Detect Absent Assertion Status with Contextual Assertion

    val documentAssembler = new DocumentAssembler()
      .setInputCol("text")
      .setOutputCol("document")

    val sentenceDetector = new SentenceDetector()
      .setInputCols(Array("document"))
      .setOutputCol("sentences")

    val tokenizer = new Tokenizer()
      .setInputCols(Array("sentences"))
      .setOutputCol("tokens")

    val embedder = WordEmbeddingsModel
      .pretrained("embeddings_clinical", "en", "clinical/models")
      .setInputCols(Array("sentences", "tokens"))
      .setOutputCol("embeddings")

    val nerTagger = MedicalNerModel
      .pretrained("ner_clinical", "en", "clinical/models")
      .setInputCols(Array("sentences", "tokens", "embeddings"))
      .setOutputCol("nerTags")

    val nerConverter = new NerConverterInternal()
      .setInputCols(Array("sentences", "tokens", "nerTags"))
      .setOutputCol("nerChunks")

    val contextualAssertionAbsent = ContextualAssertion.pretrained("contextual_assertion_absent", "en", "clinical/models")
      .setInputCols("sentences", "tokens", "nerChunks")
      .setOutputCol("assertionAbsent")

    val flattener = new Flattener()
      .setInputCols("assertionAbsent")
      .setExplodeSelectedFields(Map("assertionAbsent" -> Array("metadata.ner_chunk as ner_chunk",
        "metadata.entity",
        "begin as begin",
        "end as end",
        "metadata.ner_label as ner_label",
        "result as result")
      ))

    val emptyDataSet = Seq("").toDS().toDF("text")
    
    val pipeline = new Pipeline()
      .setStages(
        Array(documentAssembler,
                  sentenceDetector,
                  tokenizer,
                  embedder,
                  nerTagger,
                  nerConverter,
                  contextualAssertionAbsent,
                  flattener
        )).fit(emptyDataSet)

    val text = Seq("Patient resting in bed. Patient given azithromycin without any difficulty." +
      " Patient has audible wheezing, states chest tightness.No evidence of hypertension. Patient denies" +
      " nausea at this time. zofran declined. Patient is also having intermittent sweating associated " +
      "with pneumonia. Patient refused pain but tylenol still given. Neither substance abuse nor alcohol" +
      " use however cocaine once used in the last year."
    ).toDS.toDF("text")

    val dataSetResult = pipeline.transform(text)
    dataSetResult.show(false)