Drug Side Effect Classifier (BioBERT)

Description

This model is a BioBERT based classifier that can classify informal texts (such as tweets or forum posts) according to the presence of drug side effects.

Predicted Entities

Drug_AE, Other

Live Demo Open in Colab Download Copy S3 URI

How to use

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

tokenizer = Tokenizer() \
    .setInputCols(['document']) \
    .setOutputCol('token')

sequenceClassifier = MedicalBertForSequenceClassification.pretrained("bert_sequence_classifier_vop_drug_side_effect", "en", "clinical/models")\
    .setInputCols(["document",'token'])\
    .setOutputCol("prediction")

pipeline = Pipeline(stages=[
    document_assembler,
    tokenizer,
    sequenceClassifier
])

data = spark.createDataFrame(["I felt kind of dizzy after taking that medication for a month.",
                              "I took antibiotics last week and everything went well."], StringType()).toDF("text")

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

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

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

val sequenceClassifier = MedicalBertForSequenceClassification.pretrained("bert_sequence_classifier_vop_drug_side_effect", "en", "clinical/models")
    .setInputCols(Array("document","token"))
    .setOutputCol("prediction")

val pipeline = new Pipeline().setStages(Array(documenter, tokenizer, sequenceClassifier))

val data = Seq(Array("I felt kind of dizzy after taking that medication for a month.",
                      "I took antibiotics last week and everything went well.")).toDS.toDF("text")

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

Results

+--------------------------------------------------------------+---------+
|text                                                          |result   |
+--------------------------------------------------------------+---------+
|I felt kind of dizzy after taking that medication for a month.|[Drug_AE]|
|I took antibiotics last week and everything went well.        |[Other]  |
+--------------------------------------------------------------+---------+

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  precision    recall  f1-score   support
     Drug_AE   0.861111  0.788136  0.823009       118
       Other   0.875622  0.921466  0.897959       191
    accuracy   -         -         0.870550       309
   macro_avg   0.868367  0.854801  0.860484       309
weighted_avg   0.870081  0.870550  0.869337       309