Packages

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

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       |
+---------------------------------------------------------------------+-----+---+------------+--------+
Linear Supertypes
HasSimpleAnnotate[REChunkMerger], AnnotatorModel[REChunkMerger], CanBeLazy, RawAnnotator[REChunkMerger], HasOutputAnnotationCol, HasInputAnnotationCols, HasOutputAnnotatorType, ParamsAndFeaturesWritable, HasFeatures, DefaultParamsWritable, MLWritable, Model[REChunkMerger], Transformer, PipelineStage, Logging, Params, Serializable, Serializable, Identifiable, AnyRef, Any
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  3. By Inheritance
Inherited
  1. REChunkMerger
  2. HasSimpleAnnotate
  3. AnnotatorModel
  4. CanBeLazy
  5. RawAnnotator
  6. HasOutputAnnotationCol
  7. HasInputAnnotationCols
  8. HasOutputAnnotatorType
  9. ParamsAndFeaturesWritable
  10. HasFeatures
  11. DefaultParamsWritable
  12. MLWritable
  13. Model
  14. Transformer
  15. PipelineStage
  16. Logging
  17. Params
  18. Serializable
  19. Serializable
  20. Identifiable
  21. AnyRef
  22. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new REChunkMerger()
  2. new REChunkMerger(uid: String)

    uid

    a unique identifier for the instantiated AnnotatorModel

Type Members

  1. type AnnotationContent = Seq[Row]
    Attributes
    protected
    Definition Classes
    AnnotatorModel
  2. type AnnotatorType = String
    Definition Classes
    HasOutputAnnotatorType
  3. implicit class MetadataKey extends AnyRef

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def $[T](param: Param[T]): T
    Attributes
    protected
    Definition Classes
    Params
  4. def $$[T](feature: StructFeature[T]): T
    Attributes
    protected
    Definition Classes
    HasFeatures
  5. def $$[K, V](feature: MapFeature[K, V]): Map[K, V]
    Attributes
    protected
    Definition Classes
    HasFeatures
  6. def $$[T](feature: SetFeature[T]): Set[T]
    Attributes
    protected
    Definition Classes
    HasFeatures
  7. def $$[T](feature: ArrayFeature[T]): Array[T]
    Attributes
    protected
    Definition Classes
    HasFeatures
  8. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  9. def _transform(dataset: Dataset[_], recursivePipeline: Option[PipelineModel]): DataFrame
    Attributes
    protected
    Definition Classes
    AnnotatorModel
  10. def afterAnnotate(dataset: DataFrame): DataFrame
    Attributes
    protected
    Definition Classes
    AnnotatorModel
  11. def annotate(annotations: Seq[Annotation]): Seq[Annotation]
    Definition Classes
    REChunkMerger → HasSimpleAnnotate
  12. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  13. def beforeAnnotate(dataset: Dataset[_]): Dataset[_]
    Attributes
    protected
    Definition Classes
    AnnotatorModel
  14. final def checkSchema(schema: StructType, inputAnnotatorType: String): Boolean
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  15. final def clear(param: Param[_]): REChunkMerger.this.type
    Definition Classes
    Params
  16. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  17. def copy(extra: ParamMap): REChunkMerger
    Definition Classes
    RawAnnotator → Model → Transformer → PipelineStage → Params
  18. def copyValues[T <: Params](to: T, extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  19. final def defaultCopy[T <: Params](extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  20. def dfAnnotate: UserDefinedFunction
    Definition Classes
    HasSimpleAnnotate
  21. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  22. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  23. def explainParam(param: Param[_]): String
    Definition Classes
    Params
  24. def explainParams(): String
    Definition Classes
    Params
  25. final val extraInputCols: StringArrayParam
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  26. def extraValidate(structType: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  27. def extraValidateMsg: String
    Attributes
    protected
    Definition Classes
    RawAnnotator
  28. final def extractParamMap(): ParamMap
    Definition Classes
    Params
  29. final def extractParamMap(extra: ParamMap): ParamMap
    Definition Classes
    Params
  30. val features: ArrayBuffer[Feature[_, _, _]]
    Definition Classes
    HasFeatures
  31. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  32. def get[T](feature: StructFeature[T]): Option[T]
    Attributes
    protected
    Definition Classes
    HasFeatures
  33. def get[K, V](feature: MapFeature[K, V]): Option[Map[K, V]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  34. def get[T](feature: SetFeature[T]): Option[Set[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  35. def get[T](feature: ArrayFeature[T]): Option[Array[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  36. final def get[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  37. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  38. final def getDefault[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  39. def getInputCols: Array[String]
    Definition Classes
    HasInputAnnotationCols
  40. def getLazyAnnotator: Boolean
    Definition Classes
    CanBeLazy
  41. final def getOrDefault[T](param: Param[T]): T
    Definition Classes
    Params
  42. final def getOutputCol: String
    Definition Classes
    HasOutputAnnotationCol
  43. def getParam(paramName: String): Param[Any]
    Definition Classes
    Params
  44. def getSeparator: String

    Gets the separator to add between the results.

    Gets the separator to add between the results. Default: " ".

  45. final def hasDefault[T](param: Param[T]): Boolean
    Definition Classes
    Params
  46. def hasParam(paramName: String): Boolean
    Definition Classes
    Params
  47. def hasParent: Boolean
    Definition Classes
    Model
  48. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  49. def initializeLogIfNecessary(isInterpreter: Boolean, silent: Boolean): Boolean
    Attributes
    protected
    Definition Classes
    Logging
  50. def initializeLogIfNecessary(isInterpreter: Boolean): Unit
    Attributes
    protected
    Definition Classes
    Logging
  51. val inputAnnotatorTypes: Array[AnnotatorType]

    Input annotator type: CATEGORY

    Input annotator type: CATEGORY

    Definition Classes
    REChunkMerger → HasInputAnnotationCols
  52. final val inputCols: StringArrayParam
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  53. final def isDefined(param: Param[_]): Boolean
    Definition Classes
    Params
  54. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  55. final def isSet(param: Param[_]): Boolean
    Definition Classes
    Params
  56. def isTraceEnabled(): Boolean
    Attributes
    protected
    Definition Classes
    Logging
  57. val lazyAnnotator: BooleanParam
    Definition Classes
    CanBeLazy
  58. def log: Logger
    Attributes
    protected
    Definition Classes
    Logging
  59. def logDebug(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  60. def logDebug(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  61. def logError(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  62. def logError(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  63. def logInfo(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  64. def logInfo(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  65. def logName: String
    Attributes
    protected
    Definition Classes
    Logging
  66. def logTrace(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  67. def logTrace(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  68. def logWarning(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  69. def logWarning(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  70. def msgHelper(schema: StructType): String
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  71. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  72. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  73. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  74. def onWrite(path: String, spark: SparkSession): Unit
    Attributes
    protected
    Definition Classes
    ParamsAndFeaturesWritable
  75. val optionalInputAnnotatorTypes: Array[String]
    Definition Classes
    HasInputAnnotationCols
  76. val outputAnnotatorType: AnnotatorType

    Output annotator types: CHUNK

    Output annotator types: CHUNK

    Definition Classes
    REChunkMerger → HasOutputAnnotatorType
  77. final val outputCol: Param[String]
    Attributes
    protected
    Definition Classes
    HasOutputAnnotationCol
  78. lazy val params: Array[Param[_]]
    Definition Classes
    Params
  79. var parent: Estimator[REChunkMerger]
    Definition Classes
    Model
  80. def save(path: String): Unit
    Definition Classes
    MLWritable
    Annotations
    @Since( "1.6.0" ) @throws( ... )
  81. val separator: Param[String]

    Separator to add between the chunks.

    Separator to add between the chunks. Default: " ".

  82. def set[T](feature: StructFeature[T], value: T): REChunkMerger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  83. def set[K, V](feature: MapFeature[K, V], value: Map[K, V]): REChunkMerger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  84. def set[T](feature: SetFeature[T], value: Set[T]): REChunkMerger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  85. def set[T](feature: ArrayFeature[T], value: Array[T]): REChunkMerger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  86. final def set(paramPair: ParamPair[_]): REChunkMerger.this.type
    Attributes
    protected
    Definition Classes
    Params
  87. final def set(param: String, value: Any): REChunkMerger.this.type
    Attributes
    protected
    Definition Classes
    Params
  88. final def set[T](param: Param[T], value: T): REChunkMerger.this.type
    Definition Classes
    Params
  89. def setDefault[T](feature: StructFeature[T], value: () ⇒ T): REChunkMerger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  90. def setDefault[K, V](feature: MapFeature[K, V], value: () ⇒ Map[K, V]): REChunkMerger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  91. def setDefault[T](feature: SetFeature[T], value: () ⇒ Set[T]): REChunkMerger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  92. def setDefault[T](feature: ArrayFeature[T], value: () ⇒ Array[T]): REChunkMerger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  93. final def setDefault(paramPairs: ParamPair[_]*): REChunkMerger.this.type
    Attributes
    protected
    Definition Classes
    Params
  94. final def setDefault[T](param: Param[T], value: T): REChunkMerger.this.type
    Attributes
    protected[org.apache.spark.ml]
    Definition Classes
    Params
  95. def setExtraInputCols(value: Array[String]): REChunkMerger.this.type
    Definition Classes
    HasInputAnnotationCols
  96. final def setInputCols(value: String*): REChunkMerger.this.type
    Definition Classes
    HasInputAnnotationCols
  97. def setInputCols(value: Array[String]): REChunkMerger.this.type
    Definition Classes
    HasInputAnnotationCols
  98. def setLazyAnnotator(value: Boolean): REChunkMerger.this.type
    Definition Classes
    CanBeLazy
  99. final def setOutputCol(value: String): REChunkMerger.this.type
    Definition Classes
    HasOutputAnnotationCol
  100. def setParent(parent: Estimator[REChunkMerger]): REChunkMerger
    Definition Classes
    Model
  101. def setSeparator(value: String): REChunkMerger.this.type

    Sets the separator to add between the results.

    Sets the separator to add between the results. Default: " ".

  102. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  103. def toString(): String
    Definition Classes
    Identifiable → AnyRef → Any
  104. final def transform(dataset: Dataset[_]): DataFrame
    Definition Classes
    AnnotatorModel → Transformer
  105. def transform(dataset: Dataset[_], paramMap: ParamMap): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" )
  106. def transform(dataset: Dataset[_], firstParamPair: ParamPair[_], otherParamPairs: ParamPair[_]*): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" ) @varargs()
  107. final def transformSchema(schema: StructType): StructType
    Definition Classes
    RawAnnotator → PipelineStage
  108. def transformSchema(schema: StructType, logging: Boolean): StructType
    Attributes
    protected
    Definition Classes
    PipelineStage
    Annotations
    @DeveloperApi()
  109. val uid: String
    Definition Classes
    REChunkMerger → Identifiable
  110. def validate(schema: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  111. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  112. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  113. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  114. def wrapColumnMetadata(col: Column): Column
    Attributes
    protected
    Definition Classes
    RawAnnotator
  115. def write: MLWriter
    Definition Classes
    ParamsAndFeaturesWritable → DefaultParamsWritable → MLWritable

Inherited from HasSimpleAnnotate[REChunkMerger]

Inherited from AnnotatorModel[REChunkMerger]

Inherited from CanBeLazy

Inherited from RawAnnotator[REChunkMerger]

Inherited from HasOutputAnnotationCol

Inherited from HasInputAnnotationCols

Inherited from HasOutputAnnotatorType

Inherited from ParamsAndFeaturesWritable

Inherited from HasFeatures

Inherited from DefaultParamsWritable

Inherited from MLWritable

Inherited from Model[REChunkMerger]

Inherited from Transformer

Inherited from PipelineStage

Inherited from Logging

Inherited from Params

Inherited from Serializable

Inherited from Serializable

Inherited from Identifiable

Inherited from AnyRef

Inherited from Any

Parameters

Annotator types

Required input and expected output annotator types

Members

Parameter setters

Parameter getters