class IOBTagger extends AnnotatorModel[IOBTagger] with Licensed with HasSimpleAnnotate[IOBTagger]

Merges token tags and NER labels from chunks in the specified format. For example output columns as inputs from NerConverter and Tokenizer can be used to merge.

Example

Pipeline stages are defined where NER is done. NER is converted to chunks.

val data = Seq(("A 63-year-old man presents to the hospital ...")).toDF("text")
val docAssembler = new DocumentAssembler().setInputCol("text").setOutputCol("document")
val sentenceDetector = new SentenceDetector().setInputCols("document").setOutputCol("sentence")
val tokenizer = new Tokenizer().setInputCols("sentence").setOutputCol("token")
val embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models").setOutputCol("embs")
val nerModel = MedicalNerModel.pretrained("ner_jsl", "en", "clinical/models").setInputCols("sentence", "token", "embs").setOutputCol("ner")
val nerConverter = new NerConverter().setInputCols("sentence", "token", "ner").setOutputCol("ner_chunk")

Define the IOB tagger, which needs tokens and chunks as input. Show results.

val iobTagger = new IOBTagger().setInputCols("token", "ner_chunk").setOutputCol("ner_label")
val pipeline = new Pipeline().setStages(Array(docAssembler, sentenceDetector, tokenizer, embeddings, nerModel, nerConverter, iobTagger))

result.selectExpr("explode(ner_label) as a")
  .selectExpr("a.begin","a.end","a.result as chunk","a.metadata.word as word")
  .where("chunk!='O'").show(5, false)

+-----+---+-----------+-----------+
|begin|end|chunk      |word       |
+-----+---+-----------+-----------+
|5    |15 |B-Age      |63-year-old|
|17   |19 |B-Gender   |man        |
|64   |72 |B-Modifier |recurrent  |
|98   |107|B-Diagnosis|cellulitis |
|110  |119|B-Diagnosis|pneumonias |
+-----+---+-----------+-----------+
See also

Tokenizer

MedicalNerModel

NerConverter

Linear Supertypes
HasSimpleAnnotate[IOBTagger], Licensed, AnnotatorModel[IOBTagger], CanBeLazy, RawAnnotator[IOBTagger], HasOutputAnnotationCol, HasInputAnnotationCols, HasOutputAnnotatorType, ParamsAndFeaturesWritable, HasFeatures, DefaultParamsWritable, MLWritable, Model[IOBTagger], Transformer, PipelineStage, Logging, Params, Serializable, Serializable, Identifiable, AnyRef, Any
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Inherited
  1. IOBTagger
  2. HasSimpleAnnotate
  3. Licensed
  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 IOBTagger()
  2. new IOBTagger(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 extracted NER (chunks) and tags from tokens to merge

    Takes extracted NER (chunks) and tags from tokens to merge

    annotations

    a Sequence of chunks and tokens

    returns

    Tagged NER labels

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

    Input annotator types: TOKEN, CHUNK

    Input annotator types: TOKEN, CHUNK

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

    Output annotator types: NAMED_ENTITY

    Output annotator types: NAMED_ENTITY

    Definition Classes
    IOBTagger → HasOutputAnnotatorType
  74. final val outputCol: Param[String]
    Attributes
    protected
    Definition Classes
    HasOutputAnnotationCol
  75. lazy val params: Array[Param[_]]
    Definition Classes
    Params
  76. var parent: Estimator[IOBTagger]
    Definition Classes
    Model
  77. def save(path: String): Unit
    Definition Classes
    MLWritable
    Annotations
    @Since( "1.6.0" ) @throws( ... )
  78. val scheme: Param[String]

    Format of tags, either IOB or BIOES (Default: "IOB")

  79. def set[T](feature: StructFeature[T], value: T): IOBTagger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  80. def set[K, V](feature: MapFeature[K, V], value: Map[K, V]): IOBTagger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  81. def set[T](feature: SetFeature[T], value: Set[T]): IOBTagger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  82. def set[T](feature: ArrayFeature[T], value: Array[T]): IOBTagger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  83. final def set(paramPair: ParamPair[_]): IOBTagger.this.type
    Attributes
    protected
    Definition Classes
    Params
  84. final def set(param: String, value: Any): IOBTagger.this.type
    Attributes
    protected
    Definition Classes
    Params
  85. final def set[T](param: Param[T], value: T): IOBTagger.this.type
    Definition Classes
    Params
  86. def setDefault[T](feature: StructFeature[T], value: () ⇒ T): IOBTagger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  87. def setDefault[K, V](feature: MapFeature[K, V], value: () ⇒ Map[K, V]): IOBTagger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  88. def setDefault[T](feature: SetFeature[T], value: () ⇒ Set[T]): IOBTagger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  89. def setDefault[T](feature: ArrayFeature[T], value: () ⇒ Array[T]): IOBTagger.this.type
    Attributes
    protected
    Definition Classes
    HasFeatures
  90. final def setDefault(paramPairs: ParamPair[_]*): IOBTagger.this.type
    Attributes
    protected
    Definition Classes
    Params
  91. final def setDefault[T](param: Param[T], value: T): IOBTagger.this.type
    Attributes
    protected
    Definition Classes
    Params
  92. final def setInputCols(value: String*): IOBTagger.this.type
    Definition Classes
    HasInputAnnotationCols
  93. final def setInputCols(value: Array[String]): IOBTagger.this.type
    Definition Classes
    HasInputAnnotationCols
  94. def setLazyAnnotator(value: Boolean): IOBTagger.this.type
    Definition Classes
    CanBeLazy
  95. final def setOutputCol(value: String): IOBTagger.this.type
    Definition Classes
    HasOutputAnnotationCol
  96. def setParent(parent: Estimator[IOBTagger]): IOBTagger
    Definition Classes
    Model
  97. def setScheme(f: String): IOBTagger.this.type
  98. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  99. def toString(): String
    Definition Classes
    Identifiable → AnyRef → Any
  100. final def transform(dataset: Dataset[_]): DataFrame
    Definition Classes
    AnnotatorModel → Transformer
  101. def transform(dataset: Dataset[_], paramMap: ParamMap): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" )
  102. def transform(dataset: Dataset[_], firstParamPair: ParamPair[_], otherParamPairs: ParamPair[_]*): DataFrame
    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" ) @varargs()
  103. final def transformSchema(schema: StructType): StructType
    Definition Classes
    RawAnnotator → PipelineStage
  104. def transformSchema(schema: StructType, logging: Boolean): StructType
    Attributes
    protected
    Definition Classes
    PipelineStage
    Annotations
    @DeveloperApi()
  105. val uid: String
    Definition Classes
    IOBTagger → Identifiable
  106. def validate(schema: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  107. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  108. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  109. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  110. def wrapColumnMetadata(col: Column): Column
    Attributes
    protected
    Definition Classes
    RawAnnotator
  111. def write: MLWriter
    Definition Classes
    ParamsAndFeaturesWritable → DefaultParamsWritable → MLWritable

Inherited from HasSimpleAnnotate[IOBTagger]

Inherited from Licensed

Inherited from AnnotatorModel[IOBTagger]

Inherited from CanBeLazy

Inherited from RawAnnotator[IOBTagger]

Inherited from HasOutputAnnotationCol

Inherited from HasInputAnnotationCols

Inherited from HasOutputAnnotatorType

Inherited from ParamsAndFeaturesWritable

Inherited from HasFeatures

Inherited from DefaultParamsWritable

Inherited from MLWritable

Inherited from Model[IOBTagger]

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