Package edu.cmu.tetrad.search

Class FciMax

java.lang.Object
edu.cmu.tetrad.search.FciMax
All Implemented Interfaces:
IGraphSearch
@Deprecated(since="7.9", forRemoval=false) public final class FciMax extends Object implements IGraphSearch
Deprecated.
Modifies FCI to do orientation of unshielded colliders (X*-*Y*-*Z with X and Z not adjacent) using the max-P rule (see the PC-Max algorithm). This reference is relevant:

Raghu, V. K., Zhao, W., Pu, J., Leader, J. K., Wang, R., Herman, J., ... & Wilson, D. O. (2019). Feasibility of lung cancer prediction from low-dose CT scan and smoking factors using causal models. Thorax, 74(7), 643-649.

Max-P triple orientation is a method for orienting unshielded triples X*=-*Y*-*Z as one of the following: (a) Collider, X->Y<-Z, or (b) Noncollider, X-->Y-->Z, or X<-Y<-Z, or X<-Y->Z. 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, and lists the p-values for each test. Then, one chooses the conditioning set out of all of these that maximizes the p-value. If this conditioning set contains Y, then the triple is judged to be a noncollider; otherwise, it is judged to be a collider.

All unshielded triples in the graph given by FAS are judged as colliders or non-colliders and the colliders oriented. Then the final FCI orientation rules are applied, as in FCI.

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

Version:
$Id: $Id
Author:
josephramsey
See Also:

  • Constructor Summary

    Constructors
    Constructor
    Description
    FciMax(IndependenceTest independenceTest)
    Deprecated.
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    long
    getElapsedTime()
    Deprecated.
    Returns the elapsed time of search.
    IndependenceTest
    getIndependenceTest()
    Deprecated.
    Returns the independence test used in search.
    Knowledge
    getKnowledge()
    Deprecated.
    Retrieves the background knowledge that was set.
    SepsetMap
    getSepsets()
    Deprecated.
    Retrieves the map from variable pairs to sepsets from the FAS search.
    Graph
    search()
    Deprecated.
    Performs the search and returns the PAG.
    void
    setCompleteRuleSetUsed(boolean completeRuleSetUsed)
    Deprecated.
    Sets whether Zhang's complete rule set is used in the search.
    void
    setDepth(int depth)
    Deprecated.
    Sets the maximum nubmer of variables conditioned in any test.
    void
    setGuaranteePag(boolean guaranteePag)
    Deprecated.
    Sets whether to guarantee a PAG.
    void
    setKnowledge(Knowledge knowledge)
    Deprecated.
    Sets background knowledge for the search.
    void
    setMaxDiscriminatingPathLength(int maxDiscriminatingPathLength)
    Deprecated.
    Sets the maximum length of any discriminating path.
    void
    setPossibleDsepSearchDone(boolean possibleDsepSearchDone)
    Deprecated.
    Sets whether the (time-consuming) possible dsep step should be done.
    void
    setStable(boolean stable)
    Deprecated.
    Sets whether the stable option will be used for search.
    void
    setVerbose(boolean verbose)
    Deprecated.
    Sets whether verbose output should be printed.

    Methods inherited from class java.lang.Object

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

    Methods inherited from interface edu.cmu.tetrad.search.IGraphSearch

    getTest, setTest

  • Constructor Details

  • Method Details

    • search

      public Graph search() throws InterruptedException
      Deprecated.
      Performs the search and returns the PAG.
      Specified by:
      search in interface IGraphSearch
      Returns:
      This PAG.
      Throws:
      InterruptedException - if any

    • setDepth

      public void setDepth(int depth)
      Deprecated.
      Sets the maximum nubmer of variables conditioned in any test.
      Parameters:
      depth - This maximum.

    • getElapsedTime

      public long getElapsedTime()
      Deprecated.
      Returns the elapsed time of search.
      Returns:
      This time.

    • getSepsets

      public SepsetMap getSepsets()
      Deprecated.
      Retrieves the map from variable pairs to sepsets from the FAS search.
      Returns:
      This map.

    • getKnowledge

      public Knowledge getKnowledge()
      Deprecated.
      Retrieves the background knowledge that was set.
      Returns:
      This knoweldge,

    • setKnowledge

      public void setKnowledge(Knowledge knowledge)
      Deprecated.
      Sets background knowledge for the search.
      Parameters:
      knowledge - This knowledge,

    • setCompleteRuleSetUsed

      public void setCompleteRuleSetUsed(boolean completeRuleSetUsed)
      Deprecated.
      Sets whether Zhang's complete rule set is used in the search.
      Parameters:
      completeRuleSetUsed - set to true if Zhang's complete rule set should be used, false if only R1-R4 (the rule set of the original FCI) should be used. False by default.

    • setPossibleDsepSearchDone

      public void setPossibleDsepSearchDone(boolean possibleDsepSearchDone)
      Deprecated.
      Sets whether the (time-consuming) possible dsep step should be done.
      Parameters:
      possibleDsepSearchDone - True, if so.

    • setMaxDiscriminatingPathLength

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

    • setVerbose

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

    • getIndependenceTest

      public IndependenceTest getIndependenceTest()
      Deprecated.
      Returns the independence test used in search.
      Returns:
      This test.

    • setStable

      public void setStable(boolean stable)
      Deprecated.
      Sets whether the stable option will be used for search.
      Parameters:
      stable - True, if so.

    • setGuaranteePag

      public void setGuaranteePag(boolean guaranteePag)
      Deprecated.
      Sets whether to guarantee a PAG.
      Parameters:
      guaranteePag - true to guarantee a PAG, false otherwise.