Description
This pipeline is designed to:
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extract all healthcare-related entities
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assign assertion status to the extracted entities
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establish relations between the extracted entities
from the documents transferred from the patient’s sentences. In this pipeline, six NER models, one assertion model, and one relation extraction model were used to achieve those tasks.
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Clinical Entity Labels:
Gender,Employment,Age,BodyPart,Substance,Form,PsychologicalCondition,Vaccine,Drug,DateTime,ClinicalDept,Laterality,Test,AdmissionDischarge,Disease_Syndrome_Disorder,VitalTest,Dosage,Duration,RelationshipStatus,Route,Allergen,Frequency,Symptom,Procedure,HealthStatus,InjuryOrPoisoning,Modifier,Treatment,SubstanceQuantity,MedicalDevice,TestResult,Alcohol,Smoking -
Assertion Status Labels:
Present_Or_Past,Hypothetical_Or_Absent,SomeoneElse -
Relation Extraction Labels:
Drug-Dosage,Drug-Frequency,Drug-Duration,Drug-Strength,Drug-Drug,Test-TestResult,Disease_Syndrome_Disorder-Treatment,Disease_Syndrome_Disorder-Symptom,Disease_Syndrome_Disorder-Modifier,Symptom-Modifier,Disease_Syndrome_Disorder-BodyPart,Symptom-BodyPart,Procedure-DateTime,Test-DateTime,VitalTest-TestResult,Disease_Syndrome_Disorder-Drug,Treatment-Drug,Disease_Syndrome_Disorder-Procedure,Procedure-Drug,Procedure-BodyPart,Treatment-BodyPart,BodyPart-Procedure,MedicalDevice-Procedure
Predicted Entities
AdmissionDischarge, Admission_Discharge, Age, Alcohol, Allergen, BodyPart, ClinicalDept, DateTime, Disease_Syndrome_Disorder, Dosage, Drug, Duration, Employment, Form, Frequency, Gender, HealthStatus, ImagingTest, InjuryOrPoisoning, Laterality, ManualFix, MedicalDevice, Modifier, Procedure, PsychologicalCondition, RelationshipStatus, Route, Smoking, Strength, Substance, SubstanceQuantity, Symptom, Test, TestResult, Test_Result, Treatment, Units, Vaccine, Vaccine_Name, VitalTest
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("explain_clinical_doc_vop", "en", "clinical/models")
result = ner_pipeline.annotate("""I had been feeling really tired all the time and was losing weight without even trying. My doctor checked my sugar levels and they came out to be high. So, I have type 2 diabetes.
He put me on two medications - I take metformin 500 mg twice a day, and glipizide 5 mg before breakfast and dinner. I also have to watch what I eat and try to exercise more.
Now, I also have chronic acid reflux disease or GERD. Now I take daily omeprazole 20 mg to control the heartburn symptoms.""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("explain_clinical_doc_vop", "en", "clinical/models")
val result = ner_pipeline.annotate("""I had been feeling really tired all the time and was losing weight without even trying. My doctor checked my sugar levels and they came out to be high. So, I have type 2 diabetes.
He put me on two medications - I take metformin 500 mg twice a day, and glipizide 5 mg before breakfast and dinner. I also have to watch what I eat and try to exercise more.
Now, I also have chronic acid reflux disease or GERD. Now I take daily omeprazole 20 mg to control the heartburn symptoms.""")
Results
#NER Results
| | chunks | begin | end | entities |
|---:|-----------------------------|------:|----:|---------------------------|
| 0 | feeling really tired | 11 | 30 | Symptom |
| 1 | all the time | 32 | 43 | Duration |
| 2 | losing weight | 53 | 65 | Symptom |
| 3 | doctor | 91 | 96 | Employment |
| 4 | sugar levels | 109 | 120 | Test |
| 5 | high | 146 | 149 | TestResult |
| 6 | type 2 diabetes | 163 | 177 | Disease_Syndrome_Disorder |
| 7 | He | 181 | 182 | Gender |
| 8 | metformin | 219 | 227 | Drug |
| 9 | 500 mg | 229 | 234 | Strength |
| 10 | twice a day | 236 | 246 | Frequency |
| 11 | glipizide | 253 | 261 | Drug |
| 12 | 5 mg | 263 | 266 | Strength |
| 13 | before breakfast and dinner | 268 | 294 | Frequency |
| 14 | exercise | 340 | 347 | HealthStatus |
| 15 | Now | 355 | 357 | DateTime |
| 16 | chronic acid reflux disease | 372 | 398 | Disease_Syndrome_Disorder |
| 17 | GERD | 403 | 406 | Disease_Syndrome_Disorder |
| 18 | Now | 409 | 411 | DateTime |
| 19 | daily | 420 | 424 | Frequency |
| 20 | omeprazole | 426 | 435 | Drug |
| 21 | 20 mg | 437 | 441 | Strength |
| 22 | heartburn symptoms | 458 | 475 | Symptom |
#Assertion Status Results
| | chunks | entities | assertion |
|---:|-----------------------------|---------------------------|------------------------|
| 0 | feeling really tired | Symptom | Present_Or_Past |
| 1 | losing weight | Symptom | Present_Or_Past |
| 2 | sugar levels | Test | Present_Or_Past |
| 3 | high | TestResult | Present_Or_Past |
| 4 | type 2 diabetes | Disease_Syndrome_Disorder | Present_Or_Past |
| 5 | metformin | Drug | Present_Or_Past |
| 6 | glipizide | Drug | Present_Or_Past |
| 7 | exercise | HealthStatus | Hypothetical_Or_Absent |
| 8 | chronic acid reflux disease | Disease_Syndrome_Disorder | Present_Or_Past |
| 9 | GERD | Disease_Syndrome_Disorder | Present_Or_Past |
| 10 | omeprazole | Drug | Present_Or_Past |
| 11 | heartburn symptoms | Symptom | Present_Or_Past |
# Relation Extraction Results
| | sentence | entity1_begin | entity1_end | chunk1 | entity1 | entity2_begin | entity2_end | chunk2 | entity2 | relation | confidence |
|--:|:--------:|:-------------:|:-----------:|--------------|:---------:|:-------------:|:-----------:|-----------------------------|------------|-----------------|-----------:|
| 0 | 1 | 109 | 120 | sugar levels | Test | 146 | 149 | high | TestResult | Test-TestResult | 1.0 |
| 1 | 3 | 219 | 227 | metformin | Drug | 229 | 234 | 500 mg | Strength | Drug-Strength | 1.0 |
| 2 | 3 | 219 | 227 | metformin | Drug | 236 | 246 | twice a day | Frequency | Drug-Frequency | 1.0 |
| 3 | 3 | 219 | 227 | metformin | Drug | 253 | 261 | glipizide | Drug | Drug-Drug | 1.0 |
| 4 | 3 | 219 | 227 | metformin | Drug | 263 | 266 | 5 mg | Strength | Drug-Strength | 1.0 |
| 5 | 3 | 229 | 234 | 500 mg | Strength | 253 | 261 | glipizide | Drug | Strength-Drug | 1.0 |
| 6 | 3 | 253 | 261 | glipizide | Drug | 263 | 266 | 5 mg | Strength | Drug-Strength | 1.0 |
| 7 | 3 | 253 | 261 | glipizide | Drug | 268 | 294 | before breakfast and dinner | Frequency | Drug-Frequency | 1.0 |
| 8 | 6 | 420 | 424 | daily | Frequency | 426 | 435 | omeprazole | Drug | Frequency-Drug | 1.0 |
| 9 | 6 | 426 | 435 | omeprazole | Drug | 437 | 441 | 20 mg | Strength | Drug-Strength | 1.0 |
Model Information
| Model Name: | explain_clinical_doc_vop |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.2.1+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 1.8 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel
- ChunkMergeModel
- AssertionDLModel
- PerceptronModel
- DependencyParserModel
- GenericREModel