Package

org.mitre.jcarafe

crf

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package crf

Visibility
  1. Public
  2. All

Type Members

  1. abstract class AbstractInstance extends SeqElement

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  2. abstract class AbstractValuedFeatureType extends FeatureCore with Serializable

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  3. abstract class AbstractViterbi extends DecodingAlgorithm with PotentialScoring with Serializable

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  4. trait AccessSeq[T] extends Serializable

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  5. class Alphabet[A] extends Serializable

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  6. class AlphabetWithSpecialCases[A] extends Alphabet[A]

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  7. class BasicDecoder extends StdDecoder

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  8. class BasicSeqDeserialization extends Deserialization

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  9. trait BasicSeqGen extends SeqGen[String] with FactoredSeqGen[String] with XmlConversions

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  10. class BloomFilter extends Serializable

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  11. class BloomFilterBuilder extends Serializable

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  12. class BloomLexicon extends Serializable

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  13. class BuiltFeature extends Serializable

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  14. class BuiltFeatureDebug extends BuiltFeature

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  15. class CompactFeature extends FeatureCore with Serializable

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  16. class CompiledCrfInstance extends AbstractInstance

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  17. trait CondLogLikelihoodLearner[T] extends DenseTrainable[T] with CrfLearner

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  18. class CoreModel extends Serializable

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  19. abstract class CoreModelSerializer extends AnyRef

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  20. abstract class Crf extends Trainable[AbstractInstance] with PotentialScoring with Serializable

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    Top abstract class representing the core elements and functionality of a sequence-structured Conditional Random Field.

    Top abstract class representing the core elements and functionality of a sequence-structured Conditional Random Field. A Crf object is created after feature extraction has occurred.

  21. class CrfInstance extends AbstractInstance

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  22. trait CrfLearner extends AnyRef

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  23. abstract class Decoder[Obs] extends AnyRef

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  24. class DecoderPipeline extends AnyRef

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  25. abstract class DecodingAlgorithm extends Serializable

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  26. class DecodingFactoredFeatureRep[Obs] extends FactoredFeatureRep[Obs]

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  27. class DecodingNonFactoredFeatureRep[Obs] extends NonFactoredFeatureRep[Obs]

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  28. abstract class DecodingSeqGen[Obs] extends SeqGen[Obs]

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  29. abstract class DenseCRFConfidences extends DenseCrf

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  30. abstract class DenseCrf extends Crf

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    A CRF that uses a dense (rather than sparse) internal representation

  31. class DenseCrfWorker extends DenseCrf with DenseWorker

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  32. abstract class DenseGeneralizedEMCrf extends DenseCrf with GeneralizedEMCrf

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  33. class DenseGeneralizedEMCrfWorker extends DenseGeneralizedEMCrf with DenseWorker

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  34. class DenseParallelCrf extends DenseCrf with ParCrf[DenseCrfWorker] with CondLogLikelihoodLearner[AbstractInstance]

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  35. class DenseParallelGeneralizedEMCrf extends DenseGeneralizedEMCrf with ParCrf[DenseGeneralizedEMCrfWorker] with CondLogLikelihoodLearner[AbstractInstance]

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  36. abstract class DenseSemiCrf extends DenseCrf with SemiCrf

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  37. class DenseStatelessCrf extends DenseCrf with Serializable

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  38. trait DenseTrainable[T] extends Trainable[T]

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  39. trait DenseWorker extends DenseCrf

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  40. abstract class Deserialization extends AnyRef

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  41. class DirectDecoder extends AnyRef

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  42. class DirectSeqDeserialization extends Deserialization

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  43. trait DirectSeqGen extends SeqGen[String] with FactoredSeqGen[String]

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  44. abstract class DirectTrainingSeqGen[Obs] extends SeqGen[Obs]

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  45. abstract class DiskAccessSeq extends AccessSeq[AbstractInstance]

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  46. abstract class DiskInstanceSequence extends InstanceSequence

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  47. class DynamicFeatureManagerBuilder[Obs] extends FeatureManagerBuilder[Obs] with RegexParsers

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  48. class DynamicRecodeFeatureManager[Obs] extends DynamicFeatureManagerBuilder[Obs]

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    This dynamic feature manager redefines window and ngram functions to operate over the original sequence of elements in the context where we've recoded the original sequence to a selected sub-sequence with re-mapped labels.

    This dynamic feature manager redefines window and ngram functions to operate over the original sequence of elements in the context where we've recoded the original sequence to a selected sub-sequence with re-mapped labels. Design note: This could be a trait also

  49. class FactoredCachedSourceSequence[T] extends InstanceSequence

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  50. abstract class FactoredDecoder[Obs] extends Decoder[Obs]

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  51. abstract class FactoredDecodingSeqGen[Obs] extends DecodingSeqGen[Obs]

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  52. abstract class FactoredFeatureRep[Obs] extends FeatureRep[Obs]

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  53. trait FactoredSeqGen[Obs] extends SeqGen[Obs]

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  54. abstract class FactoredTrainer[O] extends Trainer[O] with LinearCRFTraining[O]

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  55. class FastNonFactoredCrfInstance extends NonFactoredCrfInstance

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  56. class Feature extends FeatureCore with Serializable

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  57. abstract class FeatureCat extends AnyRef

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  58. abstract class FeatureCore extends AnyRef

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  59. abstract class FeatureFn[Obs] extends Serializable

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    A feature function which subclasses (Int,SourceSequence[Obs],Int) => FeatureReturn.

    A feature function which subclasses (Int,SourceSequence[Obs],Int) => FeatureReturn. Essentially, this defines a function that takes three arguments, returns a FeatureReturn and also has a string name. Named feature functions are useful for tracing feature application and provide a means to compare feature functions.

  60. class FeatureManager[Obs] extends Serializable

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  61. abstract class FeatureManagerBuilder[Obs] extends Serializable

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    A FeatureManager defines includes a set of common feature function definitions.

    A FeatureManager defines includes a set of common feature function definitions. It also holds a list of actual feature function objects that are applied to a sequence of observations. Sequence labeling applications will need to create a concrete subclass of FeatureManager that specifies exactly which feature functions will be applied. This class defines a simple DSL (Domain-Specific Language) that allows the set of feature functions for a particular application to be clearly specified.

    There are also higher-order feature functions that take other feature functions as arguments to easily and compactly specify more complicated feature extraction functionality. The FeatureManager is type-parameterized by Obs which represents the observation type and Info which denotes the type of the auxilliary information (if any) associated with each observation.

    An application-specific FeatureManager should subclass this class and specify, within the body of the class definition a set of feature functions, where each function is described as a single expression that returns an instance of FeatureReturn. Below is an example:

    object MyFeatureManager extends FeatureManager[String,Map[String,String] {
      "wdFn"      as wdFn
      "capRegFn"  as regexpFn("Capitalized", "[A-Z].*".r)
      "wdNgrm1"    as wdFn ngram (-2 to 0)
      "wdNgrm2"    as wdFn ngram (-1,0,1)
      "cross1"    as wdFn ngram (-1,0) cross (regexpFn("EndIn-ed",".*ed$".r) over (-2 to 2))
    }
    

    Each top-level function consists as a String followed by the keyword method name "as" which is then followed by a feature function. That feature function may be either 1) a simple feature function such as wdFn or 2) a complex feature function created by composing other feature functions. For example, the feature function named "wdNgrm1" creates an n-gram consisting of the concatenation of the features that result from applying the wdFn feature function at the positions -2,-1 and 0 relative to the current position. The "cross1" feature function is a more complicated instance that takes the ngram computed from the words at -1 and 0 and conjoins that feature with all the features that result from applying the regular expression function that returns the feature name "EndIn-ed" (when its pattern is matched) over the relative positions -2,-1,0,1,2.

  62. abstract class FeatureRep[Obs] extends Serializable

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  63. class FeatureReturn extends Serializable

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    A list of pairs of feature names along with their value that have fired based upon the application of a feature function FeatureFn.

    A list of pairs of feature names along with their value that have fired based upon the application of a feature function FeatureFn. Specifies whether the features are node or edge features.

  64. class FeatureType extends FeatureCore with Serializable

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  65. trait GeneralizedEMCrf extends Crf

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  66. abstract class GenericNonFactoredTrainer[O] extends Trainer[O]

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  67. class HashLexicon extends HashMap[String, List[Long]] with Lexicon

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  68. class InducedFeatureMap extends Serializable

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  69. abstract class InstanceSequence extends AnyRef

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  70. class JsonDecoder extends StdDecoder

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  71. class JsonSeqDeserialization extends Deserialization

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  72. trait JsonSeqGen extends SeqGen[String] with FactoredSeqGen[String]

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    Implements methods that facilitate generating sequences from standoff representations of of data and annotations using a simple JSON-based encoding.

    Implements methods that facilitate generating sequences from standoff representations of of data and annotations using a simple JSON-based encoding. This trait is to be mixed into appropriate subclasses of SeqGen such as subclasses specialized for training or decoding.

  73. abstract class KLDivMinimizingCrf extends DenseCrf

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  74. abstract class KLDivMinimizingStochasticCrf extends StochasticCrf

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  75. trait Lexicon extends AnyRef

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  76. trait LinearCRFTraining[Obs] extends Trainer[Obs] with SeqXValidator

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  77. class LongAlphabet extends Serializable

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  78. class MaxEntModel extends Model

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  79. class MemoryAccessSeq extends AccessSeq[AbstractInstance]

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  80. class MemoryInstanceSequence extends InstanceSequence

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  81. abstract class Model extends AnyRef

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  82. case class ModelAuxiliaries(lex: Option[BloomLexicon], wdProps: Option[WordProperties], wdScores: Option[WordScores], inducedFs: Option[InducedFeatureMap]) extends Product with Serializable

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  83. case class ModelMetaData(ver: String, date: String, user: String) extends Product with Serializable

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  84. class NBinFeature extends Feature

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  85. abstract class NeuralDenseCrf extends DenseCrf with NeuralStochasticCrfScoring

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  86. class NeuralDenseCrfWorker extends NeuralDenseCrf with DenseWorker

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  87. class NeuralDenseParallelCrf extends NeuralDenseCrf with ParCrf[NeuralDenseCrfWorker] with CondLogLikelihoodLearner[AbstractInstance]

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  88. abstract class NeuralStochasticCrf extends StochasticCrf with NeuralStochasticCrfScoring

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    Extensions of "linear" CRFs that provide for (some) features to feed into a set of N hidden neurons.

    Extensions of "linear" CRFs that provide for (some) features to feed into a set of N hidden neurons. How this will work: Only some of the input features will be fed into the gates. Each FeatureType will keep track of whether that feature type goes through gates. After feature extraction has been completed and when the Neural CRF is being started up, extra parameters are added. Specifically M extra parameters where M = numGates * numNeuralFeatures. This will simply be added so that the parameter associated with feature i going into gate g is indexed at position nfs * (g+1) + i where 'nfs' is the number of input features and g is zero indexed.

  89. trait NeuralStochasticCrfScoring extends PotentialScoring

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  90. class NeuralViterbi extends Viterbi with NeuralStochasticCrfScoring

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  91. class NonFactoredCachedSourceSequence[T] extends InstanceSequence

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  92. class NonFactoredCrfInstance extends AbstractInstance

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  93. abstract class NonFactoredDecoder[Obs] extends Decoder[Obs]

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  94. abstract class NonFactoredDecodingSeqGen[Obs] extends DecodingSeqGen[Obs]

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  95. abstract class NonFactoredFeatureManager[Obs] extends AnyRef

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  96. class NonFactoredFeatureRep[Obs] extends FeatureRep[Obs]

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  97. class NonFactoredModel extends Model

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  98. class NonFactoredPreFeature extends AnyRef

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  99. abstract class NonFactoredTrainer[O] extends GenericNonFactoredTrainer[O] with LinearCRFTraining[O]

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  100. abstract class NonFactoredTrainingSeqGen[Obs] extends SeqGen[Obs]

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  101. class ObsSource[Obs] extends SeqElement

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  102. trait ParCrf[T <: DenseCrf] extends DenseCrf

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  103. trait ParallelStochastic[T <: StochasticCrf] extends StochasticCrf

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  104. trait PotentialScoring extends AnyRef

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  105. case class PreFeature(prv: Int, cur: Int, name: Long) extends Product with Serializable

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  106. trait PsaLearner[T] extends SparseTrainable[T] with CrfLearner

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  107. trait PsaLearnerWithL1[T] extends SparseTrainable[T] with CrfLearner

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  108. class RandomLongAlphabet extends LongAlphabet

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  109. class RandomNonFactoredModel extends NonFactoredModel

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  110. class RandomStdModel extends StdModel

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  111. class RecodedObsSource[Obs] extends ObsSource[Obs]

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  112. case class SectionUpdate(lambdas: Array[Double], etas: Array[Double]) extends Product with Serializable

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  113. class SelfInducibleCrfInstance extends CrfInstance

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  114. class SelfInducibleDecodingFactoredFeatureRep[Obs] extends DecodingFactoredFeatureRep[Obs]

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  115. trait SemiCrf extends Crf

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  116. class SemiRandomFsetMapping extends AnyRef

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  117. class SemiRandomFsetMappingOptimized extends AnyRef

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  118. abstract class SeqElement extends AnyRef

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  119. abstract class SeqGen[Obs] extends Serializable

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    Encapsulates functionality for creating labeled sequences.

    Encapsulates functionality for creating labeled sequences. This includes extracting features over elements in a sequence.

  120. trait SeqGenScorer[Obs] extends SeqGen[Obs]

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  121. trait SeqXValidator extends AnyRef

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  122. trait SequenceTrainable extends Trainable[AbstractInstance]

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  123. trait SgdLearner[T] extends SparseTrainable[T] with CrfLearner

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  124. trait SgdLearnerWithL1[T] extends SparseTrainable[T] with CrfLearner

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  125. class SourceSequence[Obs] extends AnyRef

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  126. class SparseStatelessCrf extends StochasticCrf with Serializable

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  127. class SparseStatelessKLDivMinimizingCrf extends KLDivMinimizingStochasticCrf with Serializable

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  128. trait SparseTrainable[T] extends Trainable[T] with Serializable

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  129. class StatelessViterbi extends AbstractViterbi with Serializable

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  130. class StaticFeatureManagerBuilder[Obs] extends FeatureManagerBuilder[Obs]

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  131. abstract class StdDecoder extends FactoredDecoder[String]

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  132. class StdModel extends Model

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  133. abstract class StdTrainer extends FactoredTrainer[String]

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  134. abstract class StochasticCrf extends Crf with SparseTrainable[AbstractInstance] with Serializable

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    A Crf that uses a sparse internal representation suitable for Stochastic Gradient Descent learning methods.

  135. abstract class StochasticGeneralizedEMCrf extends StochasticCrf with GeneralizedEMCrf

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  136. abstract class StochasticSemiCrf extends StochasticCrf with SemiCrf

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  137. class TextDecoder extends StdDecoder

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  138. class TextSeqDeserialization extends Deserialization

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  139. trait TextSeqGen extends SeqGen[String] with FactoredSeqGen[String] with XmlConversions

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    Deserialization functionality for handling text input.

    Deserialization functionality for handling text input. This uses a customized lexer to identify tokens within a body of text, identifies sentence/zone boundaries and produce annotations as inline tags. It does not use an XML parser, however, and will therefore produce and consume files that do not conform to XML.

  140. trait Trainable[T] extends Serializable

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  141. abstract class Trainer[Obs] extends AnyRef

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  142. class TrainingFactoredFeatureRep[Obs] extends FactoredFeatureRep[Obs] with Serializable

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  143. abstract class TrainingSeqGen[Obs] extends SeqGen[Obs]

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  144. class ValuedFeatureType extends AbstractValuedFeatureType

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  145. class ValuedRandomFeatureType extends AbstractValuedFeatureType

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  146. class Viterbi extends AbstractViterbi with PotentialScoring

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  147. class WordProperties extends Serializable

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  148. class WordScores extends HashMap[Long, Double] with Serializable

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  149. trait XmlConversions extends AnyRef

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  150. class XmlSeqDeserialization extends Deserialization

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  151. trait XmlSeqGen extends SeqGen[String] with FactoredSeqGen[String] with XmlConversions

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    Implements methods that facilitate generating sequences from inline XML representations of data and annotations.

    Implements methods that facilitate generating sequences from inline XML representations of data and annotations. This trait is to be mixed into appropirate subclasses of SeqGen such as subclasses specialized for training or decoding.

Value Members

  1. object BloomFilter extends Serializable

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  2. object BuiltFeature extends Serializable

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  3. object CompiledCrfInstance

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  4. object Crf extends Serializable

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    A creation of Crf.

  5. object CrfInstance

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  6. object Decoder

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  7. object DecoderPipeline

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  8. object DirectDecoder

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  9. object DirectSeqDeserialization

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  10. object FeatureFn extends Serializable

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  11. object FeatureHashMixer

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  12. object FeatureManagerBuilder extends Serializable

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  13. object FeatureReturn extends Serializable

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  14. object IncrementalMurmurHash extends Serializable

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  15. object InducedFeatureMap extends Serializable

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  16. object InducedFeatureMapProtocol

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  17. object InstSeq

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  18. object InstanceSerializations

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  19. object MaxEntSerializer extends CoreModelSerializer

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  20. object Model

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  21. object MultiFeature extends FeatureCat with Product with Serializable

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  22. object NNFeature extends FeatureCat with Product with Serializable

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  23. object NeuralCrf

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    Object used to initialize a Neural CRF.

    Object used to initialize a Neural CRF. Extra parameters and book-keeping needs to be set up.

  24. object NonFactoredSerializer extends CoreModelSerializer

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  25. object StandardSerializer extends CoreModelSerializer

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  26. object StdFeature extends FeatureCat with Product with Serializable

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  27. object TagParser extends RegexParsers

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  28. object Viterbi extends Serializable

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  29. object WordProperties extends Serializable

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Ungrouped