Description
This model extracts medical devices and clinical department mentions terms from the documents transferred from the patient’s own sentences. It is the version of ner_vop_clinical_dept model augmented with langtest library.
| test_type | before fail_count | after fail_count | before pass_count | after pass_count | minimum pass_rate | before pass_rate | after pass_rate |
|---|---|---|---|---|---|---|---|
| add_abbreviation | 143 | 121 | 258 | 280 | 60% | 64% | 70% |
| add_ocr_typo | 198 | 98 | 217 | 317 | 60% | 52% | 76% |
| lowercase | 24 | 18 | 368 | 374 | 70% | 94% | 95% |
| number_to_word | 2 | 2 | 83 | 83 | 70% | 98% | 98% |
| strip_punctuation | 3 | 4 | 413 | 412 | 70% | 99% | 99% |
| titlecase | 104 | 83 | 313 | 334 | 70% | 75% | 80% |
| uppercase | 340 | 70 | 77 | 347 | 70% | 18% | 83% |
| weighted average | 814 | 396 | 1729 | 2147 | 67% | 67.99% | 84.43% |
Predicted Entities
AdmissionDischarge, ClinicalDept, MedicalDevice
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_clinical_dept_langtest", "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([["My little brother is having surgery tomorrow in the orthopedic department. He is getting a titanium plate put in his leg to help it heal faster. Wishing him a speedy recovery!"]]).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_clinical_dept_langtest", "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("My little brother is having surgery tomorrow in the orthopedic department. He is getting a titanium plate put in his leg to help it heal faster. Wishing him a speedy recovery!").toDS.toDF("text")
val result = pipeline.fit(data).transform(data)
Results
+---------------------+-------------+
|chunk |ner_label |
+---------------------+-------------+
|orthopedic department|ClinicalDept |
|titanium plate |MedicalDevice|
+---------------------+-------------+
Model Information
| Model Name: | ner_vop_clinical_dept_langtest |
| Compatibility: | Healthcare NLP 5.1.0+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [sentence, token, embeddings] |
| Output Labels: | [ner] |
| Language: | en |
| Size: | 14.7 MB |
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 precision recall f1-score support
AdmissionDischarge 0.92 0.96 0.94 23
ClinicalDept 0.93 0.92 0.93 233
MedicalDevice 0.82 0.82 0.82 227
micro-avg 0.88 0.88 0.88 483
macro-avg 0.89 0.90 0.89 483
weighted-avg 0.88 0.88 0.88 483