Clinical Deidentification Pipeline - Obfuscation (Small)

Description

This pipeline can be used to detect the PHI information from medical texts and obfuscate (replace them with fake ones) in the resulting text. Obfuscated entities: MEDICALRECORD, ORGANIZATION, PROFESSION, HEALTHPLAN, DOCTOR, USERNAME, LOCATION-OTHER, URL, DEVICE, CITY, DATE, ZIP, STATE, PATIENT, COUNTRY, STREET, PHONE, HOSPITAL, EMAIL, IDNUM, BIOID, FAX, AGE, SSN, ACCOUNT, DLN, PLATE, VIN, LICENSE, IPADDR

Predicted Entities

MEDICALRECORD, ORGANIZATION, PROFESSION, HEALTHPLAN, DOCTOR, USERNAME, LOCATION-OTHER, URL, DEVICE, CITY, DATE, ZIP, STATE, PATIENT, COUNTRY, STREET, PHONE, HOSPITAL, EMAIL, IDNUM, BIOID, FAX, AGE, SSN, ACCOUNT, DLN, PLATE, VIN, LICENSE, IPADDR

Live Demo Open in Colab Download Copy S3 URI

How to use

from sparknlp.pretrained import PretrainedPipeline

deid_pipeline = PretrainedPipeline("clinical_deidentification_obfuscation_small", "en", "clinical/models")

result = deid_pipeline.annotate("""Name : Hendrickson, Ora, Record date: 2093-01-13, MR 719435.
Dr. John Green, ID: 1231511863, IP 203.120.223.13.
He is a 60-year-old male was admitted to the Day Hospital for cystectomy on 12/17/1993.
SSN #333-44-6666, Driver's license no: A334455B.
Phone 302-786-5227, 0295 Keats Street, San Francisco, E-MAIL: smith@gmail.com.""")

import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline

val deid_pipeline = PretrainedPipeline("clinical_deidentification_obfuscation_small", "en", "clinical/models")

val result = deid_pipeline.annotate("""Name : Hendrickson, Ora, Record date: 2093-01-13, MR 719435.
Dr. John Green, ID: 1231511863, IP 203.120.223.13.
He is a 60-year-old male was admitted to the Day Hospital for cystectomy on 12/17/1993.
SSN #333-44-6666, Driver's license no: A334455B.
Phone 302-786-5227, 0295 Keats Street, San Francisco, E-MAIL: smith@gmail.com.""")

Results

Obfuscated
------------------------------
Name : Maralyn Sago, Record date: 2093-01-31, MR 161096.
Dr. Darin Engels, ID: 9811914782, IP 003.003.003.003.
He is a 74-year-old male was admitted to the SCOTT COUNTY MEMORIAL HOSPITAL AKA SCOTT MEMORIAL for cystectomy on 01/04/1994.
SSN #956-21-3086, Driver's license no: V784696E.
Phone 952-841-3244, 11130 Parkview Circle Dr, Chesapeake, E-MAIL: Davie@yahoo.com.

Model Information

Included Models

• DocumentAssembler
• SentenceDetectorDLModel
• TokenizerModel
• WordEmbeddingsModel
• MedicalNerModel
• NerConverter
• TextMatcherModel
• RegexMatcherModel
• ChunkMergeModel
• DeIdentificationModel
• Finisher