RE Pipeline between Body Parts and Procedures

Description

This pretrained pipeline is built on the top of re_bodypart_proceduretest model.

Predicted Entities

Injury_or_Poisoning, Direction, Test, Route, Admission_Discharge, Death_Entity, Triglycerides, Oxygen_Therapy, Relationship_Status, Duration, Alcohol, Date, Drug, Hyperlipidemia, Respiration, Birth_Entity, VS_Finding, Age, Social_History_Header, Family_History_Header, Medical_Device, Labour_Delivery, BMI, Fetus_NewBorn, Temperature, Section_Header, Communicable_Disease, ImagingFindings, Psychological_Condition, Obesity, Sexually_Active_or_Sexual_Orientation, Modifier, Vaccine, Symptom, Pulse, Kidney_Disease, Oncological, EKG_Findings, Medical_History_Header, Cerebrovascular_Disease, Blood_Pressure, Diabetes, O2_Saturation, Heart_Disease, Employment, Frequency, Disease_Syndrome_Disorder, Pregnancy, RelativeDate, Procedure, Overweight, Race_Ethnicity, Hypertension, External_body_part_or_region, Imaging_Technique, Test_Result, Treatment, Substance, Clinical_Dept, LDL, Diet, Substance_Quantity, Allergen, Gender, RelativeTime, Total_Cholesterol, Internal_organ_or_component, Smoking, Vital_Signs_Header, Height, Form, Strength, Weight, Time, Dosage, HDL

Live Demo Open in Colab Download Copy S3 URI

How to use

from sparknlp.pretrained import PretrainedPipeline

pipeline = PretrainedPipeline("re_bodypart_proceduretest_pipeline", "en", "clinical/models")

pipeline.fullAnnotate("TECHNIQUE IN DETAIL: After informed consent was obtained from the patient and his mother, the chest was scanned with portable ultrasound.")

import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline

val pipeline = new PretrainedPipeline("re_bodypart_proceduretest_pipeline", "en", "clinical/models")

pipeline.fullAnnotate("TECHNIQUE IN DETAIL: After informed consent was obtained from the patient and his mother, the chest was scanned with portable ultrasound.")

import nlu
nlu.load("en.relation.bodypart_proceduretest.pipeline").predict("""TECHNIQUE IN DETAIL: After informed consent was obtained from the patient and his mother, the chest was scanned with portable ultrasound.""")

Results

| index | relations | entity1                      | entity1_begin | entity1_end | chunk1 | entity2 | entity2_end | entity2_end | chunk2              | confidence |
|-------|-----------|------------------------------|---------------|-------------|--------|---------|-------------|-------------|---------------------|------------|
| 0     | 1         | External_body_part_or_region | 94            | 98          | chest  | Test    | 117         | 135         | portable ultrasound | 1.0        |

Model Information

Included Models

• DocumentAssembler
• SentenceDetector
• TokenizerModel
• PerceptronModel
• WordEmbeddingsModel
• MedicalNerModel
• NerConverter
• DependencyParserModel
• RelationExtractionModel