Packages

•  package root

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  root

•  package com

  Definition Classes

  root

•  package johnsnowlabs

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  com

•  package nlp

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  johnsnowlabs

•  package annotators

  Definition Classes

  nlp

•  package merge

  Definition Classes

  annotators

•  class REChunkMerger extends AnnotatorModel[REChunkMerger] with HasSimpleAnnotate[REChunkMerger]

  REChunkMerger annotator merges relation chunks to create a new chunk.

  REChunkMerger annotator merges relation chunks to create a new chunk.

  Example

  val documentAssembler = new DocumentAssembler()
     .setInputCol("text")
     .setOutputCol("document")
  
  val tokenizer = new Tokenizer()
     .setInputCols(Array("document"))
     .setOutputCol("tokens")
  
  val sentencer = new SentenceDetector()
     .setInputCols(Array("document"))
     .setOutputCol("sentences")
  
  val embedder = WordEmbeddingsModel
     .pretrained("embeddings_clinical", "en", "clinical/models")
     .setInputCols(Array("document", "tokens"))
     .setOutputCol("embeddings")
  
  val posTagger = PerceptronModel
     .pretrained("pos_clinical", "en", "clinical/models")
     .setInputCols(Array("sentences", "tokens"))
     .setOutputCol("posTags")
  
  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 depencyParser = DependencyParserModel
     .pretrained("dependency_conllu", "en")
     .setInputCols(Array("document", "posTags", "tokens"))
     .setOutputCol("dependencies")
  
  val re = RelationExtractionModel
     .pretrained("re_clinical", "en", "clinical/models")
     .setInputCols(Array("embeddings", "posTags", "nerChunks", "dependencies"))
     .setOutputCol("relations_t")
  
  val REChunkMerger = new REChunkMerger()
     .setInputCols("relations_t")
     .setOutputCol("relation_chunk")
     .setSeparator(" & ")
  
  val flattener = new Flattener()
     .setInputCols("relation_chunk")
     .setExplodeSelectedFields(Map("relation_chunk" -> Array(
                                   "result as result",
                                   "begin as begin",
                                   "end as end",
                                   "metadata.relation_type as relationType",
                                   "metadata.sentence as sentence"
    )))
  
  val pipeline = new Pipeline()
     .setStages(Array(
         documentAssembler,
         sentencer,
         tokenizer,
         embedder,
         posTagger,
         nerTagger,
         nerConverter,
         depencyParser,
         re,
         REChunkMerger,
         flattener
     ))
  
  import spark.implicits._
  
  val data = Seq("A 28-year-old female with a history of gestational diabetes mellitus diagnosed eight years prior to " +
   "presentation and subsequent type two diabetes mellitus ( T2DM ). one prior episode of HTG-induced pancreatitis " +
   "three years prior to presentation , associated with an acute hepatitis , and obesity with a body mass index ")
     .toDS()
     .toDF("text")
  
  val result = pipeline.fit(data).transform(data)

  Show Results

  +---------------------------------------------------------------------+-----+---+------------+--------+
  |result                                                               |begin|end|relationType|sentence|
  +---------------------------------------------------------------------+-----+---+------------+--------+
  |gestational diabetes mellitus & subsequent type two diabetes mellitus|39   |153|TeRP        |0       |
  |gestational diabetes mellitus & T2DM                                 |39   |160|TeRP        |0       |
  |subsequent type two diabetes mellitus & T2DM                         |117  |160|TeRP        |0       |
  +---------------------------------------------------------------------+-----+---+------------+--------+

  Definition Classes

  merge

• MetadataKey

com.johnsnowlabs.nlp.annotators.merge.REChunkMerger

MetadataKey 