Package edu.cmu.tetrad.search.utils

Class TeyssierScorer

java.lang.Object

edu.cmu.tetrad.search.utils.TeyssierScorer

public class TeyssierScorer
extends Object

Implements and extends a scorer extending Teyssier, M., and Koller, D. (2012). You give it a score function and a variable ordering, and it computes the score. You can move any variable left or right, and it will keep track of the score using the Teyssier and Kohler method. You can move a variable to a new position, and you can bookmark a state and come back to it.

Teyssier, M., & Koller, D. (2012). Ordering-based search: A simple and effective algorithm for learning Bayesian networks. arXiv preprint arXiv:1207.1429.

Version:

$Id: $Id

Author:

josephramsey, bryanandrews

Constructor Summary

Constructors

Constructor	Description
TeyssierScorer(IndependenceTest test, Score score)	Constructor that takes both a test or a score.

Method Summary

Modifier and Type	Method	Description
boolean	adjacent(Node a, Node b)	Returns True iff a is adjacent to b in the current graph.
void	bookmark()	Bookmarks the current pi with index Integer.MIN_VALUE.
void	bookmark(int key)	Bookmarks the current pi as the index key.
void	clearBookmarks()	Clears all bookmarks.
boolean	clique(List<Node> W)	True iff the nodes in W form a clique in the current DAG.
boolean	collider(Node a, Node b, Node c)	Returns true iff [a, b, c] is a collider.
boolean	coveredEdge(Node x, Node y)	Returns true iff x->y or y->x is a covered edge.
Node	get(int j)	Returns the node at index j in pi.
List<NodePair>	getAdjacencies()	Returns a list of adjacent node pairs in the current graph.
Set<Node>	getAdjacentNodes(Node v)	Returns the nodes adjacent to v.
Set<Node>	getAncestors(Node node)	getAncestors.
Set<Node>	getChildren(int p)	Returns the children of a node v.
Set<Node>	getChildren(Node v)	Returns the children of a node v.
List<OrderedPair<Node>>	getEdges()	Returns a list of edges for the current graph as a list of ordered pairs.
Graph	getGraph(boolean cpDag)	Returns the DAG build for the current permutation, or its CPDAG.
int	getNumEdges()	getNumEdges.
List<Node>	getOrderShallow()	Returns the current permutation without making a copy.
Set<Node>	getParents(int p)	Returns the parents of the node at index p.
Set<Node>	getParents(Node v)	Returns the parents of a node v.
List<Node>	getPi()	Getter for the field pi.
Set<Node>	getPrefix(int i)	Retrieves a prefix of the size specified by the parameter.
List<Node>	getShuffledVariables()	getShuffledVariables.
Set<Set<Node>>	getSkeleton()	getSkeleton.
void	goToBookmark()	Retries the bookmark with key = Integer.MIN_VALUE and removes the bookmark.
void	goToBookmark(int key)	Retrieves the bookmarked state for index 'key' and removes that bookmark.
int	index(Node v)	Return the index of v in the current permutation.
void	moveTo(Node v, int toIndex)	Moves v to a new index.
boolean	parent(Node k, Node j)	parent.
double	score()	score.
double	score(List<Node> order)	Scores the given permutation.
void	setKnowledge(Knowledge knowledge)	Setter for the field knowledge.
void	setUseRaskuttiUhler(boolean useRaskuttiUhler)	Setter for the field useRaskuttiUhler.
void	setUseScore(boolean useScore)	Setter for the field useScore.
int	size()	size.
boolean	swap(Node m, Node n)	Swaps m and n in the permutation.
boolean	triangle(Node a, Node b, Node c)	Returns true iff [a, b, c] is a triangle.
boolean	tuck(Node j, Node k)	Moves j to before k and moves all the ancestors of j betwween k and j to before k.
boolean	tuck(Node k, Node... j)	Moves all j's to before k and moves all the ancestors of all ji's betwween k and ji to before k.
boolean	unshieldedCollider(Node a, Node b, Node c)	Returns true iff [a, b, c] is an unshielded collider.
boolean	unshieldedTriple(Node a, Node b, Node c)	Returns true iff [a, b, c] is an unshielded triple.

Methods inherited from class java.lang.Object

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

Constructor Details

TeyssierScorer

public TeyssierScorer(IndependenceTest test,
 Score score)

Constructor that takes both a test or a score. Only one of these is used, dependent on how the parameters are set.

Parameters:

test - The test.

score - The score

See Also:

• IndependenceTest
• Score

Method Details

setUseScore

public void setUseScore(boolean useScore)

Setter for the field useScore.

Parameters:

useScore - True if the score should be used; false if the test should be used.

setKnowledge

public void setKnowledge(Knowledge knowledge)

Setter for the field knowledge.

Parameters:

knowledge - Knowledge of forbidden edges.

setUseRaskuttiUhler

public void setUseRaskuttiUhler(boolean useRaskuttiUhler)

Setter for the field useRaskuttiUhler.

Parameters:

useRaskuttiUhler - True if Pearl's method for building a DAG should be used.

score

public double score(List<Node> order)
             throws InterruptedException

Scores the given permutation. This needs to be done initially before any move or tuck operations are performed.

Parameters:

order - The permutation to score.

Returns:

The score of it.

Throws:

InterruptedException

score

public double score()
             throws InterruptedException

score.

Returns:

The score of the current permutation.

Throws:

InterruptedException

tuck

public boolean tuck(Node j,
 Node k)

Moves j to before k and moves all the ancestors of j betwween k and j to before k.

Parameters:

j - The node to tuck.

k - The node to tuck j before.

Returns:

true if the tuck made a change.

tuck

public boolean tuck(Node k,
 Node... j)

Moves all j's to before k and moves all the ancestors of all ji's betwween k and ji to before k.

Parameters:

k - The node to tuck j before.

j - The nodes to tuck.

Returns:

true if the tuck made a change.

moveTo

public void moveTo(Node v,
 int toIndex)

Moves v to a new index.

Parameters:

v - The variable to move.

toIndex - The index to move v to.

swap

public boolean swap(Node m,
 Node n)

Swaps m and n in the permutation.

Parameters:

m - The first variable.

n - The second variable.

Returns:

True iff the swap was done.

coveredEdge

public boolean coveredEdge(Node x,
 Node y)

Returns true iff x->y or y->x is a covered edge. x->y is a covered edge if parents(x) = parents(y) \ {x}

Parameters:

x - The first variable.

y - The second variable.

Returns:

True, iff x->y or y->x is a covered edge.

getPi

public List<Node> getPi()

Getter for the field pi.

Returns:

A copy of the current permutation.

getOrderShallow

public List<Node> getOrderShallow()

Returns the current permutation without making a copy. Could be dangerous!

Returns:

the current permutation.

index

public int index(Node v)

Return the index of v in the current permutation.

Parameters:

v - The variable.

Returns:

Its index.

getParents

public Set<Node> getParents(int p)

Returns the parents of the node at index p.

Parameters:

p - The index of the node.

Returns:

Its parents.

getChildren

public Set<Node> getChildren(int p)

Returns the children of a node v.

Parameters:

p - The index of the variable.

Returns:

Its parents.

getParents

public Set<Node> getParents(Node v)

Returns the parents of a node v.

Parameters:

v - The variable.

Returns:

Its parents.

getChildren

public Set<Node> getChildren(Node v)

Returns the children of a node v.

Parameters:

v - The variable.

Returns:

Its parents.

getAdjacentNodes

public Set<Node> getAdjacentNodes(Node v)

Returns the nodes adjacent to v.

Parameters:

v - The variable.

Returns:

Its adjacent nodes.

getGraph

public Graph getGraph(boolean cpDag)

Returns the DAG build for the current permutation, or its CPDAG.

Parameters:

cpDag - True iff the CPDAG should be returned, False if the DAG.

Returns:

This graph.

getAdjacencies

public List<NodePair> getAdjacencies()

Returns a list of adjacent node pairs in the current graph.

Returns:

This list.

getAncestors

public Set<Node> getAncestors(Node node)

getAncestors.

Parameters:

node - a Node object

Returns:

a Set object

getEdges

public List<OrderedPair<Node>> getEdges()

Returns a list of edges for the current graph as a list of ordered pairs.

Returns:

This list.

getNumEdges

public int getNumEdges()

getNumEdges.

Returns:

The number of edges in the current graph.

get

public Node get(int j)

Returns the node at index j in pi.

Parameters:

j - The index.

Returns:

The node at that index.

bookmark

public void bookmark(int key)

Bookmarks the current pi as the index key.

Parameters:

key - This bookmark may be retrieved using the index 'key', an integer. This bookmark will be stored until it is retrieved and then removed.

bookmark

public void bookmark()

Bookmarks the current pi with index Integer.MIN_VALUE.

goToBookmark

public void goToBookmark(int key)

Retrieves the bookmarked state for index 'key' and removes that bookmark.

Parameters:

key - The integer key for this bookmark.

goToBookmark

public void goToBookmark()

Retries the bookmark with key = Integer.MIN_VALUE and removes the bookmark.

clearBookmarks

public void clearBookmarks()

Clears all bookmarks.

size

public int size()

size.

Returns:

The size of pi, the current permutation.

getShuffledVariables

public List<Node> getShuffledVariables()

getShuffledVariables.

Returns:

a List object

adjacent

public boolean adjacent(Node a,
 Node b)

Returns True iff a is adjacent to b in the current graph.

Parameters:

a - The first node.

b - The second node.

Returns:

True iff adj(a, b).

collider

public boolean collider(Node a,
 Node b,
 Node c)

Returns true iff [a, b, c] is a collider.

Parameters:

a - The first node.

b - The second node.

c - The third node.

Returns:

True iff a->b<-c in the current DAG.

unshieldedCollider

public boolean unshieldedCollider(Node a,
 Node b,
 Node c)

Returns true iff [a, b, c] is an unshielded collider.

Parameters:

a - The first node.

b - The second node.

c - The third node.

Returns:

True iff a->b<-c in the current DAG.

unshieldedTriple

public boolean unshieldedTriple(Node a,
 Node b,
 Node c)

Returns true iff [a, b, c] is an unshielded triple.

Parameters:

a - The first node.

b - The second node.

c - The third node.

Returns:

True iff a->b<-c in the current DAG.

triangle

public boolean triangle(Node a,
 Node b,
 Node c)

Returns true iff [a, b, c] is a triangle.

Parameters:

a - The first node.

b - The second node.

c - The third node.

Returns:

True iff adj(a, b) and adj(b, c) and adj(a, c).

clique

public boolean clique(List<Node> W)

True iff the nodes in W form a clique in the current DAG.

Parameters:

W - The nodes.

Returns:

True iff these nodes form a clique.

getPrefix

public Set<Node> getPrefix(int i)

Retrieves a prefix of the size specified by the parameter.

Parameters:

i - The size of the prefix to retrieve.

Returns:

A Set containing the prefix of size i.

getSkeleton

public Set<Set<Node>> getSkeleton()

getSkeleton.

Returns:

a Set object

parent

public boolean parent(Node k,
 Node j)

parent.

Parameters:

k - a Node object

j - a Node object

Returns:

a boolean