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* pp update

* updated md cards

* Update 2023-06-17-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md

* Update 2023-03-14-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md

* Update 2023-06-16-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md

* Update 2023-06-16-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md

* Update 2022-03-21-jsl_rd_ner_wip_greedy_clinical_pipeline_en_3_0.md

* updated md cards

* updated md

* updated md

* updated md

---------

Co-authored-by: Akar <[email protected]>
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gokhanturer and akrztrk authored Oct 3, 2024
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Expand Up @@ -22,6 +22,9 @@ This pretrained pipeline is built on the top of [jsl_rd_ner_wip_greedy_clinical]

## Predicted Entities

`Injury_or_Poisoning`, `Direction`, `Test`, `Route`, `Admission_Discharge`, `ImagingTest`, `Units`, `Death_Entity`, `Oxygen_Therapy`, `Relationship_Status`, `Triglycerides`, `Duration`, `Alcohol`, `Date`, `OtherFindings`, `BodyPart`, `Drug`, `Hyperlipidemia`, `Respiration`, `Birth_Entity`, `VS_Finding`, `Age`, `ManualFix`, `Social_History_Header`, `Family_History_Header`, `Medical_Device`, `Labour_Delivery`, `BMI`, `Fetus_NewBorn`, `Temperature`, `Section_Header`, `Communicable_Disease`, `ImagingFindings`, `Psychological_Condition`, `Obesity`, `Sexually_Active_or_Sexual_Orientation`, `Modifier`, `Vaccine`, `Symptom`, `Kidney_Disease`, `Pulse`, `Oncological`, `EKG_Findings`, `Medical_History_Header`, `Cerebrovascular_Disease`, `Blood_Pressure`, `Diabetes`, `O2_Saturation`, `Heart_Disease`, `Employment`, `Frequency`, `Disease_Syndrome_Disorder`, `Pregnancy`, `RelativeDate`, `Procedure`, `Overweight`, `Race_Ethnicity`, `Hypertension`, `Imaging_Technique`, `Test_Result`, `Treatment`, `Substance`, `Clinical_Dept`, `LDL`, `Measurements`, `Diet`, `Substance_Quantity`, `Allergen`, `Gender`, `RelativeTime`, `Score`, `Total_Cholesterol`, `Vital_Signs_Header`, `Height`, `Smoking`, `Form`, `Strength`, `Weight`, `Time`, `Dosage`, `HDL`




{:.btn-box}
Expand Down Expand Up @@ -116,4 +119,4 @@ nlu.load("en.med_ner.jsl_rd_wip_greedy.pipeline").predict("""The patient is a 21
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- NerConverterInternalModel
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Expand Up @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_cellular_biobert](https://n

## Predicted Entities

`DNA`, `protein`, `cell_type`, `cell_line`, `RNA`.



{:.btn-box}
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Expand Up @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_human_phenotype_gene_biober

## Predicted Entities

`GENE`, `HP`.



{:.btn-box}
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Expand Up @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_living_species_biobert](htt

## Predicted Entities

`SPECIES`, `HUMAN`



{:.btn-box}
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Expand Up @@ -20,6 +20,13 @@ use_language_switcher: "Python-Scala-Java"

This pretrained pipeline is built on the top of [jsl_rd_ner_wip_greedy_clinical](https://nlp.johnsnowlabs.com/2021/04/01/jsl_rd_ner_wip_greedy_clinical_en.html) model.

## Predicted Entities

`Injury_or_Poisoning`, `Direction`, `Test`, `Route`, `Admission_Discharge`, `ImagingTest`, `Units`, `Death_Entity`, `Oxygen_Therapy`, `Relationship_Status`, `Triglycerides`, `Duration`, `Alcohol`, `Date`, `OtherFindings`, `BodyPart`, `Drug`, `Hyperlipidemia`, `Respiration`, `Birth_Entity`, `VS_Finding`, `Age`, `ManualFix`, `Social_History_Header`, `Family_History_Header`, `Medical_Device`, `Labour_Delivery`, `BMI`, `Fetus_NewBorn`, `Temperature`, `Section_Header`, `Communicable_Disease`, `ImagingFindings`, `Psychological_Condition`, `Obesity`, `Sexually_Active_or_Sexual_Orientation`, `Modifier`, `Vaccine`, `Symptom`, `Kidney_Disease`, `Pulse`, `Oncological`, `EKG_Findings`, `Medical_History_Header`, `Cerebrovascular_Disease`, `Blood_Pressure`, `Diabetes`, `O2_Saturation`, `Heart_Disease`, `Employment`, `Frequency`, `Disease_Syndrome_Disorder`, `Pregnancy`, `RelativeDate`, `Procedure`, `Overweight`, `Race_Ethnicity`, `Hypertension`, `Imaging_Technique`, `Test_Result`, `Treatment`, `Substance`, `Clinical_Dept`, `LDL`, `Measurements`, `Diet`, `Substance_Quantity`, `Allergen`, `Gender`, `RelativeTime`, `Score`, `Total_Cholesterol`, `Vital_Signs_Header`, `Height`, `Smoking`, `Form`, `Strength`, `Weight`, `Time`, `Dosage`, `HDL`




{:.btn-box}
<button class="button button-orange" disabled>Live Demo</button>
<button class="button button-orange" disabled>Open in Colab</button>
Expand Down Expand Up @@ -113,4 +120,4 @@ nlu.load("en.med_ner.jsl_rd_wip_greedy.pipeline").predict("""The patient is a 21
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- NerConverterInternalModel
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java"

This pretrained pipeline is built on the top of [ner_cellular_biobert](https://nlp.johnsnowlabs.com/2021/04/01/ner_cellular_biobert_en.html) model.

## Predicted Entities

`DNA`, `protein`, `cell_type`, `cell_line`, `RNA`.

{:.btn-box}
<button class="button button-orange" disabled>Live Demo</button>
<button class="button button-orange" disabled>Open in Colab</button>
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Expand Up @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java"

This pretrained pipeline is built on the top of [ner_human_phenotype_gene_biobert](https://nlp.johnsnowlabs.com/2021/04/01/ner_human_phenotype_gene_biobert_en.html) model.

## Predicted Entities

`GENE`, `HP`.

{:.btn-box}
<button class="button button-orange" disabled>Live Demo</button>
<button class="button button-orange" disabled>Open in Colab</button>
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java"

This pretrained pipeline is built on the top of [ner_living_species_biobert](https://nlp.johnsnowlabs.com/2022/06/22/ner_living_species_biobert_en_3_0.html) model.

## Predicted Entities

`SPECIES`, `HUMAN`

{:.btn-box}
<button class="button button-orange" disabled>Live Demo</button>
<button class="button button-orange" disabled>Open in Colab</button>
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,9 @@ This pretrained pipeline is built on the top of [jsl_rd_ner_wip_greedy_clinical]

## Predicted Entities

`Injury_or_Poisoning`, `Direction`, `Test`, `Route`, `Admission_Discharge`, `ImagingTest`, `Units`, `Death_Entity`, `Oxygen_Therapy`, `Relationship_Status`, `Triglycerides`, `Duration`, `Alcohol`, `Date`, `OtherFindings`, `BodyPart`, `Drug`, `Hyperlipidemia`, `Respiration`, `Birth_Entity`, `VS_Finding`, `Age`, `ManualFix`, `Social_History_Header`, `Family_History_Header`, `Medical_Device`, `Labour_Delivery`, `BMI`, `Fetus_NewBorn`, `Temperature`, `Section_Header`, `Communicable_Disease`, `ImagingFindings`, `Psychological_Condition`, `Obesity`, `Sexually_Active_or_Sexual_Orientation`, `Modifier`, `Vaccine`, `Symptom`, `Kidney_Disease`, `Pulse`, `Oncological`, `EKG_Findings`, `Medical_History_Header`, `Cerebrovascular_Disease`, `Blood_Pressure`, `Diabetes`, `O2_Saturation`, `Heart_Disease`, `Employment`, `Frequency`, `Disease_Syndrome_Disorder`, `Pregnancy`, `RelativeDate`, `Procedure`, `Overweight`, `Race_Ethnicity`, `Hypertension`, `Imaging_Technique`, `Test_Result`, `Treatment`, `Substance`, `Clinical_Dept`, `LDL`, `Measurements`, `Diet`, `Substance_Quantity`, `Allergen`, `Gender`, `RelativeTime`, `Score`, `Total_Cholesterol`, `Vital_Signs_Header`, `Height`, `Smoking`, `Form`, `Strength`, `Weight`, `Time`, `Dosage`, `HDL`




{:.btn-box}
Expand Down Expand Up @@ -116,4 +119,4 @@ nlu.load("en.med_ner.jsl_rd_wip_greedy.pipeline").predict("""The patient is a 21
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- NerConverterInternalModel
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_cellular_biobert](https://n

## Predicted Entities

`DNA`, `protein`, `cell_type`, `cell_line`, `RNA`.



{:.btn-box}
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -20,8 +20,10 @@ use_language_switcher: "Python-Scala-Java"

This pretrained pipeline is built on the top of [ner_human_phenotype_gene_biobert](https://nlp.johnsnowlabs.com/2021/04/01/ner_human_phenotype_gene_biobert_en.html) model.


## Predicted Entities

`GENE`, `HP`.


{:.btn-box}
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ This pretrained pipeline is built on the top of [ner_living_species_biobert](htt

## Predicted Entities

`SPECIES`, `HUMAN`


{:.btn-box}
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Expand Up @@ -32,6 +32,7 @@ This pretrained pipeline maps extracted entities in the German language to ICD-1

<div class="tabs-box" markdown="1">
{% include programmingLanguageSelectScalaPythonNLU.html %}

```python
from sparknlp.pretrained import PretrainedPipeline

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Expand Up @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_living_species_biobert](htt

## Predicted Entities

`SPECIES`, `HUMAN`



{:.btn-box}
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,9 @@ This pretrained pipeline is built on the top of [jsl_rd_ner_wip_greedy_clinical]

## Predicted Entities

`Injury_or_Poisoning`, `Direction`, `Test`, `Route`, `Admission_Discharge`, `ImagingTest`, `Units`, `Death_Entity`, `Oxygen_Therapy`, `Relationship_Status`, `Triglycerides`, `Duration`, `Alcohol`, `Date`, `OtherFindings`, `BodyPart`, `Drug`, `Hyperlipidemia`, `Respiration`, `Birth_Entity`, `VS_Finding`, `Age`, `ManualFix`, `Social_History_Header`, `Family_History_Header`, `Medical_Device`, `Labour_Delivery`, `BMI`, `Fetus_NewBorn`, `Temperature`, `Section_Header`, `Communicable_Disease`, `ImagingFindings`, `Psychological_Condition`, `Obesity`, `Sexually_Active_or_Sexual_Orientation`, `Modifier`, `Vaccine`, `Symptom`, `Kidney_Disease`, `Pulse`, `Oncological`, `EKG_Findings`, `Medical_History_Header`, `Cerebrovascular_Disease`, `Blood_Pressure`, `Diabetes`, `O2_Saturation`, `Heart_Disease`, `Employment`, `Frequency`, `Disease_Syndrome_Disorder`, `Pregnancy`, `RelativeDate`, `Procedure`, `Overweight`, `Race_Ethnicity`, `Hypertension`, `Imaging_Technique`, `Test_Result`, `Treatment`, `Substance`, `Clinical_Dept`, `LDL`, `Measurements`, `Diet`, `Substance_Quantity`, `Allergen`, `Gender`, `RelativeTime`, `Score`, `Total_Cholesterol`, `Vital_Signs_Header`, `Height`, `Smoking`, `Form`, `Strength`, `Weight`, `Time`, `Dosage`, `HDL`




{:.btn-box}
Expand Down Expand Up @@ -117,4 +120,4 @@ nlu.load("en.med_ner.jsl_rd_wip_greedy.pipeline").predict("""The patient is a 21
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- NerConverterInternalModel
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_cellular_biobert](https://n

## Predicted Entities

`DNA`, `protein`, `cell_type`, `cell_line`, `RNA`.



{:.btn-box}
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_human_phenotype_gene_biober

## Predicted Entities

`GENE`, `HP`.



{:.btn-box}
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_living_species_biobert](htt

## Predicted Entities

`SPECIES`, `HUMAN`



{:.btn-box}
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java"

This advanced pipeline extracts human phenotype entities from clinical texts and utilizes the `sbiobert_base_cased_mli` Sentence Bert Embeddings to map these entities to their corresponding Human Phenotype Ontology (HPO) codes. It also returns associated codes from the following vocabularies for each HPO code: - MeSH (Medical Subject Headings)- SNOMED- UMLS (Unified Medical Language System ) - ORPHA (international reference resource for information on rare diseases and orphan drugs) - OMIM (Online Mendelian Inheritance in Man).

## Predicted Entities

`HP`

{:.btn-box}
<button class="button button-orange" disabled>Live Demo</button>
<button class="button button-orange" disabled>Open in Colab</button>
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java"

This advanced pipeline extracts clinical entities from clinical texts and utilizes the `sbiobert_base_cased_mli` Sentence Bert Embeddings to map these entities to their corresponding Medical Subject Heading (MeSH) codes.

## Predicted Entities

`TREATMENT`, `PROBLEM`, `TEST`

{:.btn-box}
<button class="button button-orange" disabled>Live Demo</button>
<button class="button button-orange" disabled>Open in Colab</button>
Expand Down
5 changes: 5 additions & 0 deletions docs/_posts/akrztrk/2024-01-18-hpo_resolver_pipeline_en.md
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Expand Up @@ -26,6 +26,10 @@ deploy:

This advanced pipeline extracts human phenotype entities from clinical texts and utilizes the `sbiobert_base_cased_mli` Sentence Bert Embeddings to map these entities to their corresponding Human Phenotype Ontology (HPO) codes. It also returns associated codes from the following vocabularies for each HPO code: - MeSH (Medical Subject Headings)- SNOMED- UMLS (Unified Medical Language System ) - ORPHA (international reference resource for information on rare diseases and orphan drugs) - OMIM (Online Mendelian Inheritance in Man).

## Predicted Entities

`HP`

{:.btn-box}
<button class="button button-orange" disabled>Live Demo</button>
<button class="button button-orange" disabled>Open in Colab</button>
Expand All @@ -45,6 +49,7 @@ This advanced pipeline extracts human phenotype entities from clinical texts and

<div class="tabs-box" markdown="1">
{% include programmingLanguageSelectScalaPythonNLU.html %}

```python

from sparknlp.pretrained import PretrainedPipeline
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4 changes: 4 additions & 0 deletions docs/_posts/akrztrk/2024-01-25-mesh_resolver_pipeline_en.md
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Expand Up @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java"

This advanced pipeline extracts clinical entities from clinical texts and utilizes the `sbiobert_base_cased_mli` Sentence Bert Embeddings to map these entities to their corresponding Medical Subject Heading (MeSH) codes.

## Predicted Entities

`TREATMENT`, `PROBLEM`, `TEST`

{:.btn-box}
<button class="button button-orange" disabled>Live Demo</button>
<button class="button button-orange" disabled>Open in Colab</button>
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java"

This advanced pipeline extracts human phenotype entities from clinical texts and utilizes the `sbiobert_base_cased_mli` Sentence Bert Embeddings to map these entities to their corresponding Human Phenotype Ontology (HPO) codes. It also returns associated codes from the following vocabularies for each HPO code: - MeSH (Medical Subject Headings)- SNOMED- UMLS (Unified Medical Language System ) - ORPHA (international reference resource for information on rare diseases and orphan drugs) - OMIM (Online Mendelian Inheritance in Man).

## Predicted Entities

`HP`

{:.btn-box}
<button class="button button-orange" disabled>Live Demo</button>
<button class="button button-orange" disabled>Open in Colab</button>
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java"

This advanced pipeline extracts clinical entities from clinical texts and utilizes the `sbiobert_base_cased_mli` Sentence Bert Embeddings to map these entities to their corresponding Medical Subject Heading (MeSH) codes.

## Predicted Entities

`TREATMENT`, `PROBLEM`, `TEST`

{:.btn-box}
<button class="button button-orange" disabled>Live Demo</button>
<button class="button button-orange" disabled>Open in Colab</button>
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,11 @@ use_language_switcher: "Python-Scala-Java"

This pretrained pipeline is built on the top of [jsl_rd_ner_wip_greedy_clinical](https://nlp.johnsnowlabs.com/2021/04/01/jsl_rd_ner_wip_greedy_clinical_en.html) model.

## Predicted Entities

`Injury_or_Poisoning`, `Direction`, `Test`, `Route`, `Admission_Discharge`, `ImagingTest`, `Units`, `Death_Entity`, `Oxygen_Therapy`, `Relationship_Status`, `Triglycerides`, `Duration`, `Alcohol`, `Date`, `OtherFindings`, `BodyPart`, `Drug`, `Hyperlipidemia`, `Respiration`, `Birth_Entity`, `VS_Finding`, `Age`, `ManualFix`, `Social_History_Header`, `Family_History_Header`, `Medical_Device`, `Labour_Delivery`, `BMI`, `Fetus_NewBorn`, `Temperature`, `Section_Header`, `Communicable_Disease`, `ImagingFindings`, `Psychological_Condition`, `Obesity`, `Sexually_Active_or_Sexual_Orientation`, `Modifier`, `Vaccine`, `Symptom`, `Kidney_Disease`, `Pulse`, `Oncological`, `EKG_Findings`, `Medical_History_Header`, `Cerebrovascular_Disease`, `Blood_Pressure`, `Diabetes`, `O2_Saturation`, `Heart_Disease`, `Employment`, `Frequency`, `Disease_Syndrome_Disorder`, `Pregnancy`, `RelativeDate`, `Procedure`, `Overweight`, `Race_Ethnicity`, `Hypertension`, `Imaging_Technique`, `Test_Result`, `Treatment`, `Substance`, `Clinical_Dept`, `LDL`, `Measurements`, `Diet`, `Substance_Quantity`, `Allergen`, `Gender`, `RelativeTime`, `Score`, `Total_Cholesterol`, `Vital_Signs_Header`, `Height`, `Smoking`, `Form`, `Strength`, `Weight`, `Time`, `Dosage`, `HDL`


{:.btn-box}
<button class="button button-orange" disabled>Live Demo</button>
<button class="button button-orange" disabled>Open in Colab</button>
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,10 @@ use_language_switcher: "Python-Scala-Java"

This pretrained pipeline is built on the top of [ner_cellular_biobert](https://nlp.johnsnowlabs.com/2021/04/01/ner_cellular_biobert_en.html) model.

## Predicted Entities

`DNA`, `protein`, `cell_type`, `cell_line`, `RNA`.

{:.btn-box}
<button class="button button-orange" disabled>Live Demo</button>
<button class="button button-orange" disabled>Open in Colab</button>
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,10 @@ use_language_switcher: "Python-Scala-Java"

This pretrained pipeline is built on the top of [ner_deid_subentity_augmented_i2b2](https://nlp.johnsnowlabs.com/2021/11/29/ner_deid_subentity_augmented_i2b2_en.html) model.

## Predicted Entities

`MEDICALRECORD`, `ORGANIZATION`, `PROFESSION`, `HEALTHPLAN`, `DOCTOR`, `USERNAME`, `URL`, `LOCATION-OTHER`, `DEVICE`, `CITY`, `DATE`, `ZIP`, `STATE`, `PATIENT`, `COUNTRY`, `STREET`, `PHONE`, `HOSPITAL`, `EMAIL`, `IDNUM`, `BIOID`, `FAX`, `AGE`

{:.btn-box}
[Live Demo](https://demo.johnsnowlabs.com/healthcare/NER_DEMOGRAPHICS/){:.button.button-orange}
[Open in Colab](https://colab.research.google.com/github/JohnSnowLabs/spark-nlp-workshop/blob/master/tutorials/streamlit_notebooks/healthcare/NER_DEMOGRAPHICS.ipynb){:.button.button-orange.button-orange-trans.co.button-icon}
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,10 @@ use_language_switcher: "Python-Scala-Java"

This pretrained pipeline is built on the top of [ner_human_phenotype_gene_biobert](https://nlp.johnsnowlabs.com/2021/04/01/ner_human_phenotype_gene_biobert_en.html) model.

## Predicted Entities

`GENE`, `HP`.

{:.btn-box}
<button class="button button-orange" disabled>Live Demo</button>
<button class="button button-orange" disabled>Open in Colab</button>
Expand Down

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