class AssertionFilterer extends AnnotatorModel[AssertionFilterer] with HasSimpleAnnotate[AssertionFilterer] with HandleExceptionParams with HasSafeAnnotate[AssertionFilterer] with FilteringParams with CheckLicense

Filters entities coming from ASSERTION type annotations and returns the CHUNKS. Filters can be set via a white list and black list on the extracted chunk, the assertion or a regular expression. White and black lists are for assertion are enabled by default. To use chunk white list, criteria has to be set to "isin". For regex, criteria has to be set to "regex".

Example

To see how the assertions are extracted, see the example for AssertionDLModel.

Define an extra step where the assertions are filtered
val assertionFilterer = new AssertionFilterer()
  .setInputCols("sentence","ner_chunk","assertion")
  .setOutputCol("filtered")
  .setCriteria("assertion")
  .setWhiteList("present")

val assertionPipeline = new Pipeline().setStages(Array(
  documentAssembler,
  sentenceDetector,
  tokenizer,
  embeddings,
  nerModel,
  nerConverter,
  clinicalAssertion,
  assertionFilterer
))

val assertionModel = assertionPipeline.fit(data)
val result = assertionModel.transform(data)

Show results:

result.selectExpr("ner_chunk.result", "assertion.result").show(3, truncate=false)
+--------------------------------+--------------------------------+
|result                          |result                          |
+--------------------------------+--------------------------------+
|[severe fever, sore throat]     |[present, present]              |
|[stomach pain]                  |[absent]                        |
|[an epidural, PCA, pain control]|[present, present, hypothetical]|
+--------------------------------+--------------------------------+

result.select("filtered.result").show(3, truncate=false)
+---------------------------+
|result                     |
+---------------------------+
|[severe fever, sore throat]|
|[]                         |
|[an epidural, PCA]         |
+---------------------------+
See also

AssertionDLModel to extract the assertions

Linear Supertypes
CheckLicense, FilteringParams, HasSafeAnnotate[AssertionFilterer], HandleExceptionParams, HasSimpleAnnotate[AssertionFilterer], AnnotatorModel[AssertionFilterer], CanBeLazy, RawAnnotator[AssertionFilterer], HasOutputAnnotationCol, HasInputAnnotationCols, HasOutputAnnotatorType, ParamsAndFeaturesWritable, HasFeatures, DefaultParamsWritable, MLWritable, Model[AssertionFilterer], Transformer, PipelineStage, Logging, Params, Serializable, Serializable, Identifiable, AnyRef, Any
Ordering
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  2. Alphabetic
  3. By Inheritance
Inherited
  1. AssertionFilterer
  2. CheckLicense
  3. FilteringParams
  4. HasSafeAnnotate
  5. HandleExceptionParams
  6. HasSimpleAnnotate
  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 AssertionFilterer()
  2. new AssertionFilterer(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]

    annotations

    a Sequence of chunks to merge

    returns

    a Sequence of Merged CHUNK Annotations

    Definition Classes
    AssertionFilterer → HasSimpleAnnotate
  12. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  13. def beforeAnnotate(dataset: Dataset[_]): Dataset[_]
    Attributes
    protected
    Definition Classes
    AnnotatorModel
  14. val blackList: StringArrayParam

    If defined, list of entities to ignore.

    If defined, list of entities to ignore. The rest will be processed

    Definition Classes
    FilteringParams
  15. val caseSensitive: BooleanParam

    Determines whether the definitions of the white listed and black listed entities are case sensitive or not.

    Determines whether the definitions of the white listed and black listed entities are case sensitive or not. If the filterValue is 'entity', 'caseSensitive' is always false. The default value is true, except: com.johnsnowlabs.nlp.annotators.chunker.AssertionFilterer

    Definition Classes
    FilteringParams
  16. final def checkSchema(schema: StructType, inputAnnotatorType: String): Boolean
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  17. def checkValidEnvironment(spark: Option[SparkSession], scopes: Seq[String]): Unit
    Definition Classes
    CheckLicense
  18. def checkValidScope(scope: String): Unit
    Definition Classes
    CheckLicense
  19. def checkValidScopeAndEnvironment(scope: String, spark: Option[SparkSession], checkLp: Boolean): Unit
    Definition Classes
    CheckLicense
  20. def checkValidScopesAndEnvironment(scopes: Seq[String], spark: Option[SparkSession], checkLp: Boolean): Unit
    Definition Classes
    CheckLicense
  21. final def clear(param: Param[_]): AssertionFilterer.this.type
    Definition Classes
    Params
  22. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  23. def copy(extra: ParamMap): AssertionFilterer
    Definition Classes
    RawAnnotator → Model → Transformer → PipelineStage → Params
  24. def copyValues[T <: Params](to: T, extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  25. val criteria: Param[String]

    It is used to how to compare black and white listed values with the result of the Annotation.

    It is used to how to compare black and white listed values with the result of the Annotation. Possible values are the following: 'isin', 'regex'. Default: isin

    • isin : Filter by the chunk
    • regex : Filter by using a regex
    Definition Classes
    FilteringParams
  26. final def defaultCopy[T <: Params](extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  27. def dfAnnotate: UserDefinedFunction
    Definition Classes
    HasSimpleAnnotate
  28. val doExceptionHandling: BooleanParam

    If true, exceptions are handled.

    If true, exceptions are handled. If exception causing data is passed to the model, a error annotation is emitted which has the exception message. Processing continues with the next one. This comes with a performance penalty.

    Definition Classes
    HandleExceptionParams
  29. val entitiesConfidence: MapFeature[String, Float]

    Pairs (entity,confidenceThreshold).

    Pairs (entity,confidenceThreshold). Filter the chunks with entities which have confidence lower than the confidence threshold.

    Definition Classes
    FilteringParams
  30. lazy val entitiesConfidenceMap: Map[String, Float]
    Definition Classes
    FilteringParams
  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. val filterValue: Param[String]

    Possible values are 'result' and 'entity'.

    Possible values are 'result' and 'entity'. If the value is 'entity', it filters the ner chunks by the ner label that you want to filter. If the value is 'result', it will filter chunks by the result of the Annotation.

    Definition Classes
    FilteringParams
  41. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  42. def get[T](feature: StructFeature[T]): Option[T]
    Attributes
    protected
    Definition Classes
    HasFeatures
  43. def get[K, V](feature: MapFeature[K, V]): Option[Map[K, V]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  44. def get[T](feature: SetFeature[T]): Option[Set[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  45. def get[T](feature: ArrayFeature[T]): Option[Array[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  46. final def get[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  47. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  48. final def getDefault[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  49. def getInputCols: Array[String]
    Definition Classes
    HasInputAnnotationCols
  50. def getLazyAnnotator: Boolean
    Definition Classes
    CanBeLazy
  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. 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. val inExceptionMode: Boolean
    Attributes
    protected
    Definition Classes
    HasSafeAnnotate
  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 types: DOCUMENT, CHUNK, ASSERTION

    Input annotator types: DOCUMENT, CHUNK, ASSERTION

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

    Output annotator types: CHUNK

    Output annotator types: CHUNK

    Definition Classes
    AssertionFilterer → HasOutputAnnotatorType
  87. final val outputCol: Param[String]
    Attributes
    protected
    Definition Classes
    HasOutputAnnotationCol
  88. lazy val params: Array[Param[_]]
    Definition Classes
    Params
  89. var parent: Estimator[AssertionFilterer]
    Definition Classes
    Model
  90. val regex: StringArrayParam

    If defined, list of regex to process the chunks (Default: Array())

    If defined, list of regex to process the chunks (Default: Array())

    Definition Classes
    FilteringParams
  91. def resolveFilter(chunkerAnnotations: Seq[Annotation]): Seq[Annotation]
    Attributes
    protected
    Definition Classes
    FilteringParams
  92. def resolveMergeFilter(a: Annotation, entityValue: String, falsePositivesArray: Array[(String, String, String)], replaceDictMap: Map[String, String] = Map.empty): Option[Annotation]
    Attributes
    protected
    Definition Classes
    FilteringParams
  93. def resolveWhiteListBlackListFilter(annotations: Seq[Annotation]): Seq[Annotation]
    Attributes
    protected
    Definition Classes
    FilteringParams
  94. def safeAnnotate(annotations: Seq[Annotation]): Seq[Annotation]

    A protected method designed to safely annotate a sequence of Annotation objects by handling exceptions.

    A protected method designed to safely annotate a sequence of Annotation objects by handling exceptions.

    annotations

    A sequence of Annotation.

    returns

    A sequence of Annotation objects after processing, potentially containing error annotations.

    Attributes
    protected
    Definition Classes
    HasSafeAnnotate
  95. def save(path: String): Unit
    Definition Classes
    MLWritable
    Annotations
    @Since( "1.6.0" ) @throws( ... )
  96. def set[T](feature: StructFeature[T], value: T): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  97. def set[K, V](feature: MapFeature[K, V], value: Map[K, V]): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  98. def set[T](feature: SetFeature[T], value: Set[T]): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  99. def set[T](feature: ArrayFeature[T], value: Array[T]): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  100. final def set(paramPair: ParamPair[_]): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    Params
  101. final def set(param: String, value: Any): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    Params
  102. final def set[T](param: Param[T], value: T): AssertionFilterer.this.type
    Definition Classes
    Params
  103. def setAllowList(list: String*): AssertionFilterer.this.type
    Definition Classes
    FilteringParams
  104. def setAllowList(list: Array[String]): AssertionFilterer.this.type
    Definition Classes
    FilteringParams
  105. def setBlackList(list: String*): AssertionFilterer.this.type
    Definition Classes
    FilteringParams
  106. def setBlackList(list: Array[String]): AssertionFilterer.this.type

    If defined, list of entities to ignore.

    If defined, list of entities to ignore. The rest will be processed.

    Definition Classes
    FilteringParams
  107. def setCaseSensitive(value: Boolean): AssertionFilterer.this.type

    Determines whether the definitions of the white listed and black listed entities are case sensitive or not.

    Determines whether the definitions of the white listed and black listed entities are case sensitive or not. If the filterValue is 'entity', 'caseSensitive' is always False. The default value is true, except: com.johnsnowlabs.nlp.annotators.chunker.AssertionFilterer

    Definition Classes
    FilteringParams
  108. def setCriteria(s: String): AssertionFilterer.this.type

    Sets criteria for how to compare black and white listed values with the result of the Annotation.

    Sets criteria for how to compare black and white listed values with the result of the Annotation. Possible values are the following: 'isin', 'regex'. Default: isin.

    Definition Classes
    FilteringParams
  109. def setDefault[T](feature: StructFeature[T], value: () ⇒ T): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  110. def setDefault[K, V](feature: MapFeature[K, V], value: () ⇒ Map[K, V]): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  111. def setDefault[T](feature: SetFeature[T], value: () ⇒ Set[T]): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  112. def setDefault[T](feature: ArrayFeature[T], value: () ⇒ Array[T]): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  113. final def setDefault(paramPairs: ParamPair[_]*): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    Params
  114. final def setDefault[T](param: Param[T], value: T): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    Params
  115. def setDenyList(list: String*): AssertionFilterer.this.type
    Definition Classes
    FilteringParams
  116. def setDenyList(list: Array[String]): AssertionFilterer.this.type
    Definition Classes
    FilteringParams
  117. def setDoExceptionHandling(value: Boolean): AssertionFilterer.this.type

    If true, exceptions are handled.

    If true, exceptions are handled. If exception causing data is passed to the model, a error annotation is emitted which has the exception message. Processing continues with the next one. This comes with a performance penalty.

    Definition Classes
    HandleExceptionParams
  118. def setEntitiesConfidence(value: Map[String, Float]): AssertionFilterer.this.type

    Unsupported method in AssertionFilterer @throw RuntimeException

    Unsupported method in AssertionFilterer @throw RuntimeException

    Definition Classes
    AssertionFiltererFilteringParams
  119. def setFilterEntity(v: String): AssertionFilterer.this.type

    Possible values are 'result' and 'entity'.

    Possible values are 'result' and 'entity'. If the value is 'entity', it filters the ner chunks by the ner label that you want to filter. If the value is 'result', it will filter chunks by the result of the Annotation.

    Definition Classes
    FilteringParams
  120. final def setInputCols(value: String*): AssertionFilterer.this.type
    Definition Classes
    HasInputAnnotationCols
  121. def setInputCols(value: Array[String]): AssertionFilterer.this.type
    Definition Classes
    HasInputAnnotationCols
  122. def setLazyAnnotator(value: Boolean): AssertionFilterer.this.type
    Definition Classes
    CanBeLazy
  123. final def setOutputCol(value: String): AssertionFilterer.this.type
    Definition Classes
    HasOutputAnnotationCol
  124. def setParent(parent: Estimator[AssertionFilterer]): AssertionFilterer
    Definition Classes
    Model
  125. def setRegex(list: String*): AssertionFilterer.this.type

    Sets the list of regexes to process the chunks.

    Sets the list of regexes to process the chunks.

    Definition Classes
    FilteringParams
  126. def setWhiteList(list: String*): AssertionFilterer.this.type
    Definition Classes
    FilteringParams
  127. def setWhiteList(list: Array[String]): AssertionFilterer.this.type

    Sets the list of entities to process.

    Sets the list of entities to process. The rest will be ignored. Do not include IOB prefix on labels.

    Definition Classes
    FilteringParams
  128. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  129. def toString(): String
    Definition Classes
    Identifiable → AnyRef → Any
  130. final def transform(dataset: Dataset[_]): DataFrame
    Definition Classes
    AnnotatorModel → Transformer
  131. def transform(dataset: Dataset[_], paramMap: ParamMap): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" )
  132. def transform(dataset: Dataset[_], firstParamPair: ParamPair[_], otherParamPairs: ParamPair[_]*): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" ) @varargs()
  133. final def transformSchema(schema: StructType): StructType
    Definition Classes
    RawAnnotator → PipelineStage
  134. def transformSchema(schema: StructType, logging: Boolean): StructType
    Attributes
    protected
    Definition Classes
    PipelineStage
    Annotations
    @DeveloperApi()
  135. val uid: String
    Definition Classes
    AssertionFilterer → Identifiable
  136. def validate(schema: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  137. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  138. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  139. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  140. val whiteList: StringArrayParam

    If defined, list of entities to process.

    If defined, list of entities to process. The rest will be ignored. Does not include IOB prefix on labels (Default: Array())

    Definition Classes
    FilteringParams
  141. def wrapColumnMetadata(col: Column): Column
    Attributes
    protected
    Definition Classes
    RawAnnotator
  142. def write: MLWriter
    Definition Classes
    ParamsAndFeaturesWritable → DefaultParamsWritable → MLWritable

Inherited from CheckLicense

Inherited from FilteringParams

Inherited from HandleExceptionParams

Inherited from HasSimpleAnnotate[AssertionFilterer]

Inherited from AnnotatorModel[AssertionFilterer]

Inherited from CanBeLazy

Inherited from RawAnnotator[AssertionFilterer]

Inherited from HasOutputAnnotationCol

Inherited from HasInputAnnotationCols

Inherited from HasOutputAnnotatorType

Inherited from ParamsAndFeaturesWritable

Inherited from HasFeatures

Inherited from DefaultParamsWritable

Inherited from MLWritable

Inherited from Model[AssertionFilterer]

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