Description
This model is a BioBERT-based Adverse Event Text Classifier and it is trained for analyzing the adverse events of drugs mentioned in health documents.
The Text Classifier model has been trained using in-house annotated health-related text that have been labeled with two different classes:
True: Text includes signs or symptoms that are unfavorable, unintended, and/or harmful in a patient who is administered a pharmaceutical product or medical device.
False: The patient did not experience something unfavorable during the course of treatment.
Predicted Entities
True, False
How to use
document_assembler = DocumentAssembler() \
.setInputCol("text") \
.setOutputCol("document")
tokenizer = Tokenizer() \
.setInputCols(["document"]) \
.setOutputCol("token")
sequence_classifier = MedicalBertForSequenceClassification.pretrained("bert_sequence_classifier_vop_adverse_event_onnx", "en", "clinical/models")\
.setInputCols(["document", "token"])\
.setOutputCol("class")
pipeline = Pipeline(stages=[
document_assembler,
tokenizer,
sequence_classifier
])
data = spark.createDataFrame([
["I am taking this medication once a day for the last 3 days. I am feeling very bad, pressure on my head, some chest pain, cramps on my neck and feel very weird. I want to reduce my blood pressure naturally. Can I stop this medication? I only took it for 5 days. I was reading here, that a lot of people has been losing weight and exercise and now they have a normal blood pressure. Please let me know, what I can do. The sides effects are horrible"],
["I go the pub about 3-4 times a week and drink quite a bit. I like socialising, been doing so for years now.Recently been getting this occasional pain from the liver area (under right ribs).It comes and goes. Could this be a sign of liver damage?When i get this pain i am usually in the pub drinking.If i press the area under my right rib cage about half way across i can feel pain. Is that pain in the Liver?"]
]).toDF("text")
model = pipeline.fit(data)
result = model.transform(data)
document_assembler = nlp.DocumentAssembler() \
.setInputCol("text") \
.setOutputCol("document")
tokenizer = nlp.Tokenizer() \
.setInputCols(["document"]) \
.setOutputCol("token")
sequenceClassifier = medical.BertForSequenceClassification.pretrained("bert_sequence_classifier_vop_adverse_event_onnx", "en", "clinical/models")\
.setInputCols(["document","token"])\
.setOutputCol("classes")
pipeline = nlp.Pipeline(stages=[
document_assembler,
tokenizer,
sequenceClassifier
])
data = spark.createDataFrame([
["I am taking this medication once a day for the last 3 days. I am feeling very bad, pressure on my head, some chest pain, cramps on my neck and feel very weird. I want to reduce my blood pressure naturally. Can I stop this medication? I only took it for 5 days. I was reading here, that a lot of people has been losing weight and exercise and now they have a normal blood pressure. Please let me know, what I can do. The sides effects are horrible"],
["I go the pub about 3-4 times a week and drink quite a bit. I like socialising, been doing so for years now.Recently been getting this occasional pain from the liver area (under right ribs).It comes and goes. Could this be a sign of liver damage?When i get this pain i am usually in the pub drinking.If i press the area under my right rib cage about half way across i can feel pain. Is that pain in the Liver?"]
]).toDF("text")
model = pipeline.fit(data)
result = model.transform(data)
val document_assembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val tokenizer = new Tokenizer()
.setInputCols(Array("document"))
.setOutputCol("token")
val sequenceClassifier = MedicalBertForSequenceClassification.pretrained("bert_sequence_classifier_vop_adverse_event_onnx", "en", "clinical/models")
.setInputCols(Array("document","token"))
.setOutputCol("class")
val pipeline = new Pipeline().setStages(Array(document_assembler, tokenizer, sequenceClassifier))
val data = Seq(Array(
"I am taking this medication once a day for the last 3 days. I am feeling very bad, pressure on my head, some chest pain, cramps on my neck and feel very weird. I want to reduce my blood pressure naturally. Can I stop this medication? I only took it for 5 days. I was reading here, that a lot of people has been losing weight and exercise and now they have a normal blood pressure. Please let me know, what I can do. The sides effects are horrible",
"I go the pub about 3-4 times a week and drink quite a bit. I like socialising, been doing so for years now.Recently been getting this occasional pain from the liver area (under right ribs).It comes and goes. Could this be a sign of liver damage? When i get this pain i am usually in the pub drinking.If i press the area under my right rib cage about half way across i can feel pain. Is that pain in the Liver?"
)).toDF("text")
val model = pipeline.fit(data)
val result = model.transform(data)
Results
+------------------------------------------------------------------------------------------------------------------------------------------------------+-------+
| text| result|
+------------------------------------------------------------------------------------------------------------------------------------------------------+-------+
|I am taking this medication once a day for the last 3 days. I am feeling very bad, pressure on my head, some chest pain, cramps on my neck and feel...| True |
|I go the pub about 3-4 times a week and drink quite a bit. I like socialising, been doing so for years now.Recently been getting this occasional pa...| False |
+------------------------------------------------------------------------------------------------------------------------------------------------------+-------+
Model Information
| Model Name: | bert_sequence_classifier_vop_adverse_event_onnx |
| Compatibility: | Healthcare NLP 6.1.1+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [document, token] |
| Output Labels: | [label] |
| Language: | en |
| Size: | 437.7 MB |
| Case sensitive: | true |