2023-06-13-recognize_entities_posology_en (#378)

* Add model 2023-06-13-recognize_entities_posology_en * Add model 2023-06-13-snomed_icd10cm_mapping_en * Add model 2023-06-13-icd10cm_umls_mapping_en * Add model 2023-06-13-mesh_umls_mapping_en * Add model 2023-06-13-clinical_deidentification_de * Add model 2023-06-13-clinical_deidentification_es * Add model 2023-06-13-snomed_umls_mapping_en * Add model 2023-06-13-rxnorm_umls_mapping_en * Add model 2023-06-13-clinical_deidentification_glove_en * Add model 2023-06-13-ner_deid_generic_augmented_pipeline_en * Add model 2023-06-13-clinical_deidentification_fr * Add model 2023-06-13-icd10_icd9_mapping_en * Add model 2023-06-13-bert_token_classifier_ner_jsl_pipeline_en * Add model 2023-06-13-clinical_deidentification_augmented_es * Add model 2023-06-13-rxnorm_mesh_mapping_en * Add model 2023-06-13-re_bodypart_directions_pipeline_en * Add model 2023-06-13-clinical_deidentification_it * Add model 2023-06-13-re_bodypart_proceduretest_pipeline_en * Add model 2023-06-13-re_human_phenotype_gene_clinical_pipeline_en * Add model 2023-06-13-re_temporal_events_clinical_pipeline_en * Add model 2023-06-13-re_temporal_events_enriched_clinical_pipeline_en * Add model 2023-06-13-re_test_problem_finding_pipeline_en * Add model 2023-06-13-re_test_result_date_pipeline_en * Add model 2023-06-13-clinical_deidentification_pt * Add model 2023-06-13-bert_sequence_classifier_binary_rct_biobert_pipeline_en * Add model 2023-06-13-icd10cm_snomed_mapping_en * Add model 2023-06-13-icdo_snomed_mapping_en * Add model 2023-06-13-rxnorm_ndc_mapping_en * Add model 2023-06-13-clinical_deidentification_ro * Add model 2023-06-13-clinical_deidentification_slim_en * Add model 2023-06-13-ner_medication_pipeline_en * Add model 2023-06-13-snomed_icdo_mapping_en * Add model 2023-06-13-ner_deid_subentity_pipeline_ar --------- Co-authored-by: Cabir40 <cabir4006@gmail.com>
JohnSnowLabs · Jun 14, 2023 · 03d9c6f · 03d9c6f
1 parent 31917c6
commit 03d9c6f
Show file tree

Hide file tree

Showing 33 changed files with 5,758 additions and 0 deletions.
diff --git a/...s/Cabir40/2023-06-13-bert_sequence_classifier_binary_rct_biobert_pipeline_en.md b/...s/Cabir40/2023-06-13-bert_sequence_classifier_binary_rct_biobert_pipeline_en.md
diff --git a/docs/_posts/Cabir40/2023-06-13-bert_token_classifier_ner_jsl_pipeline_en.md b/docs/_posts/Cabir40/2023-06-13-bert_token_classifier_ner_jsl_pipeline_en.md
@@ -0,0 +1,150 @@
+---
+layout: model
+title: Pipeline to Detect Clinical Entities (BertForTokenClassifier)
+author: John Snow Labs
+name: bert_token_classifier_ner_jsl_pipeline
+date: 2023-06-13
+tags: [ner_jsl, ner, berfortokenclassification, en, licensed]
+task: Named Entity Recognition
+language: en
+edition: Healthcare NLP 4.4.4
+spark_version: 3.4
+supported: true
+annotator: PipelineModel
+article_header:
+  type: cover
+use_language_switcher: "Python-Scala-Java"
+---
+
+## Description
+
+This pretrained pipeline is built on the top of [bert_token_classifier_ner_jsl](https://nlp.johnsnowlabs.com/2022/03/21/bert_token_classifier_ner_jsl_en_2_4.html) model.
+
+## Predicted Entities
+
+
+
+{:.btn-box}
+<button class="button button-orange" disabled>Live Demo</button>
+<button class="button button-orange" disabled>Open in Colab</button>
+[Download](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/clinical/models/bert_token_classifier_ner_jsl_pipeline_en_4.4.4_3.4_1686675054357.zip){:.button.button-orange.button-orange-trans.arr.button-icon.hidden}
+[Copy S3 URI](s3://auxdata.johnsnowlabs.com/clinical/models/bert_token_classifier_ner_jsl_pipeline_en_4.4.4_3.4_1686675054357.zip){:.button.button-orange.button-orange-trans.button-icon.button-copy-s3}
+
+## How to use
+
+<div class="tabs-box" markdown="1">
+{% include programmingLanguageSelectScalaPythonNLU.html %}
+```python
+from sparknlp.pretrained import PretrainedPipeline
+
+pipeline = PretrainedPipeline("bert_token_classifier_ner_jsl_pipeline", "en", "clinical/models")
+
+text = '''The patient is a 21-day-old Caucasian male here for 2 days of congestion - mom has been suctioning yellow discharge from the patient's nares, plus she has noticed some mild problems with his breathing while feeding (but negative for any perioral cyanosis or retractions). One day ago, mom also noticed a tactile temperature and gave the patient Tylenol. Baby-girl also has had some decreased p.o. intake. His normal breast-feeding is down from 20 minutes q.2h. to 5 to 10 minutes secondary to his respiratory congestion. He sleeps well, but has been more tired and has been fussy over the past 2 days. The parents noticed no improvement with albuterol treatments given in the ER. His urine output has also decreased; normally he has 8 to 10 wet and 5 dirty diapers per 24 hours, now he has down to 4 wet diapers per 24 hours. Mom denies any diarrhea. His bowel movements are yellow colored and soft in nature.'''
+
+result = pipeline.fullAnnotate(text)
+```
+```scala
+import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
+
+val pipeline = new PretrainedPipeline("bert_token_classifier_ner_jsl_pipeline", "en", "clinical/models")
+
+val text = "The patient is a 21-day-old Caucasian male here for 2 days of congestion - mom has been suctioning yellow discharge from the patient's nares, plus she has noticed some mild problems with his breathing while feeding (but negative for any perioral cyanosis or retractions). One day ago, mom also noticed a tactile temperature and gave the patient Tylenol. Baby-girl also has had some decreased p.o. intake. His normal breast-feeding is down from 20 minutes q.2h. to 5 to 10 minutes secondary to his respiratory congestion. He sleeps well, but has been more tired and has been fussy over the past 2 days. The parents noticed no improvement with albuterol treatments given in the ER. His urine output has also decreased; normally he has 8 to 10 wet and 5 dirty diapers per 24 hours, now he has down to 4 wet diapers per 24 hours. Mom denies any diarrhea. His bowel movements are yellow colored and soft in nature."
+
+val result = pipeline.fullAnnotate(text)
+```
+
+
+{:.nlu-block}
+```python
+import nlu
+nlu.load("en.classify.bert_token_ner_jsl.pipeline").predict("""The patient is a 21-day-old Caucasian male here for 2 days of congestion - mom has been suctioning yellow discharge from the patient's nares, plus she has noticed some mild problems with his breathing while feeding (but negative for any perioral cyanosis or retractions). One day ago, mom also noticed a tactile temperature and gave the patient Tylenol. Baby-girl also has had some decreased p.o. intake. His normal breast-feeding is down from 20 minutes q.2h. to 5 to 10 minutes secondary to his respiratory congestion. He sleeps well, but has been more tired and has been fussy over the past 2 days. The parents noticed no improvement with albuterol treatments given in the ER. His urine output has also decreased; normally he has 8 to 10 wet and 5 dirty diapers per 24 hours, now he has down to 4 wet diapers per 24 hours. Mom denies any diarrhea. His bowel movements are yellow colored and soft in nature.""")
+```
+
+</div>
+
+<div class="tabs-box" markdown="1">
+{% include programmingLanguageSelectScalaPythonNLU.html %}
+```python
+from sparknlp.pretrained import PretrainedPipeline
+
+pipeline = PretrainedPipeline("bert_token_classifier_ner_jsl_pipeline", "en", "clinical/models")
+
+text = '''The patient is a 21-day-old Caucasian male here for 2 days of congestion - mom has been suctioning yellow discharge from the patient's nares, plus she has noticed some mild problems with his breathing while feeding (but negative for any perioral cyanosis or retractions). One day ago, mom also noticed a tactile temperature and gave the patient Tylenol. Baby-girl also has had some decreased p.o. intake. His normal breast-feeding is down from 20 minutes q.2h. to 5 to 10 minutes secondary to his respiratory congestion. He sleeps well, but has been more tired and has been fussy over the past 2 days. The parents noticed no improvement with albuterol treatments given in the ER. His urine output has also decreased; normally he has 8 to 10 wet and 5 dirty diapers per 24 hours, now he has down to 4 wet diapers per 24 hours. Mom denies any diarrhea. His bowel movements are yellow colored and soft in nature.'''
+
+result = pipeline.fullAnnotate(text)
+```
+```scala
+import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
+
+val pipeline = new PretrainedPipeline("bert_token_classifier_ner_jsl_pipeline", "en", "clinical/models")
+
+val text = "The patient is a 21-day-old Caucasian male here for 2 days of congestion - mom has been suctioning yellow discharge from the patient's nares, plus she has noticed some mild problems with his breathing while feeding (but negative for any perioral cyanosis or retractions). One day ago, mom also noticed a tactile temperature and gave the patient Tylenol. Baby-girl also has had some decreased p.o. intake. His normal breast-feeding is down from 20 minutes q.2h. to 5 to 10 minutes secondary to his respiratory congestion. He sleeps well, but has been more tired and has been fussy over the past 2 days. The parents noticed no improvement with albuterol treatments given in the ER. His urine output has also decreased; normally he has 8 to 10 wet and 5 dirty diapers per 24 hours, now he has down to 4 wet diapers per 24 hours. Mom denies any diarrhea. His bowel movements are yellow colored and soft in nature."
+
+val result = pipeline.fullAnnotate(text)
+```
+
+{:.nlu-block}
+```python
+import nlu
+nlu.load("en.classify.bert_token_ner_jsl.pipeline").predict("""The patient is a 21-day-old Caucasian male here for 2 days of congestion - mom has been suctioning yellow discharge from the patient's nares, plus she has noticed some mild problems with his breathing while feeding (but negative for any perioral cyanosis or retractions). One day ago, mom also noticed a tactile temperature and gave the patient Tylenol. Baby-girl also has had some decreased p.o. intake. His normal breast-feeding is down from 20 minutes q.2h. to 5 to 10 minutes secondary to his respiratory congestion. He sleeps well, but has been more tired and has been fussy over the past 2 days. The parents noticed no improvement with albuterol treatments given in the ER. His urine output has also decreased; normally he has 8 to 10 wet and 5 dirty diapers per 24 hours, now he has down to 4 wet diapers per 24 hours. Mom denies any diarrhea. His bowel movements are yellow colored and soft in nature.""")
+```
+</div>
+
+## Results
+
+```bash
+Results
+
+
+|    | ner_chunk                        |   begin |   end | ner_label    |   confidence |
+|---:|:---------------------------------|--------:|------:|:-------------|-------------:|
+|  0 | 21-day-old                       |      17 |    26 | Age          |     0.999456 |
+|  1 | Caucasian male                   |      28 |    41 | Demographics |     0.9901   |
+|  2 | congestion                       |      62 |    71 | Symptom      |     0.997918 |
+|  3 | mom                              |      75 |    77 | Demographics |     0.999013 |
+|  4 | yellow discharge                 |      99 |   114 | Symptom      |     0.998663 |
+|  5 | nares                            |     135 |   139 | Body_Part    |     0.998609 |
+|  6 | she                              |     147 |   149 | Demographics |     0.999442 |
+|  7 | mild problems with his breathing |     168 |   199 | Symptom      |     0.930385 |
+|  8 | perioral cyanosis                |     237 |   253 | Symptom      |     0.99819  |
+|  9 | retractions                      |     258 |   268 | Symptom      |     0.999783 |
+| 10 | One day ago                      |     272 |   282 | Date_Time    |     0.999386 |
+| 11 | mom                              |     285 |   287 | Demographics |     0.999835 |
+| 12 | tactile temperature              |     304 |   322 | Symptom      |     0.999352 |
+| 13 | Tylenol                          |     345 |   351 | Drug         |     0.999762 |
+| 14 | Baby-girl                        |     354 |   362 | Age          |     0.980529 |
+| 15 | decreased p.o. intake            |     382 |   402 | Symptom      |     0.998978 |
+| 16 | His                              |     405 |   407 | Demographics |     0.999913 |
+| 17 | breast-feeding                   |     416 |   429 | Body_Part    |     0.99954  |
+| 18 | his                              |     493 |   495 | Demographics |     0.999661 |
+| 19 | respiratory congestion           |     497 |   518 | Symptom      |     0.834984 |
+| 20 | He                               |     521 |   522 | Demographics |     0.999858 |
+| 21 | tired                            |     555 |   559 | Symptom      |     0.999516 |
+| 22 | fussy                            |     574 |   578 | Symptom      |     0.997592 |
+| 23 | over the past 2 days             |     580 |   599 | Date_Time    |     0.994786 |
+| 24 | albuterol                        |     642 |   650 | Drug         |     0.999735 |
+
+
+{:.model-param}
+```
+
+{:.model-param}
+## Model Information
+
+{:.table-model}
+|---|---|
+|Model Name:|bert_token_classifier_ner_jsl_pipeline|
+|Type:|pipeline|
+|Compatibility:|Healthcare NLP 4.4.4+|
+|License:|Licensed|
+|Edition:|Official|
+|Language:|en|
+|Size:|405.0 MB|
+
+## Included Models
+
+- DocumentAssembler
+- SentenceDetectorDLModel
+- TokenizerModel
+- MedicalBertForTokenClassifier
+- NerConverterInternalModel