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, SubstanceQuantity, RaceEthnicity, Measurements, InjuryOrPoisoning, Treatment, Modifier, TestResult, MedicalDevice, Vaccine, Frequency, HealthStatus, Route, RelationshipStatus, Procedure, Duration, DateTime, AdmissionDischarge, Disease, Test, Substance, Laterality, Symptom, ClinicalDept, Dosage, Age, Drug, VitalTest, PsychologicalCondition, Form, BodyPart, Employment, Gender
Live Demo Open in Colab Download 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_emb_clinical_medium_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_medium, "en", "clinical/models")
.setInputCols(Array("sentence", "token"))
.setOutputCol("embeddings")
val ner = MedicalNerModel.pretrained("ner_vop_emb_clinical_medium_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 | 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_emb_clinical_medium_wip |
| Compatibility: | Healthcare NLP 4.4.0+ |
| 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
Allergen 0 1 8 8 0.00 0.00 0.00
SubstanceQuantity 9 14 18 27 0.39 0.33 0.36
RaceEthnicity 2 0 6 8 1.00 0.25 0.40
Measurements 41 25 33 74 0.62 0.55 0.59
InjuryOrPoisoning 66 37 51 117 0.64 0.56 0.60
Treatment 96 39 46 142 0.71 0.68 0.69
Modifier 642 268 271 913 0.71 0.70 0.70
TestResult 394 185 154 548 0.68 0.72 0.70
MedicalDevice 177 76 67 244 0.70 0.73 0.71
Vaccine 20 4 12 32 0.83 0.63 0.71
Frequency 456 144 187 643 0.76 0.71 0.73
HealthStatus 60 4 38 98 0.94 0.61 0.74
Route 24 4 12 36 0.86 0.67 0.75
RelationshipStatus 19 3 9 28 0.86 0.68 0.76
Procedure 286 91 80 366 0.76 0.78 0.77
Duration 846 227 269 1115 0.79 0.76 0.77
DateTime 1813 455 391 2204 0.80 0.82 0.81
AdmissionDischarge 19 1 8 27 0.95 0.70 0.81
Disease 1247 318 256 1503 0.80 0.83 0.81
Test 734 150 175 909 0.83 0.81 0.82
Substance 156 48 22 178 0.76 0.88 0.82
Laterality 440 91 78 518 0.83 0.85 0.84
Symptom 3069 566 630 3699 0.84 0.83 0.84
ClinicalDept 205 35 31 236 0.85 0.87 0.86
Dosage 273 42 49 322 0.87 0.85 0.86
Age 294 60 29 323 0.83 0.91 0.87
Drug 1035 188 100 1135 0.85 0.91 0.88
VitalTest 144 23 13 157 0.86 0.92 0.89
PsychologicalCondition 284 32 30 314 0.90 0.90 0.90
Form 234 32 17 251 0.88 0.93 0.91
BodyPart 2532 256 213 2745 0.91 0.92 0.92
Employment 980 65 62 1042 0.94 0.94 0.94
Gender 1174 27 20 1194 0.98 0.98 0.98
macro_avg 17771 3511 3385 21156 0.79 0.73 0.75
micro_avg 17771 3511 3385 21156 0.84 0.84 0.84