Detect Assertion Status (assertion_bert_classification_radiology)

Description

Assign assertion status to clinical entities.

Predicted Entities

Confirmed, Suspected, Negative

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How to use

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

sentence_detector = SentenceDetector()\
    .setInputCols("document")\
    .setOutputCol("sentence")

tokenizer = Tokenizer()\
    .setInputCols(["document"])\
    .setOutputCol("token")
    
embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")\
    .setInputCols(["sentence", "token"])\
    .setOutputCol("embeddings")\
    .setCaseSensitive(False)

ner = MedicalNerModel.pretrained("ner_clinical", "en", "clinical/models")\
    .setInputCols(["sentence", "token", "embeddings"])\
    .setOutputCol("ner")

ner_converter = NerConverterInternal()\
    .setInputCols(["sentence", "token", "ner"])\
    .setOutputCol("ner_chunk")\
    .setWhiteList(["PROBLEM"])
    
assertion_classifier = BertForAssertionClassification.pretrained("assertion_bert_classification_radiology", "en", "clinical/models")\
    .setInputCols(["sentence", "ner_chunk"])\
    .setOutputCol("assertion_class")
    
pipeline = Pipeline(stages=[
    document_assembler, 
    sentence_detector,
    tokenizer,
    embeddings,
    ner,
    ner_converter,
    assertion_classifier
])

text = """Patient with severe fever and sore throat.
He shows no stomach pain and he maintained on an epidural and PCA for pain control.
He also became short of breath with climbing a flight of stairs.
After CT, lung tumor located at the right lower lobe. Father with Alzheimer.
"""

data = spark.createDataFrame([[text]]).toDF("text")                         
result = pipeline.fit(data).transform(data)

# show results
result.selectExpr("explode(assertion_class) as result")\
      .selectExpr("result.metadata['ner_chunk'] as ner_chunk",
                  "result.begin as begin",
                  "result.begin as end",
                  "result.metadata['ner_label'] as ner_chunk",
                  "result.result as assertion").show(truncate=False)

# Test classifier in Spark NLP pipeline
document_assembler = nlp.DocumentAssembler() \
    .setInputCol("text") \
    .setOutputCol("document")

sentence_detector = nlp.SentenceDetector()\
    .setInputCols("document")\
    .setOutputCol("sentence")
    
tokenizer = nlp.Tokenizer() \
    .setInputCols(["sentence"]) \
    .setOutputCol("token")

embeddings = nlp.WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")\
    .setInputCols(["sentence", "token"])\
    .setOutputCol("embeddings")\
    .setCaseSensitive(False)

ner = medical.NerModel.pretrained("ner_clinical", "en", "clinical/models")\
    .setInputCols(["sentence", "token", "embeddings"])\
    .setOutputCol("ner")

ner_converter = medical.NerConverterInternal()\
    .setInputCols(["sentence", "token", "ner"])\
    .setOutputCol("ner_chunk")\
    .setWhiteList(["PROBLEM"])
    
assertion_classifier = medical.BertForAssertionClassification.pretrained("assertion_bert_classification_radiology", "en", "clinical/models")\
    .setInputCols(["sentence", "ner_chunk"])\
    .setOutputCol("assertion_class")
    
pipeline = nlp.Pipeline(stages=[
    document_assembler, 
    sentence_detector,
    tokenizer,
    embeddings,
    ner,
    ner_converter,
    assertion_classifier
])

text = """Patient with severe fever and sore throat.
He shows no stomach pain and he maintained on an epidural and PCA for pain control.
He also became short of breath with climbing a flight of stairs.
After CT, lung tumor located at the right lower lobe. Father with Alzheimer.
"""

data = spark.createDataFrame([[text]]).toDF("text")                         
result = pipeline.fit(data).transform(data)

# show results
result.selectExpr("explode(assertion_class) as result")\
      .selectExpr("result.metadata['ner_chunk'] as ner_chunk",
                  "result.begin as begin",
                  "result.begin as end",
                  "result.metadata['ner_label'] as ner_chunk",
                  "result.result as assertion").show(truncate=False)

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

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

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

val embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")
    .setInputCols(Array("sentence", "token"))
    .setOutputCol("embeddings")
    .setCaseSensitive(False)

val ner = MedicalNerModel.pretrained("ner_clinical", "en", "clinical/models")
    .setInputCols(Array("sentence", "token", "embeddings"))
    .setOutputCol("ner")

val ner_converter = new NerConverterInternal()
    .setInputCols(Array("sentence", "token", "ner"))
    .setOutputCol("ner_chunk")
    .setWhiteList(Array("PROBLEM"))
        
val assertion_classifier = BertForAssertionClassification.pretrained("assertion_bert_classification_radiology", "en", "clinical/models")
    .setInputCols(Array("document", "ner_chunk"))
    .setOutputCol("assertion_class")

val pipeline = new Pipeline().setStages(
    Array(
        document_assembler, 
        sentence_detector,
        tokenizer, 
        embeddings,
        ner,
        ner_converter,
        assertion_classifier
))

val text = """Patient with severe fever and sore throat.
He shows no stomach pain and he maintained on an epidural and PCA for pain control.
He also became short of breath with climbing a flight of stairs.
After CT, lung tumor located at the right lower lobe. Father with Alzheimer.
"""
val data = Seq(Array(text)).toDF("text")                         
val result = pipeline.fit(data).transform(data)

Results

|    | ner_chunk       |   begin |   end | ner_chunk   | assertion   |
|---:|:----------------|--------:|------:|:------------|:------------|
|  0 | severe fever    |      13 |    13 | PROBLEM     | Confirmed   |
|  1 | sore throat     |      30 |    30 | PROBLEM     | Confirmed   |
|  2 | stomach pain    |      55 |    55 | PROBLEM     | Negative    |
|  3 | pain control    |     113 |   113 | PROBLEM     | Confirmed   |
|  4 | short of breath |     142 |   142 | PROBLEM     | Confirmed   |
|  5 | lung tumor      |     202 |   202 | PROBLEM     | Confirmed   |
|  6 | Alzheimer       |     258 |   258 | PROBLEM     | Confirmed   |

Model Information

Model Name: assertion_bert_classification_radiology
Compatibility: Healthcare NLP 5.5.3+
License: Licensed
Edition: Official
Input Labels: [document, token]
Output Labels: [assertion_class]
Language: en
Size: 406.2 MB
Case sensitive: true

Benchmarking

       label  precision    recall  f1-score   support
   Confirmed      0.966     0.955     0.960      3519
    Negative      0.967     0.977     0.972       605
   Suspected      0.866     0.893     0.879      1089
    accuracy        -         -       0.944      5213
   macro-avg      0.933     0.941     0.937      5213
weighted-avg      0.945     0.944     0.945      5213