Description
This model detects molecular biology-related terms in medical texts. The model is trained with the BertForTokenClassification method from the transformers library and imported into Spark NLP.
Predicted Entities
O, B-cell_type, B-RNA, B-protein, I-protein, I-cell_line, I-RNA, I-DNA, B-cell_line, I-cell_type, B-DNA, PAD
How to use
from sparknlp.base import DocumentAssembler
from sparknlp_jsl.annotator import SentenceDetectorDLModel, MedicalBertForTokenClassifier
from sparknlp.annotator import Tokenizer, NerConverter
from pyspark.ml import Pipeline
document_assembler = (
DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
)
sentenceDetector = (
SentenceDetectorDLModel.pretrained("sentence_detector_dl","xx")
.setInputCols(["document"])
.setOutputCol("sentence")
)
tokenizer = (
Tokenizer()
.setInputCols(["sentence"])
.setOutputCol("token")
)
token_classifier = (
MedicalBertForTokenClassifier.pretrained(
"bert_token_classifier_ner_jnlpba_cellular_onnx",
"en",
"clinical/models"
)
.setInputCols(["token", "sentence"])
.setOutputCol("ner")
.setCaseSensitive(True)
)
ner_converter = (
NerConverterInternal()
.setInputCols(["sentence", "token", "ner"])
.setOutputCol("ner_chunk")
)
pipeline = Pipeline(stages=[
document_assembler,
sentenceDetector,
tokenizer,
token_classifier,
ner_converter
])
test_sentence = "The results suggest that activation of protein kinase C, but not new protein synthesis, is required for IL-2 induction of IFN-gamma and GM-CSF cytoplasmic mRNA. It also was observed that suppression of cytokine gene expression by these agents was independent of the inhibition of proliferation. These data indicate that IL-2 and IL-12 may have distinct signaling pathways leading to the induction of IFN-gammaand GM-CSFgene expression, andthatthe NK3.3 cell line may serve as a novel model for dissecting the biochemical and molecular events involved in these pathways. A functional T-cell receptor signaling pathway is required for p95vav activity. Stimulation of the T-cell antigen receptor ( TCR ) induces activation of multiple tyrosine kinases, resulting in phosphorylation of numerous intracellular substrates. One substrate is p95vav, which is expressed exclusively in hematopoietic and trophoblast cells."
data = spark.createDataFrame([[test_sentence]]).toDF("text")
model = pipeline.fit(data)
result = model.transform(data)
from johnsnowlabs import nlp, medical
document_assembler = nlp.DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
sentenceDetector = nlp.SentenceDetectorDLModel.pretrained("sentence_detector_dl","xx")\
.setInputCols(["document"])\
.setOutputCol("sentence")
tokenizer = nlp.Tokenizer()\
.setInputCols(["sentence"])\
.setOutputCol("token")
token_classifier = medical.BertForTokenClassifier.pretrained(
"bert_token_classifier_ner_jnlpba_cellular_onnx",
"en",
"clinical/models"
)\
.setInputCols(["token", "sentence"])\
.setOutputCol("ner")\
.setCaseSensitive(True)
ner_converter = medical.NerConverterInternal()\
.setInputCols(["sentence", "token", "ner"])\
.setOutputCol("ner_chunk")
pipeline = nlp.Pipeline(stages=[
document_assembler,
sentenceDetector,
tokenizer,
token_classifier,
ner_converter
])
test_sentence = "The results suggest that activation of protein kinase C, but not new protein synthesis, is required for IL-2 induction of IFN-gamma and GM-CSF cytoplasmic mRNA. It also was observed that suppression of cytokine gene expression by these agents was independent of the inhibition of proliferation. These data indicate that IL-2 and IL-12 may have distinct signaling pathways leading to the induction of IFN-gammaand GM-CSFgene expression, andthatthe NK3.3 cell line may serve as a novel model for dissecting the biochemical and molecular events involved in these pathways. A functional T-cell receptor signaling pathway is required for p95vav activity. Stimulation of the T-cell antigen receptor ( TCR ) induces activation of multiple tyrosine kinases, resulting in phosphorylation of numerous intracellular substrates. One substrate is p95vav, which is expressed exclusively in hematopoietic and trophoblast cells."
data = spark.createDataFrame([[test_sentence]]).toDF("text")
model = pipeline.fit(data)
result = model.transform(data)
import com.johnsnowlabs.nlp.base.DocumentAssembler
import com.johnsnowlabs.nlp.annotators.Tokenizer
import com.johnsnowlabs.nlp.annotators.ner.NerConverter
import com.johnsnowlabs.nlp.annotators.classifier.dl.MedicalBertForTokenClassifier
import com.johnsnowlabs.nlp.annotators.sentence_detector_dl.SentenceDetectorDLApproach
import org.apache.spark.ml.Pipeline
val documentAssembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val sentenceDetector = new SentenceDetectorDLModel()
.pretrained("sentence_detector_dl","xx")
.setInputCols("document")
.setOutputCol("sentence")
val tokenizer = new Tokenizer()
.setInputCols("document")
.setOutputCol("token")
val tokenClassifier = MedicalBertForTokenClassifier
.pretrained("bert_token_classifier_ner_jnlpba_cellular_onnx", "en", "clinical/models")
.setInputCols(Array("token", "document"))
.setOutputCol("ner")
.setCaseSensitive(true)
val nerConverter = new NerConverterInternal()
.setInputCols(Array("document", "token", "ner"))
.setOutputCol("ner_chunk")
val pipeline = new Pipeline()
.setStages(Array(
documentAssembler,
sentenceDetector,
tokenizer,
tokenClassifier,
nerConverter
))
val testSentence = "The results suggest that activation of protein kinase C, but not new protein synthesis, is required for IL-2 induction of IFN-gamma and GM-CSF cytoplasmic mRNA. It also was observed that suppression of cytokine gene expression by these agents was independent of the inhibition of proliferation. These data indicate that IL-2 and IL-12 may have distinct signaling pathways leading to the induction of IFN-gammaand GM-CSFgene expression, andthatthe NK3.3 cell line may serve as a novel model for dissecting the biochemical and molecular events involved in these pathways. A functional T-cell receptor signaling pathway is required for p95vav activity. Stimulation of the T-cell antigen receptor ( TCR ) induces activation of multiple tyrosine kinases, resulting in phosphorylation of numerous intracellular substrates. One substrate is p95vav, which is expressed exclusively in hematopoietic and trophoblast cells."
val data = Seq(testSentence).toDF("text")
val model = pipeline.fit(data)
val result = model.transform(data)
Results
+-------------------------------------+---------+
|text |entity |
+-------------------------------------+---------+
|protein kinase C |protein |
|IL-2 |protein |
|IFN-gamma and GM-CSF cytoplasmic mRNA|RNA |
|cytokine gene |DNA |
|IL-2 |protein |
|IL-12 |protein |
|IFN-gammaand |protein |
|GM-CSFgene |protein |
|NK3.3 cell line |cell_line|
|T-cell receptor |protein |
|p95vav |protein |
|T-cell antigen receptor |protein |
|TCR |protein |
|tyrosine kinases |protein |
|p95vav |protein |
|hematopoietic and trophoblast cells |cell_type|
+-------------------------------------+---------+
Model Information
| Model Name: | bert_token_classifier_ner_jnlpba_cellular_onnx |
| Compatibility: | Healthcare NLP 6.1.1+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [document, token] |
| Output Labels: | [ner] |
| Language: | en |
| Size: | 403.7 MB |
| Case sensitive: | true |
| Max sentence length: | 128 |