Packages

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

Filters entities coming from ASSERTION type annotations and returns the CHUNKS. Filters can be set via a white list on the extracted chunk, the assertion or a regular expression. White list for assertion is 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, 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
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Inherited
  1. AssertionFilterer
  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 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. final def checkSchema(schema: StructType, inputAnnotatorType: String): Boolean
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  15. def checkValidEnvironment(spark: Option[SparkContext]): Unit
    Definition Classes
    CheckLicense
  16. def checkValidScope(scope: String): Unit
    Definition Classes
    CheckLicense
  17. def checkValidScopeAndEnvironment(scope: String, spark: Option[SparkContext], checkLp: Boolean): Unit
    Definition Classes
    CheckLicense
  18. final def clear(param: Param[_]): AssertionFilterer.this.type
    Definition Classes
    Params
  19. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  20. def copy(extra: ParamMap): AssertionFilterer
    Definition Classes
    RawAnnotator → Model → Transformer → PipelineStage → Params
  21. def copyValues[T <: Params](to: T, extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  22. val criteria: Param[String]

    Tag representing dates in the obfuscate reference file (Default: "assertion")

  23. final def defaultCopy[T <: Params](extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  24. def dfAnnotate: UserDefinedFunction
    Definition Classes
    HasSimpleAnnotate
  25. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  26. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  27. def explainParam(param: Param[_]): String
    Definition Classes
    Params
  28. def explainParams(): String
    Definition Classes
    Params
  29. def extraValidate(structType: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  30. def extraValidateMsg: String
    Attributes
    protected
    Definition Classes
    RawAnnotator
  31. final def extractParamMap(): ParamMap
    Definition Classes
    Params
  32. final def extractParamMap(extra: ParamMap): ParamMap
    Definition Classes
    Params
  33. val features: ArrayBuffer[Feature[_, _, _]]
    Definition Classes
    HasFeatures
  34. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  35. def get[T](feature: StructFeature[T]): Option[T]
    Attributes
    protected
    Definition Classes
    HasFeatures
  36. def get[K, V](feature: MapFeature[K, V]): Option[Map[K, V]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  37. def get[T](feature: SetFeature[T]): Option[Set[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  38. def get[T](feature: ArrayFeature[T]): Option[Array[T]]
    Attributes
    protected
    Definition Classes
    HasFeatures
  39. final def get[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  40. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  41. final def getDefault[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  42. def getInputCols: Array[String]
    Definition Classes
    HasInputAnnotationCols
  43. def getLazyAnnotator: Boolean
    Definition Classes
    CanBeLazy
  44. final def getOrDefault[T](param: Param[T]): T
    Definition Classes
    Params
  45. final def getOutputCol: String
    Definition Classes
    HasOutputAnnotationCol
  46. def getParam(paramName: String): Param[Any]
    Definition Classes
    Params
  47. final def hasDefault[T](param: Param[T]): Boolean
    Definition Classes
    Params
  48. def hasParam(paramName: String): Boolean
    Definition Classes
    Params
  49. def hasParent: Boolean
    Definition Classes
    Model
  50. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  51. def initializeLogIfNecessary(isInterpreter: Boolean, silent: Boolean): Boolean
    Attributes
    protected
    Definition Classes
    Logging
  52. def initializeLogIfNecessary(isInterpreter: Boolean): Unit
    Attributes
    protected
    Definition Classes
    Logging
  53. val inputAnnotatorTypes: Array[AnnotatorType]

    Input annotator types: DOCUMENT, CHUNK, ASSERTION

    Input annotator types: DOCUMENT, CHUNK, ASSERTION

    Definition Classes
    AssertionFilterer → HasInputAnnotationCols
  54. final val inputCols: StringArrayParam
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  55. final def isDefined(param: Param[_]): Boolean
    Definition Classes
    Params
  56. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  57. def isLp(): Boolean
    Definition Classes
    CheckLicense
  58. final def isSet(param: Param[_]): Boolean
    Definition Classes
    Params
  59. def isTraceEnabled(): Boolean
    Attributes
    protected
    Definition Classes
    Logging
  60. val lazyAnnotator: BooleanParam
    Definition Classes
    CanBeLazy
  61. def log: Logger
    Attributes
    protected
    Definition Classes
    Logging
  62. def logDebug(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  63. def logDebug(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  64. def logError(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  65. def logError(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  66. def logInfo(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  67. def logInfo(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  68. def logName: String
    Attributes
    protected
    Definition Classes
    Logging
  69. def logTrace(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  70. def logTrace(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  71. def logWarning(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  72. def logWarning(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  73. def msgHelper(schema: StructType): String
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  74. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  75. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  76. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  77. def onWrite(path: String, spark: SparkSession): Unit
    Attributes
    protected
    Definition Classes
    ParamsAndFeaturesWritable
  78. val optionalInputAnnotatorTypes: Array[String]
    Definition Classes
    HasInputAnnotationCols
  79. val outputAnnotatorType: AnnotatorType

    Output annotator types: CHUNK

    Output annotator types: CHUNK

    Definition Classes
    AssertionFilterer → HasOutputAnnotatorType
  80. final val outputCol: Param[String]
    Attributes
    protected
    Definition Classes
    HasOutputAnnotationCol
  81. lazy val params: Array[Param[_]]
    Definition Classes
    Params
  82. var parent: Estimator[AssertionFilterer]
    Definition Classes
    Model
  83. val regex: StringArrayParam

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

  84. def save(path: String): Unit
    Definition Classes
    MLWritable
    Annotations
    @Since( "1.6.0" ) @throws( ... )
  85. def set[T](feature: StructFeature[T], value: T): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  86. def set[K, V](feature: MapFeature[K, V], value: Map[K, V]): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  87. def set[T](feature: SetFeature[T], value: Set[T]): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  88. def set[T](feature: ArrayFeature[T], value: Array[T]): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  89. final def set(paramPair: ParamPair[_]): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    Params
  90. final def set(param: String, value: Any): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    Params
  91. final def set[T](param: Param[T], value: T): AssertionFilterer.this.type
    Definition Classes
    Params
  92. def setCriteria(s: String): AssertionFilterer.this.type

    Tag representing dates in the obfuscate reference file (Default: "assertion")

  93. def setDefault[T](feature: StructFeature[T], value: () ⇒ T): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  94. def setDefault[K, V](feature: MapFeature[K, V], value: () ⇒ Map[K, V]): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  95. def setDefault[T](feature: SetFeature[T], value: () ⇒ Set[T]): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  96. def setDefault[T](feature: ArrayFeature[T], value: () ⇒ Array[T]): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  97. final def setDefault(paramPairs: ParamPair[_]*): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    Params
  98. final def setDefault[T](param: Param[T], value: T): AssertionFilterer.this.type
    Attributes
    protected
    Definition Classes
    Params
  99. final def setInputCols(value: String*): AssertionFilterer.this.type
    Definition Classes
    HasInputAnnotationCols
  100. final def setInputCols(value: Array[String]): AssertionFilterer.this.type
    Definition Classes
    HasInputAnnotationCols
  101. def setLazyAnnotator(value: Boolean): AssertionFilterer.this.type
    Definition Classes
    CanBeLazy
  102. final def setOutputCol(value: String): AssertionFilterer.this.type
    Definition Classes
    HasOutputAnnotationCol
  103. def setParent(parent: Estimator[AssertionFilterer]): AssertionFilterer
    Definition Classes
    Model
  104. def setRegex(list: String*): AssertionFilterer.this.type

    If defined, list of entities to process.

    If defined, list of entities to process. The rest will be ignored

  105. def setWhiteList(list: String*): AssertionFilterer.this.type

    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.

  106. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  107. def toString(): String
    Definition Classes
    Identifiable → AnyRef → Any
  108. final def transform(dataset: Dataset[_]): DataFrame
    Definition Classes
    AnnotatorModel → Transformer
  109. def transform(dataset: Dataset[_], paramMap: ParamMap): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" )
  110. def transform(dataset: Dataset[_], firstParamPair: ParamPair[_], otherParamPairs: ParamPair[_]*): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" ) @varargs()
  111. final def transformSchema(schema: StructType): StructType
    Definition Classes
    RawAnnotator → PipelineStage
  112. def transformSchema(schema: StructType, logging: Boolean): StructType
    Attributes
    protected
    Definition Classes
    PipelineStage
    Annotations
    @DeveloperApi()
  113. val uid: String
    Definition Classes
    AssertionFilterer → Identifiable
  114. def validate(schema: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  115. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  116. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  117. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  118. 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())

  119. def wrapColumnMetadata(col: Column): Column
    Attributes
    protected
    Definition Classes
    RawAnnotator
  120. def write: MLWriter
    Definition Classes
    ParamsAndFeaturesWritable → DefaultParamsWritable → MLWritable

Inherited from CheckLicense

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