class RelationExtractionDLModel extends AnnotatorModel[RelationExtractionDLModel] with WriteTensorflowModel with HasStorageRef with HasCaseSensitiveProperties with HasSimpleAnnotate[RelationExtractionDLModel] with CheckLicense

Extracts and classifies instances of relations between named entities. In contrast with RelationExtractionModel, RelationExtractionDLModel is based on BERT. For pretrained models please see the Models Hub for available models.

Example

Relation Extraction between body parts

This is a continuation of the RENerChunksFilter example. See that class on how to extract the relation chunks. Define the extraction model

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 re_model = RelationExtractionDLModel.pretrained("redl_bodypart_direction_biobert", "en", "clinical/models")
  .setPredictionThreshold(0.5f)
  .setInputCols("re_ner_chunks", "sentences")
  .setOutputCol("relations")

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,
  re_model
))

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(relations) as relations")
 .select(
   "relations.metadata.chunk1",
   "relations.metadata.entity1",
   "relations.metadata.chunk2",
   "relations.metadata.entity2",
   "relations.result"
 )
 .where("result != 0")
 .show(truncate=false)
+------+---------+-------------+---------------------------+------+
|chunk1|entity1  |chunk2       |entity2                    |result|
+------+---------+-------------+---------------------------+------+
|upper |Direction|brain stem   |Internal_organ_or_component|1     |
|left  |Direction|cerebellum   |Internal_organ_or_component|1     |
|right |Direction|basil ganglia|Internal_organ_or_component|1     |
+------+---------+-------------+---------------------------+------+
See also

RelationExtractionModel for ML based extraction

RENerChunksFilter on how to create inputs

Linear Supertypes
CheckLicense, HasSimpleAnnotate[RelationExtractionDLModel], HasCaseSensitiveProperties, HasStorageRef, WriteTensorflowModel, AnnotatorModel[RelationExtractionDLModel], CanBeLazy, RawAnnotator[RelationExtractionDLModel], HasOutputAnnotationCol, HasInputAnnotationCols, HasOutputAnnotatorType, ParamsAndFeaturesWritable, HasFeatures, DefaultParamsWritable, MLWritable, Model[RelationExtractionDLModel], Transformer, PipelineStage, Logging, Params, Serializable, Serializable, Identifiable, AnyRef, Any
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Inherited
  1. RelationExtractionDLModel
  2. CheckLicense
  3. HasSimpleAnnotate
  4. HasCaseSensitiveProperties
  5. HasStorageRef
  6. WriteTensorflowModel
  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 RelationExtractionDLModel()
  2. new RelationExtractionDLModel(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]

    takes a document and annotations and produces new annotations of this annotator's annotation type

    takes a document and annotations and produces new annotations of this annotator's annotation type

    annotations

    Annotations that correspond to inputAnnotationCols generated by previous annotators if any

    returns

    any number of annotations processed for every input annotation. Not necessary one to one relationship

    Definition Classes
    RelationExtractionDLModel → HasSimpleAnnotate
  12. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  13. var batchSize: IntParam
  14. def beforeAnnotate(dataset: Dataset[_]): Dataset[_]
    Definition Classes
    RelationExtractionDLModel → AnnotatorModel
  15. var bertREConfig: BertREConfig
  16. val caseSensitive: BooleanParam
    Definition Classes
    HasCaseSensitiveProperties
  17. def categorizeRelations(relations: Seq[DLRelationInstance]): Seq[(Int, Int, Float)]
    Attributes
    protected
  18. var categoryNames: StringArrayParam

    List of relation names

  19. final def checkSchema(schema: StructType, inputAnnotatorType: String): Boolean
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  20. def checkValidEnvironment(spark: Option[SparkContext]): Unit
    Definition Classes
    CheckLicense
  21. def checkValidScope(scope: String): Unit
    Definition Classes
    CheckLicense
  22. def checkValidScopeAndEnvironment(scope: String, spark: Option[SparkContext], checkLp: Boolean): Unit
    Definition Classes
    CheckLicense
  23. final def clear(param: Param[_]): RelationExtractionDLModel.this.type
    Definition Classes
    Params
  24. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  25. val configProtoBytes: IntArrayParam

    ConfigProto from tensorflow, serialized into byte array.

    ConfigProto from tensorflow, serialized into byte array. Get with config_proto.SerializeToString()

  26. def copy(extra: ParamMap): RelationExtractionDLModel
    Definition Classes
    RawAnnotator → Model → Transformer → PipelineStage → Params
  27. def copyValues[T <: Params](to: T, extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  28. def createDatabaseConnection(database: Name): RocksDBConnection
    Definition Classes
    HasStorageRef
  29. final def defaultCopy[T <: Params](extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  30. def dfAnnotate: UserDefinedFunction
    Definition Classes
    HasSimpleAnnotate
  31. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  32. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  33. def explainParam(param: Param[_]): String
    Definition Classes
    Params
  34. def explainParams(): String
    Definition Classes
    Params
  35. def extraValidate(structType: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  36. def extraValidateMsg: String
    Attributes
    protected
    Definition Classes
    RawAnnotator
  37. final def extractParamMap(): ParamMap
    Definition Classes
    Params
  38. final def extractParamMap(extra: ParamMap): ParamMap
    Definition Classes
    Params
  39. val features: ArrayBuffer[Feature[_, _, _]]
    Definition Classes
    HasFeatures
  40. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  41. def get[T](feature: StructFeature[T]): Option[T]
    Attributes
    protected
    Definition Classes
    HasFeatures
  42. def get[K, V](feature: MapFeature[K, V]): Option[Map[K, V]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  43. def get[T](feature: SetFeature[T]): Option[Set[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  44. def get[T](feature: ArrayFeature[T]): Option[Array[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  45. final def get[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  46. def getBatchSize: Int

    Number of relations to process in a batch

  47. def getCaseSensitive: Boolean
    Definition Classes
    HasCaseSensitiveProperties
  48. def getCategories(): Array[String]

    Get all categories

  49. def getCategoryName(id: Int): String

    List of relation names

  50. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  51. def getConfigProtoBytes: Option[Array[Byte]]

    ConfigProto from tensorflow, serialized into byte array.

    ConfigProto from tensorflow, serialized into byte array. Get with config_proto.SerializeToString()

  52. final def getDefault[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  53. def getInputCols: Array[String]
    Definition Classes
    HasInputAnnotationCols
  54. def getLazyAnnotator: Boolean
    Definition Classes
    CanBeLazy
  55. def getMaxSentenceLength: Int

    Max sentence length to process (Default : 128)

  56. final def getOrDefault[T](param: Param[T]): T
    Definition Classes
    Params
  57. final def getOutputCol: String
    Definition Classes
    HasOutputAnnotationCol
  58. def getParam(paramName: String): Param[Any]
    Definition Classes
    Params
  59. def getPredictionThreshold: Float

    Minimal activation of the target unit to encode a new relation instance (Default: 0.5f)

  60. def getStorageRef: String
    Definition Classes
    HasStorageRef
  61. final def hasDefault[T](param: Param[T]): Boolean
    Definition Classes
    Params
  62. def hasParam(paramName: String): Boolean
    Definition Classes
    Params
  63. def hasParent: Boolean
    Definition Classes
    Model
  64. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  65. def initializeLogIfNecessary(isInterpreter: Boolean, silent: Boolean): Boolean
    Attributes
    protected
    Definition Classes
    Logging
  66. def initializeLogIfNecessary(isInterpreter: Boolean): Unit
    Attributes
    protected
    Definition Classes
    Logging
  67. val inputAnnotatorTypes: Array[AnnotatorType]

    Input annotator types : CHUNK, DOCUMENT

    Input annotator types : CHUNK, DOCUMENT

    Definition Classes
    RelationExtractionDLModel → HasInputAnnotationCols
  68. final val inputCols: StringArrayParam
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  69. final def isDefined(param: Param[_]): Boolean
    Definition Classes
    Params
  70. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  71. def isLp(): Boolean
    Definition Classes
    CheckLicense
  72. final def isSet(param: Param[_]): Boolean
    Definition Classes
    Params
  73. def isTraceEnabled(): Boolean
    Attributes
    protected
    Definition Classes
    Logging
  74. val lazyAnnotator: BooleanParam
    Definition Classes
    CanBeLazy
  75. def log: Logger
    Attributes
    protected
    Definition Classes
    Logging
  76. def logDebug(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  77. def logDebug(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  78. def logError(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  79. def logError(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  80. def logInfo(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  81. def logInfo(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  82. def logName: String
    Attributes
    protected
    Definition Classes
    Logging
  83. def logTrace(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  84. def logTrace(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  85. def logWarning(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  86. def logWarning(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  87. val maxSentenceLength: IntParam

    Max sentence length to process (Default : 128)

  88. def model: TensorflowBertRE
  89. def msgHelper(schema: StructType): String
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  90. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  91. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  92. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  93. def onWrite(path: String, spark: SparkSession): Unit
    Definition Classes
    RelationExtractionDLModel → ParamsAndFeaturesWritable
  94. val optionalInputAnnotatorTypes: Array[String]
    Definition Classes
    HasInputAnnotationCols
  95. val outputAnnotatorType: String

    Output annotator type : CATEGORY

    Output annotator type : CATEGORY

    Definition Classes
    RelationExtractionDLModel → HasOutputAnnotatorType
  96. final val outputCol: Param[String]
    Attributes
    protected
    Definition Classes
    HasOutputAnnotationCol
  97. lazy val params: Array[Param[_]]
    Definition Classes
    Params
  98. var parent: Estimator[RelationExtractionDLModel]
    Definition Classes
    Model
  99. var predictionThreshold: FloatParam

    Minimal activation of the target unit to encode a new relation instance (Default: 0.5f)

  100. def save(path: String): Unit
    Definition Classes
    MLWritable
    Annotations
    @Since( "1.6.0" ) @throws( ... )
  101. def set[T](feature: StructFeature[T], value: T): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  102. def set[K, V](feature: MapFeature[K, V], value: Map[K, V]): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  103. def set[T](feature: SetFeature[T], value: Set[T]): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  104. def set[T](feature: ArrayFeature[T], value: Array[T]): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  105. final def set(paramPair: ParamPair[_]): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    Params
  106. final def set(param: String, value: Any): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    Params
  107. final def set[T](param: Param[T], value: T): RelationExtractionDLModel.this.type
    Definition Classes
    Params
  108. def setBatchSize(size: Int): RelationExtractionDLModel.this.type

    Set the number of relations to process in a batch.

    Set the number of relations to process in a batch. Using a larger value speeds up processing but requires more memory.

  109. def setCaseSensitive(value: Boolean): RelationExtractionDLModel.this.type
    Definition Classes
    HasCaseSensitiveProperties
  110. def setCategoryNames(categoryNames: Array[String]): RelationExtractionDLModel.this.type

    List of relation names

  111. def setConfigProtoBytes(bytes: Array[Int]): RelationExtractionDLModel.this.type

    ConfigProto from tensorflow, serialized into byte array.

    ConfigProto from tensorflow, serialized into byte array. Get with config_proto.SerializeToString()

  112. def setDefault[T](feature: StructFeature[T], value: () ⇒ T): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  113. def setDefault[K, V](feature: MapFeature[K, V], value: () ⇒ Map[K, V]): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  114. def setDefault[T](feature: SetFeature[T], value: () ⇒ Set[T]): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  115. def setDefault[T](feature: ArrayFeature[T], value: () ⇒ Array[T]): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  116. final def setDefault(paramPairs: ParamPair[_]*): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    Params
  117. final def setDefault[T](param: Param[T], value: T): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    Params
  118. final def setInputCols(value: String*): RelationExtractionDLModel.this.type
    Definition Classes
    HasInputAnnotationCols
  119. final def setInputCols(value: Array[String]): RelationExtractionDLModel.this.type
    Definition Classes
    HasInputAnnotationCols
  120. def setLazyAnnotator(value: Boolean): RelationExtractionDLModel.this.type
    Definition Classes
    CanBeLazy
  121. def setMaxSentenceLength(value: Int): RelationExtractionDLModel.this.type

    Max sentence length to process (Default : 128)

  122. final def setOutputCol(value: String): RelationExtractionDLModel.this.type
    Definition Classes
    HasOutputAnnotationCol
  123. def setParent(parent: Estimator[RelationExtractionDLModel]): RelationExtractionDLModel
    Definition Classes
    Model
  124. def setPredictionThreshold(predictionThreshold: Float): RelationExtractionDLModel.this.type

    Minimal activation of the target unit to encode a new relation instance (Default: 0.5f)

  125. def setStorageRef(value: String): RelationExtractionDLModel.this.type
    Definition Classes
    HasStorageRef
  126. def setTensorflowModel(spark: SparkSession, tf: TensorflowWrapper): RelationExtractionDLModel.this.type
  127. def setVocabulary(value: Map[String, Int]): RelationExtractionDLModel.this.type

    Vocabulary used to encode words to ids with WordPieceEncoder

  128. val storageRef: Param[String]
    Definition Classes
    HasStorageRef
  129. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  130. def toString(): String
    Definition Classes
    Identifiable → AnyRef → Any
  131. def tokenizeSentence(sentence: Sentence): WordpieceTokenizedSentence
  132. final def transform(dataset: Dataset[_]): DataFrame
    Definition Classes
    AnnotatorModel → Transformer
  133. def transform(dataset: Dataset[_], paramMap: ParamMap): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" )
  134. def transform(dataset: Dataset[_], firstParamPair: ParamPair[_], otherParamPairs: ParamPair[_]*): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" ) @varargs()
  135. final def transformSchema(schema: StructType): StructType
    Definition Classes
    RawAnnotator → PipelineStage
  136. def transformSchema(schema: StructType, logging: Boolean): StructType
    Attributes
    protected
    Definition Classes
    PipelineStage
    Annotations
    @DeveloperApi()
  137. val uid: String
    Definition Classes
    RelationExtractionDLModel → Identifiable
  138. def updateBertConfig: Unit
  139. def validate(schema: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  140. def validateStorageRef(dataset: Dataset[_], inputCols: Array[String], annotatorType: String): Unit
    Definition Classes
    HasStorageRef
  141. val vocabulary: MapFeature[String, Int]

    Vocabulary used to encode words to ids with WordPieceEncoder

  142. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  143. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  144. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  145. def wrapColumnMetadata(col: Column): Column
    Attributes
    protected
    Definition Classes
    RawAnnotator
  146. def write: MLWriter
    Definition Classes
    ParamsAndFeaturesWritable → DefaultParamsWritable → MLWritable
  147. def writeTensorflowHub(path: String, tfPath: String, spark: SparkSession, suffix: String): Unit
    Definition Classes
    WriteTensorflowModel
  148. def writeTensorflowModel(path: String, spark: SparkSession, tensorflow: TensorflowWrapper, suffix: String, filename: String, configProtoBytes: Option[Array[Byte]]): Unit
    Definition Classes
    WriteTensorflowModel
  149. def writeTensorflowModelV2(path: String, spark: SparkSession, tensorflow: TensorflowWrapper, suffix: String, filename: String, configProtoBytes: Option[Array[Byte]], savedSignatures: Option[Map[String, String]]): Unit
    Definition Classes
    WriteTensorflowModel

Inherited from CheckLicense

Inherited from HasSimpleAnnotate[RelationExtractionDLModel]

Inherited from HasCaseSensitiveProperties

Inherited from HasStorageRef

Inherited from WriteTensorflowModel

Inherited from AnnotatorModel[RelationExtractionDLModel]

Inherited from CanBeLazy

Inherited from RawAnnotator[RelationExtractionDLModel]

Inherited from HasOutputAnnotationCol

Inherited from HasInputAnnotationCols

Inherited from HasOutputAnnotatorType

Inherited from ParamsAndFeaturesWritable

Inherited from HasFeatures

Inherited from DefaultParamsWritable

Inherited from MLWritable

Inherited from Model[RelationExtractionDLModel]

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