Extract clinical problems (Voice of the Patients) - Granular version

Description

This model extracts clinical problems from the documents transferred from the patient’s own sentences using a granular taxonomy.

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

InjuryOrPoisoning, Modifier, HealthStatus, Symptom, Disease, PsychologicalCondition

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, "en", "clinical/models")\
    .setInputCols(["sentence", "token"]) \
    .setOutputCol("embeddings")                

ner = MedicalNerModel.pretrained("ner_vop_problem_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([["I"ve been experiencing joint pain and fatigue lately, so I went to the rheumatology department. After some tests, they diagnosed me with rheumatoid arthritis and started me on a treatment plan to manage the symptoms."]]).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_problem_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("I"ve been experiencing joint pain and fatigue lately, so I went to the rheumatology department. After some tests, they diagnosed me with rheumatoid arthritis and started me on a treatment plan to manage the symptoms.").toDS.toDF("text")

val result = pipeline.fit(data).transform(data)

Results

| chunk                | ner_label   |
|:---------------------|:------------|
| pain                 | Symptom     |
| fatigue              | Symptom     |
| rheumatoid arthritis | Disease     |

Model Information

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
     InjuryOrPoisoning   93  33   52    145       0.74    0.64 0.69
              Modifier  695 210  292    987       0.77    0.70 0.73
          HealthStatus   80  20   25    105       0.80    0.76 0.78
               Symptom 3669 440 1016   4685       0.89    0.78 0.83
               Disease 1708 261  262   1970       0.87    0.87 0.87
PsychologicalCondition  315  30   26    341       0.91    0.92 0.92
             macro_avg 6560 994 1673   8233       0.83    0.78 0.80
             micro_avg 6560 994 1673   8233       0.87    0.80 0.83