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, TestResult, Modifier, Route, MedicalDevice, Vaccine, RelationshipStatus, Frequency, HealthStatus, Procedure, Duration, DateTime, Disease, Test, Substance, Symptom, Laterality, Dosage, ClinicalDept, PsychologicalCondition, VitalTest, Age, Drug, BodyPart, AdmissionDischarge, Form, 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_large, "en", "clinical/models")\
.setInputCols(["sentence", "token"]) \
.setOutputCol("embeddings")
ner = MedicalNerModel.pretrained("ner_vop_emb_clinical_large_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_large, "en", "clinical/models")
.setInputCols(Array("sentence", "token"))
.setOutputCol("embeddings")
val ner = MedicalNerModel.pretrained("ner_vop_emb_clinical_large_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 |
| heartrate | VitalTest |
| homeopathy | Treatment |
| thyroid | BodyPart |
Model Information
| Model Name: | ner_vop_emb_clinical_large_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_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
Allergen 0 0 8 8 0.00 0.00 0.00
SubstanceQuantity 7 10 20 27 0.41 0.26 0.32
RaceEthnicity 2 0 6 8 1.00 0.25 0.40
Measurements 36 20 38 74 0.64 0.49 0.55
InjuryOrPoisoning 65 28 52 117 0.70 0.56 0.62
Treatment 86 27 56 142 0.76 0.61 0.67
TestResult 379 150 169 548 0.72 0.69 0.70
Modifier 644 229 269 913 0.74 0.71 0.72
Route 23 5 13 36 0.82 0.64 0.72
MedicalDevice 171 54 73 244 0.76 0.70 0.73
Vaccine 21 4 11 32 0.84 0.66 0.74
RelationshipStatus 18 2 10 28 0.90 0.64 0.75
Frequency 478 161 165 643 0.75 0.74 0.75
HealthStatus 75 19 23 98 0.80 0.77 0.78
Procedure 275 68 91 366 0.80 0.75 0.78
Duration 884 275 231 1115 0.76 0.79 0.78
DateTime 1796 397 408 2204 0.82 0.81 0.82
Disease 1258 323 245 1503 0.80 0.84 0.82
Test 752 155 157 909 0.83 0.83 0.83
Substance 152 37 26 178 0.80 0.85 0.83
Symptom 3078 547 621 3699 0.85 0.83 0.84
Laterality 425 62 93 518 0.87 0.82 0.85
Dosage 266 37 56 322 0.88 0.83 0.85
ClinicalDept 201 28 35 236 0.88 0.85 0.86
PsychologicalCondition 282 41 32 314 0.87 0.90 0.89
VitalTest 146 25 11 157 0.85 0.93 0.89
Age 295 38 28 323 0.89 0.91 0.90
Drug 1040 136 95 1135 0.88 0.92 0.90
BodyPart 2528 245 217 2745 0.91 0.92 0.92
AdmissionDischarge 24 1 3 27 0.96 0.89 0.92
Form 233 24 18 251 0.91 0.93 0.92
Employment 988 51 54 1042 0.95 0.95 0.95
Gender 1173 26 21 1194 0.98 0.98 0.98
macro_avg 17801 3225 3355 21156 0.80 0.73 0.76
micro_avg 17801 3225 3355 21156 0.85 0.84 0.84