Description
Deidentification NER (Large) is a Named Entity Recognition model that annotates text to find protected health information that may need to be deidentified. The entities it annotates are Age, Contact, Date, Id, Location, Name, and Profession. This model is trained with the ‘embeddings_clinical_medium word embeddings model, so be sure to use the same embeddings in the pipeline.
We sticked to official annotation guideline (AG) for 2014 i2b2 Deid challenge while annotating new datasets for this model. All the details regarding the nuances and explanations for AG can be found here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978170/
Predicted Entities
Live Demo Open in Colab Download Copy S3 URI
How to use
documentAssembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
sentenceDetector = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare","en","clinical/models") \
.setInputCols(["document"]) \
.setOutputCol("sentence")
tokenizer = Tokenizer()\
.setInputCols(["sentence"])\
.setOutputCol("token")
word_embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical_large", "en", "clinical/models")\
.setInputCols(["sentence", "token"])\
.setOutputCol("embeddings")
deid_ner = MedicalNerModel.pretrained('ner_deid_large_emb_clinical_large', "en", "clinical/models") \
.setInputCols(["sentence", "token", "embeddings"]) \
.setOutputCol("deid_ner")
deid_ner_converter = NerConverter() \
.setInputCols(["sentence", "token", "deid_ner"]) \
.setOutputCol("deid_ner_chunk")
deid_ner_pipeline = Pipeline(stages=[
documentAssembler,
sentenceDetector,
tokenizer,
word_embeddings,
deid_ner,
deid_ner_converter])
empty_data = spark.createDataFrame([[""]]).toDF("text")
deid_ner_model = deid_ner_pipeline.fit(empty_data)
results = deid_ner_model.transform(spark.createDataFrame([["""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. 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."""]]).toDF("text"))
val document_assembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val sentence_detector = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare","en","clinical/models")
.setInputCols("document")
.setOutputCol("sentence")
val tokenizer = new Tokenizer()
.setInputCols("sentence")
.setOutputCol("token")
val word_embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical_large", "en", "clinical/models")\
.setInputCols(Array("sentence", "token"))\
.setOutputCol("embeddings")
val deid_ner_model = MedicalNerModel.pretrained('ner_deid_large_emb_clinical_large' , "en", "clinical/models")
.setInputCols(Array("sentence", "token"))
.setOutputCol("deid_ner")
val deid_ner_converter = new NerConverter()
.setInputCols(Array("sentence", "token", "ner"))
.setOutputCol("deid_ner_chunk")
val deid_pipeline = new PipelineModel().setStages(Array(document_assembler,
sentence_detector,
tokenizer,
word_embeddings,
deid_ner_model,
deid_ner_converter))
val data = Seq(""" """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. 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."""""").toDS.toDF("text")
val result = model.fit(data).transform(data)
Results
| | chunks | begin | end | entities |
|---:|:----------------|--------:|------:|:-----------|
| 0 | Day Hospital | 258 | 269 | NAME |
| 1 | Radiology | 321 | 329 | LOCATION |
| 2 | 02/04/2003 | 341 | 350 | DATE |
| 3 | COURSE | 362 | 367 | NAME |
| 4 | Hospital | 401 | 408 | NAME |
| 5 | Urology surgery | 430 | 444 | NAME |
| 6 | On | 447 | 448 | NAME |
| 7 | Following | 1103 | 1111 | NAME |
| 8 | 02/07/2003 | 1329 | 1338 | DATE |
| 9 | Plavix daily | 1366 | 1377 | NAME |
Model Information
| Model Name: | ner_deid_large_emb_clinical_medium |
| Compatibility: | Healthcare NLP 4.3.2+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [document, token, embeddings] |
| Output Labels: | [ner] |
| Language: | en |
| Size: | 2.8 MB |
Benchmarking
precision recall f1-score support
CONTACT 0.92 0.96 0.94 126
DATE 0.99 0.99 0.99 2631
NAME 0.97 0.98 0.97 2594
AGE 0.96 0.94 0.95 284
LOCATION 0.95 0.92 0.94 1511
ID 0.93 0.95 0.94 213
PROFESSION 0.84 0.73 0.78 160
micro avg 0.97 0.96 0.97 7519
macro avg 0.94 0.92 0.93 7519
weighted avg 0.97 0.96 0.96 7519