Class SvarFges
- All Implemented Interfaces:
IGraphSearch
,DagScorer
Adapts FGES for the time series setting, assuming the data is generated by a SVAR (structural vector autoregression). The main difference is that time order is imposed, and if an edge is removed, it will also remove all homologous edges to preserve the time-repeating structure assumed by SvarFCI. Based on (but not identical to) code by Entner and Hoyer for their 2010 paper. Modified by dmalinsky 4/21/2016.
The references are as follows:
Malinsky, D., & Spirtes, P. (2018, August). Causal structure learning from multivariate time series in settings with unmeasured confounding. In Proceedings of 2018 ACM SIGKDD workshop on causal discovery (pp. 23-47). PMLR.
Entner, D., & Hoyer, P. O. (2010). On causal discovery from time series data using FCI. Probabilistic graphical models, 121-128.
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 TypeMethodDescriptionvoid
addSimilarEdges
(Node x, Node y) long
Returns the elapsed time of the search.int
The maximum of parents any nodes can have in the output pattern.int
getMinChunk
(int n) getNameNoLag
(Object obj) int
getOut()
double
Deprecated.Use the getters on the individual scores instead.double
void
removeSimilarEdges
(Node x, Node y) double
Scores the given DAG, up to a constant.search()
Greedy equivalence search: Start from the empty graph, add edges till the model is significant.void
setAdjacencies
(Graph adjacencies) Sets the set of preset adjacencies for the algorithm; edges not in this adjacencies graph will not be added.void
setExternalGraph
(Graph externalGraph) Sets the initial graph.void
setFaithfulnessAssumed
(boolean faithfulnessAssumed) Set to true if it is assumed that all path pairs with one length 1 path do not cancel.void
setKnowledge
(Knowledge knowledge) Sets the background knowledge.void
setMaxIndegree
(int maxIndegree) The maximum of parents any nodes can have in the output pattern.void
setNumCPDAGsToStore
(int numCPDAGsToStore) Sets the number of patterns to store.void
setOut
(PrintStream out) Sets the output stream that output (except for log output) should be sent to.void
setPenaltyDiscount
(double penaltyDiscount) Deprecated.Use the setters on the individual scores instead.void
setSamplePrior
(double samplePrior) Deprecated.Use the setters on the individual scores instead.void
setStructurePrior
(double expectedNumParents) Deprecated.Use the setters on the individual scores instead.void
setTrueGraph
(Graph trueGraph) If the true graph is set, asterisks will be printed in log output for the true edges.void
setVerbose
(boolean verbose) Sets whether verbose output should be produced.
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Constructor Details
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SvarFges
Construct a Score and pass it in here. The totalScore should return a positive value in case of conditional dependence and a negative values in case of conditional independence. See Chickering (2002), locally consistent scoring criterion.
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Method Details
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search
Greedy equivalence search: Start from the empty graph, add edges till the model is significant. Then start deleting edges till a minimum is achieved.- Specified by:
search
in interfaceIGraphSearch
- Returns:
- the resulting CPDAG.
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setFaithfulnessAssumed
public void setFaithfulnessAssumed(boolean faithfulnessAssumed) Set to true if it is assumed that all path pairs with one length 1 path do not cancel. -
getKnowledge
- Returns:
- the background knowledge.
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setKnowledge
Sets the background knowledge.- Parameters:
knowledge
- the knowledge object, specifying forbidden and required edges.
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getElapsedTime
public long getElapsedTime()Returns the elapsed time of the search.- Returns:
- This time.
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setTrueGraph
If the true graph is set, asterisks will be printed in log output for the true edges. -
getScore
- Returns:
- the totalScore of the given DAG, up to a constant.
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getnumCPDAGsToStore
public int getnumCPDAGsToStore()- Returns:
- the number of patterns to store.
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setNumCPDAGsToStore
public void setNumCPDAGsToStore(int numCPDAGsToStore) Sets the number of patterns to store. This should be set to zero for fast search. -
getExternalGraph
- Returns:
- the initial graph for the search. The search is initialized to this graph and proceeds from there.
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setExternalGraph
Sets the initial graph. -
setVerbose
public void setVerbose(boolean verbose) Sets whether verbose output should be produced. -
getOut
- Returns:
- the output stream that output (except for log output) should be sent to.
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setOut
Sets the output stream that output (except for log output) should be sent to. By detault System.out. -
getAdjacencies
- Returns:
- the set of preset adjacencies for the algorithm; edges not in this adjacency graph will not be added.
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setAdjacencies
Sets the set of preset adjacencies for the algorithm; edges not in this adjacencies graph will not be added. -
getPenaltyDiscount
public double getPenaltyDiscount()Deprecated.Use the getters on the individual scores instead.For BIC totalScore, a multiplier on the penalty term. For continuous searches. -
setPenaltyDiscount
public void setPenaltyDiscount(double penaltyDiscount) Deprecated.Use the setters on the individual scores instead.For BIC totalScore, a multiplier on the penalty term. For continuous searches. -
setSamplePrior
public void setSamplePrior(double samplePrior) Deprecated.Use the setters on the individual scores instead. -
setStructurePrior
public void setStructurePrior(double expectedNumParents) Deprecated.Use the setters on the individual scores instead. -
getMaxIndegree
public int getMaxIndegree()The maximum of parents any nodes can have in the output pattern.- Returns:
- -1 for unlimited.
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setMaxIndegree
public void setMaxIndegree(int maxIndegree) The maximum of parents any nodes can have in the output pattern.- Parameters:
maxIndegree
- -1 for unlimited.
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getMinChunk
public int getMinChunk(int n) -
scoreDag
Scores the given DAG, up to a constant. -
getNameNoLag
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addSimilarEdges
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removeSimilarEdges
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