipeline = new Pipeline().setStages(Array(documentAssembler, tokenizer, tokenClassifier, ner_converter))
val data = Seq("""The results have shown that the product p - choloroaniline is not a significant factor in chlorhexidine - digluconate associated erosive cystitis. "A high percentage of kanamycin - colistin and povidone - iodine irrigations were associated with erosive cystitis.""").toDS.toDF("text")
val result = pipeline.fit(data).transform(data)
import nlu
nlu.load("en.classify.token_bert.ner_chemical").predict("""The results have shown that the product p - choloroaniline is not a significant factor in chlorhexidine - digluconate associated erosive cystitis. "A high percentage of kanamycin - colistin and povidone - iodine irrigations were associated with erosive cystitis.""")
Results
+---------------------------+---------+
|chunk |ner_label|
+---------------------------+---------+
|p - choloroaniline |CHEM |
|chlorhexidine - digluconate|CHEM |
|kanamycin |CHEM |
|colistin |CHEM |
|povidone - iodine |CHEM |
+---------------------------+---------+
Model Information
| Model Name: | bert_token_classifier_ner_chemicals |
| Compatibility: | Healthcare NLP 3.3.4+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [sentence, token] |
| Output Labels: | [ner] |
| Language: | en |
| Size: | 404.3 MB |
| Case sensitive: | true |
| Max sentense length: | 512 |
Data Source
This model is trained on a custom dataset by John Snow Labs.
Benchmarking
label precision recall f1-score support
B-CHEM 0.99 0.92 0.95 30731
I-CHEM 0.99 0.93 0.96 31270
accuracy - - 0.93 62001
macro-avg 0.96 0.95 0.96 62001
weighted-avg 0.99 0.93 0.96 62001