Description
This model extracts healthcare-related terms from the documents transferred from the patient’s own sentences.
Note: ‘wip’ suffix indicates that the model development is work-in-progress and will be finalised and the model performance will improved in the upcoming releases.
Predicted Entities
TestResult, SubstanceQuantity, InjuryOrPoisoning, Treatment, Modifier, HealthStatus, MedicalDevice, Procedure, Symptom, Frequency, RelationshipStatus, Duration, Allergen, VitalTest, Disease, Dosage, AdmissionDischarge, Test, Laterality, Route, DateTime, Drug, ClinicalDept, Vaccine, Form, Substance, PsychologicalCondition, Age, BodyPart, Employment, Gender
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", "en", "clinical/models")\
.setInputCols(["sentence", "token"]) \
.setOutputCol("embeddings")
ner = MedicalNerModel.pretrained("ner_vop_wip", "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_wip", "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 |
| 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 |
| 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_wip |
| Compatibility: | Healthcare NLP 4.4.2+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [sentence, token, embeddings] |
| Output Labels: | [ner] |
| Language: | en |
| Size: | 3.9 MB |
| Dependencies: | embeddings_clinical |
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
TestResult 353 98 171 524 0.78 0.67 0.72
SubstanceQuantity 60 20 25 85 0.75 0.71 0.73
InjuryOrPoisoning 122 37 54 176 0.77 0.69 0.73
Treatment 150 30 78 228 0.83 0.66 0.74
Modifier 817 214 322 1139 0.79 0.72 0.75
HealthStatus 80 24 27 107 0.77 0.75 0.76
MedicalDevice 250 71 82 332 0.78 0.75 0.77
Procedure 576 156 129 705 0.79 0.82 0.80
Symptom 3831 858 744 4575 0.82 0.84 0.83
Frequency 865 147 214 1079 0.85 0.80 0.83
RelationshipStatus 19 2 5 24 0.90 0.79 0.84
Duration 1845 244 465 2310 0.88 0.80 0.84
Allergen 38 4 8 46 0.90 0.83 0.86
VitalTest 143 16 29 172 0.90 0.83 0.86
Disease 1745 296 270 2015 0.85 0.87 0.86
Dosage 348 48 64 412 0.88 0.84 0.86
AdmissionDischarge 29 4 5 34 0.88 0.85 0.87
Test 1064 136 144 1208 0.89 0.88 0.88
Laterality 542 68 86 628 0.89 0.86 0.88
Route 42 5 6 48 0.89 0.88 0.88
DateTime 4075 706 327 4402 0.85 0.93 0.89
Drug 1323 196 117 1440 0.87 0.92 0.89
ClinicalDept 280 25 46 326 0.92 0.86 0.89
Vaccine 37 4 5 42 0.90 0.88 0.89
Form 252 34 14 266 0.88 0.95 0.91
Substance 398 58 23 421 0.87 0.95 0.91
PsychologicalCondition 411 42 33 444 0.91 0.93 0.92
Age 529 44 53 582 0.92 0.91 0.92
BodyPart 2730 224 170 2900 0.92 0.94 0.93
Employment 1168 37 75 1243 0.97 0.94 0.95
Gender 1292 21 25 1317 0.98 0.98 0.98
macro_avg 25414 3869 3816 29230 0.86 0.84 0.85
micro_avg 25414 3869 3816 29230 0.87 0.87 0.87