Description
This model extracts countries in clinical notes using rule-based TextMatcherInternal annotator.
Predicted Entities
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")
text_matcher = TextMatcherInternalModel.pretrained("country_matcher","en","clinical/models") \
.setInputCols(["sentence", "token"])\
.setOutputCol("country_name")\
.setMergeOverlapping(True)
mathcer_pipeline = Pipeline().setStages([
documentAssembler,
sentenceDetector,
tokenizer,
text_matcher])
data = spark.createDataFrame([["""Name: Johnson, Alice, Record date: 2093-03-22, MR: 846275.
Dr. Emily Brown, IP 192.168.1.1.
She is a 55-year-old female who was admitted to the Global Hospital for hip replacement on 03/22/93.
Patient's VIN: 2HGFA165X8H123456, SSN: 444-55-8888, Driver's license no: C789012D.
Phone: (212) 555-7890, 4321 Oak Street, New York, USA, E-MAIL: alice.johnson@example.com.
Patient has traveled to Japan, France, and Australia in the past year."""]]).toDF("text")
result = mathcer_pipeline.fit(data).transform(data)
val documentAssembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val sentenceDetector = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare","en","clinical/models")
.setInputCols(Array("document"))
.setOutputCol("sentence")
val tokenizer = new Tokenizer()
.setInputCols(Array("sentence"))
.setOutputCol("token")
val text_matcher = TextMatcherInternalModel.pretrained("country_matcher","en","clinical/models")
.setInputCols(Array("sentence","token"))
.setOutputCol("country_name")
.setMergeOverlapping(true)
val mathcer_pipeline = new Pipeline().setStages(Array(
documentAssembler,
sentenceDetector,
tokenizer,
text_matcher))
val data = Seq("""Name: Johnson, Alice, Record date: 2093-03-22, MR: 846275. Dr. Emily Brown, IP 192.168.1.1. She is a 55-year-old female who was admitted to the Global Hospital for hip replacement on 03/22/93. Patient's VIN: 2HGFA165X8H123456, SSN: 444-55-8888, Driver's license no: C789012D. Phone: (212) 555-7890, 4321 Oak Street, New York, USA, E-MAIL: alice.johnson@example.com. Patient has traveled to Japan, France, and Australia in the past year.""").toDF("text")
val result = mathcer_pipeline.fit(data).transform(data)
Results
+---------+-----+---+-------+
| chunk|begin|end| label|
+---------+-----+---+-------+
| USA| 326|328|Country|
| Japan| 390|394|Country|
| France| 397|402|Country|
|Australia| 409|417|Country|
+---------+-----+---+-------+
Model Information
| Model Name: | country_matcher |
| Compatibility: | Healthcare NLP 5.3.3+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [sentence, token] |
| Output Labels: | [country_name] |
| Language: | en |
| Size: | 10.2 KB |
| Case sensitive: | false |