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update md files (#729)
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akrztrk authored Oct 30, 2023
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2 changes: 1 addition & 1 deletion docs/_posts/C-K-Loan/2021-03-29-pos_clinical_en.md
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Expand Up @@ -53,6 +53,7 @@ A [Part of Speech](https://en.wikipedia.org/wiki/Part_of_speech) classifier pred

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

```python
document_assembler = new DocumentAssembler().setInputCol("text").setOutputCol("document")
tokenizer = new Tokenizer().setInputCols("document").setOutputCol("token")
Expand Down Expand Up @@ -86,7 +87,6 @@ nlu.load('pos.clinical').predict("POS assigns each token in a sentence a grammat
+------------------------------------------+
|[NN, NNS, PND, NN, II, DD, NN, DD, JJ, NN]|
+------------------------------------------+

```

{:.model-param}
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2 changes: 0 additions & 2 deletions docs/_posts/C-K-Loan/2021-03-29-recognize_entities_posology_en.md
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Expand Up @@ -78,8 +78,6 @@ result_df
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|[[named_entity, 0, 2, O, [word -> The, confidence -> 1.0], []], [named_entity, 4, 10, O, [word -> patient, confidence -> 0.9993], []], [named_entity, 12, 14, O, [word -> was, confidence -> 1.0], []], [named_entity, 16, 25, O, [word -> perscriped, confidence -> 0.9985], []], [named_entity, 27, 30, B-Strength, [word -> 50MG, confidence -> 0.9966], []], [named_entity, 32, 40, B-Drug, [word -> penicilin, confidence -> 0.9934], []], [named_entity, 42, 44, O, [word -> for, confidence -> 0.9999], []], [named_entity, 46, 47, O, [word -> is, confidence -> 0.9468], []], [named_entity, 49, 56, O, [word -> headache, confidence -> 0.9805], []]]|
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+


```
{:.model-param}
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29 changes: 0 additions & 29 deletions .../C-K-Loan/2023-06-13-bert_sequence_classifier_binary_rct_biobert_pipeline_en.md
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Expand Up @@ -59,45 +59,16 @@ nlu.load("en.classify.bert_sequence.binary_rct_biobert.pipeline").predict("""Abs

</div>

<div class="tabs-box" markdown="1">
{% include programmingLanguageSelectScalaPythonNLU.html %}
```python
from sparknlp.pretrained import PretrainedPipeline

pipeline = PretrainedPipeline("bert_sequence_classifier_binary_rct_biobert_pipeline", "en", "clinical/models")

result = pipeline.annotate("""Abstract:Based on the American Society of Anesthesiologists' Practice Guidelines for Sedation and Analgesia by Non-Anesthesiologists (ASA-SED), a sedation training course aimed at improving medical safety was developed by the Japanese Association for Medical Simulation in 2011. This study evaluated the effect of debriefing on participants' perceptions of the essential points of the ASA-SED. A total of 38 novice doctors participated in the sedation training course during the research period. Of these doctors, 18 participated in the debriefing group, and 20 participated in non-debriefing group. Scoring of participants' guideline perceptions was conducted using an evaluation sheet (nine items, 16 points) created based on the ASA-SED. The debriefing group showed a greater perception of the ASA-SED, as reflected in the significantly higher scores on the evaluation sheet (median, 16 points) than the control group (median, 13 points; p < 0.05). No significant differences were identified before or during sedation, but the difference after sedation was significant (p < 0.05). Debriefing after sedation training courses may contribute to better perception of the ASA-SED, and may lead to enhanced attitudes toward medical safety during sedation and analgesia. """)
```
```scala
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline

val pipeline = new PretrainedPipeline("bert_sequence_classifier_binary_rct_biobert_pipeline", "en", "clinical/models")

val result = pipeline.annotate("""Abstract:Based on the American Society of Anesthesiologists' Practice Guidelines for Sedation and Analgesia by Non-Anesthesiologists (ASA-SED), a sedation training course aimed at improving medical safety was developed by the Japanese Association for Medical Simulation in 2011. This study evaluated the effect of debriefing on participants' perceptions of the essential points of the ASA-SED. A total of 38 novice doctors participated in the sedation training course during the research period. Of these doctors, 18 participated in the debriefing group, and 20 participated in non-debriefing group. Scoring of participants' guideline perceptions was conducted using an evaluation sheet (nine items, 16 points) created based on the ASA-SED. The debriefing group showed a greater perception of the ASA-SED, as reflected in the significantly higher scores on the evaluation sheet (median, 16 points) than the control group (median, 13 points; p < 0.05). No significant differences were identified before or during sedation, but the difference after sedation was significant (p < 0.05). Debriefing after sedation training courses may contribute to better perception of the ASA-SED, and may lead to enhanced attitudes toward medical safety during sedation and analgesia. """)
```

{:.nlu-block}
```python
import nlu
nlu.load("en.classify.bert_sequence.binary_rct_biobert.pipeline").predict("""Abstract:Based on the American Society of Anesthesiologists' Practice Guidelines for Sedation and Analgesia by Non-Anesthesiologists (ASA-SED), a sedation training course aimed at improving medical safety was developed by the Japanese Association for Medical Simulation in 2011. This study evaluated the effect of debriefing on participants' perceptions of the essential points of the ASA-SED. A total of 38 novice doctors participated in the sedation training course during the research period. Of these doctors, 18 participated in the debriefing group, and 20 participated in non-debriefing group. Scoring of participants' guideline perceptions was conducted using an evaluation sheet (nine items, 16 points) created based on the ASA-SED. The debriefing group showed a greater perception of the ASA-SED, as reflected in the significantly higher scores on the evaluation sheet (median, 16 points) than the control group (median, 13 points; p < 0.05). No significant differences were identified before or during sedation, but the difference after sedation was significant (p < 0.05). Debriefing after sedation training courses may contribute to better perception of the ASA-SED, and may lead to enhanced attitudes toward medical safety during sedation and analgesia. """)
```
</div>

## Results

```bash
Results


+----+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|rct |text |
+----+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|True|Abstract:Based on the American Society of Anesthesiologists' Practice Guidelines for Sedation and Analgesia by Non-Anesthesiologists (ASA-SED), a sedation training course aimed at improving medical safety was developed by the Japanese Association for Medical Simulation in 2011. This study evaluated the effect of debriefing on participants' perceptions of the essential points of the ASA-SED. A total of 38 novice doctors participated in the sedation training course during the research period. Of these doctors, 18 participated in the debriefing group, and 20 participated in non-debriefing group. Scoring of participants' guideline perceptions was conducted using an evaluation sheet (nine items, 16 points) created based on the ASA-SED. The debriefing group showed a greater perception of the ASA-SED, as reflected in the significantly higher scores on the evaluation sheet (median, 16 points) than the control group (median, 13 points; p < 0.05). No significant differences were identified before or during sedation, but the difference after sedation was significant (p < 0.05). Debriefing after sedation training courses may contribute to better perception of the ASA-SED, and may lead to enhanced attitudes toward medical safety during sedation and analgesia. |
+----+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+



{:.model-param}
```

{:.model-param}
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33 changes: 1 addition & 32 deletions docs/_posts/C-K-Loan/2023-06-13-bert_token_classifier_ner_jsl_pipeline_en.md
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Expand Up @@ -34,6 +34,7 @@ This pretrained pipeline is built on the top of [bert_token_classifier_ner_jsl](

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

```python
from sparknlp.pretrained import PretrainedPipeline

Expand Down Expand Up @@ -62,40 +63,11 @@ nlu.load("en.classify.bert_token_ner_jsl.pipeline").predict("""The patient is a

</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 |
Expand Down Expand Up @@ -123,9 +95,6 @@ Results
| 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}
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