class RENerChunksFilter extends AnnotatorModel[RENerChunksFilter] with HasSimpleAnnotate[RENerChunksFilter] with Licensed

Filters and outputs combinations of relations between extracted entities, for further processing. This annotator is especially useful to create inputs for the RelationExtractionDLModel.

Example

Define pipeline stages to extract entities

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

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

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

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

val pos_tagger = PerceptronModel.pretrained("pos_clinical", "en", "clinical/models")
  .setInputCols("sentences", "tokens")
  .setOutputCol("pos_tags")

val dependency_parser = DependencyParserModel.pretrained("dependency_conllu", "en")
  .setInputCols("sentences", "pos_tags", "tokens")
  .setOutputCol("dependencies")

val clinical_ner_tagger = MedicalNerModel.pretrained("jsl_ner_wip_greedy_clinical","en","clinical/models")
  .setInputCols("sentences", "tokens", "embeddings")
  .setOutputCol("ner_tags")

val ner_chunker = new NerConverter()
  .setInputCols("sentences", "tokens", "ner_tags")
  .setOutputCol("ner_chunks")

Define the relation pairs and the filter

val relationPairs = Array("direction-external_body_part_or_region",
                      "external_body_part_or_region-direction",
                      "direction-internal_organ_or_component",
                      "internal_organ_or_component-direction")

val re_ner_chunk_filter = new RENerChunksFilter()
    .setInputCols("ner_chunks", "dependencies")
    .setOutputCol("re_ner_chunks")
    .setMaxSyntacticDistance(4)
    .setRelationPairs(Array("internal_organ_or_component-direction"))

val trained_pipeline = new Pipeline().setStages(Array(
  documenter,
  sentencer,
  tokenizer,
  words_embedder,
  pos_tagger,
  clinical_ner_tagger,
  ner_chunker,
  dependency_parser,
  re_ner_chunk_filter
))

val data = Seq("MRI demonstrated infarction in the upper brain stem , left cerebellum and  right basil ganglia").toDF("text")
val result = trained_pipeline.fit(data).transform(data)

Show results

result.selectExpr("explode(re_ner_chunks) as re_chunks")
  .selectExpr("re_chunks.begin", "re_chunks.result", "re_chunks.metadata.entity", "re_chunks.metadata.paired_to")
  .show(6, truncate=false)
+-----+-------------+---------------------------+---------+
|begin|result       |entity                     |paired_to|
+-----+-------------+---------------------------+---------+
|35   |upper        |Direction                  |41       |
|41   |brain stem   |Internal_organ_or_component|35       |
|35   |upper        |Direction                  |59       |
|59   |cerebellum   |Internal_organ_or_component|35       |
|35   |upper        |Direction                  |81       |
|81   |basil ganglia|Internal_organ_or_component|35       |
+-----+-------------+---------------------------+---------+
See also

RelationExtractionDLModel for BERT based extraction

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

Instance Constructors

  1. new RENerChunksFilter()
  2. new RENerChunksFilter(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
    RENerChunksFilter → 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[_]): RENerChunksFilter.this.type
    Definition Classes
    Params
  16. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  17. def copy(extra: ParamMap): RENerChunksFilter
    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. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  31. def get[T](feature: StructFeature[T]): Option[T]
    Attributes
    protected
    Definition Classes
    HasFeatures
  32. def get[K, V](feature: MapFeature[K, V]): Option[Map[K, V]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  33. def get[T](feature: SetFeature[T]): Option[Set[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  34. def get[T](feature: ArrayFeature[T]): Option[Array[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  35. final def get[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  36. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  37. final def getDefault[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  38. def getInputCols: Array[String]
    Definition Classes
    HasInputAnnotationCols
  39. def getLazyAnnotator: Boolean
    Definition Classes
    CanBeLazy
  40. def getMaxSyntacticDistance: Float

    Maximal syntactic distance, as threshold (Default: 0)

  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 getRelationPairs: Array[String]

    List of dash-separated pairs of named entities ("ENTITY1-ENTITY2", e.g.

    List of dash-separated pairs of named entities ("ENTITY1-ENTITY2", e.g. "Biomarker-RelativeDay"), which will be processed

  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 : CHUNK, DEPENDENCY

    Input annotator type : CHUNK, DEPENDENCY

    Definition Classes
    RENerChunksFilter → 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. var maxSyntacticDistance: IntParam

    Maximal syntactic distance, as threshold (Default: 0)

  71. def msgHelper(schema: StructType): String
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  72. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  73. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  74. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  75. def onWrite(path: String, spark: SparkSession): Unit
    Attributes
    protected
    Definition Classes
    ParamsAndFeaturesWritable
  76. val outputAnnotatorType: String

    Output annotator type : CHUNK

    Output annotator type : CHUNK

    Definition Classes
    RENerChunksFilter → 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[RENerChunksFilter]
    Definition Classes
    Model
  80. var relationPairs: Param[String]

    List of dash-separated pairs of named entities ("ENTITY1-ENTITY2", e.g.

    List of dash-separated pairs of named entities ("ENTITY1-ENTITY2", e.g. "Biomarker-RelativeDay"), which will be processed

  81. def save(path: String): Unit
    Definition Classes
    MLWritable
    Annotations
    @Since( "1.6.0" ) @throws( ... )
  82. def set[T](feature: StructFeature[T], value: T): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  83. def set[K, V](feature: MapFeature[K, V], value: Map[K, V]): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  84. def set[T](feature: SetFeature[T], value: Set[T]): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  85. def set[T](feature: ArrayFeature[T], value: Array[T]): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  86. final def set(paramPair: ParamPair[_]): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    Params
  87. final def set(param: String, value: Any): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    Params
  88. final def set[T](param: Param[T], value: T): RENerChunksFilter.this.type
    Definition Classes
    Params
  89. def setDefault[T](feature: StructFeature[T], value: () ⇒ T): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  90. def setDefault[K, V](feature: MapFeature[K, V], value: () ⇒ Map[K, V]): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  91. def setDefault[T](feature: SetFeature[T], value: () ⇒ Set[T]): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  92. def setDefault[T](feature: ArrayFeature[T], value: () ⇒ Array[T]): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  93. final def setDefault(paramPairs: ParamPair[_]*): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    Params
  94. final def setDefault[T](param: Param[T], value: T): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    Params
  95. final def setInputCols(value: String*): RENerChunksFilter.this.type
    Definition Classes
    HasInputAnnotationCols
  96. final def setInputCols(value: Array[String]): RENerChunksFilter.this.type
    Definition Classes
    HasInputAnnotationCols
  97. def setLazyAnnotator(value: Boolean): RENerChunksFilter.this.type
    Definition Classes
    CanBeLazy
  98. def setMaxSyntacticDistance(maxSyntacticDistance: Int): RENerChunksFilter.this.type

    Maximal syntactic distance, as threshold (Default: 0)

  99. final def setOutputCol(value: String): RENerChunksFilter.this.type
    Definition Classes
    HasOutputAnnotationCol
  100. def setParent(parent: Estimator[RENerChunksFilter]): RENerChunksFilter
    Definition Classes
    Model
  101. def setRelationPairs(relationPairs: Array[String]): RENerChunksFilter.this.type

    List of dash-separated pairs of named entities ("ENTITY1-ENTITY2", e.g.

    List of dash-separated pairs of named entities ("ENTITY1-ENTITY2", e.g. "Biomarker-RelativeDay"), which will be processed

  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
    RENerChunksFilter → 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 Licensed

Inherited from HasSimpleAnnotate[RENerChunksFilter]

Inherited from AnnotatorModel[RENerChunksFilter]

Inherited from CanBeLazy

Inherited from RawAnnotator[RENerChunksFilter]

Inherited from HasOutputAnnotationCol

Inherited from HasInputAnnotationCols

Inherited from HasOutputAnnotatorType

Inherited from ParamsAndFeaturesWritable

Inherited from HasFeatures

Inherited from DefaultParamsWritable

Inherited from MLWritable

Inherited from Model[RENerChunksFilter]

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