Description
This pipeline includes Named-Entity Recognition, Assertion Status and Relation Extraction models to extract information from oncology texts. This pipeline focuses on entities related to biomarkers.
Predicted Entities
Biomarker_Result, Oncogene, Biomarker, Imaging_Test, Pathology_Test, PerformanceStatus, Drug, Test, Tumor_Finding, TargetedTherapy, Biomarker_Measurement, Duration, Chemotherapy, Oncogenes, Radiotherapy, Date, CancerModifier, Predictive_Biomarkers, HormonalTherapy, Staging, Age, Prognostic_Biomarkers, CancerSurgery, Immunotherapy, Metastasis, ResponseToTreatment, Radiological_Test, CancerDx, Radiological_Test_Result, UnspecificTherapy, Gender, Test_Result, Ethnicity, Dosage
Live Demo Open in Colab Copy S3 URI
How to use
from sparknlp.pretrained import PretrainedPipeline
pipeline = PretrainedPipeline("oncology_biomarker_pipeline", "en", "clinical/models")
pipeline.annotate("Immunohistochemistry was negative for thyroid transcription factor-1 and napsin A. The test was positive for ER and PR, and negative for HER2.")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val pipeline = new PretrainedPipeline("oncology_biomarker_pipeline", "en", "clinical/models")
val result = pipeline.fullAnnotate("""Immunohistochemistry was negative for thyroid transcription factor-1 and napsin A. The test was positive for ER and PR, and negative for HER2.""")(0)
import nlu
nlu.load("en.oncology_biomarker.pipeline").predict("""Immunohistochemistry was negative for thyroid transcription factor-1 and napsin A. The test was positive for ER and PR, and negative for HER2.""")
Results
******************** ner_oncology_wip results ********************
| chunk | ner_label |
|:-------------------------------|:-----------------|
| negative | Biomarker_Result |
| thyroid transcription factor-1 | Biomarker |
| napsin | Biomarker |
| positive | Biomarker_Result |
| ER | Biomarker |
| PR | Biomarker |
| negative | Biomarker_Result |
| HER2 | Oncogene |
******************** ner_oncology_biomarker_wip results ********************
| chunk | ner_label |
|:-------------------------------|:-----------------|
| negative | Biomarker_Result |
| thyroid transcription factor-1 | Biomarker |
| napsin A | Biomarker |
| positive | Biomarker_Result |
| ER | Biomarker |
| PR | Biomarker |
| negative | Biomarker_Result |
| HER2 | Biomarker |
******************** ner_oncology_test_wip results ********************
| chunk | ner_label |
|:-------------------------------|:-----------------|
| Immunohistochemistry | Pathology_Test |
| negative | Biomarker_Result |
| thyroid transcription factor-1 | Biomarker |
| napsin A | Biomarker |
| positive | Biomarker_Result |
| ER | Biomarker |
| PR | Biomarker |
| negative | Biomarker_Result |
| HER2 | Oncogene |
******************** ner_biomarker results ********************
| chunk | ner_label |
|:-------------------------------|:----------------------|
| Immunohistochemistry | Test |
| negative | Biomarker_Measurement |
| thyroid transcription factor-1 | Biomarker |
| napsin A | Biomarker |
| positive | Biomarker_Measurement |
| ER | Biomarker |
| PR | Biomarker |
| negative | Biomarker_Measurement |
| HER2 | Biomarker |
******************** assertion_oncology_wip results ********************
| chunk | ner_label | assertion |
|:-------------------------------|:---------------|:------------|
| Immunohistochemistry | Pathology_Test | Past |
| thyroid transcription factor-1 | Biomarker | Present |
| napsin A | Biomarker | Present |
| ER | Biomarker | Present |
| PR | Biomarker | Present |
| HER2 | Oncogene | Present |
******************** assertion_oncology_test_binary_wip results ********************
| chunk | ner_label | assertion |
|:-------------------------------|:---------------|:----------------|
| Immunohistochemistry | Pathology_Test | Medical_History |
| thyroid transcription factor-1 | Biomarker | Medical_History |
| napsin A | Biomarker | Medical_History |
| ER | Biomarker | Medical_History |
| PR | Biomarker | Medical_History |
| HER2 | Oncogene | Medical_History |
******************** re_oncology_wip results ********************
| chunk1 | entity1 | chunk2 | entity2 | relation |
|:---------------------|:-----------------|:-------------------------------|:-----------------|:--------------|
| Immunohistochemistry | Pathology_Test | negative | Biomarker_Result | O |
| negative | Biomarker_Result | thyroid transcription factor-1 | Biomarker | is_related_to |
| negative | Biomarker_Result | napsin A | Biomarker | is_related_to |
| positive | Biomarker_Result | ER | Biomarker | is_related_to |
| positive | Biomarker_Result | PR | Biomarker | is_related_to |
| positive | Biomarker_Result | HER2 | Oncogene | O |
| ER | Biomarker | negative | Biomarker_Result | O |
| PR | Biomarker | negative | Biomarker_Result | O |
| negative | Biomarker_Result | HER2 | Oncogene | is_related_to |
******************** re_oncology_granular_wip results ********************
| chunk1 | entity1 | chunk2 | entity2 | relation |
|:---------------------|:-----------------|:-------------------------------|:-----------------|:--------------|
| Immunohistochemistry | Pathology_Test | negative | Biomarker_Result | O |
| negative | Biomarker_Result | thyroid transcription factor-1 | Biomarker | is_finding_of |
| negative | Biomarker_Result | napsin A | Biomarker | is_finding_of |
| positive | Biomarker_Result | ER | Biomarker | is_finding_of |
| positive | Biomarker_Result | PR | Biomarker | is_finding_of |
| positive | Biomarker_Result | HER2 | Oncogene | is_finding_of |
| ER | Biomarker | negative | Biomarker_Result | O |
| PR | Biomarker | negative | Biomarker_Result | O |
| negative | Biomarker_Result | HER2 | Oncogene | is_finding_of |
******************** re_oncology_biomarker_result_wip results ********************
| chunk1 | entity1 | chunk2 | entity2 | relation |
|:---------------------|:-----------------|:-------------------------------|:-----------------|:--------------|
| Immunohistochemistry | Pathology_Test | negative | Biomarker_Result | is_finding_of |
| negative | Biomarker_Result | thyroid transcription factor-1 | Biomarker | is_finding_of |
| negative | Biomarker_Result | napsin A | Biomarker | is_finding_of |
| positive | Biomarker_Result | ER | Biomarker | is_finding_of |
| positive | Biomarker_Result | PR | Biomarker | is_finding_of |
| positive | Biomarker_Result | HER2 | Oncogene | O |
| ER | Biomarker | negative | Biomarker_Result | O |
| PR | Biomarker | negative | Biomarker_Result | O |
| negative | Biomarker_Result | HER2 | Oncogene | is_finding_of |
Model Information
| Model Name: | oncology_biomarker_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 4.2.2+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 1.7 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverter
- MedicalNerModel
- NerConverter
- MedicalNerModel
- NerConverter
- MedicalNerModel
- NerConverter
- ChunkMergeModel
- ChunkMergeModel
- AssertionDLModel
- AssertionDLModel
- PerceptronModel
- DependencyParserModel
- RelationExtractionModel
- RelationExtractionModel
- RelationExtractionModel