Package edu.cmu.tetrad.search

Class LvLite

java.lang.Object
edu.cmu.tetrad.search.LvLite
All Implemented Interfaces:
IGraphSearch
public final class LvLite extends Object implements IGraphSearch
The LV-Lite algorithm implements a search algorithm for learning the structure of a graphical model from observational data with latent variables. The algorithm uses the BOSS or GRaSP algorithm to get an initial CPDAG. Then it uses scoring steps to infer some unshielded colliders in the graph, then finishes with a testing step to remove extra edges and orient more unshielded colliders. Finally, the final FCI orientation is applied to the graph.
Author:
josephramsey

  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Class
    Description
    static enum 
    LvLite.ExtraEdgeRemovalStyle
    The ExtraEdgeRemovalStyle enum specifies the styles for removing extra edges.
    static enum 
    LvLite.START_WITH
    Enumeration representing different start options.

  • Constructor Summary

    Constructors
    Constructor
    Description
    LvLite(IndependenceTest test, Score score)
    LV-Lite constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    Graph
    search()
    Run the search and return s a PAG.
    void
    setAblationLeaveOutScoringStep(boolean ablationLeaveOutScoringStep)
    Sets whether the scoring step (BOSS or GRASP) should be left out during ablation.
    void
    setAblationLeaveOutTestingStep(boolean ablationLeaveOutTestingStep)
    Sets whether to the testing steps (extra edge removal and discriminating path steps) should be left out during ablation.
    void
    setCompleteRuleSetUsed(boolean completeRuleSetUsed)
    Sets whether the complete rule set should be used during the search algorithm.
    void
    setDepth(int depth)
    Sets the maximum size of the separating set used in the graph search algorithm.
    void
    setDoDiscriminatingPathColliderRule(boolean doDiscriminatingPathColliderRule)
    Sets whether the discriminating path collider rule should be used.
    void
    setDoDiscriminatingPathTailRule(boolean doDiscriminatingPathTailRule)
    Sets whether the discriminating path tail rule should be used.
    void
    setExtraEdgeRemovalStyle(LvLite.ExtraEdgeRemovalStyle extraEdgeRemovalStyle)
    Sets the style for removing extra edges.
    void
    setGuaranteePag(boolean guaranteePag)
    Sets whether to guarantee a PAG output by repairing a faulty PAG.
    void
    setKnowledge(Knowledge knowledge)
    Sets the knowledge used in search.
    void
    setMaxBlockingPathLength(int maxBlockingPathLength)
    Sets the maximum length of any discriminating path.
    void
    setMaxDdpPathLength(int maxDdpPathLength)
    Sets the maximum DDP path length.
    void
    setNumStarts(int numStarts)
    Sets the number of starts for BOSS.
    void
    setRecursionDepth(int recursionDepth)
    Sets the depth of the GRaSP if it is used.
    void
    setStartWith(LvLite.START_WITH startWith)
    Sets the algorithm to use to obtain the initial CPDAG.
    void
    setTestTimeout(long testTimeout)
    Sets the timeout for the testing steps, for the extra edge removal steps and the discriminating path steps.
    void
    setUseBes(boolean useBes)
    Sets whether to use the BES (Backward Elimination Search) algorithm during the search.
    void
    setUseDataOrder(boolean useDataOrder)
    Sets the flag indicating whether to use data order.
    void
    setVerbose(boolean verbose)
    Sets the verbosity level of the search algorithm.

    Methods inherited from class java.lang.Object

    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • LvLite

      public LvLite(IndependenceTest test, Score score)
      LV-Lite constructor. Initializes a new object of LvLite search algorithm with the given IndependenceTest and Score object.
      Parameters:
      test - The IndependenceTest object to be used for testing independence between variables.
      score - The Score object to be used for scoring DAGs.
      Throws:
      NullPointerException - if the score is null.

  • Method Details

    • search

      public Graph search()
      Run the search and return s a PAG.
      Specified by:
      search in interface IGraphSearch
      Returns:
      The PAG.

    • setMaxBlockingPathLength

      public void setMaxBlockingPathLength(int maxBlockingPathLength)
      Sets the maximum length of any discriminating path.
      Parameters:
      maxBlockingPathLength - the maximum length of any discriminating path, or -1 if unlimited.

    • setRecursionDepth

      public void setRecursionDepth(int recursionDepth)
      Sets the depth of the GRaSP if it is used.
      Parameters:
      recursionDepth - The depth of the GRaSP.

    • setGuaranteePag

      public void setGuaranteePag(boolean guaranteePag)
      Sets whether to guarantee a PAG output by repairing a faulty PAG.
      Parameters:
      guaranteePag - true if a faulty PAGs should be repaired, false otherwise

    • setStartWith

      public void setStartWith(LvLite.START_WITH startWith)
      Sets the algorithm to use to obtain the initial CPDAG.
      Parameters:
      startWith - the algorithm to use to obtain the initial CPDAG.

    • setKnowledge

      public void setKnowledge(Knowledge knowledge)
      Sets the knowledge used in search.
      Parameters:
      knowledge - This knowledge.

    • setCompleteRuleSetUsed

      public void setCompleteRuleSetUsed(boolean completeRuleSetUsed)
      Sets whether the complete rule set should be used during the search algorithm. By default, the complete rule set is not used.
      Parameters:
      completeRuleSetUsed - true if the complete rule set should be used, false otherwise

    • setVerbose

      public void setVerbose(boolean verbose)
      Sets the verbosity level of the search algorithm.
      Parameters:
      verbose - true to enable verbose mode, false to disable it

    • setNumStarts

      public void setNumStarts(int numStarts)
      Sets the number of starts for BOSS.
      Parameters:
      numStarts - The number of starts.

    • setDoDiscriminatingPathTailRule

      public void setDoDiscriminatingPathTailRule(boolean doDiscriminatingPathTailRule)
      Sets whether the discriminating path tail rule should be used.
      Parameters:
      doDiscriminatingPathTailRule - True, if so.

    • setDoDiscriminatingPathColliderRule

      public void setDoDiscriminatingPathColliderRule(boolean doDiscriminatingPathColliderRule)
      Sets whether the discriminating path collider rule should be used.
      Parameters:
      doDiscriminatingPathColliderRule - True, if so.

    • setUseBes

      public void setUseBes(boolean useBes)
      Sets whether to use the BES (Backward Elimination Search) algorithm during the search.
      Parameters:
      useBes - true to use the BES algorithm, false otherwise

    • setUseDataOrder

      public void setUseDataOrder(boolean useDataOrder)
      Sets the flag indicating whether to use data order.
      Parameters:
      useDataOrder - true if the data order should be used, false otherwise.

    • setDepth

      public void setDepth(int depth)
      Sets the maximum size of the separating set used in the graph search algorithm.
      Parameters:
      depth - the maximum size of the separating set

    • setAblationLeaveOutScoringStep

      public void setAblationLeaveOutScoringStep(boolean ablationLeaveOutScoringStep)
      Sets whether the scoring step (BOSS or GRASP) should be left out during ablation. If this step is left out, the algorithm will start with a completely connected nondirected (o-o) graph, since the subsequent steps require an initial graph that is Markov. This will make the algorithm slow.

      One cannot leave out both the testing and scoring steps of the algorithm; one or the other must be enabled.

      Parameters:
      ablationLeaveOutScoringStep - True iff the scoring step should be left out.

    • setAblationLeaveOutTestingStep

      public void setAblationLeaveOutTestingStep(boolean ablationLeaveOutTestingStep)
      Sets whether to the testing steps (extra edge removal and discriminating path steps) should be left out during ablation. If these stepw are left out, the algorithm will not remove extra edges or do discriminating path steps.

      One cannot leave out both the testing and scoring steps of the algorithm; one or the other must be enabled.

      Parameters:
      ablationLeaveOutTestingStep - the flag indicating whether to enable the ablation leave-out testing step.

    • setMaxDdpPathLength

      public void setMaxDdpPathLength(int maxDdpPathLength)
      Sets the maximum DDP path length.
      Parameters:
      maxDdpPathLength - the maximum DDP path length to set

    • setExtraEdgeRemovalStyle

      public void setExtraEdgeRemovalStyle(LvLite.ExtraEdgeRemovalStyle extraEdgeRemovalStyle)
      Sets the style for removing extra edges.
      Parameters:
      extraEdgeRemovalStyle - the style for removing extra edges

    • setTestTimeout

      public void setTestTimeout(long testTimeout)
      Sets the timeout for the testing steps, for the extra edge removal steps and the discriminating path steps.
      Parameters:
      testTimeout - the timeout for the testing steps, for the extra edge removal steps and the discriminating path steps.