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
Allergen, RaceEthnicity, SubstanceQuantity, InjuryOrPoisoning, Treatment, Modifier, HealthStatus, MedicalDevice, TestResult, RelationshipStatus, Route, Measurements, AdmissionDischarge, Frequency, Procedure, Symptom, Substance, Duration, ClinicalDept, Dosage, Disease, Vaccine, Laterality, DateTime, Drug, Test, PsychologicalCondition, VitalTest, Form, 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_medium", "en", "clinical/models")\
.setInputCols(["sentence", "token"]) \
.setOutputCol("embeddings")
ner = MedicalNerModel.pretrained("ner_vop_wip_emb_clinical_medium", "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_medium", "en", "clinical/models")
.setInputCols(Array("sentence", "token"))
.setOutputCol("embeddings")
val ner = MedicalNerModel.pretrained("ner_vop_wip_emb_clinical_medium", "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 | Treatment |
| 40 days | Duration |
| after 30 days | DateTime |
| TSH | Test |
| 0.5 | TestResult |
| now | DateTime |
| weakness | Symptom |
| depression | PsychologicalCondition |
| last week | DateTime |
| rapid | TestResult |
| heartrate | VitalTest |
| allopathy medicine | Treatment |
| homeopathy | Treatment |
| thyroid | BodyPart |
| allopathy | Treatment |
Model Information
| Model Name: | ner_vop_wip_emb_clinical_medium |
| 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_medium |
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 1296 22 21 1317 0.98 0.98 0.98
Employment 1171 43 72 1243 0.96 0.94 0.95
Vaccine 40 4 2 42 0.91 0.95 0.93
Age 536 38 46 582 0.93 0.92 0.93
PsychologicalCondition 413 35 31 444 0.92 0.93 0.93
BodyPart 2729 218 171 2900 0.93 0.94 0.93
AdmissionDischarge 29 0 5 34 1.00 0.85 0.92
Form 249 33 17 266 0.88 0.94 0.91
Drug 1298 127 142 1440 0.91 0.90 0.91
Substance 388 50 33 421 0.89 0.92 0.90
Laterality 545 58 83 628 0.90 0.87 0.89
ClinicalDept 277 24 49 326 0.92 0.85 0.88
Test 1041 121 167 1208 0.90 0.86 0.88
DateTime 4120 802 282 4402 0.84 0.94 0.88
Route 39 3 9 48 0.93 0.81 0.87
Disease 1759 338 256 2015 0.84 0.87 0.86
VitalTest 140 16 32 172 0.90 0.81 0.85
Dosage 329 42 83 412 0.89 0.80 0.84
Duration 1841 230 469 2310 0.89 0.80 0.84
Frequency 885 170 194 1079 0.84 0.82 0.83
Symptom 3771 764 804 4575 0.83 0.82 0.83
Allergen 34 2 12 46 0.94 0.74 0.83
RelationshipStatus 18 2 6 24 0.90 0.75 0.82
Procedure 555 108 150 705 0.84 0.79 0.81
HealthStatus 81 25 26 107 0.76 0.76 0.76
Modifier 799 184 340 1139 0.81 0.70 0.75
SubstanceQuantity 57 13 28 85 0.81 0.67 0.74
Treatment 135 18 93 228 0.88 0.59 0.71
InjuryOrPoisoning 117 36 59 176 0.76 0.66 0.71
TestResult 325 72 199 524 0.82 0.62 0.71
MedicalDevice 229 83 103 332 0.73 0.69 0.71
macro_avg 25246 3681 3984 29230 0.88 0.82 0.85
micro_avg 25246 3681 3984 29230 0.87 0.86 0.87