Description
This model can be used to detect normalized mentions of genes (go) and human phenotypes (hp) in medical text.
Predicted Entities
HP, GO
Live Demo Open in Colab Download
How to use
...
embeddings_clinical = BertEmbeddings.pretrained("biobert_pubmed_base_cased") .setInputCols(["sentence", "token"]) .setOutputCol("embeddings")
clinical_ner = MedicalNerModel.pretrained("ner_human_phenotype_go_biobert", "en", "clinical/models") .setInputCols(["sentence", "token", "embeddings"]) .setOutputCol("ner")
...
nlpPipeline = Pipeline(stages=[document_assembler, sentence_detector, tokenizer, embeddings_clinical, clinical_ner, ner_converter])
model = nlpPipeline.fit(spark.createDataFrame([[""]]).toDF("text"))
results = model.transform(spark.createDataFrame([["EXAMPLE_TEXT"]]).toDF("text"))
...
val embeddings_clinical = BertEmbeddings.pretrained("biobert_pubmed_base_cased")
.setInputCols(Array("sentence", "token"))
.setOutputCol("embeddings")
val ner = MedicalNerModel.pretrained("ner_human_phenotype_go_biobert", "en", "clinical/models")
.setInputCols(Array("sentence", "token", "embeddings"))
.setOutputCol("ner")
...
val pipeline = new Pipeline().setStages(Array(document_assembler, sentence_detector, tokenizer, embeddings_clinical, ner, ner_converter))
val result = pipeline.fit(Seq.empty[String]).transform(data)
Model Information
| Model Name: | ner_human_phenotype_go_biobert |
| Compatibility: | Spark NLP for Healthcare 3.0.0+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [sentence, token, embeddings] |
| Output Labels: | [ner] |
| Language: | en |