Mapping UMLS Codes with Their Corresponding CPT Codes

Description

This model maps UMLS codes to CPT codes. It is trained on the 2026AA release of the Unified Medical Language System (UMLS) dataset. CPT mapper models are removed from the Models Hub due to license restrictions and can only be shared with the users who already have a valid CPT license. Please contact support@johnsnowlabs.com for access.

Live Demo Open in Colab

How to use

document_assembler = DocumentAssembler()\
    .setInputCol("text")\
    .setOutputCol("doc")

doc2chunk = Doc2Chunk()\
    .setInputCols(["doc"])\
    .setOutputCol("ner_chunk")

mapper = ChunkMapperModel.pretrained("umls_cpt_mapper","en","clinical/models")\
    .setInputCols(["ner_chunk"])\
    .setOutputCol("mappings")

pipeline = Pipeline(stages=[document_assembler, doc2chunk, mapper])
data = spark.createDataFrame([["C0002500"],["C0002692"],["C0002866"]]).toDF("text")
result = pipeline.fit(data).transform(data)

document_assembler = nlp.DocumentAssembler()\
    .setInputCol("text")\
    .setOutputCol("doc")

doc2chunk = nlp.Doc2Chunk()\
    .setInputCols(["doc"])\
    .setOutputCol("ner_chunk")

mapper = medical.ChunkMapperModel.pretrained("umls_cpt_mapper","en","clinical/models")\
    .setInputCols(["ner_chunk"])\
    .setOutputCol("mappings")

pipeline = nlp.Pipeline(stages=[document_assembler, doc2chunk, mapper])
data = spark.createDataFrame([["C0002500"],["C0002692"],["C0002866"]]).toDF("text")
result = pipeline.fit(data).transform(data)

val documentAssembler = new DocumentAssembler()
  .setInputCol("text")
  .setOutputCol("doc")

val doc2chunk = new Doc2Chunk()
  .setInputCols(Array("doc"))
  .setOutputCol("ner_chunk")

val mapper = ChunkMapperModel.pretrained("umls_cpt_mapper","en","clinical/models")
  .setInputCols(Array("ner_chunk"))
  .setOutputCol("mappings")

val pipeline = new Pipeline().setStages(Array(documentAssembler, doc2chunk, mapper))
val data = Seq("C0002500","C0002692","C0002866").toDF("text")
val result = pipeline.fit(data).transform(data)

Results

| umls_code   |   cpt_code |
|:------------|-----------:|
| C0002500    |      80150 |
| C0002692    |      27880 |
| C0002866    |      82160 |

Model Information

Model Name:	umls_cpt_mapper
Compatibility:	Healthcare NLP 6.4.0+
License:	Licensed
Edition:	Official
Input Labels:	[ner_chunk]
Output Labels:	[mappings]
Language:	en
Size:	637.4 KB

PREVIOUSMapping UMLS Codes with Their Corresponding ATC Codes

NEXTMapping UMLS Codes with Their Corresponding HCPCS Codes