Mapping MedDRA-LLT (Lowest Level Term) Codes with Their Corresponding ICD-10 Codes

Description

This pretrained model maps MedDRA-LLT (Lowest Level Term) codes to corresponding ICD10 codes. Some of the MedDRA LLT codes map to more than ICD-10 codes. You can find all the mapped ICD-10 codes in the all_k_resolutions column in the metadata.

Predicted Entities

icd10 code

How to use


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

chunk_assembler = Doc2Chunk()\
      .setInputCols(['doc'])\
      .setOutputCol('ner_chunk')
 
mapperModel = ChunkMapperModel.load('meddra_llt_icd10_mapper')\
    .setInputCols(["ner_chunk"])\
    .setOutputCol("mappings")\
    .setRels(["icd10_code"])


mapper_pipeline = Pipeline(stages=[
    document_assembler,
    chunk_assembler,
    mapperModel
])

data = spark.createDataFrame([["10045275"], ["10067585"], ["10026182"]]).toDF("text")

mapper_model = mapper_pipeline.fit(data)
result = mapper_model.transform(data)
val document_assembler = DocumentAssembler()
      .setInputCol("text")
      .setOutputCol("doc")

val chunk_assembler = Doc2Chunk()
      .setInputCols(Array("doc"))
      .setOutputCol("ner_chunk")
 
val mapperModel = ChunkMapperModel.load("meddra_llt_icd10_mapper")
    .setInputCols(Array("ner_chunk"))
    .setOutputCol("mappings")
    .setRels(Array("icd10_code"))


val mapper_pipeline = new Pipeline().setStages(Array(
    document_assembler,
    chunk_assembler,
    mapperModel
)

val data = Seq("10045275", "10067585", "10026182").toDF("text")

val mapper_model = mapper_pipeline.fit(data)
val result = mapper_model.transform(data)

Results

+-----------+-------------------------------------------------+--------------------------------------------------------+
|meddra_code|icd10_code                                       |all_k_resolutions                                       |
+-----------+-------------------------------------------------+--------------------------------------------------------+
|10045275   |A01:Typhoid and paratyphoid fevers               |A01:Typhoid and paratyphoid fevers:::A01.0:Typhoid fever|
|10067585   |E11:Type 2 diabetes mellitus                     |E11:Type 2 diabetes mellitus:::                         |
|10026182   |C15.9:Malignant neoplasm: Oesophagus, unspecified|C15.9:Malignant neoplasm: Oesophagus, unspecified:::    |
+-----------+-------------------------------------------------+--------------------------------------------------------+

Model Information

Model Name: meddra_llt_icd10_mapper
Compatibility: Healthcare NLP 5.4.1+
License: Licensed
Edition: Official
Input Labels: [ner_chunk]
Output Labels: [mappings]
Language: en
Size: 228.0 KB

References

This model is trained with the June 2024 release of ICD-10 to MedDRA Map dataset.

To utilize this model, possession of a valid MedDRA license is requisite. If you possess one and wish to use this model, kindly contact us at support@johnsnowlabs.com.