Packages

class MultiChunk2Doc extends AnnotatorModel[MultiChunk2Doc] with HasSimpleAnnotate[MultiChunk2Doc] with WhiteAndBlackListParams with CheckLicense

MultiChunk2Doc annotator merges a given chunks to create a document. During document creation, a specific whitelist and blacklist filter can be applied, and case sensitivity can be adjusted.

See also

WhiteAndBlackListParams Additionally, specified prefix and suffix texts can be placed before and after the merged chunks in the resulting document. And a separator can be placed between the chunks.

Example

val document_assembler = new DocumentAssembler()
 .setInputCol("text").setOutputCol("document")

val sentence_detector = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare", "en", "clinical/models")
 .setInputCols("document").setOutputCol("sentence")

val tokenizer = new Tokenizer()
 .setInputCols("sentence").setOutputCol("token")

val word_embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")
 .setInputCols(Array("sentence", "token")).setOutputCol("embeddings")

val ner = MedicalNerModel.pretrained("ner_clinical_large_langtest", "en", "clinical/models")
 .setInputCols("sentence", "token", "embeddings").setOutputCol("ner")

val ner_converter = new NerConverterInternal()
 .setInputCols(Array("sentence", "token", "ner")).setOutputCol("ner_chunk")

val multi_chunk2_doc = new MultiChunk2Doc()
 .setInputCols("ner_chunk")
 .setOutputCol("new_doc")
 .setWhiteList(Array("test"))
 .setCaseSensitive(false)
 .setPrefix("<")
 .setSuffix(">")
 .setSeparator("><")

val pipeline = new Pipeline().setStages(Array(document_assembler, sentence_detector, tokenizer, word_embeddings, ner, ner_converter, multi_chunk2_doc))
import spark.implicits._
val data = Seq(
"""A 28-year-old female with a history of gestational diabetes mellitus diagnosed eight years prior to presentation and subsequent type two diabetes mellitus (T2DM),
| one prior episode of HTG-induced pancreatitis three years prior to presentation, and associated with an acute hepatitis,
| presented with a one-week history of polyuria, poor appetite, and vomiting. She was on metformin, glipizide, and dapagliflozin for T2DM and atorvastatin and gemfibrozil for HTG.
| She had been on dapagliflozin for six months at the time of presentation. Physical examination on presentation was significant for dry oral mucosa; significantly,
| her abdominal examination was benign with no tenderness, guarding, or rigidity.""".stripMargin)
.toDF("text")
val result = pipeline.fit(data).transform(data)

Show Results

result.selectExpr("explode(new_doc) as result").show(false)

+----------------------------------------------------------------------------------------------------------+
|result                                                                                                    |
+----------------------------------------------------------------------------------------------------------+
|{document, 0, 48, <Physical examination><her abdominal examination>, {document -> 0, chunk_count -> 2}, []}|
+----------------------------------------------------------------------------------------------------------+
Linear Supertypes
CheckLicense, WhiteAndBlackListParams, HasSimpleAnnotate[MultiChunk2Doc], AnnotatorModel[MultiChunk2Doc], CanBeLazy, RawAnnotator[MultiChunk2Doc], HasOutputAnnotationCol, HasInputAnnotationCols, HasOutputAnnotatorType, ParamsAndFeaturesWritable, HasFeatures, DefaultParamsWritable, MLWritable, Model[MultiChunk2Doc], Transformer, PipelineStage, Logging, Params, Serializable, Serializable, Identifiable, AnyRef, Any
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Inherited
  1. MultiChunk2Doc
  2. CheckLicense
  3. WhiteAndBlackListParams
  4. HasSimpleAnnotate
  5. AnnotatorModel
  6. CanBeLazy
  7. RawAnnotator
  8. HasOutputAnnotationCol
  9. HasInputAnnotationCols
  10. HasOutputAnnotatorType
  11. ParamsAndFeaturesWritable
  12. HasFeatures
  13. DefaultParamsWritable
  14. MLWritable
  15. Model
  16. Transformer
  17. PipelineStage
  18. Logging
  19. Params
  20. Serializable
  21. Serializable
  22. Identifiable
  23. AnyRef
  24. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new MultiChunk2Doc()
  2. new MultiChunk2Doc(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]
    Definition Classes
    MultiChunk2Doc → HasSimpleAnnotate
  12. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  13. final def beforeAnnotate(dataset: Dataset[_]): Dataset[_]
    Definition Classes
    MultiChunk2Doc → AnnotatorModel
  14. val blackList: StringArrayParam

    If defined, list of entities to ignore.

    If defined, list of entities to ignore. The rest will be processed. Should not include IOB prefix on labels. Default: Array()

    Definition Classes
    WhiteAndBlackListParams
  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. Default: true

    Definition Classes
    WhiteAndBlackListParams
  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[_]): MultiChunk2Doc.this.type
    Definition Classes
    Params
  22. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  23. def copy(extra: ParamMap): MultiChunk2Doc
    Definition Classes
    RawAnnotator → Model → Transformer → PipelineStage → Params
  24. def copyValues[T <: Params](to: T, extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  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 evaluateFilter(filter: String): Boolean

    Filter annotations by blackList and whiteList, taking into account the caseSensitive param.

    Filter annotations by blackList and whiteList, taking into account the caseSensitive param.

    Attributes
    protected
    Definition Classes
    WhiteAndBlackListParams
  30. def explainParam(param: Param[_]): String
    Definition Classes
    Params
  31. def explainParams(): String
    Definition Classes
    Params
  32. def extraValidate(structType: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  33. def extraValidateMsg: String
    Attributes
    protected
    Definition Classes
    RawAnnotator
  34. final def extractParamMap(): ParamMap
    Definition Classes
    Params
  35. final def extractParamMap(extra: ParamMap): ParamMap
    Definition Classes
    Params
  36. val features: ArrayBuffer[Feature[_, _, _]]
    Definition Classes
    HasFeatures
  37. def filterByEntityField(annotation: Annotation): Boolean

    Filter annotation by blackList and whiteList, taking into account the caseSensitive param.

    Filter annotation by blackList and whiteList, taking into account the caseSensitive param. It filters by annotation.metadata.getOrElse("entity", annotation.metadata.getOrElse("identifier", "")).toString

    returns

    Boolean

    Attributes
    protected
    Definition Classes
    WhiteAndBlackListParams
  38. def filterByEntityField(annotations: Seq[Annotation]): Seq[Annotation]

    Filter annotations by blackList and whiteList, taking into account the caseSensitive param.

    Filter annotations by blackList and whiteList, taking into account the caseSensitive param. It filters by annotation.metadata.getOrElse("entity", annotation.metadata.getOrElse("identifier", "")).toString

    Attributes
    protected
    Definition Classes
    WhiteAndBlackListParams
  39. def filterByWhiteAndBlackList(annotation: Annotation): Boolean

    Filter annotation by blackList and whiteList, taking into account the caseSensitive param.

    Filter annotation by blackList and whiteList, taking into account the caseSensitive param. It filters by annotation.result

    returns

    Boolean

    Attributes
    protected
    Definition Classes
    WhiteAndBlackListParams
  40. def filterByWhiteAndBlackList(annotations: Seq[Annotation]): Seq[Annotation]

    Filter annotations by blackList and whiteList, taking into account the caseSensitive param.

    Filter annotations by blackList and whiteList, taking into account the caseSensitive param. It filters by annotation.result

    Attributes
    protected
    Definition Classes
    WhiteAndBlackListParams
  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. def getPrefix: String

    Gets the prefix to add to the result.

    Gets the prefix to add to the result. Default: "".

  55. def getSeparator: String

    Gets the separator to add between the results.

    Gets the separator to add between the results. Default: ",".

  56. def getSuffix: String

    Gets the suffix to add to the result.

    Gets the suffix to add to the result. Default: "".

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

    Input annotator type: CHUNK

    Input annotator type: CHUNK

    Definition Classes
    MultiChunk2Doc → HasInputAnnotationCols
  64. final val inputCols: StringArrayParam
    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  65. final def isDefined(param: Param[_]): Boolean
    Definition Classes
    Params
  66. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  67. final def isSet(param: Param[_]): Boolean
    Definition Classes
    Params
  68. def isTraceEnabled(): Boolean
    Attributes
    protected
    Definition Classes
    Logging
  69. val lazyAnnotator: BooleanParam
    Definition Classes
    CanBeLazy
  70. def log: Logger
    Attributes
    protected
    Definition Classes
    Logging
  71. def logDebug(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  72. def logDebug(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  73. def logError(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  74. def logError(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  75. def logInfo(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  76. def logInfo(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  77. def logName: String
    Attributes
    protected
    Definition Classes
    Logging
  78. def logTrace(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  79. def logTrace(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  80. def logWarning(msg: ⇒ String, throwable: Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  81. def logWarning(msg: ⇒ String): Unit
    Attributes
    protected
    Definition Classes
    Logging
  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
    Attributes
    protected
    Definition Classes
    ParamsAndFeaturesWritable
  87. val optionalInputAnnotatorTypes: Array[String]
    Definition Classes
    HasInputAnnotationCols
  88. val outputAnnotatorType: AnnotatorType

    Output annotator types: DOCUMENT

    Output annotator types: DOCUMENT

    Definition Classes
    MultiChunk2Doc → 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[MultiChunk2Doc]
    Definition Classes
    Model
  92. val prefix: Param[String]

    Prefix to add to the result.

    Prefix to add to the result. Default: "".

  93. def save(path: String): Unit
    Definition Classes
    MLWritable
    Annotations
    @Since( "1.6.0" ) @throws( ... )
  94. val separator: Param[String]

    Separator to add between the chunks.

    Separator to add between the chunks. Default: ",".

  95. def set[T](feature: StructFeature[T], value: T): MultiChunk2Doc.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  96. def set[K, V](feature: MapFeature[K, V], value: Map[K, V]): MultiChunk2Doc.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  97. def set[T](feature: SetFeature[T], value: Set[T]): MultiChunk2Doc.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  98. def set[T](feature: ArrayFeature[T], value: Array[T]): MultiChunk2Doc.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  99. final def set(paramPair: ParamPair[_]): MultiChunk2Doc.this.type
    Attributes
    protected
    Definition Classes
    Params
  100. final def set(param: String, value: Any): MultiChunk2Doc.this.type
    Attributes
    protected
    Definition Classes
    Params
  101. final def set[T](param: Param[T], value: T): MultiChunk2Doc.this.type
    Definition Classes
    Params
  102. def setAllowList(list: String*): MultiChunk2Doc.this.type
    Definition Classes
    WhiteAndBlackListParams
  103. def setAllowList(list: Array[String]): MultiChunk2Doc.this.type
    Definition Classes
    WhiteAndBlackListParams
  104. def setBlackList(list: String*): MultiChunk2Doc.this.type
    Definition Classes
    WhiteAndBlackListParams
  105. def setBlackList(list: Array[String]): MultiChunk2Doc.this.type

    If defined, list of entities to ignore.

    If defined, list of entities to ignore. The rest will be processed. Should not include IOB prefix on labels. Default: Array()

    Definition Classes
    WhiteAndBlackListParams
  106. def setCaseSensitive(value: Boolean): MultiChunk2Doc.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. Default: true

    Definition Classes
    WhiteAndBlackListParams
  107. def setDefault[T](feature: StructFeature[T], value: () ⇒ T): MultiChunk2Doc.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  108. def setDefault[K, V](feature: MapFeature[K, V], value: () ⇒ Map[K, V]): MultiChunk2Doc.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  109. def setDefault[T](feature: SetFeature[T], value: () ⇒ Set[T]): MultiChunk2Doc.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  110. def setDefault[T](feature: ArrayFeature[T], value: () ⇒ Array[T]): MultiChunk2Doc.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  111. final def setDefault(paramPairs: ParamPair[_]*): MultiChunk2Doc.this.type
    Attributes
    protected
    Definition Classes
    Params
  112. final def setDefault[T](param: Param[T], value: T): MultiChunk2Doc.this.type
    Attributes
    protected
    Definition Classes
    Params
  113. def setDenyList(list: String*): MultiChunk2Doc.this.type
    Definition Classes
    WhiteAndBlackListParams
  114. def setDenyList(list: Array[String]): MultiChunk2Doc.this.type
    Definition Classes
    WhiteAndBlackListParams
  115. final def setInputCols(value: String*): MultiChunk2Doc.this.type
    Definition Classes
    HasInputAnnotationCols
  116. def setInputCols(value: Array[String]): MultiChunk2Doc.this.type
    Definition Classes
    HasInputAnnotationCols
  117. def setLazyAnnotator(value: Boolean): MultiChunk2Doc.this.type
    Definition Classes
    CanBeLazy
  118. final def setOutputCol(value: String): MultiChunk2Doc.this.type
    Definition Classes
    HasOutputAnnotationCol
  119. def setParent(parent: Estimator[MultiChunk2Doc]): MultiChunk2Doc
    Definition Classes
    Model
  120. def setPrefix(value: String): MultiChunk2Doc.this.type

    Sets the prefix to add to the result.

    Sets the prefix to add to the result. Default: "".

  121. def setSeparator(value: String): MultiChunk2Doc.this.type

    Sets the separator to add between the results.

    Sets the separator to add between the results. Default: ",".

  122. def setSuffix(value: String): MultiChunk2Doc.this.type

    Sets the suffix to add to the result.

    Sets the suffix to add to the result. Default: "".

  123. def setWhiteList(list: String*): MultiChunk2Doc.this.type
    Definition Classes
    WhiteAndBlackListParams
  124. def setWhiteList(list: Array[String]): MultiChunk2Doc.this.type

    Sets the list of entities to process.

    Sets the list of entities to process. The rest will be ignored. Should not include IOB prefix on labels. Default: Array()

    Definition Classes
    WhiteAndBlackListParams
  125. val suffix: Param[String]

    Suffix to add to the result.

    Suffix to add to the result. Default: "".

  126. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  127. def toString(): String
    Definition Classes
    Identifiable → AnyRef → Any
  128. final def transform(dataset: Dataset[_]): DataFrame
    Definition Classes
    AnnotatorModel → Transformer
  129. def transform(dataset: Dataset[_], paramMap: ParamMap): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" )
  130. def transform(dataset: Dataset[_], firstParamPair: ParamPair[_], otherParamPairs: ParamPair[_]*): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" ) @varargs()
  131. final def transformSchema(schema: StructType): StructType
    Definition Classes
    RawAnnotator → PipelineStage
  132. def transformSchema(schema: StructType, logging: Boolean): StructType
    Attributes
    protected
    Definition Classes
    PipelineStage
    Annotations
    @DeveloperApi()
  133. val uid: String
    Definition Classes
    MultiChunk2Doc → Identifiable
  134. def validate(schema: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  135. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  136. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  137. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  138. val whiteList: StringArrayParam

    If defined, list of entities to process.

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

    Definition Classes
    WhiteAndBlackListParams
  139. def wrapColumnMetadata(col: Column): Column
    Attributes
    protected
    Definition Classes
    RawAnnotator
  140. def write: MLWriter
    Definition Classes
    ParamsAndFeaturesWritable → DefaultParamsWritable → MLWritable

Inherited from CheckLicense

Inherited from WhiteAndBlackListParams

Inherited from HasSimpleAnnotate[MultiChunk2Doc]

Inherited from AnnotatorModel[MultiChunk2Doc]

Inherited from CanBeLazy

Inherited from RawAnnotator[MultiChunk2Doc]

Inherited from HasOutputAnnotationCol

Inherited from HasInputAnnotationCols

Inherited from HasOutputAnnotatorType

Inherited from ParamsAndFeaturesWritable

Inherited from HasFeatures

Inherited from DefaultParamsWritable

Inherited from MLWritable

Inherited from Model[MultiChunk2Doc]

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