Package edu.cmu.tetrad.search

Class FciMax

java.lang.Object

edu.cmu.tetrad.search.FciMax

All Implemented Interfaces:

IGraphSearch

public final class FciMax
extends Object
implements IGraphSearch

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:

• Fci
• Fas
• FciOrient
• Knowledge

Constructor Summary

Constructors

Constructor	Description
FciMax(IndependenceTest independenceTest)	Constructor.

Method Summary

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

Methods inherited from class java.lang.Object

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

Constructor Details

FciMax

public FciMax(IndependenceTest independenceTest)

Constructor.

Parameters:

independenceTest - a IndependenceTest object

Method Details

search

public Graph search()
             throws InterruptedException

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)

Sets the maximum nubmer of variables conditioned in any test.

Parameters:

depth - This maximum.

getElapsedTime

public long getElapsedTime()

Returns the elapsed time of search.

Returns:

This time.

getSepsets

public SepsetMap getSepsets()

Retrieves the map from variable pairs to sepsets from the FAS search.

Returns:

This map.

getKnowledge

public Knowledge getKnowledge()

Retrieves the background knowledge that was set.

Returns:

This knoweldge,

setKnowledge

public void setKnowledge(Knowledge knowledge)

Sets background knowledge for the search.

Parameters:

knowledge - This knowledge,

setCompleteRuleSetUsed

public void setCompleteRuleSetUsed(boolean completeRuleSetUsed)

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.

setPossibleMsepSearchDone

public void setPossibleMsepSearchDone(boolean possibleMsepSearchDone)

Sets whether the (time-consuming) possible msep step should be done.

Parameters:

possibleMsepSearchDone - True, if so.

setMaxDiscriminatingPathLength

public void setMaxDiscriminatingPathLength(int maxDiscriminatingPathLength)

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)

Sets whether verbose output should be printed.

Parameters:

verbose - True, if so.

getIndependenceTest

public IndependenceTest getIndependenceTest()

Returns the independence test used in search.

Returns:

This test.

setPcHeuristicType

public void setPcHeuristicType(PcCommon.PcHeuristicType pcHeuristicType)

Sets the FAS heuristic from PC used in search.

Parameters:

pcHeuristicType - This heuristic.

See Also:

• Pc

setStable

public void setStable(boolean stable)

Sets whether the stable option will be used for search.

Parameters:

stable - True, if so.

setGuaranteePag

public void setGuaranteePag(boolean guaranteePag)

Sets whether to guarantee a PAG.

Parameters:

guaranteePag - true to guarantee a PAG, false otherwise.