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integraal/integraal-explanation/src/main/java/fr/boreal/explanation/api/explainers/AtomicQueryExplainer.java
Edit View file @ 6c20e6d0
......@@ -28,7 +28,8 @@ public interface AtomicQueryExplainer<ExplanationType> extends QueryExplainer<Ex
/**
* Runs the pipeline (with timing) on the given dataset and queries.
*/
void pipelineWithTimer(String datasetName, Collection<Atom> queries);
void pipelineWithTimerDetailed(String datasetName, Collection<Atom> queries);
void pipelineIn2StepsWithTimer(String datasetName, Collection<Atom> queries);
}
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/configuration/StatsUtil.java
Edit View file @ 6c20e6d0
package fr.boreal.explanation.configuration;
import com.opencsv.CSVWriter;
import fr.boreal.model.kb.api.KnowledgeBase;
import java.io.ByteArrayOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintStream;
import java.nio.charset.StandardCharsets;
import java.util.*;
public class StatsUtil {
......@@ -13,8 +17,8 @@ public class StatsUtil {
static Map<String, Map<String, Map<String, Long>>> timingRecords = new TreeMap<>();
static Map<String, LinkedHashSet<String>> operationOrder = new HashMap<>();
static LinkedHashSet<String> datasetOrder = new LinkedHashSet<>();
static Map<String, Integer> datasetToFBsize = new HashMap<>();
static Map<String, Integer> rbSize = new HashMap<>();
static Map<String, Long> datasetToFBsize = new HashMap<>();
static Map<String, Integer> datasetToRBsize = new HashMap<>();
static Map<String, Integer> avgExplanationNbPerQuery = new HashMap<>();
......@@ -27,7 +31,7 @@ public class StatsUtil {
* @param operation A label describing what is being timed (e.g. "Transforming rules").
* @param datasetName The identifier for the dataset (e.g. "Dataset1").
*/
public static void timer(Runnable function, String explainerName, String operation, String datasetName) {
public static void timerSumAllQueries(Runnable function, String explainerName, String operation, String datasetName) {
long startTime = System.currentTimeMillis();
function.run();
long elapsedTime = System.currentTimeMillis() - startTime;
......@@ -40,11 +44,7 @@ public class StatsUtil {
.computeIfAbsent(explainerName, ignore -> new HashMap<>())
.computeIfAbsent(operation, ignore -> new HashMap<>());
if (!datasetNameToTime.containsKey(datasetName)) {
datasetNameToTime.put(datasetName, elapsedTime);
} else {
datasetNameToTime.put(datasetName, datasetNameToTime.get(datasetName) + elapsedTime);
}
datasetNameToTime.merge(datasetName, elapsedTime, Long::sum);
// Keep track of the order of execution
operationOrder.computeIfAbsent(explainerName, ignore -> new LinkedHashSet<>()).add(operation);
......@@ -52,12 +52,205 @@ public class StatsUtil {
// Keep track of the order of datasets
datasetOrder.add(datasetName);
}
public static void recordFBSize(String datasetName, int FBSize) {
};
public static void timerPerEachQuery(Runnable function,
String explainerName,
String operation,
String datasetName) {
long elapsedTime = -1;
if (function != null) {
long startTime = System.currentTimeMillis();
function.run();
elapsedTime = System.currentTimeMillis() - startTime;
}
System.out.printf("[Dataset=%s] %s took %d ms%n",
datasetName, operation, elapsedTime);
// 1) get-or-create the map of op-names → (dataset → time)
Map<String, Map<String, Long>> opsMap =
timingRecords.computeIfAbsent(explainerName, k -> new TreeMap<>());
// 2) count existing invocations for this op *and* this dataset
long existingCount = opsMap.entrySet().stream()
.filter(e -> {
String key = e.getKey();
boolean matchesBaseOrNumbered =
key.equals(operation) ||
key.startsWith(operation + " #");
return matchesBaseOrNumbered
&& e.getValue().containsKey(datasetName);
})
.count();
// 3) build the numbered name (first call uses bare name)
String numberedOp = existingCount == 0
? operation
: operation + " #" + existingCount;
// 4) record under that new key
Map<String, Long> datasetToTime = opsMap
.computeIfAbsent(numberedOp, k -> new TreeMap<>());
datasetToTime.put(datasetName, elapsedTime);
// 5) maintain execution order
operationOrder
.computeIfAbsent(explainerName, k -> new LinkedHashSet<>())
.add(numberedOp);
datasetOrder.add(datasetName);
}
public static void timerChasePerEachQuery(Runnable function,
KnowledgeBase kb,
String explainerName,
String operation,
String datasetName) {
long elapsedTime = -1;
long factBaseBefore = -1;
long factBaseAfter = -1;
int ruleBaseBefore = -1;
int ruleBaseAfter = -1;
if (function != null) {
factBaseBefore = kb.getFactBase().size();
ruleBaseBefore = kb.getRuleBase().getRules().size();
long startTime = System.currentTimeMillis();
function.run();
elapsedTime = System.currentTimeMillis() - startTime;
factBaseAfter = kb.getFactBase().size();
ruleBaseAfter = kb.getRuleBase().getRules().size();
}
System.out.printf("[Dataset=%s] %s took %d ms%n", datasetName, operation, elapsedTime);
// 1) Get or create timing records map
Map<String, Map<String, Long>> opsMap =
timingRecords.computeIfAbsent(explainerName, k -> new TreeMap<>());
// 2) Count existing invocations for this op and dataset
long existingCount = opsMap.entrySet().stream()
.filter(e -> {
String key = e.getKey();
boolean matchesBaseOrNumbered =
key.equals(operation) || key.startsWith(operation + " #");
return matchesBaseOrNumbered && e.getValue().containsKey(datasetName);
})
.count();
// 3) Create numbered op name
String numberedOp = existingCount == 0
? operation
: operation + " #" + existingCount;
// 4) Record execution time
Map<String, Long> datasetToTime = opsMap.computeIfAbsent(numberedOp, k -> new TreeMap<>());
datasetToTime.put(datasetName, elapsedTime);
// 5) Record fact base sizes
recordSize(explainerName, "sizeFactBaseBefore " + numberedOp, datasetName, factBaseBefore);
recordSize(explainerName, "sizeFactBaseAfter " + numberedOp, datasetName, factBaseAfter);
// 6) Record rule base sizes
recordSize(explainerName, "sizeRuleBaseBefore " + numberedOp, datasetName, ruleBaseBefore);
recordSize(explainerName, "sizeRuleBaseAfter " + numberedOp, datasetName, ruleBaseAfter);
// 7) Maintain execution order
LinkedHashSet<String> opOrderSet = operationOrder.computeIfAbsent(explainerName, k -> new LinkedHashSet<>());
opOrderSet.add(numberedOp);
opOrderSet.add("sizeFactBaseBefore " + numberedOp);
opOrderSet.add("sizeFactBaseAfter " + numberedOp);
opOrderSet.add("sizeRuleBaseBefore " + numberedOp);
opOrderSet.add("sizeRuleBaseAfter " + numberedOp);
datasetOrder.add(datasetName);
}
// Helper to store size under appropriate key
private static void recordSize(String explainerName, String fullKey, String datasetName, long size) {
Map<String, Map<String, Long>> sizeMap =
timingRecords.computeIfAbsent(explainerName, k -> new TreeMap<>());
Map<String, Long> datasetMap = sizeMap.computeIfAbsent(fullKey, k -> new TreeMap<>());
datasetMap.put(datasetName, size);
}
public static void timerMarcoAllQueries(
Runnable function,
String explainerName,
String operation,
String datasetName
) {
// 1) Capture everything sent to System.out
ByteArrayOutputStream baos = new ByteArrayOutputStream();
PrintStream oldOut = System.out;
System.setOut(new PrintStream(baos, true));
// 2) Run the function (it prints its own stats to stdout)
long startTime = System.currentTimeMillis();
function.run();
long elapsedTime = System.currentTimeMillis() - startTime;
// 3) Restore stdout
System.out.flush();
System.setOut(oldOut);
// 4) Extract the captured text
String stdout = baos.toString(StandardCharsets.UTF_8);
// 5) Parse the first “total : X.XXX” line
double totalSeconds = parseTotalSeconds(stdout);
// 6) Convert to milliseconds (long)
long totalMs = Math.round(totalSeconds * 1000);
// 7) (Optional) print a summary
System.out.printf(
"[Dataset=%s] %s total = %.3f s → %d ms%n",
datasetName, operation, totalSeconds, totalMs
);
// 8) Record _only_ the total-ms into your map
Map<String, Long> datasetTimeMap = timingRecords
.computeIfAbsent(explainerName, k -> new HashMap<>())
.computeIfAbsent(operation, k -> new HashMap<>());
datasetTimeMap.merge(datasetName, totalMs, Long::sum);
// 9) Keep your ordering structures exactly as before
operationOrder
.computeIfAbsent(explainerName, k -> new LinkedHashSet<>())
.add(operation);
datasetOrder.add(datasetName);
}
private static double parseTotalSeconds(String stdout) {
for (String line : stdout.split("\\r?\\n")) {
String trimmed = line.trim();
if (trimmed.startsWith("total")) {
int colon = trimmed.indexOf(':');
if (colon >= 0 && colon + 1 < trimmed.length()) {
String numPart = trimmed.substring(colon + 1).trim();
return Double.parseDouble(numPart);
}
}
}
throw new IllegalStateException(
"Could not find a line beginning with 'total:' in:\n" + stdout
);
}
public static void recordFBSize(String datasetName, long FBSize) {
datasetToFBsize.put(datasetName, FBSize);
};
public static void recordRBSize(String datasetName, int RBSize) {
datasetToRBsize.put(datasetName, RBSize);
};
/**
* Exports pivoted timings so that:
......@@ -77,20 +270,28 @@ public class StatsUtil {
columns.addAll(datasetOrder);
writer.writeNext(columns.toArray(new String[0]));
// 2) Record # Rules & # Facts
// for (String datasetName : datasetOrder) {
// if (operationToRecord.containsKey(datasetName)) {
// row.add(operationToRecord.get(datasetName).toString());
// } else {
// row.add("");
// }
// }
// 2) Write RB and FB Size
List<String> row = new ArrayList<>();
row.add("");
row.add("");
for (String datasetName : datasetOrder) {
if (datasetToFBsize.containsKey(datasetName) && datasetToRBsize.containsKey(datasetName)) {
row.add(datasetToFBsize.get(datasetName).toString() + "," + datasetToRBsize.get(datasetName).toString());
} else {
row.add("");
}
}
writer.writeNext(row.toArray(new String[0]));
// 3) For each explainer
for (String explainerName : timingRecords.keySet()) {
// For each operation for this explainer
writer.writeNext(new String[0]);
if (operationOrder.get(explainerName) == null) {
throw new IllegalStateException("No operations for explainer " + explainerName);
}
for (String operation : operationOrder.get(explainerName)) {
// Print explainer name and operation name
Map<String, Long> operationToRecord = timingRecords.get(explainerName).get(operation);
......@@ -99,14 +300,19 @@ public class StatsUtil {
continue;
}
List<String> row = new ArrayList<>();
row = new ArrayList<>();
row.add(explainerName);
row.add(operation);
// Then print all dataset values in order
for (String datasetName : datasetOrder) {
if (operationToRecord.containsKey(datasetName)) {
row.add(operationToRecord.get(datasetName).toString());
long value = operationToRecord.get(datasetName);
if (value < 0) {
row.add("_");
} else {
row.add(operationToRecord.get(datasetName).toString());
}
} else {
row.add("");
}
......
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/configuration/query_selection/QuerySelector.java
Edit View file @ 6c20e6d0
package fr.boreal.explanation.configuration.query_selection;
import fr.boreal.explanation.configuration.DefaultChaseForExplanations;
import fr.boreal.forward_chaining.chase.Chase;
import fr.boreal.forward_chaining.chase.ChaseBuilder;
import fr.boreal.model.kb.api.FactBase;
import fr.boreal.model.kb.api.KnowledgeBase;
import fr.boreal.model.kb.api.RuleBase;
import fr.boreal.model.kb.impl.RuleBaseImpl;
import fr.boreal.model.logicalElements.api.Atom;
import fr.boreal.model.logicalElements.api.Constant;
import fr.boreal.model.logicalElements.api.Predicate;
import fr.boreal.model.logicalElements.impl.AtomImpl;
import fr.boreal.model.rule.api.FORule;
import fr.boreal.storage.natives.SimpleInMemoryGraphStore;
import java.util.*;
import java.util.Collections;
import java.util.stream.Collectors;
public class QuerySelector {
// public static Optional<Collection<Atom>> select(KnowledgeBase kb, int nbFacts, Boolean explainFacts) {
// Collection<FORule> rules = new ArrayList<FORule>(kb.getRuleBase().getRules());
//
// RuleBase rb = new RuleBaseImpl(rules);
// FactBase fb = new SimpleInMemoryGraphStore(kb.getFactBase().getAtoms().collect(Collectors.toList()));
//
// KnowledgeBase kbCopy = Utils.copyKnowledgeBase(kb);
//
// Collection<Atom> predicateConstantAtoms = new ArrayList<Atom>();
// Collection<Constant> predicateConstants = new ArrayList<Constant>();
//
// if (!explainFacts) {
// for (FORule ruleToConstant : kbCopy.getRuleBase().getRules()) {
// for (Predicate predicateToConstant : ruleToConstant.getBody().getPredicates()) {
// if (predicateToConstant.getArity() == 1) {
// Constant constantPred = termFactory.createOrGetConstant("CONS_"+predicateToConstant.toString());
// Atom predicateConstantAtom = new AtomImpl(predicateToConstant, constantPred);
//
// kbCopy.getFactBase().add(predicateConstantAtom);
// predicateConstantAtoms.add(predicateConstantAtom);
// predicateConstants.add(constantPred);}
// }
// }
// }
//
// Chase chase = DefaultChaseForExplanations.chase(kb);
//
// int depth = 0;
//
// List<Set<Atom>> foundAxiomEntailments = new ArrayList<>();
//
// foundAxiomEntailments.add(new HashSet<>());
//
// chase.applyGlobalPretreatments();
//
// while (chase.hasNextStep()) {
// chase.applyPretreatments();
// chase.nextStep();
// chase.applyEndOfStepTreatments();
// depth++;
// foundAxiomEntailments.add(chase
// .getLastStepResults()
// .created_facts_as_factbase()
// .getAtoms()
// .collect(Collectors.toSet()));
// }
//
// System.out.println(foundAxiomEntailments);
// if (kbCopy.getFactBase().size() - predicateConstantAtoms.size() > nbFacts) {
// List<Atom> selectedAtoms = new ArrayList<>();
// for (int i = foundAxiomEntailments.size()-1; selectedAtoms.size() < nbFacts; i--) {
// if (i == -1) {
// System.out.println("Doesn't have enough entailments");
// return Optional.empty();
// } else {
// for (Atom a : foundAxiomEntailments.get(i)) {
// selectedAtoms.add(a);
// if (selectedAtoms.size() == nbFacts) {
// return Optional.of(selectedAtoms);
// }
// }
// }
// }
// }
//
// System.out.println("Doesn't have enough entailments");
// return Optional.empty();
// }
private static final Random RANDOM = new Random();
public static List<Atom> selectQueries(KnowledgeBase kb) {
Collection<FORule> rules = new ArrayList<FORule>(kb.getRuleBase().getRules());
RuleBase rb = new RuleBaseImpl(rules);
FactBase fb = new SimpleInMemoryGraphStore(kb.getFactBase().getAtoms().collect(Collectors.toList()));
Chase chase = ChaseBuilder.defaultBuilder(fb, rb)
.useObliviousChecker()
.useNaiveComputer()
.useByPredicateRuleScheduler()
.useBreadthFirstApplier()
.build().get();
List<List<Atom>> foundAxiomEntailments = new ArrayList<>();
chase.applyGlobalPretreatments();
while (chase.hasNextStep()) {
chase.applyPretreatments();
chase.nextStep();
chase.applyEndOfStepTreatments();
List<Atom> factsProduced = chase
.getLastStepResults()
.created_facts_as_factbase()
.getAtoms()
.collect(Collectors.toList());
if (!factsProduced.isEmpty()) {
foundAxiomEntailments.add(factsProduced);
}
}
List<Atom> queries = sampleQueries(foundAxiomEntailments);
Collections.shuffle(queries, RANDOM);
return queries;
}
public static List<Atom> sampleQueries(List<List<Atom>> lists) {
if (lists == null || lists.isEmpty()) {
throw new IllegalArgumentException("The outer list must not be null or empty.");
}
// how many to pick from each
final int FIRST_COUNT = 1;
final int MID_COUNT = 1;
final int LAST_COUNT = 8;
List<Atom> result = new ArrayList<>(FIRST_COUNT + MID_COUNT + LAST_COUNT);
// 1) First list
result.addAll(sampleList(lists.get(0), FIRST_COUNT));
// 2) Middle list (e.g. index = size()/2 gives 5th list when size=9)
int midIndex = lists.size() / 2;
result.addAll(sampleList(lists.get(midIndex), MID_COUNT));
// 3) Last list
result.addAll(sampleList(lists.get(lists.size() - 1), LAST_COUNT));
return result;
}
/**
* Helper to sample exactly `count` items from `list`.
* If list.size() >= count, sampling is done without replacement;
* otherwise with replacement.
*/
private static List<Atom> sampleList(List<Atom> list, int count) {
if (list == null || list.isEmpty()) {
throw new IllegalArgumentException("Sublists must not be null or empty.");
}
List<Atom> picked = new ArrayList<>(count);
if (list.size() >= count) {
// shuffle a copy and take the first 'count' items
List<Atom> copy = new ArrayList<>(list);
Collections.shuffle(copy, RANDOM);
for (int i = 0; i < count; i++) {
picked.add(copy.get(i));
}
} else {
// not enough items: sample with replacement
for (int i = 0; i < count; i++) {
picked.add(list.get(RANDOM.nextInt(list.size())));
}
}
return picked;
}
}
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/kb_gri/explainers/dynamic_gri/AbstractDynamicGRIBasedExplainer_KBGRI.java
Edit View file @ 6c20e6d0
......@@ -85,7 +85,11 @@ public abstract class AbstractDynamicGRIBasedExplainer_KBGRI<ExplanationType> im
abstract ExplanationProcessor_GRI getGMUSProcessor(Solver solver);
@Override
public void pipelineWithTimer(String datasetName, Collection<Atom> queries) {
public void pipelineWithTimerDetailed(String datasetName, Collection<Atom> queries) {
throw new NotImplementedException();
}
@Override
public void pipelineIn2StepsWithTimer(String datasetName, Collection<Atom> queries) {
throw new NotImplementedException();
}
// abstract RuleTransformer getRuleTransformer();
......
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/kb_gri/explainers/incremental_gri/AbstractIncrementalGRIBasedExplainer_KBGRI.java
Edit View file @ 6c20e6d0
......@@ -100,6 +100,10 @@ public abstract class AbstractIncrementalGRIBasedExplainer_KBGRI<ExplanationType
this.solver = solver;
}
public void staticStep() {
// there is no static step (placeholder for static util)
}
public void dynamicStep(Atom query) {
......@@ -117,11 +121,14 @@ public abstract class AbstractIncrementalGRIBasedExplainer_KBGRI<ExplanationType
if (seenRules.isEmpty()) {
transformRulesForFirstStaticKB();
chaseKBforGRI();
} else if (!seenRules.containsAll(queryAncestorRules)) {
transformUnseenRules();
chaseKBforGRI();
}
chaseKBforGRI();
// REL tracing
prepareRelTracing(query);
......@@ -143,66 +150,85 @@ public abstract class AbstractIncrementalGRIBasedExplainer_KBGRI<ExplanationType
}
public void pipelineWithTimer(String datasetName, Collection<Atom> queries) {
public void pipelineWithTimerDetailed(String datasetName, Collection<Atom> queries) {
String explainerName = this.getClass().getSimpleName() + " + " + this.solver.getClass().getSimpleName();
StatsUtil.timer(this::recordInitialFactbase, explainerName, "recordInitialFactbase", datasetName);
StatsUtil.timerSumAllQueries(this::recordInitialFactbase, explainerName, "recordInitialFactbase", datasetName);
for (Atom query : queries) {
StatsUtil.timer(() -> checkQueryInInitialFB(query), explainerName,
StatsUtil.timerSumAllQueries(() -> checkQueryInInitialFB(query), explainerName,
"checkQueryInInitialFB", datasetName);
if (!queryInInitialFB) {
if (queryAncestorRules != null) {
StatsUtil.timer(this::clearAncestorRules, explainerName,
StatsUtil.timerSumAllQueries(this::clearAncestorRules, explainerName,
"clearAncestorRules", datasetName);
}
StatsUtil.timer(() -> computeAncestorRules(query), explainerName,
StatsUtil.timerPerEachQuery(() -> computeAncestorRules(query), explainerName,
"computeAncestorRules", datasetName);
if (seenRules.isEmpty()) {
StatsUtil.timer(() -> transformRulesForFirstStaticKB(), explainerName,
StatsUtil.timerPerEachQuery(() -> transformRulesForFirstStaticKB(), explainerName,
"Transforming the rules for building GRI for first query", datasetName);
StatsUtil.timerChasePerEachQuery(this::chaseKBforGRI, staticKB, explainerName,
"chaseKBforGRI", datasetName);
StatsUtil.timerPerEachQuery(null, explainerName,
"Transforming the rules previously unseen", datasetName);
} else if (!seenRules.containsAll(queryAncestorRules)) {
StatsUtil.timer(() -> transformUnseenRules(), explainerName,
StatsUtil.timerPerEachQuery(this::transformUnseenRules, explainerName,
"Transforming the rules previously unseen", datasetName);
StatsUtil.timerChasePerEachQuery(this::chaseKBforGRI, staticKB, explainerName,
"chaseKBforGRI", datasetName);
} else {
StatsUtil.timerPerEachQuery(null, explainerName,
"Transforming the rules previously unseen", datasetName);
StatsUtil.timerChasePerEachQuery(null, staticKB, explainerName,
"chaseKBforGRI", datasetName);
}
StatsUtil.timer(this::chaseKBforGRI, explainerName,
"chaseKBforGRI", datasetName);
// filtering
StatsUtil.timer(() -> prepareRelTracing(query), explainerName,
StatsUtil.timerSumAllQueries(() -> prepareRelTracing(query), explainerName,
"prepareRelTracing", datasetName);
StatsUtil.timer(this::chaseForRELPropagation, explainerName,
StatsUtil.timerChasePerEachQuery(this::chaseForRELPropagation, dynamicKB, explainerName,
"chaseForRELPropagation", datasetName);
StatsUtil.timer(() -> encodeClauses(query), explainerName,
StatsUtil.timerSumAllQueries(() -> encodeClauses(query), explainerName,
"encodeClauses", datasetName);
if (solver instanceof MARCOGMUSSolver) {
StatsUtil.timer(this::writeMarcoGCNF, explainerName,
StatsUtil.timerSumAllQueries(this::writeMarcoGCNF, explainerName,
"writeMarcoGCNF", datasetName);
StatsUtil.timer(this::solveGMUSviaMarco, explainerName,
StatsUtil.timerMarcoAllQueries(this::solveGMUSviaMarco, explainerName,
"solveGMUSviaMarco", datasetName);
StatsUtil.timer(this::decodeGMUSesFromMarco, explainerName,
StatsUtil.timerSumAllQueries(this::decodeGMUSesFromMarco, explainerName,
"decodeGMUSesFromMarco", datasetName);
} else if (solver instanceof Sat4JSolver) {
StatsUtil.timer(this::solveGMUSviaSat4j, explainerName,
StatsUtil.timerSumAllQueries(this::solveGMUSviaSat4j, explainerName,
"solveGMUSviaSat4j", datasetName);
StatsUtil.timer(this::decodeGMUSesFromSat4j, explainerName,
StatsUtil.timerSumAllQueries(this::decodeGMUSesFromSat4j, explainerName,
"decodeGMUSesFromSat4j", datasetName
);
}
} else {
StatsUtil.timer(() -> returnExplanationForQueryInFB(query), explainerName,
StatsUtil.timerSumAllQueries(() -> returnExplanationForQueryInFB(query), explainerName,
"returnExplanationForQueryInFB", datasetName);
}
}
}
public void pipelineIn2StepsWithTimer (String datasetName, Collection<Atom> queries) {
String explainerName = this.getClass().getSimpleName() + " + " + this.solver.getClass().getSimpleName();
StatsUtil.timerPerEachQuery(this::staticStep, explainerName, "Static Step", datasetName);
for (Atom query : queries) {
StatsUtil.timerPerEachQuery(() -> dynamicStep(query), explainerName, "Dynamic Step", datasetName);
}
}
/**
* This methods takes in a query and
* (1) compute queryAncestorRules of the query
......@@ -370,5 +396,8 @@ public abstract class AbstractIncrementalGRIBasedExplainer_KBGRI<ExplanationType
explanations = getGMUSProcessor(solver).translateSAT4JGMUS(sat4jGmuses, encodingResult.factIDMap(), encodingResult.ruleIDMap());
}
public void placeHolder() {
}
abstract ExplanationProcessor_GRI getGMUSProcessor(Solver solver);
}
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/kb_gri/explainers/static_gri/AbstractStaticGRIBasedExplainer_KBGRI.java
Edit View file @ 6c20e6d0
......@@ -144,44 +144,55 @@ public abstract class AbstractStaticGRIBasedExplainer_KBGRI<ExplanationType> imp
* Pipelines
*/
public void pipelineWithTimer(String datasetName, Collection<Atom> queries) {
public void pipelineWithTimerDetailed(String datasetName, Collection<Atom> queries) {
String explainerName = this.getClass().getSimpleName() + " + " + this.solver.getClass().getSimpleName();
StatsUtil.timer(this::transformRules, explainerName, "Transforming rules", datasetName);
StatsUtil.timer(this::prepareKBforGRI, explainerName, "Preparing KB for GRI", datasetName);
StatsUtil.timer(this::chaseKBforGRI, explainerName, "Chasing on staticKB for GRI", datasetName);
StatsUtil.timer(this::recordInitialFactbase, explainerName, "Recording initial factbase", datasetName);
StatsUtil.timerSumAllQueries(this::transformRules, explainerName, "Transforming rules", datasetName);
StatsUtil.timerSumAllQueries(this::prepareKBforGRI, explainerName, "Preparing KB for GRI", datasetName);
StatsUtil.timerPerEachQuery(this::chaseKBforGRI, explainerName, "Chasing on staticKB for GRI", datasetName);
StatsUtil.timerSumAllQueries(this::recordInitialFactbase, explainerName, "Recording initial factbase", datasetName);
for (Atom query : queries) {
if (this.explanations != null) {
StatsUtil.timer(this::dynamicStepClear, explainerName,
StatsUtil.timerSumAllQueries(this::dynamicStepClear, explainerName,
"Clearing gmuses and explanations for the previous query",
datasetName);
}
StatsUtil.timer(() -> checkQueryEntailment(query), explainerName, "Check if query is entailed", datasetName);
StatsUtil.timer(() -> checkQueryInInitialFB(query), explainerName, "Check if query is already in input FB", datasetName);
StatsUtil.timerSumAllQueries(() -> checkQueryEntailment(query), explainerName, "Check if query is entailed", datasetName);
StatsUtil.timerSumAllQueries(() -> checkQueryInInitialFB(query), explainerName, "Check if query is already in input FB", datasetName);
if (queryEntailed && !queryInInitialFB) {
StatsUtil.timer(() -> prepareRelTracing(query), explainerName, "Preparing Rel Tracing", datasetName);
StatsUtil.timer(this::chaseForRELPropagation, explainerName, "Chase For Rel Tracing", datasetName);
StatsUtil.timer(() -> encodeClauses(query), explainerName, "Encoding clauses", datasetName);
StatsUtil.timerSumAllQueries(() -> prepareRelTracing(query), explainerName, "Preparing Rel Tracing", datasetName);
StatsUtil.timerPerEachQuery(this::chaseForRELPropagation, explainerName, "Chase For Rel Tracing", datasetName);
StatsUtil.timerSumAllQueries(() -> encodeClauses(query), explainerName, "Encoding clauses", datasetName);
if (solver instanceof MARCOGMUSSolver) {
StatsUtil.timer(this::writeMarcoGCNF, explainerName, "Writing GCNF", datasetName);
StatsUtil.timer(this::solveGMUSviaMarco, explainerName, "Computing GMUSes", datasetName);
StatsUtil.timer(this::decodeGMUSesFromMarco, explainerName, "Decoding GMUSes", datasetName);
StatsUtil.timerSumAllQueries(this::writeMarcoGCNF, explainerName, "Writing GCNF", datasetName);
StatsUtil.timerMarcoAllQueries(this::solveGMUSviaMarco, explainerName, "Computing GMUSes", datasetName);
StatsUtil.timerSumAllQueries(this::decodeGMUSesFromMarco, explainerName, "Decoding GMUSes", datasetName);
} else if (solver instanceof Sat4JSolver) {
StatsUtil.timer(this::solveGMUSviaSat4j, explainerName, "Computing GMUSes with sat4j", datasetName);
StatsUtil.timer(this::decodeGMUSesFromSat4j, explainerName, "Decoding GMUSes from sat4j", datasetName);
StatsUtil.timerSumAllQueries(this::solveGMUSviaSat4j, explainerName, "Computing GMUSes with sat4j", datasetName);
StatsUtil.timerSumAllQueries(this::decodeGMUSesFromSat4j, explainerName, "Decoding GMUSes from sat4j", datasetName);
}
} else if (queryInInitialFB) {
StatsUtil.timer(() -> returnExplanationForQueryInFB(query), explainerName, "Returning the explanation for query already in FB", datasetName);
StatsUtil.timerSumAllQueries(() -> returnExplanationForQueryInFB(query), explainerName, "Returning the explanation for query already in FB", datasetName);
} else {
returnEmptySetForExplanation();
}
}
}
public void pipelineIn2StepsWithTimer (String datasetName, Collection<Atom> queries) {
String explainerName = this.getClass().getSimpleName() + " + " + this.solver.getClass().getSimpleName();
StatsUtil.timerPerEachQuery(this::staticStep, explainerName, "Static Step", datasetName);
for (Atom query : queries) {
StatsUtil.timerPerEachQuery(() -> dynamicStep(query), explainerName, "Dynamic Step", datasetName);
}
}
/**
* Saturates the GRI with Tracing rules to compute relevant bodyAtoms and triggers for the query.
* Then calls the solver.
......
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/kb_gri/explainers/static_gri_baseline/AbstractStaticGRIBasedExplainer_Baseline.java 0 → 100644
Edit View file @ 6c20e6d0
package fr.boreal.explanation.kb_gri.explainers.static_gri_baseline;
import com.google.common.collect.BiMap;
import fr.boreal.explanation.api.encoders.GSATEncodingResult_GRI;
import fr.boreal.explanation.api.explainers.AtomicQueryExplainer;
import fr.boreal.explanation.api.processors.ExplanationProcessor_GRI;
import fr.boreal.explanation.api.solver.Solver;
import fr.boreal.explanation.configuration.DefaultChaseForExplanations;
import fr.boreal.explanation.configuration.StatsUtil;
import fr.boreal.explanation.kb_gri.rule_transformation.GRIRuleTransformer;
import fr.boreal.explanation.kb_gri.rule_transformation.static_gri.RulesetForStaticGRIBuildingAndTracing;
import fr.boreal.explanation.solving_enumerating.marco.MARCOGMUSSolver;
import fr.boreal.explanation.solving_enumerating.sat4j.Sat4JSolver;
import fr.boreal.model.kb.api.KnowledgeBase;
import fr.boreal.model.kb.impl.KnowledgeBaseImpl;
import fr.boreal.model.logicalElements.api.Atom;
import fr.boreal.model.logicalElements.api.Predicate;
import fr.boreal.model.logicalElements.impl.AtomImpl;
import fr.boreal.model.rule.api.FORule;
import fr.boreal.storage.natives.SimpleInMemoryGraphStore;
import fr.boreal.views.FederatedFactBase;
import java.io.File;
import java.util.Collection;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import static fr.boreal.explanation.configuration.PathFinder.ensureFilePath;
public abstract class AbstractStaticGRIBasedExplainer_Baseline<ExplanationType> implements AtomicQueryExplainer<ExplanationType> {
/**
* Attributes to be defined in the constructor
*/
private final Solver solver;
protected KnowledgeBase inputKB;
private FederatedFactBase federatedFactBase;
/**
* RuleTransforming
*/
GRIRuleTransformer ruleTransformer = GRIRuleTransformer.instance();
private RulesetForStaticGRIBuildingAndTracing transformedRB;
/**
* Static and dynamic knowledge bases
*/
protected KnowledgeBase staticKB;
protected KnowledgeBase dynamicKB;
/**
* Intermediate objects from the pipeline
*/
// check if the static step is done
boolean staticStepDone = false;
// preprocessing
java.util.function.Predicate<Atom> belongsToInitialFactbase;
boolean queryEntailed = false;
boolean queryInInitialFB = false;
// encoding
GSATEncodingResult_GRI encodingResult;
// s4j
Sat4JSolver sat4JSolver = new Sat4JSolver();
List<List<List<Integer>>> sat4jGmuses;
// marco
MARCOGMUSSolver marcoSolver = new MARCOGMUSSolver();
File gcnffile = new File(ensureFilePath("integraal-explanation/gsat.gcnf", "gsat.gcnf"));
// decoding
protected Set explanations;
protected Set<String> gmuses;
/**
* Constructor
*/
public AbstractStaticGRIBasedExplainer_Baseline(KnowledgeBase kb, Solver solver) {
ruleTransformer.clear();
inputKB = kb;
federatedFactBase = new FederatedFactBase(new SimpleInMemoryGraphStore());
this.solver = solver;
}
/**
* Static step
*/
public void staticStep() {
transformRules();
prepareKBforGRI();
chaseKBforGRI();
recordInitialFactbase();
prepareEncoding();
}
/**
* Dynamic step
*
* @param query
*
*/
public void dynamicStep(Atom query) {
if (this.explanations != null) {
dynamicStepClear();
}
checkQueryEntailment(query);
checkQueryInInitialFB(query);
if (queryEntailed & !queryInInitialFB) {
encodeClauses(query);
if (solver instanceof MARCOGMUSSolver) {
writeMarcoGCNF();
solveGMUSviaMarco();
decodeGMUSesFromMarco();
} else if (solver instanceof Sat4JSolver) {
solveGMUSviaSat4j();
decodeGMUSesFromSat4j();
}
} else if (queryInInitialFB) {
returnExplanationForQueryInFB(query);
} else {
returnEmptySetForExplanation();
}
}
private void dynamicStepClear() {
explanations.clear();
if (gmuses != null) {
gmuses.clear();
}
if (sat4jGmuses != null) {
sat4jGmuses.clear();
}
}
/*
* Pipelines
*/
public void pipelineWithTimerDetailed(String datasetName, Collection<Atom> queries) {
String explainerName = this.getClass().getSimpleName() + " + " + this.solver.getClass().getSimpleName();
StatsUtil.timerSumAllQueries(this::transformRules, explainerName, "Transforming rules", datasetName);
StatsUtil.timerSumAllQueries(this::prepareKBforGRI, explainerName, "Preparing KB for GRI", datasetName);
StatsUtil.timerSumAllQueries(this::chaseKBforGRI, explainerName, "Chasing on staticKB for GRI", datasetName);
StatsUtil.timerSumAllQueries(this::recordInitialFactbase, explainerName, "Recording initial factbase", datasetName);
StatsUtil.timerSumAllQueries(this::prepareEncoding, explainerName, "Preparing Encoding", datasetName);
for (Atom query : queries) {
if (this.explanations != null) {
StatsUtil.timerSumAllQueries(this::dynamicStepClear, explainerName,
"Clearing gmuses and explanations for the previous query",
datasetName);
}
StatsUtil.timerSumAllQueries(() -> checkQueryEntailment(query), explainerName, "Check if query is entailed", datasetName);
StatsUtil.timerSumAllQueries(() -> checkQueryInInitialFB(query), explainerName, "Check if query is already in input FB", datasetName);
if (queryEntailed && !queryInInitialFB) {
StatsUtil.timerSumAllQueries(() -> encodeClauses(query), explainerName, "Encoding clauses", datasetName);
if (solver instanceof MARCOGMUSSolver) {
StatsUtil.timerSumAllQueries(this::writeMarcoGCNF, explainerName, "Writing GCNF", datasetName);
StatsUtil.timerMarcoAllQueries(this::solveGMUSviaMarco, explainerName, "Computing GMUSes", datasetName);
StatsUtil.timerSumAllQueries(this::decodeGMUSesFromMarco, explainerName, "Decoding GMUSes", datasetName);
} else if (solver instanceof Sat4JSolver) {
StatsUtil.timerSumAllQueries(this::solveGMUSviaSat4j, explainerName, "Computing GMUSes with sat4j", datasetName);
StatsUtil.timerSumAllQueries(this::decodeGMUSesFromSat4j, explainerName, "Decoding GMUSes from sat4j", datasetName);
}
} else if (queryInInitialFB) {
StatsUtil.timerSumAllQueries(() -> returnExplanationForQueryInFB(query), explainerName, "Returning the explanation for query already in FB", datasetName);
} else {
returnEmptySetForExplanation();
}
}
}
public void pipelineIn2StepsWithTimer (String datasetName, Collection<Atom> queries) {
String explainerName = this.getClass().getSimpleName() + " + " + this.solver.getClass().getSimpleName();
StatsUtil.timerPerEachQuery(this::staticStep, explainerName, "Static Step", datasetName);
for (Atom query : queries) {
StatsUtil.timerPerEachQuery(() -> dynamicStep(query), explainerName, "Dynamic Step", datasetName);
}
}
/**
* Saturates the GRI with Tracing rules to compute relevant bodyAtoms and triggers for the query.
* Then calls the solver.
*
* @param query
* @return
*/
public Set<ExplanationType> getAllExplanations(Atom query) {
if (!staticStepDone) {
staticStep();
staticStepDone = true;
}
dynamicStep(query);
return explanations;
}
public void transformRules() {
this.transformedRB = ruleTransformer.createStaticGRIBuildingRB(inputKB);
}
public void prepareKBforGRI() {
this.staticKB = new KnowledgeBaseImpl(inputKB.getFactBase(), transformedRB.getStaticRuleBase());
}
public void chaseKBforGRI() {
DefaultChaseForExplanations.chase(this.staticKB);
}
public void recordInitialFactbase() {
belongsToInitialFactbase = atom -> staticKB.getFactBase().contains(atom);
}
public void checkQueryEntailment(Atom query) {
Atom queryWithFuncId = GRIRuleTransformer.instance().createAtomWithStoredFnTermIdentifier(query);
if (staticKB.getFactBase().contains(queryWithFuncId)) {
queryEntailed = true;
}
}
public void returnEmptySetForExplanation() {
explanations = Set.of();
}
public void checkQueryInInitialFB(Atom query) {
if (belongsToInitialFactbase.test(query)) {
queryInInitialFB = true;
}
}
public void returnExplanationForQueryInFB(Atom query) {
explanations = getGMUSProcessor(solver).getQueryIsInTheIntitialFactbaseExplanation(query);
}
/**
* Prepares a dynamic KB that can be used for tracing relevant atoms for the input query.
* The dynamic KB uses a federated factbase ; inferences will be put on the local storage, which can be eas
*/
public void prepareEncoding() {
SimpleInMemoryGraphStore encodingFB = new SimpleInMemoryGraphStore();
BiMap<FORule, Predicate> ruleToEdgePredicateMap = ruleTransformer.getRuleToEdgePredicateMap();
BiMap<FORule, Predicate> ruleToRelEdgePredicateMap = ruleTransformer.getRuleToRelEdgePredicateMap();
for (Iterator<Predicate> itp = staticKB.getFactBase().getPredicates(); itp.hasNext(); ) {
Predicate p = itp.next();
if (p.label().endsWith("+")) {
for (Iterator<Atom> ita = staticKB.getFactBase().getAtomsByPredicate(p); ita.hasNext(); ) {
Atom a = ita.next();
encodingFB.add(new AtomImpl(GRIRuleTransformer.REL, a.getTerm(a.getPredicate().arity() - 1)));
}
}
}
for (FORule r : inputKB.getRuleBase().getRules()) {
Predicate p = ruleToEdgePredicateMap.get(r);
for (Iterator<Atom> ita = staticKB.getFactBase().getAtomsByPredicate(p); ita.hasNext(); ) {
Atom a = ita.next();
encodingFB.add(new AtomImpl(ruleToRelEdgePredicateMap.get(r), a.getTerms()));
}
}
dynamicKB = new KnowledgeBaseImpl(encodingFB, transformedRB.getDynamicRuleBase());
}
public void encodeClauses(Atom query) {
encodingResult = getGMUSProcessor(solver).getEncoder().encode(dynamicKB, query, belongsToInitialFactbase);
}
public void writeMarcoGCNF() {
marcoSolver.writeGCNF(encodingResult.propVarIDMap(), encodingResult.clauses(), encodingResult.nbGroup());
}
public void solveGMUSviaMarco() {
gmuses = marcoSolver.getGMUSes(gcnffile);
}
public void decodeGMUSesFromMarco() {
explanations = getGMUSProcessor(solver).translateMARCOGMUS(gmuses, encodingResult.factIDMap(), encodingResult.ruleIDMap());
}
public void solveGMUSviaSat4j() {
sat4jGmuses = sat4JSolver.enumerateGMUSes(encodingResult.clauses());
}
public void decodeGMUSesFromSat4j() {
explanations = getGMUSProcessor(solver).translateSAT4JGMUS(sat4jGmuses, encodingResult.factIDMap(), encodingResult.ruleIDMap());
}
abstract ExplanationProcessor_GRI getGMUSProcessor(Solver solver);
}
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/kb_gri/explainers/static_gri_baseline/FactSupportExplainer_Baseline.java 0 → 100644
Edit View file @ 6c20e6d0
package fr.boreal.explanation.kb_gri.explainers.static_gri_baseline;
import fr.boreal.explanation.api.processors.ExplanationProcessor_GRI;
import fr.boreal.explanation.api.solver.Solver;
import fr.boreal.explanation.kb_gri.processors.FactSupportGMUSProcessor_KBGRI;
import fr.boreal.explanation.solving_enumerating.marco.MARCOGMUSSolver;
import fr.boreal.model.kb.api.FactBase;
import fr.boreal.model.kb.api.KnowledgeBase;
/**
* Computes fact-support explanations for a knowledge base and a ground atomic query
*/
public class FactSupportExplainer_Baseline extends AbstractStaticGRIBasedExplainer_Baseline<FactBase> {
public FactSupportExplainer_Baseline(KnowledgeBase kb) {
super(kb, new MARCOGMUSSolver());
}
public FactSupportExplainer_Baseline(KnowledgeBase kb, Solver solver) {
super(kb, solver);
}
@Override
ExplanationProcessor_GRI getGMUSProcessor(Solver solver) {
return new FactSupportGMUSProcessor_KBGRI(solver);
}
}
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/kb_gri/explainers/static_gri_baseline/KBSupportExplainer_Baseline.java 0 → 100644
Edit View file @ 6c20e6d0
package fr.boreal.explanation.kb_gri.explainers.static_gri_baseline;
import fr.boreal.explanation.api.processors.ExplanationProcessor_GRI;
import fr.boreal.explanation.api.solver.Solver;
import fr.boreal.explanation.kb_gri.processors.KBSupportGMUSProcessor_KBGRI;
import fr.boreal.explanation.solving_enumerating.marco.MARCOGMUSSolver;
import fr.boreal.model.kb.api.KnowledgeBase;
/**
* Computes kb-support explanations for a knowledge base and a ground atomic query
*/
public class KBSupportExplainer_Baseline extends AbstractStaticGRIBasedExplainer_Baseline<KnowledgeBase> {
public KBSupportExplainer_Baseline(KnowledgeBase kb) {
super(kb, new MARCOGMUSSolver());
}
public KBSupportExplainer_Baseline(KnowledgeBase kb, Solver solver) {
super(kb,solver);
}
@Override
ExplanationProcessor_GRI getGMUSProcessor(Solver solver) {
return new KBSupportGMUSProcessor_KBGRI(solver);
}
}
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/kb_gri/explainers/static_gri_baseline/RuleSupportExplainer_Baseline.java 0 → 100644
Edit View file @ 6c20e6d0
package fr.boreal.explanation.kb_gri.explainers.static_gri_baseline;
import fr.boreal.explanation.api.processors.ExplanationProcessor_GRI;
import fr.boreal.explanation.api.solver.Solver;
import fr.boreal.explanation.kb_gri.processors.RuleSupportGMUSProcessor_KBGRI;
import fr.boreal.explanation.solving_enumerating.marco.MARCOGMUSSolver;
import fr.boreal.model.kb.api.KnowledgeBase;
import fr.boreal.model.kb.api.RuleBase;
/**
* Computes rule-support explanations for a knowledge base and a ground atomic query
*/
public class RuleSupportExplainer_Baseline extends AbstractStaticGRIBasedExplainer_Baseline<RuleBase> {
public RuleSupportExplainer_Baseline(KnowledgeBase kb) {
super(kb, new MARCOGMUSSolver());
}
public RuleSupportExplainer_Baseline(KnowledgeBase kb, Solver solver) {
super(kb, solver);
}
@Override
ExplanationProcessor_GRI getGMUSProcessor(Solver solver) {
return new RuleSupportGMUSProcessor_KBGRI(solver);
}
}
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/kb_gri/explainers/why_provenance/FactSupportProvenanceExplainer_KBGRI.java
Edit View file @ 6c20e6d0
......@@ -17,7 +17,13 @@ public class FactSupportProvenanceExplainer_KBGRI implements AtomicQueryExplaine
}
@Override
public void pipelineWithTimer(String datasetName, Collection<Atom> queries) {
public void pipelineWithTimerDetailed(String datasetName, Collection<Atom> queries) {
throw new NotImplementedException();
}
@Override
public void pipelineIn2StepsWithTimer(String datasetName, Collection<Atom> queries) {
throw new NotImplementedException();
}
}
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/pipeline_with_timer/compareExplainers.java
Edit View file @ 6c20e6d0
......@@ -3,14 +3,17 @@ package fr.boreal.explanation.pipeline_with_timer;
import fr.boreal.explanation.InternalDLGPParser;
import fr.boreal.explanation.api.explainers.AtomicQueryExplainer;
import fr.boreal.explanation.configuration.StatsUtil;
import fr.boreal.explanation.configuration.query_selection.QuerySelector;
import fr.boreal.explanation.kb_gri.explainers.incremental_gri.KBSupportExplainer_IncrementalKBGRI;
import fr.boreal.explanation.kb_gri.explainers.static_gri.FactSupportExplainer_KBGRI;
import fr.boreal.explanation.kb_gri.explainers.static_gri.KBSupportExplainer_KBGRI;
import fr.boreal.explanation.kb_gri.explainers.static_gri.RuleSupportExplainer_KBGRI;
import fr.boreal.explanation.kb_gri.explainers.static_gri_baseline.KBSupportExplainer_Baseline;
import fr.boreal.explanation.solving_enumerating.sat4j.Sat4JSolver;
import fr.boreal.explanation.tracker_gri.explainers.FactSupportExplainer_TrackerGRI;
import fr.boreal.explanation.tracker_gri.explainers.KBSupportExplainer_TrackerGRI;
import fr.boreal.explanation.tracker_gri.explainers.RuleSupportExplainer_TrackerGRI;
import fr.boreal.explanation.tracker_gri.explainers.UnambiguousProofTreeWhyProvenanceExplainer_TrackerGRI;
import fr.boreal.model.kb.api.KnowledgeBase;
import fr.boreal.model.logicalElements.api.Atom;
......@@ -23,47 +26,35 @@ public class compareExplainers {
/*
input
*/
static String benchPath = new File("").getAbsolutePath() + "/integraal/integraal-explanation/src/test/resources/AAAI_datasets/";
static String benchPath = "integraal-explanation/src/test/resources/ruleml24/";
// static String benchPath = "integraal-explanation/src/test/resources/mowl-bench-main/";
public static List<String> datasets = List.of(
// "algorithmTypes",
// "DataEncoding",
// "HARMONISE",
// "NEMO_annotation_properties",
// "Ontology1260916270538",
// "platformOntology",
// "snoopy",
// "transitive-ancestor",
// "catalogue",
// "ddex",
// "ncbi_rank",
// "oil",
// "Ontology-Kassel-Material",
// "PlatOntology",
// "socialsimulationdescription",
// "WNAffect"
// "andersen_1000",
"andersen_10000"//,
// "andersen_100000", // dropped as it is too large for now
// "andersen_5000",
// "andersen_50000",
// "csda_httpd", // dropped as it is too large for now
// "csda_linux", // dropped as it is too large for now
// "csda_postgresql", // dropped as it is too large for now
/* "doctors_q01_100k",
"doctors_q02_100k",
"doctors_q03_100k",
"doctors_q04_100k",
"doctors_q05_100k",
"doctors_q06_100k",
"doctors_q07_100k",
"galen_15",
"galen_25",
"galen_40",
"galen_50",
"graph_analytics_bitcoin",
"graph_analytics_facebook"*/
"warmup",
// "218a127c-8d13-40af-9957-63c28b0a091e_elontology",
// "3cb9dec1-627b-496f-b49a-543dd1c77837_snoopy",
// "b80a039c-8975-4928-b45f-017126159882_sification",
// "98523b14-b04e-4af0-9597-15a297e226eb_taEncoding",
// "d09d7487-43dd-452a-976a-b69bc44d9b06_onOntology",
// "08cb4085-d900-4f82-8fa8-f523e382008d_ESG_test_1",
// "04c0af47-ff23-4761-8a4e-8fec2389f89f_ESG_test_2",
// "0b1f5620-f71d-4a01-8a16-d1818f69c187_ncbi_rank",
// "7b46d780-2032-46e3-ac89-90ab183e22aa_properties",
// "bb6535f4-d6a3-4197-a678-7f464e737862_properties",
// "4c3c8c62-d8f4-42c0-a96c-c994ece58345_catalogue",
// "734871d0-bf0d-47b3-bc19-b484567f5f4f_rmOntology",
// "93c3774c-58c0-4fa9-a592-539c130ee2d7_AlgorithmTypes",
// "f8a8e732-205b-4703-b568-2ce69e524055_instances",
// "f32019cc-43f3-49ce-b4f2-235f7db97132_oil",
// "8ee7a7f5-ad8c-4ac5-afbe-207e3ff285c8_HARMONISE",
// "ddd6d023-65dd-429a-a01f-2784c1d61f65_WNAffect",
"2d09369e-392a-4ef2-a7c9-28334cbdc6f8_ddex",
"dce07111-010a-450b-8c3a-2d55a8b48a21_LSCOM",
"3b327e7f-0409-4f52-8e69-7062a62f7ba1_undin_area",
"c669669d-7a04-410c-9474-1f6e46230556_BioLinks",
"1dd81ef3-1e3e-4b2f-9bd0-230123497968_atOntology",
"80bf8685-0e15-4780-8e61-7130e4e777c6_00Ontology",
"ab726941-765f-4e5e-b6c9-2d51b652e841_00Ontology"
);
......@@ -71,21 +62,20 @@ public class compareExplainers {
static KnowledgeBase inputKB;
enum AtomicQueryExplainerType {
TRACKER_GRI_KB_MARCO,
// STATIC_GRI_FB_MARCO,
// STATIC_GRI_RB_MARCO,
STATIC_GRI_KB_MARCO,
STATIC_GRI_FB_MARCO,
STATIC_GRI_RB_MARCO,
STATIC_GRI_KB_S4J,
STATIC_GRI_FB_S4J,
STATIC_GRI_RB_S4J,
TRACKER_GRI_FB_MARCO,
TRACKER_GRI_RB_MARCO,
TRACKER_GRI_FB_S4J,
TRACKER_GRI_KB_S4J,
TRACKER_GRI_RB_S4J,
INCREMENTAL_GRI_KB_MARCO
// STATIC_GRI_KB_S4J,
// STATIC_GRI_FB_S4J,
// STATIC_GRI_RB_S4J,
// TRACKER_GRI_FB_MARCO,
// TRACKER_GRI_KB_MARCO,
// TRACKER_GRI_RB_MARCO,
// TRACKER_GRI_FB_S4J,
// TRACKER_GRI_KB_S4J,
// TRACKER_GRI_RB_S4J,
INCREMENTAL_GRI_KB_MARCO,
// BASELINE_GRI_KB_MARCO
// TRACKER_GRI_UNAMBIGUOUS_PROOF_TREE_WHY_PROVENANCE
}
......@@ -93,19 +83,20 @@ public class compareExplainers {
AtomicQueryExplainerType type,
KnowledgeBase kb) {
return switch (type) {
case STATIC_GRI_FB_MARCO -> new FactSupportExplainer_KBGRI(kb);
case STATIC_GRI_RB_MARCO -> new RuleSupportExplainer_KBGRI(kb);
// case STATIC_GRI_FB_MARCO -> new FactSupportExplainer_KBGRI(kb);
// case STATIC_GRI_RB_MARCO -> new RuleSupportExplainer_KBGRI(kb);
case STATIC_GRI_KB_MARCO -> new KBSupportExplainer_KBGRI(kb);
case STATIC_GRI_KB_S4J -> new KBSupportExplainer_KBGRI(kb, new Sat4JSolver());
case STATIC_GRI_FB_S4J -> new FactSupportExplainer_KBGRI(kb, new Sat4JSolver());
case STATIC_GRI_RB_S4J -> new RuleSupportExplainer_KBGRI(kb, new Sat4JSolver());
case TRACKER_GRI_FB_MARCO -> new FactSupportExplainer_TrackerGRI(kb);
case TRACKER_GRI_KB_MARCO -> new KBSupportExplainer_TrackerGRI(kb);
case TRACKER_GRI_RB_MARCO -> new RuleSupportExplainer_TrackerGRI(kb);
case TRACKER_GRI_FB_S4J -> new FactSupportExplainer_TrackerGRI(kb, new Sat4JSolver());
case TRACKER_GRI_KB_S4J -> new KBSupportExplainer_TrackerGRI(kb, new Sat4JSolver());
case TRACKER_GRI_RB_S4J -> new RuleSupportExplainer_TrackerGRI(kb, new Sat4JSolver());
// case STATIC_GRI_KB_S4J -> new KBSupportExplainer_KBGRI(kb, new Sat4JSolver());
// case STATIC_GRI_FB_S4J -> new FactSupportExplainer_KBGRI(kb, new Sat4JSolver());
// case STATIC_GRI_RB_S4J -> new RuleSupportExplainer_KBGRI(kb, new Sat4JSolver());
// case TRACKER_GRI_FB_MARCO -> new FactSupportExplainer_TrackerGRI(kb);
// case TRACKER_GRI_KB_MARCO -> new KBSupportExplainer_TrackerGRI(kb);
// case TRACKER_GRI_RB_MARCO -> new RuleSupportExplainer_TrackerGRI(kb);
// case TRACKER_GRI_FB_S4J -> new FactSupportExplainer_TrackerGRI(kb, new Sat4JSolver());
// case TRACKER_GRI_KB_S4J -> new KBSupportExplainer_TrackerGRI(kb, new Sat4JSolver());
// case TRACKER_GRI_RB_S4J -> new RuleSupportExplainer_TrackerGRI(kb, new Sat4JSolver());
case INCREMENTAL_GRI_KB_MARCO -> new KBSupportExplainer_IncrementalKBGRI(kb);
// case BASELINE_GRI_KB_MARCO -> new KBSupportExplainer_Baseline(kb);
// case TRACKER_GRI_UNAMBIGUOUS_PROOF_TREE_WHY_PROVENANCE -> new UnambiguousProofTreeWhyProvenanceExplainer_TrackerGRI(kb);
};
}
......@@ -114,26 +105,35 @@ public class compareExplainers {
StatsUtil.clearStats();
for (AtomicQueryExplainerType type : AtomicQueryExplainerType.values()) {
for (String datasetName : datasets) {
inputKB = loadKB(datasetName);
Collection<Atom> queries = loadQuery(datasetName);
AtomicQueryExplainer<?> explainer = getExplainer(type, inputKB);
// Collection<Atom> queries = loadQuery(datasetName);
Collection<Atom> queries = QuerySelector.selectQueries(inputKB);
System.out.println("Loading KB completed");
explainer.pipelineWithTimer(datasetName, queries);
StatsUtil.recordFBSize(datasetName, inputKB.getFactBase().size());
StatsUtil.recordRBSize(datasetName, inputKB.getRuleBase().getRules().size());
explainer.pipelineWithTimerDetailed(datasetName, queries);
// explainer.pipelineIn2StepsWithTimer(datasetName, queries);
}
}
StatsUtil.exportPivotStatsToCSV("timings.csv");
StatsUtil.exportPivotStatsToCSV("ruleml24_timings.csv");
}
static KnowledgeBase loadKB(String ontology_name) throws FileNotFoundException {
return InternalDLGPParser.ParserForDLGP.parseKB(
new File(benchPath +ontology_name+"/"+ontology_name+".dlgp"));
new File(benchPath +ontology_name+"/"+ontology_name+"_kb.dlgp"));
}
static Collection<Atom> loadQuery(String ontology_name) throws FileNotFoundException {
return InternalDLGPParser.ParserForDLGP.parseQueries(
new File(benchPath +ontology_name+"/"+ontology_name+"_query_5.dlgp"));
new File(benchPath +ontology_name+"/"+ontology_name+"_queries.dlgp"));
}
}
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/solving_enumerating/marco/MARCOGMUSSolver.java
Edit View file @ 6c20e6d0
......@@ -106,9 +106,9 @@ public class MARCOGMUSSolver implements Solver {
ProcessBuilder build = new ProcessBuilder().redirectErrorStream(true);
String command;
if (timeout == 0)
build.command(ensureFilePath("integraal-explanation/MARCO-MUS/marco.py", "MARCO-MUS/marco.py"), "-v", "-b", "MUSes", gcnfFile.getAbsolutePath(), " -a");
build.command(ensureFilePath("integraal-explanation/MARCO-MUS/marco.py", "MARCO-MUS/marco.py"), "-s", "-v", "-b", "MUSes", gcnfFile.getAbsolutePath());
else
build.command(ensureFilePath("integraal-explanation/MARCO-MUS/marco.py", "MARCO-MUS/marco.py"), "-v", "-b", "MUSes", "-T", Long.toString(timeout), gcnfFile.getAbsolutePath(), " -a");
build.command(ensureFilePath("integraal-explanation/MARCO-MUS/marco.py", "MARCO-MUS/marco.py"), "-a", "-v", "-b", "MUSes", "-T", Long.toString(timeout), gcnfFile.getAbsolutePath());
Process proc;
try {
proc = build.start();
......
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/tracker_gri/explainers/AbstractStaticGRIBasedExplainer_TrackerGRI.java
Edit View file @ 6c20e6d0
......@@ -119,37 +119,46 @@ public abstract class AbstractStaticGRIBasedExplainer_TrackerGRI<ExplanationType
}
}
@Override
public void pipelineIn2StepsWithTimer (String datasetName, Collection<Atom> queries) {
String explainerName = this.getClass().getSimpleName() + " + " + this.solver.getClass().getSimpleName();
StatsUtil.timerPerEachQuery(this::staticStep, explainerName, "Static Step", datasetName);
for (Atom query : queries) {
StatsUtil.timerPerEachQuery(() -> dynamicStep(query), explainerName, "Dynamic Step", datasetName);
}
}
public void pipelineWithTimer(String datasetName, Collection<Atom> queries) {
@Override
public void pipelineWithTimerDetailed(String datasetName, Collection<Atom> queries) {
String explainerName = this.getClass().getSimpleName() + " + " + this.solver.getClass().getSimpleName();
StatsUtil.timer(this::recordInitialFactbase, explainerName, "Recording initial factbase", datasetName);
StatsUtil.timer(this::trackerChase, explainerName, "Chase for building lineage tracker", datasetName);
StatsUtil.timerSumAllQueries(this::recordInitialFactbase, explainerName, "Recording initial factbase", datasetName);
StatsUtil.timerSumAllQueries(this::trackerChase, explainerName, "Chase for building lineage tracker", datasetName);
for (Atom query : queries) {
if (this.explanations != null) {
StatsUtil.timer(this::dynamicStepClear, explainerName,
StatsUtil.timerSumAllQueries(this::dynamicStepClear, explainerName,
"Clearing gmuses and explanations for the previous query",
datasetName);
}
StatsUtil.timer(() -> checkQueryEntailment(query), explainerName, "Check if query is entailed", datasetName);
StatsUtil.timer(() -> checkQueryInInitialFB(query), explainerName, "Check if query is already in input FB", datasetName);
StatsUtil.timerSumAllQueries(() -> checkQueryEntailment(query), explainerName, "Check if query is entailed", datasetName);
StatsUtil.timerSumAllQueries(() -> checkQueryInInitialFB(query), explainerName, "Check if query is already in input FB", datasetName);
if (queryEntailed && !queryInInitialFB) {
StatsUtil.timer(() -> encodeTrackerClauses(query), explainerName, "Preparing Rel Tracing", datasetName);
StatsUtil.timerSumAllQueries(() -> encodeTrackerClauses(query), explainerName, "Preparing Rel Tracing", datasetName);
if (solver instanceof MARCOGMUSSolver) {
StatsUtil.timer(this::writeMarcoGCNF, explainerName, "Writing GCNF", datasetName);
StatsUtil.timer(this::solveGMUSviaMarco, explainerName, "Computing GMUSes", datasetName);
StatsUtil.timer(this::decodeGMUSesFromMarco, explainerName, "Decoding GMUSes", datasetName);
StatsUtil.timerSumAllQueries(this::writeMarcoGCNF, explainerName, "Writing GCNF", datasetName);
StatsUtil.timerSumAllQueries(this::solveGMUSviaMarco, explainerName, "Computing GMUSes", datasetName);
StatsUtil.timerSumAllQueries(this::decodeGMUSesFromMarco, explainerName, "Decoding GMUSes", datasetName);
} else if (solver instanceof Sat4JSolver) {
StatsUtil.timer(this::solveGMUSviaSat4j, explainerName, "Computing GMUSes with sat4j", datasetName);
StatsUtil.timer(this::decodeGMUSesFromSat4j, explainerName, "Decoding GMUSes from sat4j", datasetName);
StatsUtil.timerSumAllQueries(this::solveGMUSviaSat4j, explainerName, "Computing GMUSes with sat4j", datasetName);
StatsUtil.timerSumAllQueries(this::decodeGMUSesFromSat4j, explainerName, "Decoding GMUSes from sat4j", datasetName);
}
} else if (queryInInitialFB) {
StatsUtil.timer(() -> returnExplanationForQueryInFB(query), explainerName, "Preparing Rel Tracing", datasetName);
StatsUtil.timerSumAllQueries(() -> returnExplanationForQueryInFB(query), explainerName, "Preparing Rel Tracing", datasetName);
} else {
returnEmptySetForExplanation();
}
......
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/tracker_gri/explainers/UnambiguousProofTreeWhyProvenanceExplainer_TrackerGRI.java
Edit View file @ 6c20e6d0
......@@ -82,7 +82,12 @@ public class UnambiguousProofTreeWhyProvenanceExplainer_TrackerGRI implements At
}
@Override
public void pipelineWithTimer(String datasetName, Collection<Atom> queries) {
public void pipelineWithTimerDetailed(String datasetName, Collection<Atom> queries) {
throw new NotImplementedException();
}
@Override
public void pipelineIn2StepsWithTimer(String datasetName, Collection<Atom> queries) {
throw new NotImplementedException();
}
......
integraal/integraal-explanation/src/main/java/module-info.java
Edit View file @ 6c20e6d0
......@@ -17,4 +17,8 @@ module fr.boreal.explanation {
requires jfreechart;
requires com.opencsv;
requires commons.collections;
exports fr.boreal.explanation.api.explainers;
exports fr.boreal.explanation.kb_gri.explainers.static_gri;
exports fr.boreal.explanation.kb_gri.explainers.incremental_gri;
exports fr.boreal.explanation.tracker_gri.explainers;
}
\ No newline at end of file
integraal/integraal-explanation/src/test/java/fr/boreal/test/explanation/TestData.java
Edit View file @ 6c20e6d0
......@@ -103,13 +103,13 @@ public class TestData {
public static String mowl_bench_path = "./src/test/resources/mowl-bench-main/";
public static List<String> default_mowl_bench_datasets = List.of(
"algorithmTypes"
// "DataEncoding",
// "HARMONISE",
// "NEMO_annotation_properties",
// "Ontology1260916270538",
// "platformOntology",
// "snoopy",
"algorithmTypes",
"DataEncoding",
"HARMONISE",
"NEMO_annotation_properties",
"Ontology1260916270538",
"platformOntology",
"snoopy"
// "transitive-ancestor"
// "catalogue",
// "ddex",
......
integraal/integraal-explanation/src/test/java/fr/boreal/test/explanation/check_same_explanation/KBSupport_MowlOntologyTest.java
Edit View file @ 6c20e6d0
......@@ -4,6 +4,7 @@ import fr.boreal.explanation.InternalDLGPParser;
import fr.boreal.explanation.api.explainers.AtomicQueryExplainer;
import fr.boreal.explanation.kb_gri.explainers.incremental_gri.KBSupportExplainer_IncrementalKBGRI;
import fr.boreal.explanation.kb_gri.explainers.static_gri.KBSupportExplainer_KBGRI;
import fr.boreal.explanation.kb_gri.explainers.static_gri_baseline.KBSupportExplainer_Baseline;
import fr.boreal.explanation.solving_enumerating.sat4j.Sat4JSolver;
import fr.boreal.explanation.tracker_gri.explainers.KBSupportExplainer_TrackerGRI;
import fr.boreal.model.kb.api.KnowledgeBase;
......@@ -36,7 +37,8 @@ public class KBSupport_MowlOntologyTest {
STATIC_GRI_KB_S4J,
TRACKER_STATIC_GRI_KB_MARCO,
TRACKER_STATIC_GRI_KB_S4J,
INCREMENTAL_GRI_KB_MARCO
INCREMENTAL_GRI_KB_MARCO,
BASELINE_GRI_KB_MARCO
}
static AtomicQueryExplainer<?> getExplainer(
AtomicQueryExplainerType type,
......@@ -47,6 +49,7 @@ public class KBSupport_MowlOntologyTest {
case TRACKER_STATIC_GRI_KB_MARCO -> new KBSupportExplainer_TrackerGRI(kb);
case TRACKER_STATIC_GRI_KB_S4J -> new KBSupportExplainer_TrackerGRI(kb, new Sat4JSolver());
case INCREMENTAL_GRI_KB_MARCO -> new KBSupportExplainer_IncrementalKBGRI(kb);
case BASELINE_GRI_KB_MARCO -> new KBSupportExplainer_Baseline(kb);
};
}
......
integraal/integraal-explanation/src/test/java/fr/boreal/test/explanation/unit_tests/explainer/kb_gri_baseline_marco/FactSupportExplainerTest.java 0 → 100644
Edit View file @ 6c20e6d0
package fr.boreal.test.explanation.unit_tests.explainer.kb_gri_baseline_marco;
import fr.boreal.explanation.kb_gri.explainers.static_gri.FactSupportExplainer_KBGRI;
import fr.boreal.explanation.kb_gri.explainers.static_gri_baseline.FactSupportExplainer_Baseline;
import fr.boreal.explanation.kb_gri.rule_transformation.GRIRuleTransformer;
import fr.boreal.model.kb.api.FactBase;
import fr.boreal.model.kb.api.KnowledgeBase;
import fr.boreal.model.kb.api.RuleBase;
import fr.boreal.model.kb.impl.KnowledgeBaseImpl;
import fr.boreal.model.kb.impl.RuleBaseImpl;
import fr.boreal.model.logicalElements.api.Atom;
import fr.boreal.model.logicalElements.api.Predicate;
import fr.boreal.storage.natives.SimpleInMemoryGraphStore;
import fr.boreal.test.explanation.TestData;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import java.util.List;
import java.util.Set;
public class FactSupportExplainerTest {
FactSupportExplainer_Baseline explainer;
GRIRuleTransformer griRuleTransformer = GRIRuleTransformer.instance();
Predicate REL = GRIRuleTransformer.REL;
@BeforeEach
public void setUp() {
}
@Test
public void FactSupportExplainerTestCyclic3() {
Atom query = TestData.ta;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.pa));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r1_px_qx,TestData.r10_qx_tx, TestData.r11_tx_px));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new FactSupportExplainer_Baseline(kb);
Set<FactBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase1 = new SimpleInMemoryGraphStore(Set.of(TestData.pa));
Assertions.assertTrue(explanations.contains(expectedFactBase1), "(Completeness issue) Explanation missing: " + expectedFactBase1);
Assertions.assertEquals(1, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void FactSupportExplainerTestCyclic2() {
Atom query = TestData.qa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.pa));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r1_px_qx,TestData.r10_qx_tx, TestData.r11_tx_px));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new FactSupportExplainer_Baseline(kb);
Set<FactBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase1 = new SimpleInMemoryGraphStore(Set.of(TestData.pa));
Assertions.assertTrue(explanations.contains(expectedFactBase1), "(Completeness issue) Explanation missing: " + expectedFactBase1);
Assertions.assertEquals(1, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void FactSupportExplainerTestCyclic1() {
Atom query = TestData.qa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.pa));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r1_px_qx,TestData.r9_qx_px));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new FactSupportExplainer_Baseline(kb);
Set<FactBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase1 = new SimpleInMemoryGraphStore(Set.of(TestData.pa));
Assertions.assertTrue(explanations.contains(expectedFactBase1), "(Completeness issue) Explanation missing: " + expectedFactBase1);
Assertions.assertEquals(1, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void FactSupportExplainerTest4() {
Atom query = TestData.pa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.saa, TestData.sab));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r6_sxy_px,TestData.r7_sxx_px));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new FactSupportExplainer_Baseline(kb);
Set<FactBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase1 = new SimpleInMemoryGraphStore(Set.of(TestData.saa));
FactBase expectedFactBase2 = new SimpleInMemoryGraphStore(Set.of(TestData.sab));
Assertions.assertTrue(explanations.contains(expectedFactBase1), "(Completeness issue) Explanation missing: " + expectedFactBase1);
Assertions.assertTrue(explanations.contains(expectedFactBase2), "(Completeness issue) Explanation missing: " + expectedFactBase2);
Assertions.assertEquals(2, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void FactSupportExplainerTest3() {
Atom query = TestData.qa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.saa, TestData.sbc, TestData.tab));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r6_sxy_px, TestData.r7_sxx_px, TestData.r8_pxpytxy_qx));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new FactSupportExplainer_Baseline(kb);
Set<FactBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase = new SimpleInMemoryGraphStore(Set.of(TestData.saa, TestData.sbc, TestData.tab));
Assertions.assertTrue(explanations.contains(expectedFactBase), "(Completeness issue) Explanation missing: " + expectedFactBase);
Assertions.assertEquals(1, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void FactSupportExplainerTest2() {
Atom query = TestData.qa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.saa, TestData.sbc, TestData.tab));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r6_sxy_px, TestData.r7_sxx_px, TestData.r8_pxpytxy_qx));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new FactSupportExplainer_Baseline(kb);
Set<FactBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase = new SimpleInMemoryGraphStore(Set.of(TestData.saa, TestData.sbc, TestData.tab));
Assertions.assertTrue(explanations.contains(expectedFactBase), "(Completeness issue) Explanation missing: " + expectedFactBase);
Assertions.assertEquals(1, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void FactSupportExplainerTest1() {
Atom query = TestData.qa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.pa, TestData.ta));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r1_px_qx, TestData.r4_qx_txy));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new FactSupportExplainer_Baseline(kb);
Set<FactBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase = new SimpleInMemoryGraphStore(Set.of(TestData.pa));
Assertions.assertTrue(explanations.contains(expectedFactBase), "(Completeness issue) Explanation missing: " + expectedFactBase);
Assertions.assertEquals(1, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void QueryNotEntailedTest() {
Atom query = TestData.sa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.pa, TestData.ta));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r1_px_qx, TestData.r4_qx_txy));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new FactSupportExplainer_Baseline(kb);
Set<FactBase> explanations = explainer.getAllExplanations(query);
Assertions.assertEquals(0, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void QueryInFactBaseTest() {
Atom query = TestData.pa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.pa, TestData.ta));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r1_px_qx, TestData.r4_qx_txy));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new FactSupportExplainer_Baseline(kb);
Set<FactBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase = new SimpleInMemoryGraphStore(Set.of(TestData.pa));
Assertions.assertTrue(explanations.contains(expectedFactBase), "(Completeness issue) Explanation missing: " + expectedFactBase);
Assertions.assertEquals(1, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
}
integraal/integraal-explanation/src/test/java/fr/boreal/test/explanation/unit_tests/explainer/kb_gri_baseline_marco/KBSupportExplainerTest.java 0 → 100644
Edit View file @ 6c20e6d0
package fr.boreal.test.explanation.unit_tests.explainer.kb_gri_baseline_marco;
import fr.boreal.explanation.kb_gri.explainers.static_gri.KBSupportExplainer_KBGRI;
import fr.boreal.explanation.kb_gri.explainers.static_gri_baseline.KBSupportExplainer_Baseline;
import fr.boreal.explanation.kb_gri.rule_transformation.GRIRuleTransformer;
import fr.boreal.model.kb.api.FactBase;
import fr.boreal.model.kb.api.KnowledgeBase;
import fr.boreal.model.kb.api.RuleBase;
import fr.boreal.model.kb.impl.KnowledgeBaseImpl;
import fr.boreal.model.kb.impl.RuleBaseImpl;
import fr.boreal.model.logicalElements.api.Atom;
import fr.boreal.model.logicalElements.api.Predicate;
import fr.boreal.storage.natives.SimpleInMemoryGraphStore;
import fr.boreal.test.explanation.TestData;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import java.util.List;
import java.util.Set;
public class KBSupportExplainerTest {
KBSupportExplainer_Baseline explainer;
GRIRuleTransformer griRuleTransformer = GRIRuleTransformer.instance();
Predicate REL = GRIRuleTransformer.REL;
@BeforeEach
public void setUp() {
}
@Test
public void KBSupportExplainerTestCyclic3() {
Atom query = TestData.ta;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.pa));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r1_px_qx,TestData.r10_qx_tx, TestData.r11_tx_px));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new KBSupportExplainer_Baseline(kb);
Set<KnowledgeBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase1 = new SimpleInMemoryGraphStore(Set.of(TestData.pa));
RuleBase expectedRuleBase1 = new RuleBaseImpl(Set.of(TestData.r1_px_qx, TestData.r10_qx_tx));
KnowledgeBase expectedExpl1 = new KnowledgeBaseImpl(expectedFactBase1, expectedRuleBase1);
Assertions.assertTrue(explanations.contains(expectedExpl1), "(Completeness issue) Explanation missing: " + expectedExpl1);
Assertions.assertEquals(1, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void KBSupportExplainerTestCyclic2() {
Atom query = TestData.qa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.pa));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r1_px_qx,TestData.r10_qx_tx, TestData.r11_tx_px));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new KBSupportExplainer_Baseline(kb);
Set<KnowledgeBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase1 = new SimpleInMemoryGraphStore(Set.of(TestData.pa));
RuleBase expectedRuleBase1 = new RuleBaseImpl(Set.of(TestData.r1_px_qx));
KnowledgeBase expectedExpl1 = new KnowledgeBaseImpl(expectedFactBase1, expectedRuleBase1);
Assertions.assertTrue(explanations.contains(expectedExpl1), "(Completeness issue) Explanation missing: " + expectedExpl1);
Assertions.assertEquals(1, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void KBSupportExplainerTestCyclic1() {
Atom query = TestData.qa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.pa));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r1_px_qx,TestData.r9_qx_px));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new KBSupportExplainer_Baseline(kb);
Set<KnowledgeBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase1 = new SimpleInMemoryGraphStore(Set.of(TestData.pa));
RuleBase expectedRuleBase1 = new RuleBaseImpl(Set.of(TestData.r1_px_qx));
KnowledgeBase expectedExpl1 = new KnowledgeBaseImpl(expectedFactBase1, expectedRuleBase1);
Assertions.assertTrue(explanations.contains(expectedExpl1), "(Completeness issue) Explanation missing: " + expectedExpl1);
Assertions.assertEquals(1, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void KBSupportExplainerTest4() {
Atom query = TestData.pa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.saa, TestData.sab));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r6_sxy_px,TestData.r7_sxx_px));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new KBSupportExplainer_Baseline(kb);
Set<KnowledgeBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase1 = new SimpleInMemoryGraphStore(Set.of(TestData.saa));
RuleBase expectedRuleBase1 = new RuleBaseImpl(Set.of(TestData.r6_sxy_px));
KnowledgeBase expectedExpl1 = new KnowledgeBaseImpl(expectedFactBase1, expectedRuleBase1);
FactBase expectedFactBase2 = new SimpleInMemoryGraphStore(Set.of(TestData.sab));
RuleBase expectedRuleBase2 = new RuleBaseImpl(Set.of(TestData.r6_sxy_px));
KnowledgeBase expectedExpl2 = new KnowledgeBaseImpl(expectedFactBase2, expectedRuleBase2);
FactBase expectedFactBase3 = new SimpleInMemoryGraphStore(Set.of(TestData.saa));
RuleBase expectedRuleBase3 = new RuleBaseImpl(Set.of(TestData.r7_sxx_px));
KnowledgeBase expectedExpl3 = new KnowledgeBaseImpl(expectedFactBase3, expectedRuleBase3);
Assertions.assertTrue(explanations.contains(expectedExpl1), "(Completeness issue) Explanation missing: " + expectedExpl1);
Assertions.assertTrue(explanations.contains(expectedExpl2), "(Completeness issue) Explanation missing: " + expectedExpl2);
Assertions.assertTrue(explanations.contains(expectedExpl3), "(Completeness issue) Explanation missing: " + expectedExpl3);
Assertions.assertEquals(3, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void KBSupportExplainerTest3() {
Atom query = TestData.qa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.saa, TestData.sbc, TestData.tab));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r6_sxy_px, TestData.r7_sxx_px, TestData.r8_pxpytxy_qx));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new KBSupportExplainer_Baseline(kb);
Set<KnowledgeBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase = new SimpleInMemoryGraphStore(Set.of(TestData.saa, TestData.sbc, TestData.tab));
RuleBase expectedRuleBase = new RuleBaseImpl(Set.of(TestData.r6_sxy_px,TestData.r8_pxpytxy_qx));
KnowledgeBase expectedExpl = new KnowledgeBaseImpl(expectedFactBase, expectedRuleBase);
Assertions.assertTrue(explanations.contains(expectedExpl), "(Completeness issue) Explanation missing: " + expectedExpl);
Assertions.assertEquals(1, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void KBSupportExplainerTest2() {
Atom query = TestData.qa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.saa, TestData.sbc, TestData.tab));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r6_sxy_px, TestData.r7_sxx_px, TestData.r8_pxpytxy_qx));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new KBSupportExplainer_Baseline(kb);
Set<KnowledgeBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase = new SimpleInMemoryGraphStore(Set.of(TestData.saa, TestData.sbc, TestData.tab));
RuleBase expectedRuleBase = new RuleBaseImpl(Set.of(TestData.r6_sxy_px,TestData.r8_pxpytxy_qx));
KnowledgeBase expectedExpl = new KnowledgeBaseImpl(expectedFactBase, expectedRuleBase);
Assertions.assertTrue(explanations.contains(expectedExpl), "(Completeness issue) Explanation missing: " + expectedExpl);
Assertions.assertEquals(1, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void KBSupportExplainerTest1() {
Atom query = TestData.qa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.pa, TestData.ta));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r1_px_qx, TestData.r4_qx_txy));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new KBSupportExplainer_Baseline(kb);
Set<KnowledgeBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase = new SimpleInMemoryGraphStore(Set.of(TestData.pa));
RuleBase expectedRuleBase = new RuleBaseImpl(Set.of(TestData.r1_px_qx));
KnowledgeBase expectedExpl = new KnowledgeBaseImpl(expectedFactBase, expectedRuleBase);
Assertions.assertTrue(explanations.contains(expectedExpl), "(Completeness issue) Explanation missing: " + expectedExpl);
Assertions.assertEquals(1, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void QueryNotEntailedTest() {
Atom query = TestData.sa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.pa, TestData.ta));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r1_px_qx, TestData.r4_qx_txy));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new KBSupportExplainer_Baseline(kb);
Set<KnowledgeBase> explanations = explainer.getAllExplanations(query);
Assertions.assertEquals(0, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
@Test
public void QueryInFactBaseTest() {
Atom query = TestData.pa;
FactBase factBase = new SimpleInMemoryGraphStore(List.of(TestData.pa, TestData.ta));
RuleBase ruleBase = new RuleBaseImpl(List.of(TestData.r1_px_qx, TestData.r4_qx_txy));
KnowledgeBase kb = new KnowledgeBaseImpl(factBase, ruleBase);
explainer = new KBSupportExplainer_Baseline(kb);
Set<KnowledgeBase> explanations = explainer.getAllExplanations(query);
FactBase expectedFactBase = new SimpleInMemoryGraphStore(Set.of(TestData.pa));
RuleBase expectedRuleBase = new RuleBaseImpl(Set.of());
KnowledgeBase expectedExpl = new KnowledgeBaseImpl(expectedFactBase, expectedRuleBase);
Assertions.assertTrue(explanations.contains(expectedExpl), "(Completeness issue) Explanation missing: " + expectedExpl);
Assertions.assertEquals(1, explanations.size(), "(Soundness issue) identify non-explanation as explanation");
}
}