Extract Demographic Entities from Voice of the Patient Documents (embeddings_clinical)

Description

This model extracts demographic terms from the documents transferred from the patient’s own sentences.

Predicted Entities

Gender, Employment, RaceEthnicity, Age, Substance, RelationshipStatus, SubstanceQuantity

Live Demo Open in Colab Download 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_vop_demographic", "en", "clinical/models") \
    .setInputCols(["sentence", "token", "embeddings"]) \
    .setOutputCol("ner")

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

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

data = spark.createDataFrame([["My grandma, who's 85 and Black, just had a pacemaker implanted in the cardiology department. The doctors say it'll help regulate her heartbeat and prevent future complications."]]).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_vop_demographic", "en", "clinical/models")
    .setInputCols(Array("sentence", "token", "embeddings"))
    .setOutputCol("ner")
    
val ner_converter = new NerConverterInternal()
    .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("My grandma, who's 85 and Black, just had a pacemaker implanted in the cardiology department. The doctors say it'll help regulate her heartbeat and prevent future complications.").toDS.toDF("text")

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

Results

| chunk   | ner_label     |
|:--------|:--------------|
| grandma | Gender        |
| 85      | Age           |
| Black   | RaceEthnicity |
| doctors | Employment    |
| her     | Gender        |

Model Information

References

In-house annotated health-related text in colloquial language.

Sample text from the training dataset

Hello,I’m 20 year old girl. I’m diagnosed with hyperthyroid 1 month ago. I was feeling weak, light headed,poor digestion, panic attacks, depression, left chest pain, increased heart rate, rapidly weight loss, from 4 months. Because of this, I stayed in the hospital and just discharged from hospital. I had many other blood tests, brain mri, ultrasound scan, endoscopy because of some dumb doctors bcs they were not able to diagnose actual problem. Finally I got an appointment with a homeopathy doctor finally he find that i was suffering from hyperthyroid and my TSH was 0.15 T3 and T4 is normal . Also i have b12 deficiency and vitamin D deficiency so I’m taking weekly supplement of vitamin D and 1000 mcg b12 daily. I’m taking homeopathy medicine for 40 days and took 2nd test after 30 days. My TSH is 0.5 now. I feel a little bit relief from weakness and depression but I’m facing with 2 new problem from last week that is breathtaking problem and very rapid heartrate. I just want to know if i should start allopathy medicine or homeopathy is okay? Bcs i heard that thyroid take time to start recover. So please let me know if both of medicines take same time. Because some of my friends advising me to start allopathy and never take a chance as i can develop some serious problems.Sorry for my poor english😐Thank you.

Benchmarking

             label   tp  fp  fn  total  precision  recall   f1
            Gender 1296  30  21   1317       0.98    0.98 0.98
        Employment 1183  70  60   1243       0.94    0.95 0.95
     RaceEthnicity   30   1   3     33       0.97    0.91 0.94
               Age  533  44  49    582       0.92    0.92 0.92
         Substance  386  49  35    421       0.89    0.92 0.90
RelationshipStatus   21   3   3     24       0.88    0.88 0.88
 SubstanceQuantity   61  14  24     85       0.81    0.72 0.76
         macro_avg 3510 211 195   3705       0.91    0.90 0.90
         micro_avg 3510 211 195   3705       0.94    0.95 0.95