Description
Assign assertion status to clinical entities extracted by NER based on their context in the text.
Predicted Entities
absent, present, conditional, associated_with_someone_else, hypothetical, possible.
Live Demo Open in Colab Copy S3 URI
How to use
documentAssembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
sentenceDetector = SentenceDetector()\
.setInputCols(["document"])\
.setOutputCol("sentence")
tokenizer = Tokenizer()\
.setInputCols(["sentence"])\
.setOutputCol("token")
word_embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")\
.setInputCols(["sentence", "token"])\
.setOutputCol("embeddings")
clinical_ner = MedicalNerModel.pretrained("ner_clinical", "en", "clinical/models") \
.setInputCols(["sentence", "token", "embeddings"]) \
.setOutputCol("ner")
ner_converter = NerConverter() \
.setInputCols(["sentence", "token", "ner"]) \
.setOutputCol("ner_chunk")
clinical_assertion = AssertionDLModel.pretrained("assertion_dl", "en", "clinical/models") \
.setInputCols(["sentence", "ner_chunk", "embeddings"]) \
.setOutputCol("assertion")
nlpPipeline = Pipeline(stages=[
documentAssembler,
sentenceDetector,
tokenizer,
word_embeddings,
clinical_ner,
ner_converter,
clinical_assertion
])
data = spark.createDataFrame([["The human KCNJ9 (Kir 3.3, GIRK3) is a member of the G-protein-activated inwardly rectifying potassium (GIRK) channel family.', 'Here we describe the genomicorganization of the KCNJ9 locus on chromosome 1q21-23 as a candidate gene forType II diabetes mellitus in the Pima Indian population.', 'The gene spansapproximately 7.6 kb and contains one noncoding and two coding exons separated byapproximately 2.2 and approximately 2.6 kb introns, respectively.', 'We identified14 single nucleotide polymorphisms (SNPs), including one that predicts aVal366Ala substitution, and an 8 base-pair', '(bp) insertion/deletion.', 'Ourexpression studies revealed the presence of the transcript in various humantissues including pancreas, and two major insulin-responsive tissues: fat andskeletal muscle.', 'The characterization of the KCNJ9 gene should facilitate furtherstudies on the function of the KCNJ9 protein and allow evaluation of thepotential role of the locus in Type II diabetes."]]).toDF("text")
model = nlpPipeline.fit(data)
result = model.transform(data)
val documentAssembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val sentenceDetector = new SentenceDetector()
.setInputCols("document")
.setOutputCol("sentence")
val tokenizer = new Tokenizer()
.setInputCols("sentence")
.setOutputCol("token")
val word_embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")
.setInputCols(Array("sentence", "token"))
.setOutputCol("embeddings")
val clinical_ner = MedicalNerModel.pretrained("ner_clinical", "en", "clinical/models")
.setInputCols(Array("sentence", "token", "embeddings"))
.setOutputCol("ner")
val ner_converter = new NerConverter()
.setInputCols(Array("sentence", "token", "ner"))
.setOutputCol("ner_chunk")
val clinical_assertion = AssertionDLModel.pretrained("assertion_dl", "en", "clinical/models")
.setInputCols(Array("sentence", "ner_chunk", "embeddings"))
.setOutputCol("assertion")
val nlpPipeline = new Pipeline().setStages(Array(
documentAssembler,
sentenceDetector,
tokenizer,
word_embeddings,
clinical_ner,
ner_converter,
clinical_assertion
))
val text = """The human KCNJ9 (Kir 3.3, GIRK3) is a member of the G-protein-activated inwardly rectifying potassium (GIRK) channel family.', 'Here we describe the genomicorganization of the KCNJ9 locus on chromosome 1q21-23 as a candidate gene forType II diabetes mellitus in the Pima Indian population.', 'The gene spansapproximately 7.6 kb and contains one noncoding and two coding exons separated byapproximately 2.2 and approximately 2.6 kb introns, respectively.', 'We identified14 single nucleotide polymorphisms (SNPs), including one that predicts aVal366Ala substitution, and an 8 base-pair', '(bp) insertion/deletion.', 'Ourexpression studies revealed the presence of the transcript in various humantissues including pancreas, and two major insulin-responsive tissues: fat andskeletal muscle.', 'The characterization of the KCNJ9 gene should facilitate furtherstudies on the function of the KCNJ9 protein and allow evaluation of thepotential role of the locus in Type II diabetes."""
val data = Seq(text).toDS.toDF("text")
val results = pipeline.fit(data).transform(data)
import nlu
nlu.load("en.assert").predict("""The human KCNJ9 (Kir 3.3, GIRK3) is a member of the G-protein-activated inwardly rectifying potassium (GIRK) channel family.', 'Here we describe the genomicorganization of the KCNJ9 locus on chromosome 1q21-23 as a candidate gene forType II diabetes mellitus in the Pima Indian population.', 'The gene spansapproximately 7.6 kb and contains one noncoding and two coding exons separated byapproximately 2.2 and approximately 2.6 kb introns, respectively.', 'We identified14 single nucleotide polymorphisms (SNPs), including one that predicts aVal366Ala substitution, and an 8 base-pair', '(bp) insertion/deletion.', 'Ourexpression studies revealed the presence of the transcript in various humantissues including pancreas, and two major insulin-responsive tissues: fat andskeletal muscle.', 'The characterization of the KCNJ9 gene should facilitate furtherstudies on the function of the KCNJ9 protein and allow evaluation of thepotential role of the locus in Type II diabetes.""")
Results
+-----------------------------------------------------------+---------+-----------+
|chunk |ner_label|assertion |
+-----------------------------------------------------------+---------+-----------+
|the G-protein-activated inwardly rectifying potassium (GIRK|TREATMENT|conditional|
|the genomicorganization |TREATMENT|present |
|a candidate gene forType II diabetes mellitus |PROBLEM |present |
|byapproximately |TREATMENT|present |
|single nucleotide polymorphisms |TREATMENT|present |
|aVal366Ala substitution |TREATMENT|present |
|insertion/deletion |PROBLEM |present |
|'Ourexpression studies |TEST |present |
|the transcript in various humantissues |PROBLEM |present |
|fat andskeletal muscle |PROBLEM |possible |
|furtherstudies |PROBLEM |present |
|the KCNJ9 protein |TREATMENT|present |
|evaluation |TEST |possible |
|Type II diabetes |PROBLEM |present |
+-----------------------------------------------------------+---------+-----------+
Model Information
| Model Name: | assertion_dl |
| Compatibility: | Spark NLP 2.7.2+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [document, chunk, embeddings] |
| Output Labels: | [assertion] |
| Language: | en |
Data Source
Trained with augmented version of i2b2 dataset.
Benchmarking
| | label | tp | fp | fn | prec | rec | f1 |
|---:|:-----------------------------|------:|-----:|-----:|---------:|---------:|---------:|
| 0 | absent | 791 | 47 | 80 | 0.943914 | 0.908152 | 0.925688 |
| 1 | present | 2499 | 169 | 120 | 0.936657 | 0.954181 | 0.945338 |
| 2 | conditional | 23 | 19 | 21 | 0.547619 | 0.522727 | 0.534884 |
| 3 | associated_with_someone_else | 38 | 2 | 11 | 0.95 | 0.77551 | 0.853933 |
| 4 | hypothetical | 163 | 19 | 21 | 0.895604 | 0.88587 | 0.89071 |
| 5 | possible | 119 | 61 | 64 | 0.661111 | 0.650273 | 0.655647 |
| 6 | Macro-average | 3633 | 317 | 317 | 0.822484 | 0.782786 | 0.802144 |
| 7 | Micro-average | 3633 | 317 | 317 | 0.919747 | 0.919747 | 0.919747 |