class PosologyREModel extends RelationExtractionModel with HasStorageRef with ParamsAndFeaturesWritable with Licensed

Instantiated RelationExtractionModel for extracting relationships between different recognized drug entitites. This class is not intended to be directly used, please use the RelationExtractionModel instead. Possible values are "DRUG-DOSAGE", "DRUG-ADE", "DRUG-FORM", "DRUG-FREQUENCY", "DRUG-ROUTE", "DRUG-REASON", "DRUG-STRENGTH", "DRUG-DURATION". Please see the Models Hub for available models.

See also

RelationExtractionModel to use the model

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

Instance Constructors

  1. new PosologyREModel()
  2. new PosologyREModel(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
    RelationExtractionModelGenericClassifierModel → HasSimpleAnnotate
  12. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  13. def beforeAnnotate(dataset: Dataset[_]): Dataset[_]
    Definition Classes
    RelationExtractionModelGenericClassifierModel → AnnotatorModel
  14. def categorizeRel(relation: RelationInstance): (Long, Float)
  15. final def checkSchema(schema: StructType, inputAnnotatorType: String): Boolean
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  16. final def clear(param: Param[_]): PosologyREModel.this.type
    Definition Classes
    Params
  17. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  18. def copy(extra: ParamMap): GenericClassifierModel
    Definition Classes
    RawAnnotator → Model → Transformer → PipelineStage → Params
  19. def copyValues[T <: Params](to: T, extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  20. def createDatabaseConnection(database: Name): RocksDBConnection
    Definition Classes
    HasStorageRef
  21. final def defaultCopy[T <: Params](extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  22. def dfAnnotate: UserDefinedFunction
    Definition Classes
    HasSimpleAnnotate
  23. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  24. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  25. def explainParam(param: Param[_]): String
    Definition Classes
    Params
  26. def explainParams(): String
    Definition Classes
    Params
  27. def extraValidate(structType: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  28. def extraValidateMsg: String
    Attributes
    protected
    Definition Classes
    RawAnnotator
  29. final def extractParamMap(): ParamMap
    Definition Classes
    Params
  30. final def extractParamMap(extra: ParamMap): ParamMap
    Definition Classes
    Params
  31. val featureScaling: Param[String]

    Feature scaling method.

    Feature scaling method. Possible values are 'zscore', 'minmax' or empty (no scaling)

    Definition Classes
    GenericClassifierModel
  32. val features: ArrayBuffer[Feature[_, _, _]]
    Definition Classes
    HasFeatures
  33. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  34. def get[T](feature: StructFeature[T]): Option[T]
    Attributes
    protected
    Definition Classes
    HasFeatures
  35. def get[K, V](feature: MapFeature[K, V]): Option[Map[K, V]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  36. def get[T](feature: SetFeature[T]): Option[Set[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  37. def get[T](feature: ArrayFeature[T]): Option[Array[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  38. final def get[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  39. def getCategories(): Array[String]
    Definition Classes
    GenericClassifierModel
  40. def getCategoryName(id: Int): String
  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 getEncoder: GenericClassifierDataEncoder
    Definition Classes
    GenericClassifierModel
  44. def getFeatureScaling: String

    Get feature scaling method

    Get feature scaling method

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

    Maximal syntactic distance, as threshold (Default: 0)

    Maximal syntactic distance, as threshold (Default: 0)

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

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

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

    Definition Classes
    RelationExtractionModel
  52. 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

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

    Input annotator types : WORD_EMBEDDINGS, POS, CHUNK, DEPENDENCY

    Input annotator types : WORD_EMBEDDINGS, POS, CHUNK, DEPENDENCY

    Definition Classes
    RelationExtractionModelGenericClassifierModel → HasInputAnnotationCols
  61. final val inputCols: StringArrayParam
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  62. final def isDefined(param: Param[_]): Boolean
    Definition Classes
    Params
  63. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  64. final def isSet(param: Param[_]): Boolean
    Definition Classes
    Params
  65. def isTraceEnabled(): Boolean
    Attributes
    protected
    Definition Classes
    Logging
  66. val lazyAnnotator: BooleanParam
    Definition Classes
    CanBeLazy
  67. def loadModel(sparkSession: SparkSession, tfModel: TensorflowWrapper, categories: Array[String], encoder: GenericClassifierDataEncoder, nerTags: Array[String]): PosologyREModel.this.type
    Definition Classes
    RelationExtractionModel
  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

    Maximal syntactic distance, as threshold (Default: 0)

    Maximal syntactic distance, as threshold (Default: 0)

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

    Output annotator types : CATEGORY

    Output annotator types : CATEGORY

    Definition Classes
    RelationExtractionModelGenericClassifierModel → 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[GenericClassifierModel]
    Definition Classes
    Model
  91. var predictionThreshold: FloatParam

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

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

    Definition Classes
    RelationExtractionModel
  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

    Definition Classes
    RelationExtractionModel
  93. def save(path: String): Unit
    Definition Classes
    MLWritable
    Annotations
    @Since( "1.6.0" ) @throws( ... )
  94. def scaleFeatures(features: Array[Array[Float]]): Array[Array[Float]]
    Attributes
    protected
    Definition Classes
    GenericClassifierModel
  95. def set[T](feature: StructFeature[T], value: T): PosologyREModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  96. def set[K, V](feature: MapFeature[K, V], value: Map[K, V]): PosologyREModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  97. def set[T](feature: SetFeature[T], value: Set[T]): PosologyREModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  98. def set[T](feature: ArrayFeature[T], value: Array[T]): PosologyREModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  99. final def set(paramPair: ParamPair[_]): PosologyREModel.this.type
    Attributes
    protected
    Definition Classes
    Params
  100. final def set(param: String, value: Any): PosologyREModel.this.type
    Attributes
    protected
    Definition Classes
    Params
  101. final def set[T](param: Param[T], value: T): PosologyREModel.this.type
    Definition Classes
    Params
  102. def setCategoryNames(categoryNames: Array[String]): PosologyREModel.this.type
    Definition Classes
    GenericClassifierModel
  103. def setDefault[T](feature: StructFeature[T], value: () ⇒ T): PosologyREModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  104. def setDefault[K, V](feature: MapFeature[K, V], value: () ⇒ Map[K, V]): PosologyREModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  105. def setDefault[T](feature: SetFeature[T], value: () ⇒ Set[T]): PosologyREModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  106. def setDefault[T](feature: ArrayFeature[T], value: () ⇒ Array[T]): PosologyREModel.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  107. final def setDefault(paramPairs: ParamPair[_]*): PosologyREModel.this.type
    Attributes
    protected
    Definition Classes
    Params
  108. final def setDefault[T](param: Param[T], value: T): PosologyREModel.this.type
    Attributes
    protected
    Definition Classes
    Params
  109. def setEncoder(encoder: GenericClassifierDataEncoder): PosologyREModel.this.type
    Definition Classes
    GenericClassifierModel
  110. def setFeatureScaling(featureScaling: String): PosologyREModel.this.type

    Set the feature scaling method.

    Set the feature scaling method. Possible values are 'zscore', 'minmax' or empty (no scaling)

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

    Maximal syntactic distance, as threshold (Default: 0)

    Maximal syntactic distance, as threshold (Default: 0)

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

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

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

    Definition Classes
    RelationExtractionModel
  118. def setRelationPairs(relationPairs: Array[String]): PosologyREModel.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

    Definition Classes
    RelationExtractionModel
  119. def setStorageRef(value: String): PosologyREModel.this.type
    Definition Classes
    HasStorageRef
  120. def setTensorflowModel(spark: SparkSession, tf: TensorflowWrapper): PosologyREModel.this.type
    Definition Classes
    GenericClassifierModel
  121. val storageRef: Param[String]
    Definition Classes
    HasStorageRef
  122. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  123. def toString(): String
    Definition Classes
    Identifiable → AnyRef → Any
  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
    PosologyREModelRelationExtractionModelGenericClassifierModel → Identifiable
  130. def validate(schema: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  131. def validateStorageRef(dataset: Dataset[_], inputCols: Array[String], annotatorType: String): Unit
    Definition Classes
    HasStorageRef
  132. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  133. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  134. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  135. def wrapColumnMetadata(col: Column): Column
    Attributes
    protected
    Definition Classes
    RawAnnotator
  136. def write: MLWriter
    Definition Classes
    ParamsAndFeaturesWritable → DefaultParamsWritable → MLWritable
  137. def writeTensorflowHub(path: String, tfPath: String, spark: SparkSession, suffix: String): Unit
    Definition Classes
    WriteTensorflowModel
  138. def writeTensorflowModel(path: String, spark: SparkSession, tensorflow: TensorflowWrapper, suffix: String, filename: String, configProtoBytes: Option[Array[Byte]]): Unit
    Definition Classes
    PosologyREModel → WriteTensorflowModel
  139. def writeTensorflowModelV2(path: String, spark: SparkSession, tensorflow: TensorflowWrapper, suffix: String, filename: String, configProtoBytes: Option[Array[Byte]]): Unit
    Definition Classes
    WriteTensorflowModel

Inherited from RelationExtractionModel

Inherited from GenericClassifierModel

Inherited from Licensed

Inherited from HasSimpleAnnotate[GenericClassifierModel]

Inherited from WriteTensorflowModel

Inherited from HasStorageRef

Inherited from AnnotatorModel[GenericClassifierModel]

Inherited from CanBeLazy

Inherited from RawAnnotator[GenericClassifierModel]

Inherited from HasOutputAnnotationCol

Inherited from HasInputAnnotationCols

Inherited from HasOutputAnnotatorType

Inherited from ParamsAndFeaturesWritable

Inherited from HasFeatures

Inherited from DefaultParamsWritable

Inherited from MLWritable

Inherited from Model[GenericClassifierModel]

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