Description
Pretrained named entity recognition deep learning model for Drugs. The model combines dosage, strength, form, and route into a single entity: Drug. The SparkNLP deep learning model (NerDL) is inspired by a former state of the art model for NER: Chiu & Nicols, Named Entity Recognition with Bidirectional LSTM-CNN.
Predicted Entities
DRUG
Live Demo Open in Colab Copy S3 URI
How to use
Use as part of an nlp pipeline with the following stages: DocumentAssembler, SentenceDetector, Tokenizer, WordEmbeddingsModel, NerDLModel. Add the NerConverter to the end of the pipeline to convert entity tokens into full entity chunks.
document_assembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
sentence_detector = SentenceDetector()\
.setInputCols(["document"])\
.setOutputCol("sentence")
tokenizer = Tokenizer()\
.setInputCols(["sentence"])\
.setOutputCol("token")
# Clinical word embeddings trained on PubMED dataset
word_embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")\
.setInputCols(["sentence", "token"])\
.setOutputCol("embeddings")
clinical_ner = NerDLModel.pretrained("ner_drugs_large", "en", "clinical/models") \
.setInputCols(["sentence", "token", "embeddings"]) \
.setOutputCol("ner")
ner_converter = NerConverter() \
.setInputCols(["sentence", "token", "ner"]) \
.setOutputCol("ner_chunk")
nlpPipeline = Pipeline(stages=[document_assembler, sentence_detector, tokenizer, word_embeddings, clinical_ner, ner_converter])
data = spark.createDataFrame([["""The patient is a 40-year-old white male who presents with a chief complaint of 'chest pain'. The patient is diabetic and has a prior history of coronary artery disease. The patient presents today stating that his chest pain started yesterday evening and has been somewhat intermittent. He has been advised Aspirin 81 milligrams QDay. Humulin N. insulin 50 units in a.m. HCTZ 50 mg QDay. Nitroglycerin 1/150 sublingually PRN chest pain."""]]).toDF("text")
result = nlpPipeline.fit(data).transform(data)
val document_assembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val sentence_detector = new SentenceDetector()
.setInputCols("document")
.setOutputCol("sentence")
val tokenizer = new Tokenizer()
.setInputCols("sentence")
.setOutputCol("token")
# Clinical word embeddings trained on PubMED dataset
val word_embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")
.setInputCols(Array("sentence", "token"))
.setOutputCol("embeddings")
val ner = NerDLModel.pretrained("ner_drugs_large", "en", "clinical/models")
.setInputCols(Array("sentence", "token", "embeddings"))
.setOutputCol("ner")
val ner_converter = new NerConverter()
.setInputCols(Array("sentence", "token", "ner"))
.setOutputCol("ner_chunk")
val pipeline = new Pipeline().setStages(Array(document_assembler, sentence_detector, tokenizer, word_embeddings, ner, ner_converter))
val data = Seq("""The patient is a 40-year-old white male who presents with a chief complaint of 'chest pain'. The patient is diabetic and has a prior history of coronary artery disease. The patient presents today stating that his chest pain started yesterday evening and has been somewhat intermittent. He has been advised Aspirin 81 milligrams QDay. Humulin N. insulin 50 units in a.m. HCTZ 50 mg QDay. Nitroglycerin 1/150 sublingually PRN chest pain.""").toDS.toDF("text")
val result = pipeline.fit(data).transform(data)
Results
The output is a dataframe with a sentence per row and a "ner" column containing all of the entity labels in the sentence, entity character indices, and other metadata.
+--------------------------------+---------+
|chunk |ner_label|
+--------------------------------+---------+
|Aspirin 81 milligrams |DRUG |
|Humulin N |DRUG |
|insulin 50 units |DRUG |
|HCTZ 50 mg |DRUG |
|Nitroglycerin 1/150 sublingually|DRUG |
+--------------------------------+---------+
Model Information
| Model Name: | ner_drugs_large_en_2.6.0_2.4 |
| Type: | ner |
| Compatibility: | Spark NLP 2.7.1+ |
| Edition: | Official |
| License: | Licensed |
| Input Labels: | [sentence,token, embeddings] |
| Output Labels: | [ner] |
| Language: | [en] |
| Case sensitive: | false |
Data Source
Trained on augmented version of i2b2_med7 + FDA with ‘embeddings_clinical’. https://www.i2b2.org/NLP/Medication
Benchmarking
Since this NER model is crafted from ner_posology but reduced to single entity, no benchmark is applicable.