Description
This model maps extracted medical entities to Healthcare Common Procedure Coding System (HCPCS) codes using ‘sbiobert_base_cased_mli’ sentence embeddings.
Predicted Entities
HCPCS Codes
Live Demo Open in Colab Copy S3 URI
How to use
documentAssembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("ner_chunk")
sbert_embedder = BertSentenceEmbeddings\
.pretrained('sbiobert_base_cased_mli', 'en','clinical/models')\
.setInputCols(["ner_chunk"])\
.setOutputCol("sentence_embeddings")
hcpcs_resolver = SentenceEntityResolverModel\
.pretrained("sbiobertresolve_hcpcs", "en", "clinical/models") \
.setInputCols(["ner_chunk", "sentence_embeddings"]) \
.setOutputCol("hcpcs_code")\
.setDistanceFunction("EUCLIDEAN")
hcpcs_pipeline = Pipeline(
stages = [
documentAssembler,
sbert_embedder,
hcpcs_resolver])
data = spark.createDataFrame([["Breast prosthesis, mastectomy bra, with integrated breast prosthesis form, unilateral, any size, any type"]]).toDF("text")
results = hcpcs_pipeline.fit(data).transform(data)
val documentAssembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("ner_chunk")
val sbert_embedder = BertSentenceEmbeddings
.pretrained("sbiobert_base_cased_mli", "en","clinical/models")
.setInputCols(Array("ner_chunk"))
.setOutputCol("sentence_embeddings")
val hcpcs_resolver = SentenceEntityResolverModel
.pretrained("sbiobertresolve_hcpcs", "en", "clinical/models")
.setInputCols(Array("ner_chunk", "sentence_embeddings"))
.setOutputCol("hcpcs_code")
.setDistanceFunction("EUCLIDEAN")
val hcpcs_pipeline = new Pipeline().setStages(Array(documentAssembler, sbert_embedder, hcpcs_resolver))
val data = Seq("Breast prosthesis, mastectomy bra, with integrated breast prosthesis form, unilateral, any size, any type").toDF("text")
val results = hcpcs_pipeline.fit(data).transform(data)
import nlu
nlu.load("en.resolve.hcpcs").predict("""Breast prosthesis, mastectomy bra, with integrated breast prosthesis form, unilateral, any size, any type""")
Results
+--+---------------------------------------------------------------------------------------------------------+----------+----------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| |ner_chunk |hcpcs_code|all_codes |resolutions |
+--+---------------------------------------------------------------------------------------------------------+----------+----------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|0 |Breast prosthesis, mastectomy bra, with integrated breast prosthesis form, unilateral, any size, any type|L8001 |[L8001, L8002, L8000, L8033, L8032, ...]|'Breast prosthesis, mastectomy bra, with integrated breast prosthesis form, unilateral, any size, any type', 'Breast prosthesis, mastectomy bra, with integrated breast prosthesis form, bilateral, any size, any type', 'Breast prosthesis, mastectomy bra, without integrated breast prosthesis form, any size, any type', 'Nipple prosthesis, custom fabricated, reusable, any material, any type, each', ...|
+--+---------------------------------------------------------------------------------------------------------+----------+----------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
Model Information
| Model Name: | sbiobertresolve_hcpcs |
| Compatibility: | Healthcare NLP 3.4.0+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [sentence_embeddings] |
| Output Labels: | [hcpcs_code] |
| Language: | en |
| Size: | 21.5 MB |
| Case sensitive: | false |