Description
This pretrained pipeline is built on the top of ner_deid_augmented model.
Live Demo Open in Colab Copy S3 URI
How to use
from sparknlp.pretrained import PretrainedPipeline
pipeline = PretrainedPipeline("ner_deid_augmented_pipeline", "en", "clinical/models")
pipeline.annotate("HISTORY OF PRESENT ILLNESS: Mr. Smith is a 60-year-old white male veteran with multiple comorbidities, who has a history of bladder cancer diagnosed approximately two years ago by the VA Hospital, Dr. John Green (2347165768). He underwent a resection there. He was to be admitted to the Day Hospital for cystectomy. He was seen in Urology Clinic and Radiology Clinic on 02/04/2003. HOSPITAL COURSE: Mr. Smith presented to the Day Hospital in anticipation for Urology surgery. On evaluation, EKG, echocardiogram was abnormal, a Cardiology consult was obtained. A cardiac adenosine stress MRI was then proceeded, same was positive for inducible ischemia, mild-to-moderate inferolateral subendocardial infarction with peri-infarct ischemia. In addition, inducible ischemia seen in the inferior lateral septum. Mr. Smith underwent a left heart catheterization, which revealed two vessel coronary artery disease. The RCA, proximal was 95% stenosed and the distal 80% stenosed. The mid LAD was 85% stenosed and the distal LAD was 85% stenosed. There was four Multi-Link Vision bare metal stents placed to decrease all four lesions to 0%. Following intervention, Mr. Smith was admitted to 7 Ardmore Tower under Cardiology Service under the direction of Dr. Hart. Mr. Smith had a noncomplicated post-intervention hospital course. He was stable for discharge home on 02/07/2003 with instructions to take Plavix daily for one month and Urology is aware of the same.")
val pipeline = new PretrainedPipeline("ner_deid_augmented_pipeline", "en", "clinical/models")
pipeline.annotate("HISTORY OF PRESENT ILLNESS: Mr. Smith is a 60-year-old white male veteran with multiple comorbidities, who has a history of bladder cancer diagnosed approximately two years ago by the VA Hospital, Dr. John Green (2347165768). He underwent a resection there. He was to be admitted to the Day Hospital for cystectomy. He was seen in Urology Clinic and Radiology Clinic on 02/04/2003. HOSPITAL COURSE: Mr. Smith presented to the Day Hospital in anticipation for Urology surgery. On evaluation, EKG, echocardiogram was abnormal, a Cardiology consult was obtained. A cardiac adenosine stress MRI was then proceeded, same was positive for inducible ischemia, mild-to-moderate inferolateral subendocardial infarction with peri-infarct ischemia. In addition, inducible ischemia seen in the inferior lateral septum. Mr. Smith underwent a left heart catheterization, which revealed two vessel coronary artery disease. The RCA, proximal was 95% stenosed and the distal 80% stenosed. The mid LAD was 85% stenosed and the distal LAD was 85% stenosed. There was four Multi-Link Vision bare metal stents placed to decrease all four lesions to 0%. Following intervention, Mr. Smith was admitted to 7 Ardmore Tower under Cardiology Service under the direction of Dr. Hart. Mr. Smith had a noncomplicated post-intervention hospital course. He was stable for discharge home on 02/07/2003 with instructions to take Plavix daily for one month and Urology is aware of the same.")
import nlu
nlu.load("en.deid.ner_augmented.pipeline").predict("""HISTORY OF PRESENT ILLNESS: Mr. Smith is a 60-year-old white male veteran with multiple comorbidities, who has a history of bladder cancer diagnosed approximately two years ago by the VA Hospital, Dr. John Green (2347165768). He underwent a resection there. He was to be admitted to the Day Hospital for cystectomy. He was seen in Urology Clinic and Radiology Clinic on 02/04/2003. HOSPITAL COURSE: Mr. Smith presented to the Day Hospital in anticipation for Urology surgery. On evaluation, EKG, echocardiogram was abnormal, a Cardiology consult was obtained. A cardiac adenosine stress MRI was then proceeded, same was positive for inducible ischemia, mild-to-moderate inferolateral subendocardial infarction with peri-infarct ischemia. In addition, inducible ischemia seen in the inferior lateral septum. Mr. Smith underwent a left heart catheterization, which revealed two vessel coronary artery disease. The RCA, proximal was 95% stenosed and the distal 80% stenosed. The mid LAD was 85% stenosed and the distal LAD was 85% stenosed. There was four Multi-Link Vision bare metal stents placed to decrease all four lesions to 0%. Following intervention, Mr. Smith was admitted to 7 Ardmore Tower under Cardiology Service under the direction of Dr. Hart. Mr. Smith had a noncomplicated post-intervention hospital course. He was stable for discharge home on 02/07/2003 with instructions to take Plavix daily for one month and Urology is aware of the same.""")
Results
+---------------+---------+
|chunk |ner_label|
+---------------+---------+
|Smith |NAME |
|VA Hospital |LOCATION |
|John Green |NAME |
|2347165768 |ID |
|Day Hospital |LOCATION |
|02/04/2003 |DATE |
|Smith |NAME |
|Day Hospital |LOCATION |
|Smith |NAME |
|Smith |NAME |
|7 Ardmore Tower|LOCATION |
|Hart |NAME |
|Smith |NAME |
|02/07/2003 |DATE |
+---------------+---------+
Model Information
| Model Name: | ner_deid_augmented_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