Description
This relation extraction model links Biomarker and Oncogene extractions to their corresponding Biomarker_Result extractions.
Predicted Entities
is_finding_of, O
How to use
document_assembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
sentence_detector = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare","en","clinical/models")\
.setInputCols(["document"])\
.setOutputCol("sentence")
tokenizer = Tokenizer() \
.setInputCols(["sentence"]) \
.setOutputCol("token")
word_embeddings = WordEmbeddingsModel().pretrained("embeddings_clinical", "en", "clinical/models")\
.setInputCols(["sentence", "token"]) \
.setOutputCol("embeddings")
ner = MedicalNerModel.pretrained("ner_oncology_wip", "en", "clinical/models") \
.setInputCols(["sentence", "token", "embeddings"]) \
.setOutputCol("ner")
ner_converter = NerConverter() \
.setInputCols(["sentence", "token", "ner"]) \
.setOutputCol("ner_chunk")
pos_tagger = PerceptronModel.pretrained("pos_clinical", "en", "clinical/models") \
.setInputCols(["sentence", "token"]) \
.setOutputCol("pos_tags")
dependency_parser = DependencyParserModel.pretrained("dependency_conllu", "en") \
.setInputCols(["sentence", "pos_tags", "token"]) \
.setOutputCol("dependencies")
re_model = RelationExtractionModel.pretrained("re_oncology_biomarker_result", "en", "clinical/models") \
.setInputCols(["embeddings", "pos_tags", "ner_chunk", "dependencies"]) \
.setOutputCol("relation_extraction") \
.setRelationPairs(['Biomarker-Biomarker_Result', 'Biomarker_Result-Biomarker', 'Oncogene-Biomarker_Result', 'Biomarker_Result-Oncogene']) \
.setMaxSyntacticDistance(10)
pipeline = Pipeline(stages=[document_assembler,
sentence_detector,
tokenizer,
word_embeddings,
ner,
ner_converter,
pos_tagger,
dependency_parser,
re_model])
data = spark.createDataFrame([["Immunohistochemistry was negative for thyroid transcription factor-1 and napsin A. The test was positive for ER and PR, and negative for HER2."]]).toDF("text")
result = pipeline.fit(data).transform(data)
val document_assembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val sentence_detector = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare","en","clinical/models")
.setInputCols(Array("document"))
.setOutputCol("sentence")
val tokenizer = new Tokenizer()
.setInputCols(Array("sentence"))
.setOutputCol("token")
val word_embeddings = WordEmbeddingsModel().pretrained("embeddings_clinical", "en", "clinical/models")
.setInputCols(Array("sentence", "token"))
.setOutputCol("embeddings")
val ner = MedicalNerModel.pretrained("ner_oncology_wip", "en", "clinical/models")
.setInputCols(Array("sentence", "token", "embeddings"))
.setOutputCol("ner")
val ner_converter = new NerConverter()
.setInputCols(Array("sentence", "token", "ner"))
.setOutputCol("ner_chunk")
val pos_tagger = PerceptronModel.pretrained("pos_clinical", "en", "clinical/models")
.setInputCols(Array("sentence", "token"))
.setOutputCol("pos_tags")
val dependency_parser = DependencyParserModel.pretrained("dependency_conllu", "en")
.setInputCols(Array("sentence", "pos_tags", "token"))
.setOutputCol("dependencies")
val re_model = RelationExtractionModel.pretrained("re_oncology_biomarker_result", "en", "clinical/models")
.setInputCols(Array("embeddings", "pos_tags", "ner_chunk", "dependencies"))
.setOutputCol("relation_extraction")
.setRelationPairs(Array("Biomarker-Biomarker_Result", "Biomarker_Result-Biomarker", "Oncogene-Biomarker_Result", "Biomarker_Result-Oncogene"))
.setMaxSyntacticDistance(10)
val pipeline = new Pipeline().setStages(Array(document_assembler,
sentence_detector,
tokenizer,
word_embeddings,
ner,
ner_converter,
pos_tagger,
dependency_parser,
re_model))
val data = Seq("Immunohistochemistry was negative for thyroid transcription factor-1 and napsin A. The test was positive for ER and PR, and negative for HER2.").toDS.toDF("text")
val result = pipeline.fit(data).transform(data)
Results
chunk1 entity1 chunk2 entity2 relation confidence
negative Biomarker_Result thyroid transcription factor-1 Biomarker is_finding_of 0.99925953
negative Biomarker_Result napsin Biomarker is_finding_of 0.98856175
positive Biomarker_Result ER Biomarker is_finding_of 0.9833266
positive Biomarker_Result PR Biomarker is_finding_of 0.94771445
positive Biomarker_Result HER2 Oncogene O 0.96865135
ER Biomarker negative Biomarker_Result O 0.998276
PR Biomarker negative Biomarker_Result O 0.98595536
negative Biomarker_Result HER2 Oncogene is_finding_of 0.99124444
Model Information
| Model Name: | re_oncology_biomarker_result |
| Type: | re |
| Compatibility: | Healthcare NLP 5.4.0+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [embeddings, pos_tags, train_ner_chunks, dependencies] |
| Output Labels: | [relations] |
| Language: | en |
| Size: | 265.8 KB |
References
In-house annotated oncology case reports.
Benchmarking
label recall precision f1
O 0.88 0.95 0.91
is_finding_of 0.95 0.89 0.92
macro-avg 0.92 0.92 0.92