Package edu.cmu.tetrad.search.work_in_progress

Class FasLofs

java.lang.Object

edu.cmu.tetrad.search.work_in_progress.FasLofs

All Implemented Interfaces:

IGraphSearch

public final class FasLofs
extends Object
implements IGraphSearch

Runs Fast Adjacency Search (FAS) and then orients each edge using the robust skew orientation algorithm. Checks are done for adding two-cycles. The two-cycle checks do not require non-Gaussianity. The robust skew orientation of edges left or right does.

Moving this to the work_in_progress package because the functionality can be generalized. Instead of hard-coding FAS, an arbitrary algorithm can be used to obtain adjacencies. Instead of hard-coding robust skew, and arbitrary algorithm can be used to to pairwise orientation. Instead of orienting all edges, an option can be given to just orient the edges that are unoriented in the input graph (see, e.g., PC LiNGAM). This was an early attempt at this. For BOSS-LiNGAM, see this paper:

Hoyer, P. O., Hyvarinen, A., Scheines, R., Spirtes, P. L., Ramsey, J., Lacerda, G., & Shimizu, S. (2012). Causal discovery of linear acyclic models with arbitrary distributions. arXiv preprint arXiv:1206.3260.

Version:

$Id: $Id

Author:

josephramsey

See Also:

• Fas
• Fask

Constructor Summary

Constructors

Constructor	Description
FasLofs(DataSet dataSet, Lofs.Rule rule)	Constructor for FasLofs.

Method Summary

Modifier and Type	Method	Description
int	getDepth()	Getter for the field depth.
long	getElapsedTime()	getElapsedTime.
Knowledge	getKnowledge()	Getter for the field knowledge.
double	getPenaltyDiscount()	Getter for the field penaltyDiscount.
Graph	search()	Runs the search on the concatenated data, returning a graph, possibly cyclic, possibly with two-cycles.
void	setDepth(int depth)	Setter for the field depth.
void	setKnowledge(Knowledge knowledge)	Setter for the field knowledge.
void	setPenaltyDiscount(double penaltyDiscount)	Setter for the field penaltyDiscount.

Methods inherited from class java.lang.Object

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

Constructor Details

FasLofs

public FasLofs(DataSet dataSet,
 Lofs.Rule rule)

Constructor for FasLofs.

Parameters:

dataSet - These datasets to analyze.

rule - a Lofs.Rule object

Method Details

search

public Graph search()
             throws InterruptedException

Runs the search on the concatenated data, returning a graph, possibly cyclic, possibly with two-cycles. Runs the fast adjacency search (FAS, Spirtes et al., 2000) follows by a modification of the robust skew rule (Pairwise Likelihood Ratios for Estimation of Non-Gaussian Structural Equation Models, Smith and Hyvarinen), together with some heuristics for orienting two-cycles.

Specified by:

search in interface IGraphSearch

Returns:

the graph. Some of the edges may be undirected (though it shouldn't be many in most cases) and some of the adjacencies may be two-cycles.

Throws:

InterruptedException - if any.

getDepth

public int getDepth()

Getter for the field depth.

Returns:

The depth of search for the Fast Adjacency Search (FAS).

setDepth

public void setDepth(int depth)

Setter for the field depth.

Parameters:

depth - The depth of search for the Fast Adjacency Search (S). The default is -1. unlimited. Making this too high may results in statistical errors.

getElapsedTime

public long getElapsedTime()

getElapsedTime.

Returns:

The elapsed time in milliseconds.

getPenaltyDiscount

public double getPenaltyDiscount()

Getter for the field penaltyDiscount.

Returns:

Returns the penalty discount used for the adjacency search. The default is 1, though a higher value is recommended, say, 2, 3, or 4.

setPenaltyDiscount

public void setPenaltyDiscount(double penaltyDiscount)

Setter for the field penaltyDiscount.

Parameters:

penaltyDiscount - Sets the penalty discount used for the adjacency search. The default is 1, though a higher value is recommended, say, 2, 3, or 4.

getKnowledge

public Knowledge getKnowledge()

Getter for the field knowledge.

Returns:

the current knowledge.

setKnowledge

public void setKnowledge(Knowledge knowledge)

Setter for the field knowledge.

Parameters:

knowledge - Knowledge of forbidden and required edges.