Description
This pipeline can be used to detect and label smoking-related entities within medical text. Smoking/Tobacco typically involves inhaling smoke from burning tobacco, a highly addictive substance.
Predicted Entities
TOBACO_USE
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("ner_tobaco_use_benchmark_pipeline", "en", "clinical/models")
text = """SOCIAL HISTORY : The patient is a nonsmoker . Denies any alcohol or illicit drug use . The patient does live with his family .
SOCIAL HISTORY : The patient smokes approximately 2 packs per day times greater than 40 years . He does drink occasional alcohol approximately 5 to 6 alcoholic drinks per month . He denies any drug use . He is a retired liquor store owner .
SOCIAL HISTORY : Patient admits alcohol use , Drinking is described as heavy , Patient denies illegal drug use , Patient denies STD history , Patient denies tobacco use .
SOCIAL HISTORY : The patient is employed in the finance department . He is a nonsmoker . He does consume alcohol on the weekend as much as 3 to 4 alcoholic beverages per day on the weekends . He denies any IV drug use or abuse .
SOCIAL HISTORY : She is married .Employed with the US Post Office .She is a mother of three . Denies tobacco , alcohol or illicit drug use . MEDICATIONS . Coumadin 1 mg daily .Last INR was on Tuesday , August 14 , 2007 , and her INR was 2.3.2 . Amiodarone 100 mg p.o . daily .
"""
result = ner_pipeline.fullAnnotate(text)
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = nlp.PretrainedPipeline("ner_tobaco_use_benchmark_pipeline", "en", "clinical/models")
text = """SOCIAL HISTORY : The patient is a nonsmoker . Denies any alcohol or illicit drug use . The patient does live with his family .
SOCIAL HISTORY : The patient smokes approximately 2 packs per day times greater than 40 years . He does drink occasional alcohol approximately 5 to 6 alcoholic drinks per month . He denies any drug use . He is a retired liquor store owner .
SOCIAL HISTORY : Patient admits alcohol use , Drinking is described as heavy , Patient denies illegal drug use , Patient denies STD history , Patient denies tobacco use .
SOCIAL HISTORY : The patient is employed in the finance department . He is a nonsmoker . He does consume alcohol on the weekend as much as 3 to 4 alcoholic beverages per day on the weekends . He denies any IV drug use or abuse .
SOCIAL HISTORY : She is married .Employed with the US Post Office .She is a mother of three . Denies tobacco , alcohol or illicit drug use . MEDICATIONS . Coumadin 1 mg daily .Last INR was on Tuesday , August 14 , 2007 , and her INR was 2.3.2 . Amiodarone 100 mg p.o . daily .
"""
result = ner_pipeline.fullAnnotate(text)
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("ner_tobaco_use_benchmark_pipeline", "en", "clinical/models")
val text = """SOCIAL HISTORY : The patient is a nonsmoker . Denies any alcohol or illicit drug use . The patient does live with his family .
SOCIAL HISTORY : The patient smokes approximately 2 packs per day times greater than 40 years . He does drink occasional alcohol approximately 5 to 6 alcoholic drinks per month . He denies any drug use . He is a retired liquor store owner .
SOCIAL HISTORY : Patient admits alcohol use , Drinking is described as heavy , Patient denies illegal drug use , Patient denies STD history , Patient denies tobacco use .
SOCIAL HISTORY : The patient is employed in the finance department . He is a nonsmoker . He does consume alcohol on the weekend as much as 3 to 4 alcoholic beverages per day on the weekends . He denies any IV drug use or abuse .
SOCIAL HISTORY : She is married .Employed with the US Post Office .She is a mother of three . Denies tobacco , alcohol or illicit drug use . MEDICATIONS . Coumadin 1 mg daily .Last INR was on Tuesday , August 14 , 2007 , and her INR was 2.3.2 . Amiodarone 100 mg p.o . daily .
"""
val result = ner_pipeline.fullAnnotate(text)
Results
| | chunk | begin | end | ner_label |
|---:|:----------|--------:|------:|:------------|
| 0 | nonsmoker | 34 | 42 | TOBACO_USE |
| 1 | smokes | 156 | 161 | TOBACO_USE |
| 2 | tobacco | 525 | 531 | TOBACO_USE |
| 3 | nonsmoker | 616 | 624 | TOBACO_USE |
| 4 | tobacco | 869 | 875 | TOBACO_USE |
Model Information
Model Name: | ner_tobaco_use_benchmark_pipeline |
Type: | pipeline |
Compatibility: | Healthcare NLP 5.5.3+ |
License: | Licensed |
Edition: | Official |
Language: | en |
Size: | 1.7 GB |
Included Models
- DocumentAssembler
- SentenceDetector
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel
- ChunkMergeModel
Benchmarking
label precision recall f1-score support
O 1.000 1.000 1.000 82397
TOBACO_USE 1.000 0.994 0.997 174
accuracy - - 1.000 82571
macro-avg 1.000 0.997 0.999 82571
weighted-avg 1.000 1.000 1.000 82571