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2022-12-01-oncology_general_pipeline_en (#13178)
* Add model 2022-12-01-oncology_general_pipeline_en * Add model 2022-12-01-oncology_diagnosis_pipeline_en * Add model 2022-12-01-oncology_biomarker_pipeline_en * Add model 2022-12-01-oncology_therapy_pipeline_en Co-authored-by: mauro-nievoff <mauro.nievasoffidani@gmail.com>
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docs/_posts/mauro-nievoff/2022-12-01-oncology_biomarker_pipeline_en.md
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| --- | ||
| layout: model | ||
| title: Oncology Pipeline for Biomarkers | ||
| author: John Snow Labs | ||
| name: oncology_biomarker_pipeline | ||
| date: 2022-12-01 | ||
| tags: [licensed, pipeline, oncology, biomarker, en] | ||
| task: Named Entity Recognition | ||
| language: en | ||
| edition: Healthcare NLP 4.2.2 | ||
| spark_version: 3.0 | ||
| supported: true | ||
| article_header: | ||
| type: cover | ||
| use_language_switcher: "Python-Scala-Java" | ||
| --- | ||
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| ## Description | ||
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| 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. | ||
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| {:.btn-box} | ||
| <button class="button button-orange" disabled>Live Demo</button> | ||
| [Open in Colab](https://colab.research.google.com/github/JohnSnowLabs/spark-nlp-workshop/blob/master/tutorials/Certification_Trainings/Healthcare/27.Oncology_Model.ipynb){:.button.button-orange.button-orange-trans.co.button-icon} | ||
| [Download](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/clinical/models/oncology_biomarker_pipeline_en_4.2.2_3.0_1669902355525.zip){:.button.button-orange.button-orange-trans.arr.button-icon} | ||
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| ## How to use | ||
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| <div class="tabs-box" markdown="1"> | ||
| {% include programmingLanguageSelectScalaPythonNLU.html %} | ||
| ```python | ||
| from sparknlp.pretrained import PretrainedPipeline | ||
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| pipeline = PretrainedPipeline("oncology_biomarker_pipeline", "en", "clinical/models") | ||
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| 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.") | ||
| ``` | ||
| ```scala | ||
| import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline | ||
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| val pipeline = new PretrainedPipeline("oncology_biomarker_pipeline", "en", "clinical/models") | ||
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| 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) | ||
| ``` | ||
| </div> | ||
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| ## Results | ||
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| ```bash | ||
| ******************** ner_oncology_wip results ******************** | ||
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| | 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 | | ||
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| ******************** ner_oncology_biomarker_wip results ******************** | ||
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| | 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 | | ||
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| ******************** ner_oncology_test_wip results ******************** | ||
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| | 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 | | ||
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| ******************** ner_biomarker results ******************** | ||
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| | 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 | | ||
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| ******************** assertion_oncology_wip results ******************** | ||
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| | 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 | | ||
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| ******************** assertion_oncology_test_binary_wip results ******************** | ||
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| | 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 | | ||
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| ******************** re_oncology_wip results ******************** | ||
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| | 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 | | ||
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| ******************** re_oncology_granular_wip results ******************** | ||
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| | 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 | | ||
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| ******************** re_oncology_biomarker_result_wip results ******************** | ||
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| | 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 | | ||
| ``` | ||
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| {:.model-param} | ||
| ## Model Information | ||
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| {:.table-model} | ||
| |---|---| | ||
| |Model Name:|oncology_biomarker_pipeline| | ||
| |Type:|pipeline| | ||
| |Compatibility:|Healthcare NLP 4.2.2+| | ||
| |License:|Licensed| | ||
| |Edition:|Official| | ||
| |Language:|en| | ||
| |Size:|1.7 GB| | ||
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| ## Included Models | ||
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| - DocumentAssembler | ||
| - SentenceDetectorDLModel | ||
| - TokenizerModel | ||
| - WordEmbeddingsModel | ||
| - MedicalNerModel | ||
| - NerConverter | ||
| - MedicalNerModel | ||
| - NerConverter | ||
| - MedicalNerModel | ||
| - NerConverter | ||
| - MedicalNerModel | ||
| - NerConverter | ||
| - ChunkMergeModel | ||
| - ChunkMergeModel | ||
| - AssertionDLModel | ||
| - AssertionDLModel | ||
| - PerceptronModel | ||
| - DependencyParserModel | ||
| - RelationExtractionModel | ||
| - RelationExtractionModel | ||
| - RelationExtractionModel |
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