class RENerChunksFilter extends AnnotatorModel[RENerChunksFilter] with ParamsAndFeaturesReadable[RENerChunksFilter] with HasSimpleAnnotate[RENerChunksFilter] with CheckLicense

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
CheckLicense, HasSimpleAnnotate[RENerChunksFilter], ParamsAndFeaturesReadable[RENerChunksFilter], DefaultParamsReadable[RENerChunksFilter], MLReadable[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
Ordering
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  3. By Inheritance
Inherited
  1. RENerChunksFilter
  2. CheckLicense
  3. HasSimpleAnnotate
  4. ParamsAndFeaturesReadable
  5. DefaultParamsReadable
  6. MLReadable
  7. AnnotatorModel
  8. CanBeLazy
  9. RawAnnotator
  10. HasOutputAnnotationCol
  11. HasInputAnnotationCols
  12. HasOutputAnnotatorType
  13. ParamsAndFeaturesWritable
  14. HasFeatures
  15. DefaultParamsWritable
  16. MLWritable
  17. Model
  18. Transformer
  19. PipelineStage
  20. Logging
  21. Params
  22. Serializable
  23. Serializable
  24. Identifiable
  25. AnyRef
  26. 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 addReader(reader: (RENerChunksFilter, String, SparkSession) ⇒ Unit): Unit
    Definition Classes
    ParamsAndFeaturesReadable
  11. def afterAnnotate(dataset: DataFrame): DataFrame
    Attributes
    protected
    Definition Classes
    AnnotatorModel
  12. def annotate(annotations: Seq[Annotation]): Seq[Annotation]
    Definition Classes
    RENerChunksFilter → HasSimpleAnnotate
  13. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  14. def beforeAnnotate(dataset: Dataset[_]): Dataset[_]
    Attributes
    protected
    Definition Classes
    AnnotatorModel
  15. final def checkSchema(schema: StructType, inputAnnotatorType: String): Boolean
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  16. def checkValidEnvironment(spark: Option[SparkContext]): Unit
    Definition Classes
    CheckLicense
  17. def checkValidScope(scope: String): Unit
    Definition Classes
    CheckLicense
  18. def checkValidScopeAndEnvironment(scope: String, spark: Option[SparkContext], checkLp: Boolean): Unit
    Definition Classes
    CheckLicense
  19. final def clear(param: Param[_]): RENerChunksFilter.this.type
    Definition Classes
    Params
  20. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  21. def copy(extra: ParamMap): RENerChunksFilter
    Definition Classes
    RawAnnotator → Model → Transformer → PipelineStage → Params
  22. def copyValues[T <: Params](to: T, extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  23. final def defaultCopy[T <: Params](extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  24. def dfAnnotate: UserDefinedFunction
    Definition Classes
    HasSimpleAnnotate
  25. var docLevelRelations: BooleanParam
  26. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  27. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  28. def explainParam(param: Param[_]): String
    Definition Classes
    Params
  29. def explainParams(): String
    Definition Classes
    Params
  30. def extraValidate(structType: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  31. def extraValidateMsg: String
    Attributes
    protected
    Definition Classes
    RawAnnotator
  32. final def extractParamMap(): ParamMap
    Definition Classes
    Params
  33. final def extractParamMap(extra: ParamMap): ParamMap
    Definition Classes
    Params
  34. val features: ArrayBuffer[Feature[_, _, _]]
    Definition Classes
    HasFeatures
  35. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  36. def get[T](feature: StructFeature[T]): Option[T]
    Attributes
    protected
    Definition Classes
    HasFeatures
  37. def get[K, V](feature: MapFeature[K, V]): Option[Map[K, V]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  38. def get[T](feature: SetFeature[T]): Option[Set[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  39. def get[T](feature: ArrayFeature[T]): Option[Array[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  40. final def get[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  41. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  42. final def getDefault[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  43. def getDocLevelRelations: Boolean

    Include relations between entities from different sentences (Default: False)

  44. def getInputCols: Array[String]
    Definition Classes
    HasInputAnnotationCols
  45. def getLazyAnnotator: Boolean
    Definition Classes
    CanBeLazy
  46. def getMaxSyntacticDistance: Float

    Maximal syntactic distance, as threshold (Default: 0)

  47. final def getOrDefault[T](param: Param[T]): T
    Definition Classes
    Params
  48. final def getOutputCol: String
    Definition Classes
    HasOutputAnnotationCol
  49. def getParam(paramName: String): Param[Any]
    Definition Classes
    Params
  50. 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

  51. final def hasDefault[T](param: Param[T]): Boolean
    Definition Classes
    Params
  52. def hasParam(paramName: String): Boolean
    Definition Classes
    Params
  53. def hasParent: Boolean
    Definition Classes
    Model
  54. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  55. def initializeLogIfNecessary(isInterpreter: Boolean, silent: Boolean): Boolean
    Attributes
    protected
    Definition Classes
    Logging
  56. def initializeLogIfNecessary(isInterpreter: Boolean): Unit
    Attributes
    protected
    Definition Classes
    Logging
  57. val inputAnnotatorTypes: Array[AnnotatorType]

    Input annotator type : CHUNK, DEPENDENCY

    Input annotator type : CHUNK, DEPENDENCY

    Definition Classes
    RENerChunksFilter → HasInputAnnotationCols
  58. final val inputCols: StringArrayParam
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  59. final def isDefined(param: Param[_]): Boolean
    Definition Classes
    Params
  60. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  61. def isLp(): Boolean
    Definition Classes
    CheckLicense
  62. final def isSet(param: Param[_]): Boolean
    Definition Classes
    Params
  63. def isTraceEnabled(): Boolean
    Attributes
    protected
    Definition Classes
    Logging
  64. val lazyAnnotator: BooleanParam
    Definition Classes
    CanBeLazy
  65. def load(path: String): RENerChunksFilter
    Definition Classes
    MLReadable
    Annotations
    @Since( "1.6.0" )
  66. def log: Logger
    Attributes
    protected
    Definition Classes
    Logging
  67. def logDebug(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  68. def logDebug(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  69. def logError(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  70. def logError(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  71. def logInfo(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  72. def logInfo(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  73. def logName: String
    Attributes
    protected
    Definition Classes
    Logging
  74. def logTrace(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  75. def logTrace(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  76. def logWarning(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  77. def logWarning(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  78. var maxSyntacticDistance: IntParam

    Maximal syntactic distance, as threshold (Default: 0)

  79. def msgHelper(schema: StructType): String
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  80. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  81. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  82. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  83. def onWrite(path: String, spark: SparkSession): Unit
    Attributes
    protected
    Definition Classes
    ParamsAndFeaturesWritable
  84. val optionalInputAnnotatorTypes: Array[String]
    Definition Classes
    HasInputAnnotationCols
  85. val outputAnnotatorType: String

    Output annotator type : CHUNK

    Output annotator type : CHUNK

    Definition Classes
    RENerChunksFilter → HasOutputAnnotatorType
  86. final val outputCol: Param[String]
    Attributes
    protected
    Definition Classes
    HasOutputAnnotationCol
  87. lazy val params: Array[Param[_]]
    Definition Classes
    Params
  88. var parent: Estimator[RENerChunksFilter]
    Definition Classes
    Model
  89. def processAnnotations(annotations: Seq[Annotation]): Seq[Annotation]
  90. def read: MLReader[RENerChunksFilter]
    Definition Classes
    ParamsAndFeaturesReadable → DefaultParamsReadable → MLReadable
  91. 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

  92. def save(path: String): Unit
    Definition Classes
    MLWritable
    Annotations
    @Since( "1.6.0" ) @throws( ... )
  93. def set[T](feature: StructFeature[T], value: T): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  94. def set[K, V](feature: MapFeature[K, V], value: Map[K, V]): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  95. def set[T](feature: SetFeature[T], value: Set[T]): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  96. def set[T](feature: ArrayFeature[T], value: Array[T]): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  97. final def set(paramPair: ParamPair[_]): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    Params
  98. final def set(param: String, value: Any): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    Params
  99. final def set[T](param: Param[T], value: T): RENerChunksFilter.this.type
    Definition Classes
    Params
  100. def setDefault[T](feature: StructFeature[T], value: () ⇒ T): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  101. def setDefault[K, V](feature: MapFeature[K, V], value: () ⇒ Map[K, V]): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  102. def setDefault[T](feature: SetFeature[T], value: () ⇒ Set[T]): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  103. def setDefault[T](feature: ArrayFeature[T], value: () ⇒ Array[T]): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  104. final def setDefault(paramPairs: ParamPair[_]*): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    Params
  105. final def setDefault[T](param: Param[T], value: T): RENerChunksFilter.this.type
    Attributes
    protected
    Definition Classes
    Params
  106. def setDocLevelRelations(docLevelRelations: Boolean): RENerChunksFilter.this.type

    Include relations between entities from different sentences (Default: False).

    Include relations between entities from different sentences (Default: False). If it set to True, then then the sentence ids of all entities is set to 0, i.e. the sentences are merged together. The original sentence ids are preserved in the metadata as 'orig_sentence'. The dependency annotations are not affected. Mind that the model which is used to extract relations may not be able to process texts that exceed a given length. It is generally a bad idea to search for relations between entities spanning more than 100 words unless using a model which is specifically trained on such data.

  107. final def setInputCols(value: String*): RENerChunksFilter.this.type
    Definition Classes
    HasInputAnnotationCols
  108. final def setInputCols(value: Array[String]): RENerChunksFilter.this.type
    Definition Classes
    HasInputAnnotationCols
  109. def setLazyAnnotator(value: Boolean): RENerChunksFilter.this.type
    Definition Classes
    CanBeLazy
  110. def setMaxSyntacticDistance(maxSyntacticDistance: Int): RENerChunksFilter.this.type

    Maximal syntactic distance, as threshold (Default: 0).

    Maximal syntactic distance, as threshold (Default: 0). This constraint may not work well if setDocLevelRelations is set to True, because dependency parsers are poor at detecting syntactic relations across multiple sentences.

  111. final def setOutputCol(value: String): RENerChunksFilter.this.type
    Definition Classes
    HasOutputAnnotationCol
  112. def setParent(parent: Estimator[RENerChunksFilter]): RENerChunksFilter
    Definition Classes
    Model
  113. 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

  114. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  115. def toString(): String
    Definition Classes
    Identifiable → AnyRef → Any
  116. final def transform(dataset: Dataset[_]): DataFrame
    Definition Classes
    AnnotatorModel → Transformer
  117. def transform(dataset: Dataset[_], paramMap: ParamMap): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" )
  118. def transform(dataset: Dataset[_], firstParamPair: ParamPair[_], otherParamPairs: ParamPair[_]*): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" ) @varargs()
  119. final def transformSchema(schema: StructType): StructType
    Definition Classes
    RawAnnotator → PipelineStage
  120. def transformSchema(schema: StructType, logging: Boolean): StructType
    Attributes
    protected
    Definition Classes
    PipelineStage
    Annotations
    @DeveloperApi()
  121. val uid: String
    Definition Classes
    RENerChunksFilter → Identifiable
  122. def validate(schema: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  123. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  124. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  125. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  126. def wrapColumnMetadata(col: Column): Column
    Attributes
    protected
    Definition Classes
    RawAnnotator
  127. def write: MLWriter
    Definition Classes
    ParamsAndFeaturesWritable → DefaultParamsWritable → MLWritable

Inherited from CheckLicense

Inherited from HasSimpleAnnotate[RENerChunksFilter]

Inherited from ParamsAndFeaturesReadable[RENerChunksFilter]

Inherited from DefaultParamsReadable[RENerChunksFilter]

Inherited from MLReadable[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