Pipeline to Detect Radiology Concepts (WIP Greedy)

Description

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

Predicted Entities

Injury_or_Poisoning, Direction, Test, Route, Admission_Discharge, ImagingTest, Units, Death_Entity, Oxygen_Therapy, Relationship_Status, Triglycerides, Duration, Alcohol, Date, OtherFindings, BodyPart, Drug, Hyperlipidemia, Respiration, Birth_Entity, VS_Finding, Age, ManualFix, 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, Kidney_Disease, Pulse, 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, Imaging_Technique, Test_Result, Treatment, Substance, Clinical_Dept, LDL, Measurements, Diet, Substance_Quantity, Allergen, Gender, RelativeTime, Score, Total_Cholesterol, Vital_Signs_Header, Height, Smoking, Form, Strength, Weight, Time, Dosage, HDL

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How to use

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

pipeline.annotate("Bilateral breast ultrasound was subsequently performed, which demonstrated an ovoid mass measuring approximately 0.5 x 0.5 x 0.4 cm in diameter located within the anteromedial aspect of the left shoulder. This mass demonstrates isoechoic echotexture to the adjacent muscle, with no evidence of internal color flow. This may represent benign fibrous tissue or a lipoma.")
val pipeline = new PretrainedPipeline("jsl_rd_ner_wip_greedy_clinical_pipeline", "en", "clinical/models")

pipeline.annotate("Bilateral breast ultrasound was subsequently performed, which demonstrated an ovoid mass measuring approximately 0.5 x 0.5 x 0.4 cm in diameter located within the anteromedial aspect of the left shoulder. This mass demonstrates isoechoic echotexture to the adjacent muscle, with no evidence of internal color flow. This may represent benign fibrous tissue or a lipoma.")
import nlu
nlu.load("en.med_ner.jsl_rd_wip_greedy.pipeline").predict("""Bilateral breast ultrasound was subsequently performed, which demonstrated an ovoid mass measuring approximately 0.5 x 0.5 x 0.4 cm in diameter located within the anteromedial aspect of the left shoulder. This mass demonstrates isoechoic echotexture to the adjacent muscle, with no evidence of internal color flow. This may represent benign fibrous tissue or a lipoma.""")

Results

+---------------------+-------------------------+
|chunks               |entities                 |
+---------------------+-------------------------+
|Bilateral            |Direction                |
|breast               |BodyPart                 |
|ultrasound           |ImagingTest              |
|ovoid mass           |Symptom                  |
|anteromedial aspect  |Direction                |
|left                 |Direction                |
|shoulder             |BodyPart                 |
|mass                 |Symptom                  |
|isoechoic echotexture|ImagingFindings          |
|adjacent muscle      |BodyPart                 |
|internal color flow  |Symptom                  |
|benign fibrous tissue|Symptom                  |
|lipoma               |Disease_Syndrome_Disorder|
+---------------------+-------------------------+

Model Information

Model Name: jsl_rd_ner_wip_greedy_clinical_pipeline
Type: pipeline
Compatibility: Healthcare NLP 3.4.1+
License: Licensed
Edition: Official
Language: en
Size: 1.7 GB

Included Models

  • DocumentAssembler
  • SentenceDetectorDLModel
  • TokenizerModel
  • WordEmbeddingsModel
  • MedicalNerModel
  • NerConverter