Extract Biomarkers and their Results

Description

This model extracts mentions of biomarkers and biomarker results from oncology texts.

Definitions of Predicted Entities:

  • Biomarker: Biological molecules that indicate the presence or absence of cancer, or the type of cancer (including oncogenes).
  • Biomarker_Result: Terms or values that are identified as the result of a biomarkers.

Predicted Entities

Biomarker, Biomarker_Result

Live Demo Open in Colab Copy S3 URI

How to use

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

sentence_detector = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare","en","clinical/models")\
    .setInputCols(["document"])\
    .setOutputCol("sentence")

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

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

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

ner_converter = NerConverter() \
    .setInputCols(["sentence", "token", "ner"]) \
    .setOutputCol("ner_chunk")

pipeline = Pipeline(stages=[document_assembler,
                            sentence_detector,
                            tokenizer,
                            word_embeddings,
                            ner,
                            ner_converter])

data = spark.createDataFrame([["The results of immunohistochemical examination showed that she tested negative for CK7, synaptophysin (Syn), chromogranin A (CgA), Muc5AC, human epidermal growth factor receptor-2 (HER2), and Muc6; positive for CK20, Muc1, Muc2, E-cadherin, and p53; the Ki-67 index was about 87%."]]).toDF("text")

result = pipeline.fit(data).transform(data)
val document_assembler = new DocumentAssembler()
    .setInputCol("text")
    .setOutputCol("document")
    
val sentence_detector = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare","en","clinical/models")
    .setInputCols("document")
    .setOutputCol("sentence")
    
val tokenizer = new Tokenizer()
    .setInputCols("sentence")
    .setOutputCol("token")
    
val word_embeddings = WordEmbeddingsModel().pretrained("embeddings_clinical", "en", "clinical/models")
    .setInputCols(Array("sentence", "token"))
    .setOutputCol("embeddings")                
    
val ner = MedicalNerModel.pretrained("ner_oncology_biomarker", "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,
                            word_embeddings,
                            ner,
                            ner_converter))    

val data = Seq("The results of immunohistochemical examination showed that she tested negative for CK7, synaptophysin (Syn), chromogranin A (CgA), Muc5AC, human epidermal growth factor receptor-2 (HER2), and Muc6; positive for CK20, Muc1, Muc2, E-cadherin, and p53; the Ki-67 index was about 87%.").toDS.toDF("text")

val result = pipeline.fit(data).transform(data)
import nlu
nlu.load("en.med_ner.oncology_biomarker").predict("""The results of immunohistochemical examination showed that she tested negative for CK7, synaptophysin (Syn), chromogranin A (CgA), Muc5AC, human epidermal growth factor receptor-2 (HER2), and Muc6; positive for CK20, Muc1, Muc2, E-cadherin, and p53; the Ki-67 index was about 87%.""")

Results

| chunk                                    | ner_label        |
|:-----------------------------------------|:-----------------|
| negative                                 | Biomarker_Result |
| CK7                                      | Biomarker        |
| synaptophysin                            | Biomarker        |
| Syn                                      | Biomarker        |
| chromogranin A                           | Biomarker        |
| CgA                                      | Biomarker        |
| Muc5AC                                   | Biomarker        |
| human epidermal growth factor receptor-2 | Biomarker        |
| HER2                                     | Biomarker        |
| Muc6                                     | Biomarker        |
| positive                                 | Biomarker_Result |
| CK20                                     | Biomarker        |
| Muc1                                     | Biomarker        |
| Muc2                                     | Biomarker        |
| E-cadherin                               | Biomarker        |
| p53                                      | Biomarker        |
| Ki-67 index                              | Biomarker        |
| 87%                                      | Biomarker_Result |

Model Information

Model Name: ner_oncology_biomarker
Compatibility: Healthcare NLP 4.2.2+
License: Licensed
Edition: Official
Input Labels: [sentence, token, embeddings]
Output Labels: [ner]
Language: en
Size: 34.3 MB

References

In-house annotated oncology case reports.

Benchmarking

           label   tp  fp  fn  total  precision  recall   f1
Biomarker_Result 1030 148 415   1445       0.87    0.71 0.79
       Biomarker 1685 272 279   1964       0.86    0.86 0.86
       macro_avg 2715 420 694   3409       0.87    0.79 0.82
       micro_avg 2715 420 694   3409       0.87    0.80 0.83