Package edu.cmu.tetrad.search

Class SpFci

java.lang.Object

edu.cmu.tetrad.search.SpFci

All Implemented Interfaces:

IGraphSearch

public final class SpFci
extends Object
implements IGraphSearch

Uses SP in place of FGES for the initial step in the GFCI algorithm. This tends to produce an accurate PAG than GFCI as a result, for the latent variables case. This is a simple substitution; the reference for GFCI is here:

J.M. Ogarrio and P. Spirtes and J. Ramsey, "A Hybrid Causal Search Algorithm for Latent Variable Models," JMLR 2016. Here, SP has been substituted for FGES.

The reference for the SP algorithm is here:

Raskutti, G., & Uhler, C. (2018). Learning directed acyclic graph models based on sparsest permutations. Stat, 7(1), e183.

For SP only a score is needed, but there are steps in GFCI that require a test, so for this method, both a test and a score need to be given.

Note that SP considers all permutations of the algorithm, which is exponential in the number of variables. So SP is limited to about 10 variables.

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

Version:

$Id: $Id

Author:

josephramsey, bryan andrews

See Also:

• Grasp
• GFci
• Sp
• Knowledge
• FciOrient

Constructor Summary

Constructors

Constructor	Description
SpFci(IndependenceTest test, Score score)	Constructor; requires by ta test and a score, over the same variables.

Method Summary

Modifier and Type	Method	Description
IndependenceTest	getIndependenceTest()	Returns the independence test used in search.
Knowledge	getKnowledge()	Returns the knowledge.
int	getMaxDegree()	Returns The maximum indegree of the output graph.
int	getMaxDiscriminatingPathLength()	Returns the maximum length of any discriminating path, or -1 of unlimited.
boolean	isCompleteRuleSetUsed()	Returns whether the complete rule set is used.
Graph	search()	Runs the search and returns the discovered PAG.
void	setCompleteRuleSetUsed(boolean completeRuleSetUsed)	Sets whether Zhang's complete rule set is used.
void	setDepth(int depth)	Sets the maximum number of variables conditioned on.
void	setGuaranteePag(boolean guaranteePag)	Sets whether the search should guarantee the output is a legal PAG.
void	setKnowledge(Knowledge knowledge)	Sets the knoweldge used in the search.
void	setMaxDegree(int maxDegree)	Sets the max degree of the search.
void	setMaxDiscriminatingPathLength(int maxDiscriminatingPathLength)	Sets the maximum length of any discriminating path.
void	setOut(PrintStream out)	Sets the output stream used to print.
void	setSepsetFinderMethod(int sepsetFinderMethod)	Sets the method to use for finding sepsets, 1 = greedy, 2 = min-p., 3 = max-p, default min-p.
void	setVerbose(boolean verbose)	Sets whether verbose output is printed.

Methods inherited from class java.lang.Object

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

Constructor Details

SpFci

public SpFci(IndependenceTest test,
 Score score)

Constructor; requires by ta test and a score, over the same variables.

Parameters:

test - The test.

score - The score.

Method Details

search

public Graph search()
             throws InterruptedException

Runs the search and returns the discovered PAG.

Specified by:

search in interface IGraphSearch

Returns:

This PAG.

Throws:

InterruptedException - if any.

getMaxDegree

public int getMaxDegree()

Returns The maximum indegree of the output graph.

Returns:

This maximum.

setMaxDegree

public void setMaxDegree(int maxDegree)

Sets the max degree of the search.

Parameters:

maxDegree - This maximum.

getKnowledge

public Knowledge getKnowledge()

Returns the knowledge.

Returns:

This knowledge.

setKnowledge

public void setKnowledge(Knowledge knowledge)

Sets the knoweldge used in the search.

Parameters:

knowledge - This knowledge.

isCompleteRuleSetUsed

public boolean isCompleteRuleSetUsed()

Returns whether the complete rule set is used.

Returns:

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.

setCompleteRuleSetUsed

public void setCompleteRuleSetUsed(boolean completeRuleSetUsed)

Sets whether Zhang's complete rule set is used.

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.

getMaxDiscriminatingPathLength

public int getMaxDiscriminatingPathLength()

Returns the maximum length of any discriminating path, or -1 of unlimited.

Returns:

This length.

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 is printed.

Parameters:

verbose - True, if so.

getIndependenceTest

public IndependenceTest getIndependenceTest()

Returns the independence test used in search.

Returns:

This test.

setOut

public void setOut(PrintStream out)

Sets the output stream used to print. Unused, but the implementation needs to be here.

Parameters:

out - This print stream.

setDepth

public void setDepth(int depth)

Sets the maximum number of variables conditioned on.

Parameters:

depth - This maximum.

setGuaranteePag

public void setGuaranteePag(boolean guaranteePag)

Sets whether the search should guarantee the output is a legal PAG.

Parameters:

guaranteePag - True, if so.

setSepsetFinderMethod

public void setSepsetFinderMethod(int sepsetFinderMethod)

Sets the method to use for finding sepsets, 1 = greedy, 2 = min-p., 3 = max-p, default min-p.

Parameters:

sepsetFinderMethod - the method to use for finding sepsets