Package edu.cmu.tetrad.search

Class PermutationSearch

java.lang.Object

edu.cmu.tetrad.search.PermutationSearch

public class PermutationSearch
extends Object

Implements common elements of a permutation search. The specific parts for each permutation search are implemented as a SuborderSearch.

This class specifically handles an optimization for tiered knowledge, whereby tiers in the knowledge can be searched one at a time in order from the lowest to highest, taking all variables from previous tiers as a fixed for a later tier. This allows these permutation searches to search over many more variables than otherwise, so long as tiered knowledge is available to organize the search.

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

Author:

bryanandrews

See Also:

• SuborderSearch
• Boss
• Sp
• Knowledge

Constructor Summary

Constructors

Constructor	Description
PermutationSearch(SuborderSearch suborderSearch)	Constructs a new PermutationSearch using the given SuborderSearch.

Method Summary

Modifier and Type	Method	Description
boolean	getCpdag()	Retrieves the value of cpdag.
static Graph	getGraph(List<Node> nodes, Map<Node,Set<Node>> parents, boolean cpDag)	Construct a graph given a specification of the parents for each node.
static Graph	getGraph(List<Node> nodes, Map<Node,Set<Node>> parents, Knowledge knowledge, boolean cpDag)	Constructs a graph given a specification of the parents for each node.
GrowShrinkTree	getGST(Node node)	Retrieves the GrowShrinkTree (GST) associated with the given Node.
List<Node>	getOrder()	Retrieves the order list.
List<Node>	getVariables()	Retrieves the list of variables.
Graph	search()	Performs a search for a graph using the default options.
Graph	search(boolean cpdag)	Performe the search and return a CPDAG.
void	setCpdag(boolean cpdag)	Sets the flag indicating whether a CPDAG (partially directed acyclic graph) is wanted or not.
void	setKnowledge(Knowledge knowledge)	Sets the knowledge to be used for the search.
void	setOrder(List<Node> order)	Sets the order list for the search.
void	setSeed(long seed)	Sets the seed value used for generating random numbers.

Methods inherited from class java.lang.Object

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

Constructor Details

PermutationSearch

public PermutationSearch(SuborderSearch suborderSearch)

Constructs a new PermutationSearch using the given SuborderSearch.

Parameters:

suborderSearch - The SuborderSearch (see).

See Also:

• SuborderSearch

Method Details

getGraph

public static Graph getGraph(List<Node> nodes,
 Map<Node,Set<Node>> parents,
 boolean cpDag)

Construct a graph given a specification of the parents for each node.

Parameters:

nodes - The nodes.

parents - A map from each node to its parents.

cpDag - Whether a CPDAG is wanted, if false, a DAG.

Returns:

The constructed graph.

getGraph

public static Graph getGraph(List<Node> nodes,
 Map<Node,Set<Node>> parents,
 Knowledge knowledge,
 boolean cpDag)

Constructs a graph given a specification of the parents for each node.

Parameters:

nodes - The nodes.

parents - A map from each node to its parents.

knowledge - the knowledge to use to construct the graph.

cpDag - Whether a CPDAG is wanted, if false, a DAG.

Returns:

The construted graph.

search

public Graph search()
             throws InterruptedException

Performs a search for a graph using the default options. Returns the resulting graph.

Returns:

The constructed CPDAG.

Throws:

InterruptedException

search

public Graph search(boolean cpdag)
             throws InterruptedException

Performe the search and return a CPDAG.

Parameters:

cpdag - True a CPDAG is wanted, if false, a DAG.

Returns:

The CPDAG.

Throws:

InterruptedException

getOrder

public List<Node> getOrder()

Retrieves the order list.

Returns:

The order list.

setOrder

public void setOrder(List<Node> order)

Sets the order list for the search.

Parameters:

order - The order list to set. Must contain all variables.

Throws:

AssertionError - If the order list does not contain all variables.

getGST

public GrowShrinkTree getGST(Node node)

Retrieves the GrowShrinkTree (GST) associated with the given Node.

Parameters:

node - The Node whose GST is to be retrieved.

Returns:

The GrowShrinkTree associated with the given Node.

getVariables

public List<Node> getVariables()

Retrieves the list of variables.

Returns:

The list of variables.

setKnowledge

public void setKnowledge(Knowledge knowledge)

Sets the knowledge to be used for the search.

Parameters:

knowledge - The knowledge to be set.

getCpdag

public boolean getCpdag()

Retrieves the value of cpdag.

Returns:

The value of the cpdag flag.

setCpdag

public void setCpdag(boolean cpdag)

Sets the flag indicating whether a CPDAG (partially directed acyclic graph) is wanted or not.

Parameters:

cpdag - The value indicating whether a CPDAG is wanted or not.

setSeed

public void setSeed(long seed)

Sets the seed value used for generating random numbers.

Parameters:

seed - The seed value to set.