Description
This model extracts healthcare-related terms from the documents transferred from the patient’s own sentences. It is the version of ner_vop model augmented with langtest library.
| test_type | before fail_count | after fail_count | before pass_count | after pass_count | minimum pass_rate | before pass_rate | after pass_rate |
|---|---|---|---|---|---|---|---|
| add_ocr_typo | 3230 | 1015 | 1520 | 3735 | 70% | 32% | 79% |
| add_typo | 1088 | 942 | 3472 | 3645 | 70% | 76% | 79% |
| lowercase | 413 | 346 | 4043 | 4110 | 70% | 91% | 92% |
| titlecase | 2424 | 1364 | 2382 | 3442 | 70% | 50% | 72% |
| uppercase | 4361 | 1433 | 445 | 3373 | 70% | 9% | 70% |
| weighted average | 11516 | 5100 | 11862 | 18305 | 70% | 50.74% | 78.21% |
Predicted Entities
Gender, Employment, Age, BodyPart, Substance, Form, PsychologicalCondition, Vaccine, Drug, DateTime, ClinicalDept, Laterality, Test, AdmissionDischarge, Disease, VitalTest, Dosage, Duration, RelationshipStatus, Route, Allergen, Frequency, Symptom, Procedure, HealthStatus, InjuryOrPoisoning, Modifier, Treatment, SubstanceQuantity, MedicalDevice, TestResult
How to use
document_assembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
sentence_detector = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare", "en", "clinical/models")\
.setInputCols(["document"])\
.setOutputCol("sentence")
tokenizer = Tokenizer() \
.setInputCols(["sentence"]) \
.setOutputCol("token")
word_embeddings = WordEmbeddingsModel().pretrained("embeddings_clinical", "en", "clinical/models")\
.setInputCols(["sentence", "token"]) \
.setOutputCol("embeddings")
ner = MedicalNerModel.pretrained("ner_vop_langtest", "en", "clinical/models") \
.setInputCols(["sentence", "token", "embeddings"]) \
.setOutputCol("ner")
ner_converter = NerConverterInternal() \
.setInputCols(["sentence", "token", "ner"]) \
.setOutputCol("ner_chunk")
pipeline = Pipeline(stages=[document_assembler,
sentence_detector,
tokenizer,
word_embeddings,
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 = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare", "en", "clinical/models")
.setInputCols("document")
.setOutputCol("sentence")
val tokenizer = new Tokenizer()
.setInputCols("sentence")
.setOutputCol("token")
val word_embeddings = WordEmbeddingsModel().pretrained("embeddings_clinical", "en", "clinical/models")
.setInputCols(Array("sentence", "token"))
.setOutputCol("embeddings")
val ner = MedicalNerModel.pretrained("ner_vop_langtest", "en", "clinical/models")
.setInputCols(Array("sentence", "token", "embeddings"))
.setOutputCol("ner")
val ner_converter = new NerConverterInternal()
.setInputCols(Array("sentence", "token", "ner"))
.setOutputCol("ner_chunk")
val pipeline = new Pipeline().setStages(Array(document_assembler,
sentence_detector,
tokenizer,
word_embeddings,
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.").toDS.toDF("text")
val result = pipeline.fit(data).transform(data)
Results
+--------------------+----------------------+
|chunk |ner_label |
+--------------------+----------------------+
|20 year old |Age |
|girl |Gender |
|hyperthyroid |Disease |
|1 month ago |DateTime |
|weak |Symptom |
|light |Symptom |
|digestion |Symptom |
|panic attacks |PsychologicalCondition|
|depression |PsychologicalCondition|
|left |Laterality |
|chest |BodyPart |
|pain |Symptom |
|increased |TestResult |
|heart rate |VitalTest |
|rapidly |Modifier |
|weight loss |Symptom |
|4 months |Duration |
|hospital |ClinicalDept |
|discharged |AdmissionDischarge |
|hospital |ClinicalDept |
|blood tests |Test |
|brain |BodyPart |
|mri |Test |
|ultrasound scan |Test |
|endoscopy |Procedure |
|doctors |Employment |
|homeopathy doctor |Employment |
|he |Gender |
|hyperthyroid |Disease |
|TSH |Test |
|0.15 |TestResult |
|T3 |Test |
|T4 |Test |
|normal |TestResult |
|b12 deficiency |Disease |
|vitamin D deficiency|Disease |
|weekly |Frequency |
|supplement |Drug |
|vitamin D |Drug |
|1000 mcg |Dosage |
|b12 |Drug |
|daily |Frequency |
|homeopathy medicine |Drug |
|40 days |Duration |
|2nd test |Test |
|after 30 days |DateTime |
|TSH |Test |
|0.5 |TestResult |
|now |DateTime |
|weakness |Symptom |
|depression |PsychologicalCondition|
|last week |DateTime |
|rapid heartrate |Symptom |
|allopathy medicine |Drug |
|homeopathy |Treatment |
|thyroid |BodyPart |
|allopathy |Treatment |
+--------------------+----------------------+
Model Information
| Model Name: | ner_vop_langtest |
| Compatibility: | Healthcare NLP 5.1.1+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [sentence, token, embeddings] |
| Output Labels: | [ner] |
| Language: | en |
| Size: | 14.7 MB |
References
In-house annotated health-related text in colloquial language.
Sample text from the training dataset
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.
Benchmarking
label precision recall f1-score support
AdmissionDischarge 0.78 0.78 0.78 32
Age 0.83 0.87 0.85 248
Allergen 0.86 0.41 0.56 29
BodyPart 0.91 0.92 0.91 2089
ClinicalDept 0.93 0.83 0.88 184
DateTime 0.82 0.86 0.84 1599
Disease 0.81 0.83 0.82 1140
Dosage 0.79 0.80 0.80 238
Drug 0.89 0.86 0.87 897
Duration 0.81 0.75 0.78 802
Employment 0.96 0.92 0.94 831
Form 0.90 0.89 0.90 207
Frequency 0.80 0.67 0.73 499
Gender 0.98 0.98 0.98 1047
HealthStatus 0.77 0.81 0.79 72
InjuryOrPoisoning 0.73 0.64 0.68 102
Laterality 0.79 0.89 0.84 397
MedicalDevice 0.69 0.72 0.70 190
Modifier 0.80 0.70 0.75 839
Procedure 0.85 0.72 0.78 297
PsychologicalCondition 0.89 0.90 0.90 272
RelationshipStatus 1.00 0.90 0.95 10
Route 0.79 0.67 0.72 33
Substance 0.88 0.82 0.85 281
SubstanceQuantity 0.88 0.49 0.63 43
Symptom 0.87 0.82 0.84 2690
Test 0.83 0.79 0.81 590
TestResult 0.71 0.72 0.71 367
Treatment 0.81 0.67 0.74 104
Vaccine 0.92 0.86 0.89 14
VitalTest 0.76 0.74 0.75 74
micro-avg 0.86 0.83 0.85 16217
macro-avg 0.84 0.78 0.80 16217
weighted-avg 0.86 0.83 0.84 16217