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

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
Licensed, 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
Ordering
  1. Grouped
  2. Alphabetic
  3. By Inheritance
Inherited
  1. RelationExtractionDLModel
  2. Licensed
  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
  1. Hide All
  2. Show All
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. def beforeAnnotate(dataset: Dataset[_]): Dataset[_]
    Attributes
    protected
    Definition Classes
    AnnotatorModel
  14. var bertREConfig: BertREConfig
  15. val caseSensitive: BooleanParam
    Definition Classes
    HasCaseSensitiveProperties
  16. def categorizeRel(relation: DLRelationInstance): (Int, Int, Float)
    Attributes
    protected
  17. var categoryNames: StringArrayParam

    List of relation names

  18. final def checkSchema(schema: StructType, inputAnnotatorType: String): Boolean
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  19. final def clear(param: Param[_]): RelationExtractionDLModel.this.type
    Definition Classes
    Params
  20. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  21. val configProtoBytes: IntArrayParam

    ConfigProto from tensorflow, serialized into byte array.

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

  22. def copy(extra: ParamMap): RelationExtractionDLModel
    Definition Classes
    RawAnnotator → Model → Transformer → PipelineStage → Params
  23. def copyValues[T <: Params](to: T, extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  24. def createDatabaseConnection(database: Name): RocksDBConnection
    Definition Classes
    HasStorageRef
  25. final def defaultCopy[T <: Params](extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  26. def dfAnnotate: UserDefinedFunction
    Definition Classes
    HasSimpleAnnotate
  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. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  37. def get[T](feature: StructFeature[T]): Option[T]
    Attributes
    protected
    Definition Classes
    HasFeatures
  38. def get[K, V](feature: MapFeature[K, V]): Option[Map[K, V]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  39. def get[T](feature: SetFeature[T]): Option[Set[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  40. def get[T](feature: ArrayFeature[T]): Option[Array[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  41. final def get[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  42. def getCaseSensitive: Boolean
    Definition Classes
    HasCaseSensitiveProperties
  43. def getCategories(): Array[String]

    Get all categories

  44. def getCategoryName(id: Int): String

    List of relation names

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

    ConfigProto from tensorflow, serialized into byte array.

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

  47. final def getDefault[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  48. def getInputCols: Array[String]
    Definition Classes
    HasInputAnnotationCols
  49. def getLazyAnnotator: Boolean
    Definition Classes
    CanBeLazy
  50. def getMaxSentenceLength: Int

    Max sentence length to process (Default : 128)

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

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

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

    Input annotator types : CHUNK, DOCUMENT

    Input annotator types : CHUNK, DOCUMENT

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

    Max sentence length to process (Default : 128)

  82. def model: TensorflowBertRE
  83. def msgHelper(schema: StructType): String
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  84. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  85. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  86. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  87. def onWrite(path: String, spark: SparkSession): Unit
    Definition Classes
    RelationExtractionDLModel → ParamsAndFeaturesWritable
  88. val outputAnnotatorType: String

    Output annotator type : CATEGORY

    Output annotator type : CATEGORY

    Definition Classes
    RelationExtractionDLModel → HasOutputAnnotatorType
  89. final val outputCol: Param[String]
    Attributes
    protected
    Definition Classes
    HasOutputAnnotationCol
  90. lazy val params: Array[Param[_]]
    Definition Classes
    Params
  91. var parent: Estimator[RelationExtractionDLModel]
    Definition Classes
    Model
  92. var predictionThreshold: FloatParam

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

  93. def save(path: String): Unit
    Definition Classes
    MLWritable
    Annotations
    @Since( "1.6.0" ) @throws( ... )
  94. def set[T](feature: StructFeature[T], value: T): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  95. def set[K, V](feature: MapFeature[K, V], value: Map[K, V]): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  96. def set[T](feature: SetFeature[T], value: Set[T]): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  97. def set[T](feature: ArrayFeature[T], value: Array[T]): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  98. final def set(paramPair: ParamPair[_]): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    Params
  99. final def set(param: String, value: Any): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    Params
  100. final def set[T](param: Param[T], value: T): RelationExtractionDLModel.this.type
    Definition Classes
    Params
  101. def setCaseSensitive(value: Boolean): RelationExtractionDLModel.this.type
    Definition Classes
    HasCaseSensitiveProperties
  102. def setCategoryNames(categoryNames: Array[String]): RelationExtractionDLModel.this.type

    List of relation names

  103. 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()

  104. def setDefault[T](feature: StructFeature[T], value: () ⇒ T): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  105. def setDefault[K, V](feature: MapFeature[K, V], value: () ⇒ Map[K, V]): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  106. def setDefault[T](feature: SetFeature[T], value: () ⇒ Set[T]): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  107. def setDefault[T](feature: ArrayFeature[T], value: () ⇒ Array[T]): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  108. final def setDefault(paramPairs: ParamPair[_]*): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    Params
  109. final def setDefault[T](param: Param[T], value: T): RelationExtractionDLModel.this.type
    Attributes
    protected
    Definition Classes
    Params
  110. final def setInputCols(value: String*): RelationExtractionDLModel.this.type
    Definition Classes
    HasInputAnnotationCols
  111. final def setInputCols(value: Array[String]): RelationExtractionDLModel.this.type
    Definition Classes
    HasInputAnnotationCols
  112. def setLazyAnnotator(value: Boolean): RelationExtractionDLModel.this.type
    Definition Classes
    CanBeLazy
  113. def setMaxSentenceLength(value: Int): RelationExtractionDLModel.this.type

    Max sentence length to process (Default : 128)

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

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

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

    Vocabulary used to encode words to ids with WordPieceEncoder

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

    Vocabulary used to encode words to ids with WordPieceEncoder

  134. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  135. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  136. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  137. def wrapColumnMetadata(col: Column): Column
    Attributes
    protected
    Definition Classes
    RawAnnotator
  138. def write: MLWriter
    Definition Classes
    ParamsAndFeaturesWritable → DefaultParamsWritable → MLWritable
  139. def writeTensorflowHub(path: String, tfPath: String, spark: SparkSession, suffix: String): Unit
    Definition Classes
    WriteTensorflowModel
  140. def writeTensorflowModel(path: String, spark: SparkSession, tensorflow: TensorflowWrapper, suffix: String, filename: String, configProtoBytes: Option[Array[Byte]]): Unit
    Definition Classes
    WriteTensorflowModel
  141. def writeTensorflowModelV2(path: String, spark: SparkSession, tensorflow: TensorflowWrapper, suffix: String, filename: String, configProtoBytes: Option[Array[Byte]]): Unit
    Definition Classes
    WriteTensorflowModel

Inherited from Licensed

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