Description
This model is a BioBERT-based Age Group Text Classifier and it is trained for analyzing the age group of a person mentioned in health documents. Age of the person may or may not be mentioned explicitly in the training dataset.
The Text Classifier model has been trained using in-house annotated health-related text that have been labeled with three different classes:
Adult: A person who is fully grown or developed. Typically refers to someone who is 18 years or older,
Child: Requires intervention, urgent, not life-threatening cases.
Unknown: Not possible to comprehend/figure out the age group from the given text.
Predicted Entities
Adult, Child, Unknown
How to use
document_assembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
tokenizer = Tokenizer() \
.setInputCols(["document"]) \
.setOutputCol("token")
sequenceClassifier = MedicalBertForSequenceClassification.pretrained("bert_sequence_classifier_age_group", "en", "clinical/models")\
.setInputCols(["document",'token'])\
.setOutputCol("prediction")
clf_Pipeline = Pipeline(stages=[
document_assembler,
tokenizer,
sequenceClassifier])
data = spark.createDataFrame([["""A patient presented with complaints of chest pain and shortness of breath. The medical history revealed the patient had a smoking habit for over 30 years, and was diagnosed with hypertension two years ago. After a detailed physical examination, the doctor found a noticeable wheeze on lung auscultation and prescribed a spirometry test, which showed irreversible airway obstruction. The patient was diagnosed with Chronic obstructive pulmonary disease (COPD) caused by smoking."""],
["""My 4.5 year old has been poorly this week with a cold and thismorning he saw the doctors because he was up in the night last night saying his ear hurt and she said he has an ear infection.She said it's most likely viral but could be bacterial.Mostly they clear on their own.Watch and see about antibiotics.So we held off yestetday and today to see how be went and he perkes up today but then has gone downhill this evening saying his ear hurts still and he just feels poorly."""],
["""Hi have chronic gastritis from 4 month(confirmed by endoscopy).I do not have acid reflux.Only dull ache above abdomen and left side of chest.I am on reberprozole and librax.My question is whether chronic gastritis is curable or is it a lifetime condition?I am loosing hope because this dull ache is not going away.Please please reply"""]
]).toDF("text")
result = clf_Pipeline.fit(data).transform(data)
val document_assembler =new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val tokenizer = new Tokenizer()
.setInputCols("document")
.setOutputCol("token")
val sequenceClassifier = new MedicalBertForSequenceClassification.pretrained("bert_sequence_classifier_age_group", "en", "clinical/models")
.setInputCols("token")
.setOutputCol("prediction")
val clf_Pipeline = new Pipeline().setStages(Array(document_assembler, tokenizer, sequenceClassifier))
val data = Seq(Array("A patient presented with complaints of chest pain and shortness of breath. The medical history revealed the patient had a smoking habit for over 30 years, and was diagnosed with hypertension two years ago. After a detailed physical examination, the doctor found a noticeable wheeze on lung auscultation and prescribed a spirometry test, which showed irreversible airway obstruction. The patient was diagnosed with Chronic obstructive pulmonary disease (COPD) caused by smoking.", "My 4.5 year old has been poorly this week with a cold and thismorning he saw the doctors because he was up in the night last night saying his ear hurt and she said he has an ear infection.She said it's most likely viral but could be bacterial.Mostly they clear on their own.Watch and see about antibiotics.So we held off yestetday and today to see how be went and he perkes up today but then has gone downhill this evening saying his ear hurts still and he just feels poorly.", "Hi have chronic gastritis from 4 month(confirmed by endoscopy).I do not have acid reflux.Only dull ache above abdomen and left side of chest.I am on reberprozole and librax.My question is whether chronic gastritis is curable or is it a lifetime condition?I am loosing hope because this dull ache is not going away.Please please reply")).toDS().toDF("text")
val result = clf_Pipeline.fit(data).transform(data)
Results
+------------------------------------------------------------------------------------------------------------------------------------------------------+---------+
| text| result|
+------------------------------------------------------------------------------------------------------------------------------------------------------+---------+
|A patient presented with complaints of chest pain and shortness of breath. The medical history revealed the patient had a smoking habit for over 30...| [Adult]|
|My 4.5 year old has been poorly this week with a cold and thismorning he saw the doctors because he was up in the night last night saying his ear h...| [Child]|
|Hi have chronic gastritis from 4 month(confirmed by endoscopy).I do not have acid reflux.Only dull ache above abdomen and left side of chest.I am o...|[Unknown]|
+------------------------------------------------------------------------------------------------------------------------------------------------------+---------+
Model Information
| Model Name: | bert_sequence_classifier_age_group |
| Compatibility: | Healthcare NLP 5.0.1+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [document, token] |
| Output Labels: | [prediction] |
| Language: | en |
| Size: | 406.4 MB |
| Case sensitive: | true |
| Max sentence length: | 512 |
References
In-house annotated health-related text.
Benchmarking
label precision recall f1-score support
Adult 0.95 0.95 0.95 360
Child 0.96 0.93 0.94 188
Unknown 0.93 0.94 0.94 359
accuracy - - 0.94 907
macro avg 0.95 0.94 0.94 907
weighted avg 0.94 0.94 0.94 907