Sentence Entity Resolver for billable ICD10-CM HCC codes (Slim)

Description

This model maps extracted medical entities to ICD10-CM codes using sbiobert_base_cased_mli Sentence Bert Embeddings. This model has been augmented with synonyms and synonyms having low cosine similarity are dropped, making the model slim.

Predicted Entities

Outputs 7-digit billable ICD codes. In the result, look for aux_label parameter in the metadata to get HCC status. The HCC status can be divided to get further information: billable status, hcc status, and hcc score.

For example, in the example shared below the billable status is 1, hcc status is 1, and hcc score is 8.

Live Demo Open in Colab Download

How to use

document_assembler = DocumentAssembler().setInputCol("text").setOutputCol("document")

sbert_embedder = BertSentenceEmbeddings\
    .pretrained("sbiobert_base_cased_mli","en","clinical/models")\
    .setInputCols(["document"])\
    .setOutputCol("sbert_embeddings")

icd10_resolver = SentenceEntityResolverModel\
    .pretrained("sbiobertresolve_icd10cm_slim_billable_hcc","en", "clinical/models")\
    .setInputCols(["document", "sbert_embeddings"])\
    .setOutputCol("icd10cm_code")\
    .setDistanceFunction("EUCLIDEAN")\
    .setReturnCosineDistances(True)

bert_pipeline_icd = Pipeline(stages = [document_assembler, sbert_embedder, icd10_resolver])

data = spark.createDataFrame([["metastatic lung cancer"]]).toDF("text")

results = bert_pipeline_icd.fit(data).transform(data)
val document_assembler = DocumentAssembler()
    .setInputCol("text")
    .setOutputCol("document")

val sbert_embedder = BertSentenceEmbeddings
    .pretrained("sbiobert_base_cased_mli","en","clinical/models")
    .setInputCols(Array("document"))
    .setOutputCol("sbert_embeddings")

val icd10_resolver = SentenceEntityResolverModel
    .pretrained("sbiobertresolve_icd10cm_slim_billable_hcc","en", "clinical/models")
    .setInputCols(Array("document", "sbert_embeddings"))
    .setOutputCol("icd10cm_code")
    .setDistanceFunction("EUCLIDEAN")
    .setReturnCosineDistances(True)

val bert_pipeline_icd = new Pipeline().setStages(Array(document_assembler, sbert_embedder, icd10_resolver))

val data = Seq("metastatic lung cancer").toDF("text")

val result = bert_pipeline_icd.fit(data).transform(data)

Results

|    | chunks                 | code   | resolutions                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | all_codes                                                                                              | billable_hcc_status_score   | all_distances                                                                                                            |
|---:|:-----------------------|:-------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------|:----------------------------|:-------------------------------------------------------------------------------------------------------------------------|
|  0 | metastatic lung cancer | C7800  | ['cancer metastatic to lung', 'metastasis from malignant tumor of lung', 'cancer metastatic to left lung', 'history of cancer metastatic to lung', 'metastatic cancer', 'history of cancer metastatic to lung (situation)', 'metastatic adenocarcinoma to bilateral lungs', 'cancer metastatic to chest wall', 'metastatic malignant neoplasm to left lower lobe of lung', 'metastatic carcinoid tumour', 'cancer metastatic to respiratory tract', 'metastatic carcinoid tumor'] | ['C7800', 'C349', 'C7801', 'Z858', 'C800', 'Z8511', 'C780', 'C798', 'C7802', 'C799', 'C7830', 'C7B00'] | ['1', '1', '8']             | ['0.0464', '0.0829', '0.0852', '0.0860', '0.0914', '0.0989', '0.1133', '0.1220', '0.1220', '0.1253', '0.1249', '0.1260'] |

Model Information

Model Name: sbiobertresolve_icd10cm_slim_billable_hcc
Compatibility: Spark NLP for Healthcare 3.0.4+
License: Licensed
Edition: Official
Input Labels: [sentence_embeddings]
Output Labels: [icd10cm_code]
Language: en
Case sensitive: false