Description
This model extracts healthcare-related terms from the documents transferred from the patient’s own sentences.
Predicted Entities
Gender, Employment, BodyPart, Vaccine, Age, PsychologicalCondition, Form, Substance, ClinicalDept, Drug, AdmissionDischarge, DateTime, Test, Laterality, Route, Disease, VitalTest, Dosage, Duration, Frequency, Allergen, Symptom, Procedure, RelationshipStatus, HealthStatus, Modifier, MedicalDevice, SubstanceQuantity, InjuryOrPoisoning, TestResult, Treatment
Live Demo Open in Colab Copy S3 URI
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_large", "en", "clinical/models")\
.setInputCols(["sentence", "token"]) \
.setOutputCol("embeddings")
ner = MedicalNerModel.pretrained("ner_vop_emb_clinical_large", "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_large", "en", "clinical/models")
.setInputCols(Array("sentence", "token"))
.setOutputCol("embeddings")
val ner = MedicalNerModel.pretrained("ner_vop_emb_clinical_large", "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 |
| 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 | TestResult |
| heartrate | VitalTest |
| homeopathy | Treatment |
| thyroid | BodyPart |
Model Information
| Model Name: | ner_vop_emb_clinical_large |
| Compatibility: | Healthcare NLP 4.4.3+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [sentence, token, embeddings] |
| Output Labels: | [ner] |
| Language: | en |
| Size: | 3.9 MB |
| Dependencies: | embeddings_clinical_large |
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 tp fp fn total precision recall f1
Gender 1293 17 24 1317 0.99 0.98 0.98
Employment 1184 52 59 1243 0.96 0.95 0.96
BodyPart 2731 204 169 2900 0.93 0.94 0.94
Vaccine 40 5 2 42 0.89 0.95 0.92
Age 536 42 46 582 0.93 0.92 0.92
PsychologicalCondition 411 38 33 444 0.92 0.93 0.92
Form 248 33 18 266 0.88 0.93 0.91
Substance 394 60 27 421 0.87 0.94 0.90
ClinicalDept 291 37 35 326 0.89 0.89 0.89
Drug 1342 230 98 1440 0.85 0.93 0.89
AdmissionDischarge 28 1 6 34 0.97 0.82 0.89
DateTime 3998 579 404 4402 0.87 0.91 0.89
Test 1043 116 165 1208 0.90 0.86 0.88
Laterality 566 101 62 628 0.85 0.90 0.87
Route 41 5 7 48 0.89 0.85 0.87
Disease 1747 269 268 2015 0.87 0.87 0.87
VitalTest 151 25 21 172 0.86 0.88 0.87
Dosage 342 51 70 412 0.87 0.83 0.85
Duration 1943 302 367 2310 0.87 0.84 0.85
Frequency 910 208 169 1079 0.81 0.84 0.83
Allergen 33 1 13 46 0.97 0.72 0.83
Symptom 3557 517 1018 4575 0.87 0.78 0.82
Procedure 576 132 129 705 0.81 0.82 0.82
RelationshipStatus 18 2 6 24 0.90 0.75 0.82
HealthStatus 79 23 28 107 0.77 0.74 0.76
Modifier 805 213 334 1139 0.79 0.71 0.75
MedicalDevice 240 70 92 332 0.77 0.72 0.75
SubstanceQuantity 57 15 28 85 0.79 0.67 0.73
InjuryOrPoisoning 116 28 60 176 0.81 0.66 0.73
TestResult 353 95 171 524 0.79 0.67 0.73
Treatment 134 44 94 228 0.75 0.59 0.66
macro_avg 25207 3515 4023 29230 0.87 0.83 0.85
micro_avg 25207 3515 4023 29230 0.88 0.86 0.87