Class Fas
- All Implemented Interfaces:
IFas
,IGraphSearch
Implements the Fast Adjacency Search (FAS), which is the adjacency search of the PC algorithm (see). This is a useful algorithm in many contexts, including as the first step of FCI (see).
The idea of FAS is that at a given stage of the search, an edge X*-*Y is removed from the graph if X _||_ Y | S, where S is a subset of size d either of adj(X) or of adj(Y), where d is the depth of the search. The fast adjacency search performs this procedure for each pair of adjacent edges in the graph and for each depth d = 0, 1, 2, ..., d1, where d1 is either the maximum depth or else the first such depth at which no edges can be removed. The interpretation of this adjacency search is different for different algorithm, depending on the assumptions of the algorithm. A mapping from {x, y} to S({x, y}) is returned for edges x *-* y that have been removed.
FAS may optionally use a heuristic from Causation, Prediction and Search, which (like PC-Stable) renders the output invariant to the order of the input variables.
This algorithm was described in the earlier edition of this book:
Spirtes, P., Glymour, C. N., Scheines, R., & Heckerman, D. (2000). Causation, prediction, and search. MIT press.
This class is configured to respect knowledge of forbidden and required edges, including knowledge of temporal tiers.
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiongetAmbiguousTriples
(Node node) There are no ambiguous triples for this search, for any nodes.long
Returns the elapsed time of the search.getNodes()
Returns the nodes from the test.int
Returns the number of independence tests that were done.Returns the sepsets that were discovered in the search.search()
Runs the search and returns the resulting (undirected) graph.Discovers all adjacencies in data.void
setDepth
(int depth) Sets the depth of the search, which is the maximum number of variables that ben be conditioned on in any conditional independence test.void
setKnowledge
(Knowledge knowledge) Sets the knowledge to be used in the search.void
setOut
(PrintStream out) sets the print stream to send text to.void
setPcHeuristicType
(PcCommon.PcHeuristicType pcHeuristic) void
setStable
(boolean stable) Sets whether the stable adjacency search should be used.void
setVerbose
(boolean verbose) Sets whether verbose output should be printed.
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Constructor Details
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Fas
Constructor.- Parameters:
test
- The test to use for oracle conditional independence test results.
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Method Details
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search
Runs the search and returns the resulting (undirected) graph.- Specified by:
search
in interfaceIGraphSearch
- Returns:
- This graph.
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search
Discovers all adjacencies in data. The procedure is to remove edges in the graph which connect pairs of variables which are independent, conditional on some other set of variables in the graph (the "sepset"). These are removed in tiers. First, edges which are independent conditional on zero other variables are removed, then edges which are independent conditional on one other variable are removed, then two, then three, and so on, until no more edges can be removed from the graph. The edges which remain in the graph after this procedure are the adjacencies in the data.- Parameters:
nodes
- A list of nodes to search over.- Returns:
- An undirected graph that summarizes the conditional independencies that obtain in the data.
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setDepth
public void setDepth(int depth) Sets the depth of the search, which is the maximum number of variables that ben be conditioned on in any conditional independence test. -
setKnowledge
Sets the knowledge to be used in the search.- Specified by:
setKnowledge
in interfaceIFas
- Parameters:
knowledge
- This knowledge.- See Also:
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getNumIndependenceTests
public int getNumIndependenceTests()Returns the number of independence tests that were done.- Specified by:
getNumIndependenceTests
in interfaceIFas
- Returns:
- This number.
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getSepsets
Returns the sepsets that were discovered in the search. A 'sepset' for test X _||_ Y | Z1,...,Zm would be {Z1,...,Zm}- Specified by:
getSepsets
in interfaceIFas
- Returns:
- A map of these sepsets indexed by {X, Y}.
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setVerbose
public void setVerbose(boolean verbose) Sets whether verbose output should be printed.- Specified by:
setVerbose
in interfaceIFas
- Parameters:
verbose
- True iff the case.
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getElapsedTime
public long getElapsedTime()Returns the elapsed time of the search.- Specified by:
getElapsedTime
in interfaceIFas
- Returns:
- This elapsed time.
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getNodes
Returns the nodes from the test. -
getAmbiguousTriples
There are no ambiguous triples for this search, for any nodes.- Specified by:
getAmbiguousTriples
in interfaceIFas
- Parameters:
node
- The nodes in question.- Returns:
- An empty list.
- See Also:
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setOut
Description copied from interface:IFas
sets the print stream to send text to. -
setPcHeuristicType
- Parameters:
pcHeuristic
- Which PC heuristic to use (see Causation, Prediction and Search). Default is PcHeuristicType.NONE.- See Also:
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setStable
public void setStable(boolean stable) Sets whether the stable adjacency search should be used. Default is false. Default is false. See the following reference for this:
Colombo, D., & Maathuis, M. H. (2014). Order-independent constraint-based causal structure learning. J. Mach. Learn. Res., 15(1), 3741-3782.
- Parameters:
stable
- True iff the case.
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