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joe-work-2024-8-12 #1801

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merged 6 commits into from
Aug 13, 2024
Merged

joe-work-2024-8-12 #1801

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452a426
Remove redundant and unused parameters
jdramsey Aug 12, 2024
3d9aee9
Remove redundant ablation parameter and add logging
jdramsey Aug 12, 2024
2108ac4
Refactor FCI to handle unshielded triples and repair faulty PAGs
jdramsey Aug 13, 2024
3106aa9
Enhance FCI algorithms with discriminating path rules.
jdramsey Aug 13, 2024
4931a4f
Enhance FCI configurations with new settings
jdramsey Aug 13, 2024
0b690a1
Add cyclicity check parameter to repairFaultyPag method
jdramsey Aug 13, 2024
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6 changes: 0 additions & 6 deletions tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Bfci.java
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Expand Up @@ -122,9 +122,6 @@ public Graph runSearch(DataModel dataModel, Parameters parameters) {
search.setRepairFaultyPag(parameters.getBoolean(Params.REPAIR_FAULTY_PAG));
search.setVerbose(parameters.getBoolean(Params.VERBOSE));

// Ablation
search.setLeaveOutFinalOrientation(parameters.getBoolean(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION));

search.setKnowledge(knowledge);

search.setNumStarts(parameters.getInt(Params.NUM_STARTS));
Expand Down Expand Up @@ -191,9 +188,6 @@ public List<String> getParameters() {
// Parameters
params.add(Params.NUM_STARTS);

// Ablation
params.add(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION);

return params;
}

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6 changes: 0 additions & 6 deletions tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Cfci.java
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Expand Up @@ -103,9 +103,6 @@ public Graph runSearch(DataModel dataModel, Parameters parameters) {
search.setMaxPathLength(parameters.getInt(Params.MAX_PATH_LENGTH));
search.setVerbose(parameters.getBoolean(Params.VERBOSE));

// Ablation
search.setLeaveOutFinalOrientation(parameters.getBoolean(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION));

return search.search();
}

Expand Down Expand Up @@ -159,9 +156,6 @@ public List<String> getParameters() {

parameters.add(Params.VERBOSE);

// Ablation
parameters.add(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION);

return parameters;
}

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6 changes: 0 additions & 6 deletions tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Fci.java
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Expand Up @@ -112,9 +112,6 @@ public Graph runSearch(DataModel dataModel, Parameters parameters) {
search.setStable(parameters.getBoolean(Params.STABLE_FAS));
search.setRepairFaultyPag(parameters.getBoolean(Params.REPAIR_FAULTY_PAG));

// Ablation
search.setLeaveOutFinalOrientation(parameters.getBoolean(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION));

return search.search();
}

Expand Down Expand Up @@ -169,9 +166,6 @@ public List<String> getParameters() {
parameters.add(Params.TIME_LAG);
parameters.add(Params.REPAIR_FAULTY_PAG);

// Ablation
parameters.add(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION);

parameters.add(Params.VERBOSE);

return parameters;
Expand Down
8 changes: 2 additions & 6 deletions tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/FciMax.java
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Expand Up @@ -108,11 +108,9 @@ public Graph runSearch(DataModel dataModel, Parameters parameters) {
search.setDoDiscriminatingPathColliderRule(parameters.getBoolean(Params.DO_DISCRIMINATING_PATH_COLLIDER_RULE));
search.setPossibleMsepSearchDone(parameters.getBoolean(Params.POSSIBLE_MSEP_DONE));
search.setPcHeuristicType(pcHeuristicType);
search.setRepairFaultyPag(parameters.getBoolean(Params.REPAIR_FAULTY_PAG));
search.setVerbose(parameters.getBoolean(Params.VERBOSE));

// Ablation
search.setLeaveOutFinalOrientation(parameters.getBoolean(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION));

return search.search();
}

Expand Down Expand Up @@ -162,14 +160,12 @@ public List<String> getParameters() {
parameters.add(Params.DO_DISCRIMINATING_PATH_TAIL_RULE);
parameters.add(Params.DO_DISCRIMINATING_PATH_COLLIDER_RULE);
parameters.add(Params.POSSIBLE_MSEP_DONE);
parameters.add(Params.REPAIR_FAULTY_PAG);
// parameters.add(Params.PC_HEURISTIC);
parameters.add(Params.TIME_LAG);

parameters.add(Params.VERBOSE);

// Ablation
parameters.add(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION);

return parameters;
}

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10 changes: 2 additions & 8 deletions tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Gfci.java
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Expand Up @@ -105,12 +105,9 @@ public Graph runSearch(DataModel dataModel, Parameters parameters) {
search.setDoDiscriminatingPathTailRule(parameters.getBoolean(Params.DO_DISCRIMINATING_PATH_TAIL_RULE));
search.setDoDiscriminatingPathColliderRule(parameters.getBoolean(Params.DO_DISCRIMINATING_PATH_COLLIDER_RULE));
search.setNumThreads(parameters.getInt(Params.NUM_THREADS));
search.setRepairFaultyPag(parameters.getBoolean(Params.REPAIR_FAULTY_PAG));
search.setRepairFaultyPag(parameters.getBoolean(Params.REMOVE_ALMOST_CYCLES));
search.setOut(System.out);

// Ablation
search.setAblationLeaveOutFinalOrientation(parameters.getBoolean(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION));

return search.search();
}

Expand Down Expand Up @@ -166,12 +163,9 @@ public List<String> getParameters() {
parameters.add(Params.DO_DISCRIMINATING_PATH_COLLIDER_RULE);
parameters.add(Params.POSSIBLE_MSEP_DONE);
parameters.add(Params.TIME_LAG);
parameters.add(Params.REPAIR_FAULTY_PAG);
parameters.add(Params.REMOVE_ALMOST_CYCLES);
parameters.add(Params.NUM_THREADS);

// Ablation
parameters.add(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION);

parameters.add(Params.VERBOSE);
return parameters;
}
Expand Down
10 changes: 2 additions & 8 deletions tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/GraspFci.java
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Expand Up @@ -132,12 +132,9 @@ public Graph runSearch(DataModel dataModel, Parameters parameters) {

// General
search.setVerbose(parameters.getBoolean(Params.VERBOSE));
search.setRepairFaultyPag(parameters.getBoolean(Params.REPAIR_FAULTY_PAG));
search.setRepairFaultyPag(parameters.getBoolean(Params.REMOVE_ALMOST_CYCLES));
search.setKnowledge(this.knowledge);

// Ablation
search.setLeaveOutFinalOrientation(parameters.getBoolean(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION));

return search.search();
}

Expand Down Expand Up @@ -204,12 +201,9 @@ public List<String> getParameters() {
// General
params.add(Params.TIME_LAG);
params.add(Params.SEED);
params.add(Params.REPAIR_FAULTY_PAG);
params.add(Params.REMOVE_ALMOST_CYCLES);
params.add(Params.VERBOSE);

// Ablation
params.add(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION);

return params;
}

Expand Down
12 changes: 6 additions & 6 deletions tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/LvLite.java
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Original file line number Diff line number Diff line change
Expand Up @@ -153,11 +153,11 @@ public Graph runSearch(DataModel dataModel, Parameters parameters) {
search.setDepth(parameters.getInt(Params.DEPTH));
search.setMaxDdpPathLength(parameters.getInt(Params.MAX_PATH_LENGTH));
search.setTestTimeout(parameters.getLong(Params.TEST_TIMEOUT));
search.setRepairFaultyPag(parameters.getBoolean(Params.REPAIR_FAULTY_PAG));

// Ablation
search.setAblationLeaveOutTestingStep(parameters.getBoolean(Params.ABLATION_LEAVE_OUT_TESTING_STEP));
// search.ablationSetLeaveOutFinalOrientation(parameters.getBoolean(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION));

search.setAblationLeaveOutScoringStep(parameters.getBoolean(Params.ABLATION_LEAVE_OUT_SCORING_STEP));
search.setAblationLeaveOutTestingStep(parameters.getBoolean(Params.ABLATION_LEAVE_OUT_TESTING_STEPS));

if (parameters.getInt(Params.LV_LITE_STARTS_WITH) == 1) {
search.setStartWith(edu.cmu.tetrad.search.LvLite.START_WITH.BOSS);
Expand All @@ -170,7 +170,6 @@ public Graph runSearch(DataModel dataModel, Parameters parameters) {
// General
search.setVerbose(parameters.getBoolean(Params.VERBOSE));
search.setKnowledge(this.knowledge);
search.setRepairFaultyPag(parameters.getBoolean(Params.REPAIR_FAULTY_PAG));

return search.search();
}
Expand Down Expand Up @@ -231,12 +230,13 @@ public List<String> getParameters() {
params.add(Params.GRASP_DEPTH);
params.add(Params.MAX_BLOCKING_PATH_LENGTH);
params.add(Params.DEPTH);
params.add(Params.ABLATION_LEAVE_OUT_TESTING_STEP);
params.add(Params.ABLATION_LEAVE_OUT_SCORING_STEP);
params.add(Params.ABLATION_LEAVE_OUT_TESTING_STEPS);
params.add(Params.MAX_PATH_LENGTH);
params.add(Params.REPAIR_FAULTY_PAG);

// General
params.add(Params.TIME_LAG);
params.add(Params.REPAIR_FAULTY_PAG);
params.add(Params.VERBOSE);
params.add(Params.TEST_TIMEOUT);

Expand Down
6 changes: 0 additions & 6 deletions tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Rfci.java
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Original file line number Diff line number Diff line change
Expand Up @@ -98,9 +98,6 @@ public Graph runSearch(DataModel dataModel, Parameters parameters) {
search.setMaxPathLength(parameters.getInt(Params.MAX_PATH_LENGTH));
search.setVerbose(parameters.getBoolean(Params.VERBOSE));

// Ablation
search.setLeaveOutFinalOrientation(parameters.getBoolean(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION));

return search.search();
}

Expand Down Expand Up @@ -146,9 +143,6 @@ public List<String> getParameters() {

parameters.add(Params.VERBOSE);

// Ablation
parameters.add(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION);

return parameters;
}

Expand Down
14 changes: 5 additions & 9 deletions tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/SpFci.java
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Expand Up @@ -112,22 +112,20 @@ public Graph runSearch(DataModel dataModel, Parameters parameters) {
search.setKnowledge(this.knowledge);
search.setMaxPathLength(parameters.getInt(Params.MAX_PATH_LENGTH));
search.setCompleteRuleSetUsed(parameters.getBoolean(Params.COMPLETE_RULE_SET_USED));
search.setDoDiscriminatingPathColliderRule(parameters.getBoolean(Params.DO_DISCRIMINATING_PATH_COLLIDER_RULE));
search.setDoDiscriminatingPathTailRule(parameters.getBoolean(Params.DO_DISCRIMINATING_PATH_TAIL_RULE));
search.setDoDiscriminatingPathCollideRule(parameters.getBoolean(Params.DO_DISCRIMINATING_PATH_COLLIDER_RULE));
search.setRepairFaultyPag(parameters.getBoolean(Params.REPAIR_FAULTY_PAG));
search.setVerbose(parameters.getBoolean(Params.VERBOSE));
search.setOut(System.out);

// Ablation
search.setLeaveOutFinalOrientation(parameters.getBoolean(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION));

return search.search();
}

/**
* Returns the comparison graph created by converting a true directed graph into a partially directed acyclic graph
* (PAG).
*
* @param graph The true directed graph, if there is one.
* @param graph The true, directed graph, if there is one.
* @return The comparison graph as a partially directed acyclic graph (PAG).
*/
@Override
Expand Down Expand Up @@ -168,15 +166,13 @@ public List<String> getParameters() {
params.add(Params.SEPSET_FINDER_METHOD);
params.add(Params.MAX_PATH_LENGTH);
params.add(Params.COMPLETE_RULE_SET_USED);
params.add(Params.DO_DISCRIMINATING_PATH_TAIL_RULE);
params.add(Params.DO_DISCRIMINATING_PATH_COLLIDER_RULE);
params.add(Params.DO_DISCRIMINATING_PATH_TAIL_RULE);
params.add(Params.DEPTH);
params.add(Params.TIME_LAG);
params.add(Params.REPAIR_FAULTY_PAG);
params.add(Params.VERBOSE);

// Ablation
params.add(Params.ABLATATION_LEAVE_OUT_FINAL_ORIENTATION);

// Flags
params.add(Params.VERBOSE);

Expand Down
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