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

Filters entities' dependency relations.

The annotator filters desired relation pairs (defined by the parameter realtionPairs), and store those on the output column. Filtering the possible relations can be useful to perform additional analysis for a specific use case (e.g., checking adverse drug reactions and drug realations), which can be the input for further analysis using a pretrained RelationExtractionDLModel.

For example, the ner_clinical NER model can identify PROBLEM, TEST, and TREATMENT entities. By using this annotator, one can filter (select) the relations between PROBLEM and TREATMENT entities only, removing any relation between the other entities, to further analyze the associations between clinical problems and treatments.

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], 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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Inherited
  1. RENerChunksFilter
  2. CheckLicense
  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. def checkValidEnvironment(spark: Option[SparkSession], scopes: Seq[String]): Unit
    Definition Classes
    CheckLicense
  16. def checkValidScope(scope: String): Unit
    Definition Classes
    CheckLicense
  17. def checkValidScopeAndEnvironment(scope: String, spark: Option[SparkSession], checkLp: Boolean): Unit
    Definition Classes
    CheckLicense
  18. def checkValidScopesAndEnvironment(scopes: Seq[String], spark: Option[SparkSession], 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. val directionSensitive: BooleanParam

    If it is true, only relations in the form of "ENTITY1-ENTITY2" will be considered, If it is false, both "ENTITY1-ENTITY2" and "ENTITY2-ENTITY1" relations will be considered,

  26. var docLevelRelations: BooleanParam

    Whether to include relations between entities from different sentences (Default: False).

  27. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  28. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  29. def explainParam(param: Param[_]): String
    Definition Classes
    Params
  30. def explainParams(): String
    Definition Classes
    Params
  31. def extraValidate(structType: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  32. def extraValidateMsg: String
    Attributes
    protected
    Definition Classes
    RawAnnotator
  33. final def extractParamMap(): ParamMap
    Definition Classes
    Params
  34. final def extractParamMap(extra: ParamMap): ParamMap
    Definition Classes
    Params
  35. val features: ArrayBuffer[Feature[_, _, _]]
    Definition Classes
    HasFeatures
  36. val filterByTokenDistance: IntParam

    filtering criterion based on number of token between entities.

    filtering criterion based on number of token between entities. Model only finds relations that have fewer than the specified number of tokens between them.

  37. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  38. def get[T](feature: StructFeature[T]): Option[T]
    Attributes
    protected
    Definition Classes
    HasFeatures
  39. def get[K, V](feature: MapFeature[K, V]): Option[Map[K, V]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  40. def get[T](feature: SetFeature[T]): Option[Set[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  41. def get[T](feature: ArrayFeature[T]): Option[Array[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  42. final def get[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  43. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  44. final def getDefault[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  45. def getDirectionSensitive: Boolean

    Gets the directionSensitive

  46. def getDocLevelRelations: Boolean

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

  47. def getInputCols: Array[String]
    Definition Classes
    HasInputAnnotationCols
  48. def getLazyAnnotator: Boolean
    Definition Classes
    CanBeLazy
  49. def getMaxSyntacticDistance: Float

    Maximal syntactic distance, as threshold (Default: 0)

  50. final def getOrDefault[T](param: Param[T]): T
    Definition Classes
    Params
  51. final def getOutputCol: String
    Definition Classes
    HasOutputAnnotationCol
  52. def getParam(paramName: String): Param[Any]
    Definition Classes
    Params
  53. 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

  54. def getRelationPairsCaseSensitive: Boolean

    Gets the case sensitivity of relation pairs

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

    Input annotator type : CHUNK, DEPENDENCY

    Input annotator type : CHUNK, DEPENDENCY

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

    Maximum syntactic distance between a pair of named entities to consider them as a relation.

    Maximum syntactic distance between a pair of named entities to consider them as a relation.

    Increase this value if you want to consider relations between entities that are far away, but be careful as it may add false positives (Default: 0).

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

    Output annotator type : CHUNK

    Output annotator type : CHUNK

    Definition Classes
    RENerChunksFilter → HasOutputAnnotatorType
  88. final val outputCol: Param[String]
    Attributes
    protected
    Definition Classes
    HasOutputAnnotationCol
  89. lazy val params: Array[Param[_]]
    Definition Classes
    Params
  90. var parent: Estimator[RENerChunksFilter]
    Definition Classes
    Model
  91. def processAnnotations(annotations: Seq[Annotation]): Seq[Annotation]
  92. 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. If not set, all relations between the entities will be considered.

  93. var relationPairsCaseSensitive: BooleanParam

    Determines whether relation pairs are case sensitive

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

    If it is true, only relations in the form of "ENTITY1-ENTITY2" will be considered, If it is false, both "ENTITY1-ENTITY2" and "ENTITY2-ENTITY1" relations will be considered,

  109. 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.

  110. def setFilterByTokenDistance(value: Int): RENerChunksFilter.this.type

    filtering criterion based on number of token between entities.

    filtering criterion based on number of token between entities. Model only finds relations that have fewer than the specified number of tokens between them

  111. final def setInputCols(value: String*): RENerChunksFilter.this.type
    Definition Classes
    HasInputAnnotationCols
  112. def setInputCols(value: Array[String]): RENerChunksFilter.this.type
    Definition Classes
    HasInputAnnotationCols
  113. def setLazyAnnotator(value: Boolean): RENerChunksFilter.this.type
    Definition Classes
    CanBeLazy
  114. 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.

  115. final def setOutputCol(value: String): RENerChunksFilter.this.type
    Definition Classes
    HasOutputAnnotationCol
  116. def setParent(parent: Estimator[RENerChunksFilter]): RENerChunksFilter
    Definition Classes
    Model
  117. 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

  118. def setRelationPairsCaseSensitive(value: Boolean): RENerChunksFilter.this.type

    Sets the case sensitivity of relation pairs

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

Inherited from CheckLicense

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