Description
This pretrained model maps HPO codes to their related extraocular movements (EOM). It also returns all the possible EOMs in the all_k_resolutions
in the metadata.
How to use
document_assembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
chunk_assembler = Doc2Chunk()\
.setInputCols(["document"])\
.setOutputCol("hpo_code")
mapperModel = ChunkMapperModel.pretrained("hpo_code_eom_mapper", "en", "clinical/models")\
.setInputCols(["hpo_code"])\
.setOutputCol("mappings")\
.setRels(["eom"])
mapper_pipeline = Pipeline(stages=[
document_assembler,
chunk_assembler,
mapperModel
])
data = spark.createDataFrame([["HP:0000154"],["HP:0400001"],["HP:0009765"]]).toDF("text")
result = mapper_pipeline.fit(data).transform(data)
document_assembler = nlp.DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
chunk_assembler = nlp.Doc2Chunk()\
.setInputCols(["document"])\
.setOutputCol("hpo_code")
mapperModel = medical.ChunkMapperModel.pretrained("hpo_code_eom_mapper", "en", "clinical/models")\
.setInputCols(["hpo_code"])\
.setOutputCol("mappings")\
.setRels(["eom"])
mapper_pipeline = nlp.Pipeline(stages=[
document_assembler,
chunk_assembler,
mapperModel
])
data = spark.createDataFrame([["HP:0000154"],["HP:0400001"],["HP:0009765"]]).toDF("text")
result = mapper_pipeline.fit(data).transform(data)
val document_assembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val chunk_assembler = new Doc2Chunk()
.setInputCols("document")
.setOutputCol("hpo_code")
val mapperModel = ChunkMapperModel.pretrained("hpo_code_eom_mapper", "en", "clinical/models")
.setInputCols("hpo_code")
.setOutputCol("mappings")
.setRels(Array("eom"))
val mapper_pipeline = new Pipeline().setStages(Array(
document_assembler,
chunk_assembler,
mapperModel
))
val data = Seq("HP:0000154","HP:0400001","HP:0009765").toDF("text")
val result = mapper_pipeline.fit(data).transform(data)
Results
+----------+--------------------+-----------------------+
| hpo_code| eom| all_k_resolutions|
+----------+--------------------+-----------------------+
|HP:0000154|EOM:a6a2d57a281ead72|EOM:a6a2d57a281ead72:::|
|HP:0400001|EOM:8a5493c72e0dd13c|EOM:8a5493c72e0dd13c:::|
|HP:0009765|EOM:49acd433e354541b|EOM:49acd433e354541b:::|
+----------+--------------------+-----------------------+
Model Information
Model Name: | hpo_code_eom_mapper |
Compatibility: | Healthcare NLP 6.0.4+ |
License: | Licensed |
Edition: | Official |
Input Labels: | [ner_chunk] |
Output Labels: | [mappings] |
Language: | en |
Size: | 10.3 KB |
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