Description
Zero-shot Named Entity Recognition (NER) enables the identification of entities in text with minimal effort. By leveraging pre-trained language models and contextual understanding, zero-shot NER extends entity recognition capabilities to new domains and languages. While the model card includes default labels as examples, it is important to highlight that users are not limited to these labels. The model is designed to support any set of entity labels, allowing users to adapt it to their specific use cases. For best results, it is recommended to use labels that are conceptually similar to the provided defaults.
Predicted Entities
AdmissionDischarge, Age, Allergen, BodyPart, ClinicalDept, DateTime, Disease,
Dosage, Drug, Duration, Employment, Form, Frequency, Gender, Laterality, MedicalDevice,
Modifier, Procedure, PsychologicalCondition, RaceEthnicity, Substance, Symptom, Test,
Treatment, Vaccine
How to use
document_assembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
sentence_detector = SentenceDetector()\
.setInputCols(["document"])\
.setOutputCol("sentence")
tokenizer = Tokenizer()\
.setInputCols(["sentence"])\
.setOutputCol("token")
labels = [
'AdmissionDischarge', 'Age', 'Allergen','BodyPart','ClinicalDept','DateTime','Disease',
'Dosage','Drug','Duration','Employment','Form','Frequency','Gender','Laterality','MedicalDevice',
'Modifier','Procedure','PsychologicalCondition','RaceEthnicity','Substance','Symptom','Test',
'Treatment','Vaccine']
pretrained_zero_shot_ner = PretrainedZeroShotNER().pretrained("zeroshot_ner_vop_medium", "en", "clinical/models")\
.setInputCols("sentence", "token")\
.setOutputCol("ner")\
.setPredictionThreshold(0.5)\
.setLabels(labels)
ner_converter = NerConverterInternal()\
.setInputCols("sentence", "token", "ner")\
.setOutputCol("ner_chunk")
pipeline = Pipeline().setStages([
document_assembler,
sentence_detector,
tokenizer,
pretrained_zero_shot_ner,
ner_converter
])
data = spark.createDataFrame([["""Hello,I'm 20 year old girl. I'm diagnosed with hyperthyroid 1 month ago. I was feeling weak, light headed,poor digestion, panic attacks, depression, left chest pain, increased heart rate, rapidly weight loss, from 4 months. Because of this, I stayed in the hospital and just discharged from hospital. I had many other blood tests, brain mri, ultrasound scan, endoscopy because of some dumb doctors bcs they were not able to diagnose actual problem. Finally I got an appointment with a homeopathy doctor finally he find that i was suffering from hyperthyroid and my TSH was 0.15 T3 and T4 is normal . Also i have b12 deficiency and vitamin D deficiency so I'm taking weekly supplement of vitamin D and 1000 mcg b12 daily. I'm taking homeopathy medicine for 40 days and took 2nd test after 30 days. My TSH is 0.5 now. I feel a little bit relief from weakness and depression but I'm facing with 2 new problem from last week that is breathtaking problem and very rapid heartrate. I just want to know if i should start allopathy medicine or homeopathy is okay? Bcs i heard that thyroid take time to start recover. So please let me know if both of medicines take same time. Because some of my friends advising me to start allopathy and never take a chance as i can develop some serious problems.Sorry for my poor english😐Thank you."""]]).toDF("text")
result = pipeline.fit(data).transform(data)
document_assembler = nlp.DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
sentence_detector = nlp.SentenceDetector()\
.setInputCols(["document"])\
.setOutputCol("sentence")
tokenizer = nlp.Tokenizer()\
.setInputCols(["sentence"])\
.setOutputCol("token")
labels = [
'AdmissionDischarge', 'Age', 'Allergen','BodyPart','ClinicalDept','DateTime','Disease',
'Dosage','Drug','Duration','Employment','Form','Frequency','Gender','Laterality','MedicalDevice',
'Modifier','Procedure','PsychologicalCondition','RaceEthnicity','Substance','Symptom','Test',
'Treatment','Vaccine']
pretrained_zero_shot_ner = medical.PretrainedZeroShotNER().pretrained("zeroshot_ner_vop_medium", "en", "clinical/models")\
.setInputCols("sentence", "token")\
.setOutputCol("ner")\
.setPredictionThreshold(0.5)\
.setLabels(labels)
ner_converter = medical.NerConverterInternal()\
.setInputCols("sentence", "token", "ner")\
.setOutputCol("ner_chunk")
pipeline = nlp.Pipeline().setStages([
document_assembler,
sentence_detector,
tokenizer,
pretrained_zero_shot_ner,
ner_converter
])
data = spark.createDataFrame([["""Hello,I'm 20 year old girl. I'm diagnosed with hyperthyroid 1 month ago. I was feeling weak, light headed,poor digestion, panic attacks, depression, left chest pain, increased heart rate, rapidly weight loss, from 4 months. Because of this, I stayed in the hospital and just discharged from hospital. I had many other blood tests, brain mri, ultrasound scan, endoscopy because of some dumb doctors bcs they were not able to diagnose actual problem. Finally I got an appointment with a homeopathy doctor finally he find that i was suffering from hyperthyroid and my TSH was 0.15 T3 and T4 is normal . Also i have b12 deficiency and vitamin D deficiency so I'm taking weekly supplement of vitamin D and 1000 mcg b12 daily. I'm taking homeopathy medicine for 40 days and took 2nd test after 30 days. My TSH is 0.5 now. I feel a little bit relief from weakness and depression but I'm facing with 2 new problem from last week that is breathtaking problem and very rapid heartrate. I just want to know if i should start allopathy medicine or homeopathy is okay? Bcs i heard that thyroid take time to start recover. So please let me know if both of medicines take same time. Because some of my friends advising me to start allopathy and never take a chance as i can develop some serious problems.Sorry for my poor english😐Thank you."""]]).toDF("text")
result = pipeline.fit(data).transform(data)
val document_assembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val sentence_detector = new SentenceDetector()
.setInputCols("document")
.setOutputCol("sentence")
val tokenizer = new Tokenizer()
.setInputCols("sentence")
.setOutputCol("token")
labels = Array(
"AdmissionDischarge", "Age", "Allergen", "BodyPart", "ClinicalDept", "DateTime", "Disease",
"Dosage", "Drug", "Duration", "Employment", "Form", "Frequency", "Gender", "Laterality", "MedicalDevice",
"Modifier", "Procedure", "PsychologicalCondition", "RaceEthnicity", "Substance", "Symptom", "Test",
"Treatment", "Vaccine")
val pretrained_zero_shot_ner = PretrainedZeroShotNER().pretrained("zeroshot_ner_vop_medium", "en", "clinical/models")
.setInputCols(Array("sentence", "token"))
.setOutputCol("ner")
.setPredictionThreshold(0.5)
.setLabels(labels)
val ner_converter = new NerConverterInternal()
.setInputCols(Array("sentence", "token", "ner"))
.setOutputCol("ner_chunk")
val pipeline = new Pipeline().setStages(Array(
document_assembler,
sentence_detector,
tokenizer,
pretrained_zero_shot_ner,
ner_converter
))
val data = Seq([["""Hello,I'm 20 year old girl. I'm diagnosed with hyperthyroid 1 month ago. I was feeling weak, light headed,poor digestion, panic attacks, depression, left chest pain, increased heart rate, rapidly weight loss, from 4 months. Because of this, I stayed in the hospital and just discharged from hospital. I had many other blood tests, brain mri, ultrasound scan, endoscopy because of some dumb doctors bcs they were not able to diagnose actual problem. Finally I got an appointment with a homeopathy doctor finally he find that i was suffering from hyperthyroid and my TSH was 0.15 T3 and T4 is normal . Also i have b12 deficiency and vitamin D deficiency so I'm taking weekly supplement of vitamin D and 1000 mcg b12 daily. I'm taking homeopathy medicine for 40 days and took 2nd test after 30 days. My TSH is 0.5 now. I feel a little bit relief from weakness and depression but I'm facing with 2 new problem from last week that is breathtaking problem and very rapid heartrate. I just want to know if i should start allopathy medicine or homeopathy is okay? Bcs i heard that thyroid take time to start recover. So please let me know if both of medicines take same time. Because some of my friends advising me to start allopathy and never take a chance as i can develop some serious problems.Sorry for my poor english😐Thank you."""]]).toDF("text")
val result = pipeline.fit(data).transform(data)
Results
+--------------------+-----+----+----------------------+----------+
|chunk |begin|end |ner_label |confidence|
+--------------------+-----+----+----------------------+----------+
|20 year old |11 |21 |Age |0.90626055|
|girl |23 |26 |Gender |0.9872349 |
|hyperthyroid |48 |59 |Disease |0.5882809 |
|1 month ago |61 |71 |DateTime |0.89972264|
|weak |88 |91 |Symptom |0.94134945|
|light |94 |98 |Symptom |0.8042566 |
|digestion |112 |120 |Symptom |0.80794823|
|panic attacks |123 |135 |PsychologicalCondition|0.6966042 |
|depression |138 |147 |PsychologicalCondition|0.8788635 |
|left |150 |153 |Laterality |0.9769653 |
|chest |155 |159 |BodyPart |0.9179944 |
|pain |161 |164 |Symptom |0.9488603 |
|heart rate |177 |186 |Test |0.852903 |
|weight loss |197 |207 |Symptom |0.8533222 |
|4 months |216 |223 |Duration |0.91566205|
|hospital |259 |266 |ClinicalDept |0.9460183 |
|discharged |277 |286 |AdmissionDischarge |0.9330801 |
|hospital |293 |300 |ClinicalDept |0.9106594 |
|blood tests |320 |330 |Test |0.9211605 |
|brain |333 |337 |BodyPart |0.56395924|
|mri |339 |341 |Test |0.5211516 |
|ultrasound scan |344 |358 |Test |0.9587256 |
|endoscopy |361 |369 |Test |0.56992483|
|doctors |392 |398 |Employment |0.70382017|
|homeopathy doctor |487 |503 |Employment |0.8384213 |
|he |513 |514 |Gender |0.9115307 |
|hyperthyroid |547 |558 |Disease |0.7546066 |
|TSH |567 |569 |Test |0.9506327 |
|T4 |587 |588 |Test |0.5156918 |
|b12 deficiency |614 |627 |Disease |0.74625975|
|vitamin D deficiency|633 |652 |Disease |0.6932099 |
|weekly |668 |673 |Frequency |0.9117316 |
|vitamin D |689 |697 |Drug |0.9248756 |
|1000 mcg |703 |710 |Dosage |0.955836 |
|b12 |712 |714 |Drug |0.74509525|
|daily |716 |720 |Frequency |0.87319267|
|40 days |758 |764 |Duration |0.90739 |
|after 30 days |784 |796 |DateTime |0.5512618 |
|TSH |802 |804 |Test |0.9578176 |
|now |813 |815 |DateTime |0.8912383 |
|weakness |850 |857 |Symptom |0.9487599 |
|depression |863 |872 |PsychologicalCondition|0.92137915|
|last week |913 |921 |DateTime |0.889882 |
|heartrate |967 |975 |Test |0.59811634|
|thyroid |1075 |1081|BodyPart |0.87814385|
+--------------------+-----+----+----------------------+----------+
Model Information
| Model Name: | zeroshot_ner_vop_medium |
| Compatibility: | Healthcare NLP 5.5.1+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 711.8 MB |
Benchmarking
label precision recall f1-score support
AdmissionDischarge 0.6562 0.8400 0.7368 25
Age 0.9151 0.9513 0.9328 657
Allergen 0.4500 0.8000 0.5760 45
BodyPart 0.8746 0.9429 0.9074 2870
ClinicalDept 0.7930 0.8831 0.8356 308
DateTime 0.8785 0.8118 0.8438 4489
Disease 0.7933 0.7746 0.7839 2081
Dosage 0.5358 0.8423 0.6550 444
Drug 0.7968 0.8836 0.8379 1340
Duration 0.7361 0.8400 0.7846 2225
Employment 0.9137 0.9268 0.9202 1257
Form 0.6570 0.9150 0.7648 247
Frequency 0.7031 0.8986 0.7889 1144
Gender 0.9445 0.9670 0.9556 1303
Laterality 0.7016 0.9009 0.7889 535
MedicalDevice 0.6979 0.6381 0.6667 315
Modifier 0.4495 0.8186 0.5803 1141
O 0.9747 0.9576 0.9661 113762
Procedure 0.6328 0.6022 0.6171 641
PsychologicalCondition 0.8365 0.8124 0.8243 485
RaceEthnicity 0.8182 0.9310 0.8710 29
Substance 0.7509 0.8833 0.8117 454
Symptom 0.8088 0.7952 0.8020 4629
Test 0.8572 0.7759 0.8146 1486
Treatment 0.5600 0.5957 0.5773 188
Vaccine 0.9000 0.5000 0.6429 36
accuracy - - 0.9340 142136
macro avg 0.7552 0.8265 0.7802 142136
weighted avg 0.9399 0.9340 0.9359 142136