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  • John Snow Labs
  • Jul 06, 2022

Detect PHI for Generic Deidentification in Romanian (BERT)

  • deidentification
  • bert
  • phi
  • ner
  • generic
  • ro
  • licensed

Description

Named Entity Recognition annotators allow for a generic model to be trained by using a Deep Learning architecture (Char CNNs - BiLSTM - CRF - word embeddings) inspired on a former state of the art model for NER: Chiu & Nicols, Named Entity Recognition with Bidirectional LSTM,CNN.

Deidentification NER (Romanian) is a Named Entity Recognition model that annotates text to find protected health information that may need to be de-identified. It is trained with bert_base_cased embeddings and can detect 7 generic entities.

This NER model is trained with a combination of custom datasets with several data augmentation mechanisms.

Predicted Entities

AGE, CONTACT, DATE, ID, LOCATION, NAME, PROFESSION

Live Demo Open in Colab Copy S3 URI

How to use

documentAssembler = DocumentAssembler()\
        .setInputCol("text")\
        .setOutputCol("document")
        
sentenceDetector = SentenceDetector()\
        .setInputCols(["document"])\
        .setOutputCol("sentence")

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

embeddings = BertEmbeddings.pretrained("bert_base_cased", "ro")\
	.setInputCols(["sentence","token"])\
	.setOutputCol("word_embeddings")

clinical_ner = MedicalNerModel.pretrained("ner_deid_generic_bert", "ro", "clinical/models")\
	.setInputCols(["sentence","token","word_embeddings"])\
	.setOutputCol("ner")

ner_converter = NerConverter()\
	.setInputCols(["sentence", "token", "ner"])\
	.setOutputCol("ner_chunk")
    
nlpPipeline = Pipeline(stages=[
        documentAssembler, 
        sentenceDetector, 
        tokenizer, 
        embeddings, 
        clinical_ner, 
        ner_converter])

text = """
Spitalul Pentru Ochi de Deal, Drumul Oprea Nr. 972 Vaslui, 737405 România
Tel: +40(235)413773
Data setului de analize: 25 May 2022 15:36:00
Nume si Prenume : BUREAN MARIA, Varsta: 77
Medic : Agota Evelyn Tımar
C.N.P : 2450502264401"""

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

results = nlpPipeline.fit(data).transform(data)

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

val sentenceDetector = new SentenceDetector()
        .setInputCols(Array("document"))
        .setOutputCol("sentence")

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

val embeddings = BertEmbeddings.pretrained("bert_base_cased", "ro")
	.setInputCols(Array("sentence","token"))
	.setOutputCol("word_embeddings")

val clinical_ner = MedicalNerModel.pretrained("ner_deid_generic_bert", "ro", "clinical/models")
        .setInputCols(Array("sentence","token","word_embeddings"))
        .setOutputCol("ner")

val ner_converter = new NerConverter()
	.setInputCols(Array("sentence", "token", "ner"))
	.setOutputCol("ner_chunk")
	
val pipeline = new Pipeline().setStages(Array(
        documentAssembler, 
        sentenceDetector, 
        tokenizer, 
        embeddings, 
        clinical_ner, 
        ner_converter))

val text = """Spitalul Pentru Ochi de Deal, Drumul Oprea Nr. 972 Vaslui, 737405 România
Tel: +40(235)413773
Data setului de analize: 25 May 2022 15:36:00
Nume si Prenume : BUREAN MARIA, Varsta: 77
Medic : Agota Evelyn Tımar
C.N.P : 2450502264401"""

val data = Seq(text).toDS.toDF("text")

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

import nlu
nlu.load("ro.med_ner.deid_generic_bert").predict("""
Spitalul Pentru Ochi de Deal, Drumul Oprea Nr. 972 Vaslui, 737405 România
Tel: +40(235)413773
Data setului de analize: 25 May 2022 15:36:00
Nume si Prenume : BUREAN MARIA, Varsta: 77
Medic : Agota Evelyn Tımar
C.N.P : 2450502264401""")

Results

+----------------------------+---------+
|chunk                       |ner_label|
+----------------------------+---------+
|Spitalul Pentru Ochi de Deal|LOCATION |
|Drumul Oprea Nr             |LOCATION |
|972                         |LOCATION |
|Vaslui                      |LOCATION |
|737405                      |LOCATION |
|+40(235)413773              |CONTACT  |
|25 May 2022                 |DATE     |
|BUREAN MARIA                |NAME     |
|77                          |AGE      |
|Agota Evelyn Tımar          |NAME     |
|2450502264401               |ID       |
+----------------------------+---------+

Model Information

Model Name: ner_deid_generic_bert
Compatibility: Healthcare NLP 3.5.0+
License: Licensed
Edition: Official
Input Labels: [sentence, token, embeddings]
Output Labels: [ner]
Language: ro
Size: 16.5 MB

References

  • Custom John Snow Labs datasets
  • Data augmentation techniques

Benchmarking

       label  precision    recall  f1-score   support
         AGE       0.95      0.97      0.96      1186
     CONTACT       0.99      0.98      0.98       366
        DATE       0.96      0.92      0.94      4518
          ID       1.00      1.00      1.00       679
    LOCATION       0.91      0.90      0.90      1683
        NAME       0.93      0.96      0.94      2916
  PROFESSION       0.87      0.85      0.86       161
   micro-avg       0.94      0.94      0.94     11509
   macro-avg       0.94      0.94      0.94     11509
weighted-avg       0.95      0.94      0.94     11509