Relation Extraction between Treatment-Issue Entities and Drinking-Smoking Status

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 RegexTokenizer()
    .setInputCols("sentence")
    .setOutputCol("token")
    .setPattern("\\s+|(?=[-.:;*+,\(\)\/$&%\\[\\]])|(?<=[-.:;*+,\(\)\/$&%\\[\\]])")

val embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")
    .setInputCols(Array("sentence", "token"))
    .setOutputCol("embeddings")

val ner_model = MedicalNerModel.pretrained("ner_alcohol_smoking", "en", "clinical/models")
    .setInputCols(Array("sentence", "token","embeddings"))
    .setOutputCol("ner")

val ner_converter = new NerConverterInternal()
    .setInputCols(Array("sentence", "token", "ner"))
    .setOutputCol("ner_chunk")

val pos_tagger = PerceptronModel()
    .pretrained("pos_clinical", "en", "clinical/models")
    .setInputCols(Array("sentence", "token"))
    .setOutputCol("pos_tags")

val dependency_parser = DependencyParserModel()
    .pretrained("dependency_conllu", "en")
    .setInputCols(Array("sentence", "pos_tags", "token"))
    .setOutputCol("dependencies")

val clinical_re_Model = RelationExtractionModel()
    .pretrained("re_alcohol_smoking_clinical_wip", "en", "clinical/models")
    .setInputCols(Array("embeddings", "pos_tags", "ner_chunk", "dependencies"))
    .setOutputCol("relations")\
    .setMaxSyntacticDistance(4)\
    .setRelationPairs(Array("Cessation_Treatment-Drinking_Status",
    "Withdrawal_Treatment-Drinking_Status",
    "Cessation_Treatment-Smoking_Status",
    "Withdrawal_Treatment-Smoking_Status",
    "Neurologic_Issues-Drinking_Status",
    "Neurologic_Issues-Smoking_Status",
    "Psychiatric_Issues-Drinking_Status",
    "Psychiatric_Issues-Smoking_Status",
    "Cardiovascular_Issues-Drinking_Status",
    "Cardiovascular_Issues-Smoking_Status",
    "Respiratory_Issues-Drinking_Status",
    "Respiratory_Issues-Smoking_Status",
    "GUT_Issues-Drinking_Status",
    "GUT_Issues-Smoking_Status",
    "Other_Health_Issues-Drinking_Status",
    "Other_Health_Issues-Smoking_Status"))

val re_pipeline = new Pipeline().setStages(Array(
    document_assembler,
    sentence_detector,
    tokenizer,
    embeddings,
    ner_model,
    ner_converter,
    pos_tagger,
    dependency_parser,
    clinical_re_Model
))

val text = Seq("""Pulmonary Function Tests: Demonstrates airflow limitation consistent with chronic obstructive pulmonary disease
 (COPD). Diagnosis: Acute exacerbation of COPD secondary to smoking.
 Diagnosis: Alcoholic fatty liver disease and smoking-related respiratory symptoms.Management: The patient received alcohol cessation counseling and support services to address her alcohol use disorder. She was also provided with smoking cessation pharmacotherapy and behavioral interventions to help her quit smoking.""").toDF("text")


val lmodel = LightPipeline(model)
val annotations = lmodel.fullAnnotate(text)