class IOBTagger extends AnnotatorModel[IOBTagger] with CheckLicense 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], CheckLicense, AnnotatorModel[IOBTagger], CanBeLazy, RawAnnotator[IOBTagger], HasOutputAnnotationCol, HasInputAnnotationCols, HasOutputAnnotatorType, ParamsAndFeaturesWritable, HasFeatures, DefaultParamsWritable, MLWritable, Model[IOBTagger], Transformer, PipelineStage, Logging, Params, Serializable, Serializable, Identifiable, AnyRef, Any
Ordering
  1. Grouped
  2. Alphabetic
  3. By Inheritance
Inherited
  1. IOBTagger
  2. HasSimpleAnnotate
  3. CheckLicense
  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
  1. Hide All
  2. Show All
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. 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[_]): IOBTagger.this.type
    Definition Classes
    Params
  19. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  20. def copy(extra: ParamMap): IOBTagger
    Definition Classes
    RawAnnotator → Model → Transformer → PipelineStage → Params
  21. def copyValues[T <: Params](to: T, extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  22. final def defaultCopy[T <: Params](extra: ParamMap): T
    Attributes
    protected
    Definition Classes
    Params
  23. def dfAnnotate: UserDefinedFunction
    Definition Classes
    HasSimpleAnnotate
  24. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  25. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  26. def explainParam(param: Param[_]): String
    Definition Classes
    Params
  27. def explainParams(): String
    Definition Classes
    Params
  28. def extraValidate(structType: StructType): Boolean
    Attributes
    protected
    Definition Classes
    RawAnnotator
  29. def extraValidateMsg: String
    Attributes
    protected
    Definition Classes
    RawAnnotator
  30. final def extractParamMap(): ParamMap
    Definition Classes
    Params
  31. final def extractParamMap(extra: ParamMap): ParamMap
    Definition Classes
    Params
  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. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  40. final def getDefault[T](param: Param[T]): Option[T]
    Definition Classes
    Params
  41. def getInputCols: Array[String]
    Definition Classes
    HasInputAnnotationCols
  42. def getLazyAnnotator: Boolean
    Definition Classes
    CanBeLazy
  43. final def getOrDefault[T](param: Param[T]): T
    Definition Classes
    Params
  44. final def getOutputCol: String
    Definition Classes
    HasOutputAnnotationCol
  45. def getParam(paramName: String): Param[Any]
    Definition Classes
    Params
  46. final def hasDefault[T](param: Param[T]): Boolean
    Definition Classes
    Params
  47. def hasParam(paramName: String): Boolean
    Definition Classes
    Params
  48. def hasParent: Boolean
    Definition Classes
    Model
  49. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  50. def initializeLogIfNecessary(isInterpreter: Boolean, silent: Boolean): Boolean
    Attributes
    protected
    Definition Classes
    Logging
  51. def initializeLogIfNecessary(isInterpreter: Boolean): Unit
    Attributes
    protected
    Definition Classes
    Logging
  52. val inputAnnotatorTypes: Array[AnnotatorType]

    Input annotator types: TOKEN, CHUNK

    Input annotator types: TOKEN, CHUNK

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

    Output annotator types: NAMED_ENTITY

    Output annotator types: NAMED_ENTITY

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

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

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

Inherited from HasSimpleAnnotate[IOBTagger]

Inherited from CheckLicense

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