class Mapper2Chunk extends AnnotatorModel[Mapper2Chunk] with HasSimpleAnnotate[Mapper2Chunk]

This annotator converts 'LABELED_DEPENDENCY' type annotations coming from ChunkMapper into 'CHUNK' type to create new chunk-type column, compatible with annotators that use chunk type as input.

Example

Define dataset

 val testText = "Patient resting in bed. Patient given azithromycin without any difficulty." +
" Patient denies nausea at this time. zofran declined. Patient is also having intermittent sweating "

val testDataSet = Seq(testText).toDS.toDF("text")

Define a pipeline

 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 chunkerMapper = ChunkMapperModel.pretrained("drug_action_treatment_mapper", "en", "clinical/models")
   .setInputCols("nerChunks")
   .setOutputCol("relations")
   .setRels(Array("action"))
   .setAllowMultiTokenChunk(true)
   .setEnableCharFingerprintMatching(true)

val mapper2Chunk = new Mapper2Chunk()
   .setInputCols("relations")
   .setOutputCol("chunk")

val flattener = new Flattener()
   .setInputCols("chunk")
   .setExplodeSelectedFields(Map("chunk" -> Array("result as result",
                                                  "metadata.__trained__ as chunk",
                                                  "metadata.relation as relation",
                                                  "annotatorType as annotatorType")))
val pipeline = new Pipeline()
   .setStages(Array(
         documentAssembler,
         sentenceDetector,
         tokenizer,
         embedder,
         nerTagger,
         nerConverter,
         chunkerMapper,
         mapper2Chunk,
         flattener
           )).fit(testDataSet)

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

  +---------------+------------+--------+-------------+
  |result         |chunk       |relation|annotatorType|
  +---------------+------------+--------+-------------+
  |bactericidal   |azithromycin|action  |chunk        |
  |NONE           |null        |null    |chunk        |
  |antiemetic     |nausea      |action  |chunk        |
  |anti-abstinence|zofran      |action  |chunk        |
  |NONE           |null        |null    |chunk        |
  +---------------+------------+--------+-------------+
Linear Supertypes
HasSimpleAnnotate[Mapper2Chunk], AnnotatorModel[Mapper2Chunk], CanBeLazy, RawAnnotator[Mapper2Chunk], HasOutputAnnotationCol, HasInputAnnotationCols, HasOutputAnnotatorType, ParamsAndFeaturesWritable, HasFeatures, DefaultParamsWritable, MLWritable, Model[Mapper2Chunk], Transformer, PipelineStage, Logging, Params, Serializable, Serializable, Identifiable, AnyRef, Any
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  3. By Inheritance
Inherited
  1. Mapper2Chunk
  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 Mapper2Chunk()
  2. new Mapper2Chunk(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

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
    Mapper2Chunk → 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[_]): Mapper2Chunk.this.type
    Definition Classes
    Params
  16. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  17. def copy(extra: ParamMap): Mapper2Chunk
    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. def extraValidate(structType: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  26. def extraValidateMsg: String
    Attributes
    protected
    Definition Classes
    RawAnnotator
  27. final def extractParamMap(): ParamMap
    Definition Classes
    Params
  28. final def extractParamMap(extra: ParamMap): ParamMap
    Definition Classes
    Params
  29. val features: ArrayBuffer[Feature[_, _, _]]
    Definition Classes
    HasFeatures
  30. val filterNoneValues: BooleanParam

    When set to true, annotations with the result 'NONE' will be filtered out

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

    Input annotator type: LABELED_DEPENDENCY

    Input annotator type: LABELED_DEPENDENCY

    Definition Classes
    Mapper2Chunk → HasInputAnnotationCols
  51. final val inputCols: StringArrayParam
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  52. final def isDefined(param: Param[_]): Boolean
    Definition Classes
    Params
  53. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  54. final def isSet(param: Param[_]): Boolean
    Definition Classes
    Params
  55. def isTraceEnabled(): Boolean
    Attributes
    protected
    Definition Classes
    Logging
  56. val lazyAnnotator: BooleanParam
    Definition Classes
    CanBeLazy
  57. def log: Logger
    Attributes
    protected
    Definition Classes
    Logging
  58. def logDebug(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  59. def logDebug(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  60. def logError(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  61. def logError(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  62. def logInfo(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  63. def logInfo(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  64. def logName: String
    Attributes
    protected
    Definition Classes
    Logging
  65. def logTrace(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  66. def logTrace(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  67. def logWarning(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  68. def logWarning(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  69. def msgHelper(schema: StructType): String
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  70. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  71. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  72. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  73. def onWrite(path: String, spark: SparkSession): Unit
    Attributes
    protected
    Definition Classes
    ParamsAndFeaturesWritable
  74. val optionalInputAnnotatorTypes: Array[String]
    Definition Classes
    HasInputAnnotationCols
  75. val outputAnnotatorType: AnnotatorType

    Output annotator types: CHUNK

    Output annotator types: CHUNK

    Definition Classes
    Mapper2Chunk → HasOutputAnnotatorType
  76. final val outputCol: Param[String]
    Attributes
    protected
    Definition Classes
    HasOutputAnnotationCol
  77. lazy val params: Array[Param[_]]
    Definition Classes
    Params
  78. var parent: Estimator[Mapper2Chunk]
    Definition Classes
    Model
  79. def save(path: String): Unit
    Definition Classes
    MLWritable
    Annotations
    @Since( "1.6.0" ) @throws( ... )
  80. def set[T](feature: StructFeature[T], value: T): Mapper2Chunk.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  81. def set[K, V](feature: MapFeature[K, V], value: Map[K, V]): Mapper2Chunk.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  82. def set[T](feature: SetFeature[T], value: Set[T]): Mapper2Chunk.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  83. def set[T](feature: ArrayFeature[T], value: Array[T]): Mapper2Chunk.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  84. final def set(paramPair: ParamPair[_]): Mapper2Chunk.this.type
    Attributes
    protected
    Definition Classes
    Params
  85. final def set(param: String, value: Any): Mapper2Chunk.this.type
    Attributes
    protected
    Definition Classes
    Params
  86. final def set[T](param: Param[T], value: T): Mapper2Chunk.this.type
    Definition Classes
    Params
  87. def setDefault[T](feature: StructFeature[T], value: () ⇒ T): Mapper2Chunk.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  88. def setDefault[K, V](feature: MapFeature[K, V], value: () ⇒ Map[K, V]): Mapper2Chunk.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  89. def setDefault[T](feature: SetFeature[T], value: () ⇒ Set[T]): Mapper2Chunk.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  90. def setDefault[T](feature: ArrayFeature[T], value: () ⇒ Array[T]): Mapper2Chunk.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  91. final def setDefault(paramPairs: ParamPair[_]*): Mapper2Chunk.this.type
    Attributes
    protected
    Definition Classes
    Params
  92. final def setDefault[T](param: Param[T], value: T): Mapper2Chunk.this.type
    Attributes
    protected[org.apache.spark.ml]
    Definition Classes
    Params
  93. def setFilterNoneValues(value: Boolean): Mapper2Chunk.this.type
  94. final def setInputCols(value: String*): Mapper2Chunk.this.type
    Definition Classes
    HasInputAnnotationCols
  95. def setInputCols(value: Array[String]): Mapper2Chunk.this.type
    Definition Classes
    HasInputAnnotationCols
  96. def setLazyAnnotator(value: Boolean): Mapper2Chunk.this.type
    Definition Classes
    CanBeLazy
  97. final def setOutputCol(value: String): Mapper2Chunk.this.type
    Definition Classes
    HasOutputAnnotationCol
  98. def setParent(parent: Estimator[Mapper2Chunk]): Mapper2Chunk
    Definition Classes
    Model
  99. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  100. def toString(): String
    Definition Classes
    Identifiable → AnyRef → Any
  101. final def transform(dataset: Dataset[_]): DataFrame
    Definition Classes
    AnnotatorModel → Transformer
  102. def transform(dataset: Dataset[_], paramMap: ParamMap): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" )
  103. def transform(dataset: Dataset[_], firstParamPair: ParamPair[_], otherParamPairs: ParamPair[_]*): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" ) @varargs()
  104. final def transformSchema(schema: StructType): StructType
    Definition Classes
    RawAnnotator → PipelineStage
  105. def transformSchema(schema: StructType, logging: Boolean): StructType
    Attributes
    protected
    Definition Classes
    PipelineStage
    Annotations
    @DeveloperApi()
  106. val uid: String
    Definition Classes
    Mapper2Chunk → Identifiable
  107. def validate(schema: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  108. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  109. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  110. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  111. def wrapColumnMetadata(col: Column): Column
    Attributes
    protected
    Definition Classes
    RawAnnotator
  112. def write: MLWriter
    Definition Classes
    ParamsAndFeaturesWritable → DefaultParamsWritable → MLWritable

Inherited from HasSimpleAnnotate[Mapper2Chunk]

Inherited from AnnotatorModel[Mapper2Chunk]

Inherited from CanBeLazy

Inherited from RawAnnotator[Mapper2Chunk]

Inherited from HasOutputAnnotationCol

Inherited from HasInputAnnotationCols

Inherited from HasOutputAnnotatorType

Inherited from ParamsAndFeaturesWritable

Inherited from HasFeatures

Inherited from DefaultParamsWritable

Inherited from MLWritable

Inherited from Model[Mapper2Chunk]

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

Annotator types

Required input and expected output annotator types

param

Ungrouped