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2022-12-01-oncology_general_pipeline_en #13178

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Add model 2022-12-01-oncology_general_pipeline_en
mauro-nievoff Dec 1, 2022
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Add model 2022-12-01-oncology_diagnosis_pipeline_en
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Add model 2022-12-01-oncology_biomarker_pipeline_en
mauro-nievoff Dec 1, 2022
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214 changes: 214 additions & 0 deletions 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"
---

## 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.

{:.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}

## How to use



<div class="tabs-box" markdown="1">
{% include programmingLanguageSelectScalaPythonNLU.html %}
```python
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.")
```
```scala
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)
```
</div>

## Results

```bash
******************** 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-param}
## Model Information

{:.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|

## Included Models

- 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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