Description
This model is a BioBERT-based classifier that can classify the sections within the abstracts of scientific articles regarding randomized clinical trials (RCT).
Predicted Entities
BACKGROUND, CONCLUSIONS, METHODS, OBJECTIVE, RESULTS
How to use
document_assembler = DocumentAssembler() \
.setInputCol("text") \
.setOutputCol("document")
tokenizer = Tokenizer() \
.setInputCols(["document"]) \
.setOutputCol("token")
sequenceClassifier_loaded = MedicalBertForSequenceClassification.pretrained("bert_sequence_classifier_rct_biobert", "en", "clinical/models")\
.setInputCols(["document",'token'])\
.setOutputCol("class")
pipeline = Pipeline(stages=[
document_assembler,
tokenizer,
sequenceClassifier_loaded
])
data = spark.createDataFrame([["""Previous attempts to prevent all the unwanted postoperative responses to major surgery with an epidural hydrophilic opioid , morphine , have not succeeded . The authors ' hypothesis was that the lipophilic opioid fentanyl , infused epidurally close to the spinal-cord opioid receptors corresponding to the dermatome of the surgical incision , gives equal pain relief but attenuates postoperative hormonal and metabolic responses more effectively than does systemic fentanyl ."""]]).toDF("text")
result = pipeline.fit(data).transform(data)
val documenter = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val tokenizer = new Tokenizer()
.setInputCols("document")
.setOutputCol("token")
val sequenceClassifier = MedicalBertForSequenceClassification.pretrained("bert_sequence_classifier_rct_biobert", "en", "clinical/models")
.setInputCols(Array("document","token"))
.setOutputCol("class")
val pipeline = new Pipeline().setStages(Array(documenter, tokenizer, sequenceClassifier))
val data = Seq("Previous attempts to prevent all the unwanted postoperative responses to major surgery with an epidural hydrophilic opioid , morphine , have not succeeded . The authors ' hypothesis was that the lipophilic opioid fentanyl , infused epidurally close to the spinal-cord opioid receptors corresponding to the dermatome of the surgical incision , gives equal pain relief but attenuates postoperative hormonal and metabolic responses more effectively than does systemic fentanyl .").toDF("text")
val result = pipeline.fit(data).transform(data)
import nlu
nlu.load("en.med_ner.clinical_trials").predict("""Previous attempts to prevent all the unwanted postoperative responses to major surgery with an epidural hydrophilic opioid , morphine , have not succeeded . The authors ' hypothesis was that the lipophilic opioid fentanyl , infused epidurally close to the spinal-cord opioid receptors corresponding to the dermatome of the surgical incision , gives equal pain relief but attenuates postoperative hormonal and metabolic responses more effectively than does systemic fentanyl .""")
Results
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------+
|text |class |
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------+
|[Previous attempts to prevent all the unwanted postoperative responses to major surgery with an epidural hydrophilic opioid , morphine , have not succeeded . The authors ' hypothesis was that the lipophilic opioid fentanyl , infused epidurally close to the spinal-cord opioid receptors corresponding to the dermatome of the surgical incision , gives equal pain relief but attenuates postoperative hormonal and metabolic responses more effectively than does systemic fentanyl .]|[BACKGROUND]|
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------+
Model Information
| Model Name: | bert_sequence_classifier_rct_biobert |
| Compatibility: | Healthcare NLP 3.4.1+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [document, token] |
| Output Labels: | [class] |
| Language: | en |
| Size: | 406.0 MB |
| Case sensitive: | true |
| Max sentence length: | 128 |
References
https://arxiv.org/abs/1710.06071
Benchmarking
label precision recall f1-score support
BACKGROUND 0.77 0.86 0.81 2000
CONCLUSIONS 0.96 0.95 0.95 2000
METHODS 0.96 0.98 0.97 2000
OBJECTIVE 0.85 0.77 0.81 2000
RESULTS 0.98 0.95 0.96 2000
accuracy 0.9 0.9 0.9 10000
macro-avg 0.9 0.9 0.9 10000
weighted-avg 0.9 0.9 0.9 10000