Detect Assertion Status from Opioid Entities

val document_assembler = new DocumentAssembler()
    .setInputCol("text")
    .setOutputCol("document")
    
val sentence_detector = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare","en","clinical/models")
    .setInputCols(Array("document"))
    .setOutputCol("sentence")
    
val tokenizer = new Tokenizer()
    .setInputCols(Array("sentence"))
    .setOutputCol("token")
    
val word_embeddings = WordEmbeddingsModel().pretrained("embeddings_clinical", "en", "clinical/models")
    .setInputCols(Array("sentence", "token"))
    .setOutputCol("embeddings")                
    
val ner_model = MedicalNerModel.pretrained("ner_opioid", "en", "clinical/models")
    .setInputCols(Array("sentence", "token", "embeddings"))
    .setOutputCol("ner")
    
val ner_converter = new NerConverterInternal()
    .setInputCols(Array("sentence", "token", "ner"))
    .setOutputCol("ner_chunk")


val assertion = AssertionDLModel.pretrained("assertion_opioid_wip", "en", "clinical/models")
    .setInputCols(Array("sentence", "ner_chunk", "embeddings"))
    .setOutputCol("assertion")
        
val pipeline = new Pipeline().setStages(Array(document_assembler,
                                              sentence_detector,
                                              tokenizer,
                                              word_embeddings,
                                              ner_model,
                                              ner_converter,
                                              assertion))

val data = Seq("""The patient with a history of substance abuse presented with clinical signs indicative of opioid overdose, including constricted pupils, cyanotic lips, drowsiness, and confusion. Immediate assessment and intervention were initiated to address the patient's symptoms and stabilize their condition. Close monitoring for potential complications, such as respiratory depression, was maintained throughout the course of treatment.""",
                """The patient presented to the rehabilitation facility with a documented history of opioid abuse, primarily stemming from misuse of prescription percocet pills intended for their partner's use. Initial assessment revealed withdrawal symptoms consistent with opioid dependency.""",
               """The patient was brought to the clinic exhibiting symptoms consistent with opioid withdrawal, despite denying any illicit drug use. Upon further questioning, the patient revealed using tramadol for chronic pain management.""").toDF("text")

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