Package edu.cmu.tetrad.search

Class Cpc

java.lang.Object
edu.cmu.tetrad.search.Cpc
All Implemented Interfaces:
IGraphSearch
public final class Cpc extends Object implements IGraphSearch

Implements a convervative version of PC, in which the Markov condition is assumed but faithfulness is tested locally. The reference is here:

Ramsey, J., Zhang, J., & Spirtes, P. L. (2012). Adjacency-faithfulness and conservative causal inference. arXiv preprint arXiv:1206.6843.

Conservative triple orientation is a method for orienting unshielded triples X*-*Y*-*Z as one of the following: (a) Collider, X->Y<-Z, (b) Noncollider, X-->Y-->Z, or X<-Y<-Z, or X<-Y->Z, (c) ambiguous between (a) or (b). One does this by conditioning on subsets of adj(X) or adj(Z). One first checks conditional independence of X and Z conditional on each of these subsets, then lists all of these subsets conditional on which X and Z are *independent*, then looks thoough this list to see if Y is in them. If Y is in all of these subset, the triple is judged to be a noncollider; if it is in none of these subsets, the triple is judged to be a collider, and if it is in some of these subsets and not in others of the subsets, then it is judged to be ambiguous.

Ambiguous triple are marked in the final graph using an underline, and the final graph is called an "e-pattern", and represents a collection of CPDAGs. To find an element of this collection, one first needs to choose for each ambiguous triple whether it should be a collider or a noncollider and then run the Meek rules given the result of these decisions.

See setter methods for "knobs" you can turn to control the output of PC and their defaults.

*

This class is configured to respect knowledge of forbidden and required edges, including knowledge of temporal tiers.

Author:
josephramsey (this version).
See Also:

  • Constructor Summary

    Constructors
    Constructor
    Description
    Cpc(IndependenceTest independenceTest)
    Constructs a CPC algorithm that uses the given independence test as oracle.

  • Method Summary

    Modifier and Type
    Method
    Description
    Set<Edge>
    getAdjacencies()
    Returns the edges in the search graph as a set of undirected edges.
    Set<Triple>
    getAmbiguousTriples()
    Returns the set of ambiguous triples found during the most recent run of the algorithm.
    int
    getDepth()
    Returns the depth of the search--that is, the maximum number of variables conditioned on in any conditional independence test.
    long
    getElapsedTime()
    Returns the elapsed time of search in milliseconds, after search() has been run.
    Graph
    getGraph()
    The graph that's constructed during the search.
    IndependenceTest
    getIndependenceTest()
    Rreturn the independence test used in the search, set in the constructor.
    Knowledge
    getKnowledge()
    Returns the knowledge specification used in the search.
    SepsetMap
    getSepsets()
    Returns a map for x _||_ y | z1,..,zn from {x, y} to {z1,...,zn}.
    void
    meekPreventCycles(boolean meekPreventCycles)
    Sets to true just in case edges will not be added if they would create cycles.
    Graph
    search()
    Runs CPC starting with a fully connected graph over all the variables in the domain of the independence test.
    void
    setConflictRule(PcCommon.ConflictRule conflictRule)
    Sets which conflict rule to use for resolving collider orientation conflicts.
    void
    setDepth(int depth)
    Sets the maximum number of variables conditioned on in any conditional independence test.
    void
    setKnowledge(Knowledge knowledge)
    Sets the knowledge specification used in the search.
    void
    setPcHeuristicType(PcCommon.PcHeuristicType pcHeuristicType)
    Sets the PC heuristic type.
    void
    setStable(boolean stable)
    Sets whether the stable adjacency search should be used.
    void
    setVerbose(boolean verbose)
    Sets whether verbose output should be printed.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • Cpc

      public Cpc(IndependenceTest independenceTest)
      Constructs a CPC algorithm that uses the given independence test as oracle. This does not make a copy of the independence test, for fear of duplicating the data set!
      Parameters:
      independenceTest - The test to user for oracle conditional independence information.

  • Method Details

    • search

      public Graph search()
      Runs CPC starting with a fully connected graph over all the variables in the domain of the independence test. See PC for caveats. The number of possible cycles and bidirected edges is far less with CPC than with PC.
      Specified by:
      search in interface IGraphSearch
      Returns:
      The e-pattern for the search, which is a graphical representation of a set of possible CPDAGs.

    • meekPreventCycles

      public void meekPreventCycles(boolean meekPreventCycles)
      Sets to true just in case edges will not be added if they would create cycles.
      Parameters:
      meekPreventCycles - True, if so.

    • getElapsedTime

      public long getElapsedTime()
      Returns the elapsed time of search in milliseconds, after search() has been run.
      Returns:
      This time.

    • getKnowledge

      public Knowledge getKnowledge()
      Returns the knowledge specification used in the search. Non-null.
      Returns:
      this knowledge.

    • setKnowledge

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

    • getIndependenceTest

      public IndependenceTest getIndependenceTest()
      Rreturn the independence test used in the search, set in the constructor.
      Returns:
      This.

    • getDepth

      public int getDepth()
      Returns the depth of the search--that is, the maximum number of variables conditioned on in any conditional independence test.
      Returns:
      This.

    • setDepth

      public void setDepth(int depth)
      Sets the maximum number of variables conditioned on in any conditional independence test. If set to -1, the value of 1000 will be used. May not be set to Integer.MAX_VALUE, due to a Java bug on multicore systems.
      Parameters:
      depth - This maximum.

    • getAmbiguousTriples

      public Set<Triple> getAmbiguousTriples()
      Returns the set of ambiguous triples found during the most recent run of the algorithm. Non-null after a call to search().
      Returns:
      This set.

    • getAdjacencies

      public Set<Edge> getAdjacencies()
      Returns the edges in the search graph as a set of undirected edges.
      Returns:
      These edges.

    • getSepsets

      public SepsetMap getSepsets()
      Returns a map for x _||_ y | z1,..,zn from {x, y} to {z1,...,zn}.
      Returns:
      This map.

    • getGraph

      public Graph getGraph()
      The graph that's constructed during the search.
      Returns:
      This graph.

    • setVerbose

      public void setVerbose(boolean verbose)
      Sets whether verbose output should be printed.
      Parameters:
      verbose - True, if so.

    • setStable

      public void setStable(boolean stable)

      Sets whether the stable adjacency search should be used. Default is false. Default is false. See the following reference for this:

      Colombo, D., & Maathuis, M. H. (2014). Order-independent constraint-based causal structure learning. J. Mach. Learn. Res., 15(1), 3741-3782.

      Parameters:
      stable - True iff the case.

    • setConflictRule

      public void setConflictRule(PcCommon.ConflictRule conflictRule)
      Sets which conflict rule to use for resolving collider orientation conflicts.
      Parameters:
      conflictRule - The rule.
      See Also:

    • setPcHeuristicType

      public void setPcHeuristicType(PcCommon.PcHeuristicType pcHeuristicType)
      Sets the PC heuristic type. Default = NONE.
      Parameters:
      pcHeuristicType - The type.
      See Also: