Description
Detect different types of species of bacteria in text using pretrained NER model.
Predicted Entities
SPECIES
Live Demo Open in Colab Download
How to use
...
embeddings_clinical = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models") .setInputCols(["sentence", "token"]) .setOutputCol("embeddings")
clinical_ner = MedicalNerModel.pretrained("ner_bacterial_species", "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 = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")
.setInputCols(Array("sentence", "token"))
.setOutputCol("embeddings")
val ner = MedicalNerModel.pretrained("ner_bacterial_species", "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_bacterial_species |
| Compatibility: | Spark NLP for Healthcare 3.0.0+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [sentence, token, embeddings] |
| Output Labels: | [ner] |
| Language: | en |
Benchmarking
+-------+------+-----+-----+------+---------+------+------+
| entity| tp| fp| fn| total|precision|recall| f1|
+-------+------+-----+-----+------+---------+------+------+
|SPECIES|1396.0|265.0|414.0|1810.0| 0.8405|0.7713|0.8044|
+-------+------+-----+-----+------+---------+------+------+
+------------------+
| macro|
+------------------+
|0.8043791414577931|
+------------------+
+------------------+
| micro|
+------------------+
|0.8043791414577931|
+------------------+