Description
This pretrained model maps HPO codes to related genes. It also returns all the possible genes 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_gene_mapper", "en", "clinical/models")\
.setInputCols(["hpo_code"])\
.setOutputCol("mappings")\
.setRels(["gene"])
mapper_pipeline = Pipeline(stages=[
document_assembler,
chunk_assembler,
mapperModel
])
data = spark.createDataFrame([["HP:0000002"],["HP:6001080"],["HP:0009484"]]).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_gene_mapper", "en", "clinical/models")\
.setInputCols(["hpo_code"])\
.setOutputCol("mappings")\
.setRels(["gene"])
mapper_pipeline = nlp.Pipeline(stages=[
document_assembler,
chunk_assembler,
mapperModel
])
data = spark.createDataFrame([["HP:0000002"],["HP:6001080"],["HP:0009484"]]).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_gene_mapper", "en", "clinical/models")
.setInputCols("hpo_code")
.setOutputCol("mappings")
.setRels(Array("gene"))
val mapper_pipeline = new Pipeline().setStages(Array(
document_assembler,
chunk_assembler,
mapperModel
))
val data = Seq("HP:0000002","HP:6001080","HP:0009484").toDF("text")
val result = mapper_pipeline.fit(data).transform(data)
Results
+----------+-------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| hpo_code| gene| all_k_resolutions|
+----------+-------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|HP:0000002| DUSP6|DUSP6:::FGF8:::FGFR1:::GNRH1:::GNRHR:::KISS1:::LRP5:::NHLH2:::TAC3:::TACR3:::FGF17:::NOG:::COPB2:::HS6ST1:::NSMF:::CHD7:::WDR11:::PROK2:::SPRY4:::KISS1R:::TMEM67:::PROKR2|
|HP:6001080|HSD11B1| HSD11B1:::|
|HP:0009484| SHH| SHH:::LMBR1|
+----------+-------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
Model Information
Model Name: | hpo_code_gene_mapper |
Compatibility: | Healthcare NLP 6.0.4+ |
License: | Licensed |
Edition: | Official |
Input Labels: | [ner_chunk] |
Output Labels: | [mappings] |
Language: | en |
Size: | 920.9 KB |