Package edu.cmu.tetrad.search.work_in_progress

Class Kpc

java.lang.Object

edu.cmu.tetrad.search.work_in_progress.Kpc

All Implemented Interfaces:

IGraphSearch

public class Kpc
extends Object
implements IGraphSearch

Kernelized PC algorithm. This is the same as the PC class, the nonparametric kernel-based HSIC test is used for independence testing and the parameters for this test can be set directly when Kpc is initialized.

Moving this to the work_in_progress package because it has not been tested in a very long time, and there is another option available that has been tested, namely, to run PC using the KCI test due to Kun Zhang.

Version:

$Id: $Id

Author:

Robert Tillman.

Constructor Summary

Constructors

Constructor	Description
Kpc(DataSet dataset, double alpha)	Constructs a new PC search using for the given dataset.

Method Summary

Modifier and Type	Method	Description
double	getAlpha()	Gets the getModel significance level.
int	getDepth()	Getter for the field depth.
long	getElapsedTime()	Getter for the field elapsedTime.
IndependenceTest	getIndependenceTest()	Getter for the field independenceTest.
Knowledge	getKnowledge()	Getter for the field knowledge.
int	getPerms()	Gets the getModel number of bootstrap samples used
double	getPrecision()	Gets the getModel precision for the Incomplete Cholesky
SepsetMap	getSepset()	Getter for the field sepset.
Set<Triple>	getUnshieldedColliders()	Getter for the field unshieldedColliders.
Set<Triple>	getUnshieldedNoncolliders()	Getter for the field unshieldedNoncolliders.
boolean	isGuaranteeCpdag()	Checks if guaranteeCpdag is set to true.
Graph	search()	Runs PC starting with a complete graph over all nodes of the given conditional independence test, using the given independence test and knowledge and returns the resultant graph.
Graph	search(List<Node> nodes)	Runs PC starting with a commplete graph over the given list of nodes, using the given independence test and knowledge and returns the resultant graph.
void	setAlpha(double alpha)	Sets the significance level at which independence judgments should be made.
void	setDepth(int depth)	Sets the depth of the search--that is, the maximum number of conditioning nodes for any conditional independence checked.
void	setGuaranteeCpdag(boolean guaranteeCpdag)	Sets the flag to determine whether to guarantee a CPDAG (Consensus Partially Directed Acyclic Graph) result in the search.
void	setKnowledge(Knowledge knowledge)	Sets the knowledge specification to be used in the search.
void	setPerms(int perms)	Set the number of bootstrap samples to use
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

Kpc

public Kpc(DataSet dataset,
 double alpha)

Constructs a new PC search using for the given dataset.

Parameters:

dataset - The oracle for conditional independence facts. This does not make a copy of the independence test, for fear of duplicating the data set!

alpha - a double

Method Details

isGuaranteeCpdag

public boolean isGuaranteeCpdag()

Checks if guaranteeCpdag is set to true.

Returns:

true if guaranteeCpdag is set to true, otherwise false

setGuaranteeCpdag

public void setGuaranteeCpdag(boolean guaranteeCpdag)

Sets the flag to determine whether to guarantee a CPDAG (Consensus Partially Directed Acyclic Graph) result in the search.

Parameters:

guaranteeCpdag - true if guarantee CPDAG result should be ensured, false otherwise

getIndependenceTest

public IndependenceTest getIndependenceTest()

Getter for the field independenceTest.

Returns:

the independence test being used in the search.

getKnowledge

public Knowledge getKnowledge()

Getter for the field knowledge.

Returns:

the knowledge specification used in the search. Non-null.

setKnowledge

public void setKnowledge(Knowledge knowledge)

Sets the knowledge specification to be used in the search. May not be null.

Parameters:

knowledge - a Knowledge object

getSepset

public SepsetMap getSepset()

Getter for the field sepset.

Returns:

the sepset map from the most recent search. Non-null after the first call to search().

getDepth

public int getDepth()

Getter for the field depth.

Returns:

the getModel depth of search--that is, the maximum number of conditioning nodes for any conditional independence checked.

setDepth

public void setDepth(int depth)

Sets the depth of the search--that is, the maximum number of conditioning nodes for any conditional independence checked.

Parameters:

depth - The depth of the search. The default is 1000. A value of -1 may be used to indicate that the depth should be high (1000). A value of Integer.MAX_VALUE may not be used, due to a bug on multi-core machines.

search

public Graph search()
             throws InterruptedException

Runs PC starting with a complete graph over all nodes of the given conditional independence test, using the given independence test and knowledge and returns the resultant graph. The returned graph will be a CPDAG if the independence information is consistent with the hypothesis that there are no latent common causes. It may, however, contain cycles or bidirected edges if this assumption is not born out, either due to the actual presence of latent common causes, or due to statistical errors in conditional independence judgments.

Specified by:

search in interface IGraphSearch

Returns:

a Graph object

Throws:

InterruptedException - if any.

search

public Graph search(List<Node> nodes)
             throws InterruptedException

Runs PC starting with a commplete graph over the given list of nodes, using the given independence test and knowledge and returns the resultant graph. The returned graph will be a CPDAG if the independence information is consistent with the hypothesis that there are no latent common causes. It may, however, contain cycles or bidirected edges if this assumption is not born out, either due to the actual presence of latent common causes, or due to statistical errors in conditional independence judgments.

All of the given nodes must be in the domain of the given conditional independence test.

Parameters:

nodes - a List object

Returns:

a Graph object

Throws:

InterruptedException

getElapsedTime

public long getElapsedTime()

Getter for the field elapsedTime.

Returns:

the elapsed time of the search, in milliseconds.

getUnshieldedColliders

public Set<Triple> getUnshieldedColliders()

Getter for the field unshieldedColliders.

Returns:

the set of unshielded colliders in the graph returned by search(). Non-null after search is called.

getUnshieldedNoncolliders

public Set<Triple> getUnshieldedNoncolliders()

Getter for the field unshieldedNoncolliders.

Returns:

the set of unshielded noncolliders in the graph returned by search(). Non-null after search is called.

setVerbose

public void setVerbose(boolean verbose)

Sets whether verbose output should be printed.

Parameters:

verbose - True, if so.

getAlpha

public double getAlpha()

Gets the getModel significance level.

Returns:

a double

setAlpha

public void setAlpha(double alpha)

Sets the significance level at which independence judgments should be made.

Parameters:

alpha - a double

getPrecision

public double getPrecision()

Gets the getModel precision for the Incomplete Cholesky

Returns:

a double

getPerms

public int getPerms()

Gets the getModel number of bootstrap samples used

Returns:

a int

setPerms

public void setPerms(int perms)

Set the number of bootstrap samples to use

Parameters:

perms - a int