108 files changed, 3583 insertions, 1884 deletions
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/ActionFactory.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/ActionFactory.java
deleted file mode 100644
index 524c2f55..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/ActionFactory.java
+++ /dev/null
@@ -1,14 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse;
-import org.eclipse.collections.api.block.procedure.Procedure;
-import tools.refinery.store.model.Model;
-import tools.refinery.store.tuple.Tuple;
-public interface ActionFactory {
-        Procedure<Tuple> prepare(Model model);
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/DesignSpaceExplorationAdapter.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/DesignSpaceExplorationAdapter.java
deleted file mode 100644
index ab87ddd5..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/DesignSpaceExplorationAdapter.java
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse;
-import tools.refinery.store.adapter.ModelAdapter;
-import tools.refinery.store.dse.internal.TransformationRule;
-import tools.refinery.store.map.Version;
-import tools.refinery.store.dse.internal.Activation;
-import tools.refinery.store.dse.internal.DesignSpaceExplorationBuilderImpl;
-import tools.refinery.store.dse.objectives.Fitness;
-import tools.refinery.store.dse.objectives.ObjectiveComparatorHelper;
-import tools.refinery.store.tuple.Tuple;
-import tools.refinery.store.tuple.Tuple1;
-import java.util.Collection;
-import java.util.List;
-import java.util.Random;
-public interface DesignSpaceExplorationAdapter extends ModelAdapter {
-        @Override
-        DesignSpaceExplorationStoreAdapter getStoreAdapter();
-        static DesignSpaceExplorationBuilder builder() {
-                return new DesignSpaceExplorationBuilderImpl();
-        }
-        Collection<Version> explore();
-        public int getModelSize();
-        public Tuple1 createObject();
-        public Tuple deleteObject(Tuple tuple);
-        public boolean checkGlobalConstraints();
-        public boolean backtrack();
-        public boolean backtrack(String reason);
-        public Fitness getFitness();
-        public void newSolution();
-        public int getDepth();
-        public Collection<Activation> getUntraversedActivations();
-        public boolean fireActivation(Activation activation);
-        public boolean fireRandomActivation();
-        public List<Version> getTrajectory();
-        public boolean isCurrentStateAlreadyTraversed();
-        public ObjectiveComparatorHelper getObjectiveComparatorHelper();
-        public void restoreTrajectory(List<Version>  trajectory);
-        public void setRandom(Random random);
-        public void setRandom(long seed);
-        public List<Version> getSolutions();
-        void addTransformationRule(TransformationRule transformationRule);
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/DesignSpaceExplorationBuilder.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/DesignSpaceExplorationBuilder.java
deleted file mode 100644
index 4def5cb2..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/DesignSpaceExplorationBuilder.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse;
-import tools.refinery.store.adapter.ModelAdapterBuilder;
-import tools.refinery.store.query.dnf.RelationalQuery;
-import tools.refinery.store.dse.internal.TransformationRule;
-import tools.refinery.store.dse.objectives.Objective;
-import java.util.Collection;
-import java.util.List;
-public interface DesignSpaceExplorationBuilder extends ModelAdapterBuilder {
-        default DesignSpaceExplorationBuilder transformations(TransformationRule... transformationRules) {
-                return transformations(List.of(transformationRules));
-        }
-        default DesignSpaceExplorationBuilder transformations(Collection<? extends TransformationRule> transformationRules) {
-                transformationRules.forEach(this::transformation);
-                return this;
-        }
-        default DesignSpaceExplorationBuilder globalConstraints(RelationalQuery... globalConstraints) {
-                return globalConstraints(List.of(globalConstraints));
-        }
-        default DesignSpaceExplorationBuilder globalConstraints(Collection<RelationalQuery> globalConstraints) {
-                globalConstraints.forEach(this::globalConstraint);
-                return this;
-        }
-        default DesignSpaceExplorationBuilder objectives(Objective... objectives) {
-                return objectives(List.of(objectives));
-        }
-        default DesignSpaceExplorationBuilder objectives(Collection<? extends Objective> objectives) {
-                objectives.forEach(this::objective);
-                return this;
-        }
-        DesignSpaceExplorationBuilder transformation(TransformationRule transformationRule);
-        DesignSpaceExplorationBuilder globalConstraint(RelationalQuery globalConstraint);
-        DesignSpaceExplorationBuilder objective(Objective objective);
-        DesignSpaceExplorationBuilder strategy(Strategy strategy);
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/DesignSpaceExplorationStoreAdapter.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/DesignSpaceExplorationStoreAdapter.java
deleted file mode 100644
index 0252748d..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/DesignSpaceExplorationStoreAdapter.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse;
-import tools.refinery.store.adapter.ModelStoreAdapter;
-import tools.refinery.store.dse.internal.TransformationRule;
-import tools.refinery.store.dse.objectives.Objective;
-import tools.refinery.store.model.Model;
-import tools.refinery.store.query.dnf.RelationalQuery;
-import java.util.List;
-import java.util.Set;
-public interface DesignSpaceExplorationStoreAdapter extends ModelStoreAdapter {
-        @Override
-        DesignSpaceExplorationAdapter createModelAdapter(Model model);
-        Set<TransformationRule> getTransformationSpecifications();
-        Set<RelationalQuery> getGlobalConstraints();
-        List<Objective> getObjectives();
-        Strategy getStrategy();
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/Strategy.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/Strategy.java
deleted file mode 100644
index c60a4410..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/Strategy.java
+++ /dev/null
@@ -1,13 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse;
-public interface Strategy {
-        void initialize(DesignSpaceExplorationAdapter designSpaceExplorationAdapter);
-        void explore();
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/Activation.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/Activation.java
deleted file mode 100644
index 1893ce2e..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/Activation.java
+++ /dev/null
@@ -1,14 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse.internal;
-import tools.refinery.store.tuple.Tuple;
-public record Activation(TransformationRule transformationRule, Tuple activation) {
-        public boolean fire() {
-                return transformationRule.fireActivation(activation);
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/DesignSpaceExplorationAdapterImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/DesignSpaceExplorationAdapterImpl.java
deleted file mode 100644
index 1ae09916..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/DesignSpaceExplorationAdapterImpl.java
+++ /dev/null
@@ -1,303 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2010-2014, Miklos Foldenyi, Andras Szabolcs Nagy, Abel Hegedus, Akos Horvath, Zoltan Ujhelyi and Daniel Varro
- * Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
- * This program and the accompanying materials are made available under the
- * terms of the Eclipse Public License v. 2.0 which is available at
- * http://www.eclipse.org/legal/epl-v20.html.
- *
- * SPDX-License-Identifier: EPL-2.0
- *******************************************************************************/
-package tools.refinery.store.dse.internal;
-import tools.refinery.store.map.Version;
-import tools.refinery.store.model.Interpretation;
-import tools.refinery.store.model.Model;
-import tools.refinery.store.query.ModelQueryAdapter;
-import tools.refinery.store.query.dnf.Query;
-import tools.refinery.store.query.dnf.RelationalQuery;
-import tools.refinery.store.dse.DesignSpaceExplorationAdapter;
-import tools.refinery.store.dse.DesignSpaceExplorationStoreAdapter;
-import tools.refinery.store.dse.Strategy;
-import tools.refinery.store.dse.objectives.Fitness;
-import tools.refinery.store.dse.objectives.Objective;
-import tools.refinery.store.dse.objectives.ObjectiveComparatorHelper;
-import tools.refinery.store.query.resultset.ResultSet;
-import tools.refinery.store.representation.Symbol;
-import tools.refinery.store.tuple.Tuple;
-import tools.refinery.store.tuple.Tuple1;
-import tools.refinery.visualization.ModelVisualizerAdapter;
-import java.util.*;
-public class DesignSpaceExplorationAdapterImpl implements DesignSpaceExplorationAdapter {
-        static final Symbol<Integer> NODE_COUNT_SYMBOL = Symbol.of("MODEL_SIZE", 0, Integer.class, 0);
-        private final Model model;
-        private final ModelQueryAdapter queryEngine;
-        private final DesignSpaceExplorationStoreAdapterImpl storeAdapter;
-        private final Set<TransformationRule> transformationRules;
-        private final Set<RelationalQuery> globalConstraints;
-        private final List<Objective> objectives;
-        private final LinkedHashSet<ResultSet<Boolean>> globalConstraintResultSets = new LinkedHashSet<>();
-        private final Interpretation<Integer> sizeInterpretation;
-        private final Strategy strategy;
-        private ObjectiveComparatorHelper objectiveComparatorHelper;
-        private List<Version> trajectory = new ArrayList<>();
-        private Map<Version, Version> parents = new HashMap<>();
-        private final List<Version> solutions = new ArrayList<>();
-        private Map<Version, List<Activation>> statesAndTraversedActivations;
-        @SuppressWarnings("squid:S2245")
-        private Random random = new Random();
-        private boolean isNewState = false;
-        private final boolean isVisualizationEnabled;
-        private final ModelVisualizerAdapter modelVisualizerAdapter;
-        private final Map<Version, Fitness> fitnessCache = new HashMap<>();
-        public DesignSpaceExplorationAdapterImpl(Model model, DesignSpaceExplorationStoreAdapterImpl storeAdapter) {
-                this.model = model;
-                this.storeAdapter = storeAdapter;
-                this.sizeInterpretation = model.getInterpretation(NODE_COUNT_SYMBOL);
-                queryEngine = model.getAdapter(ModelQueryAdapter.class);
-                globalConstraints = storeAdapter.getGlobalConstraints();
-                for (var constraint : globalConstraints) {
-                        globalConstraintResultSets.add(queryEngine.getResultSet(constraint));
-                }
-                transformationRules = storeAdapter.getTransformationSpecifications();
-                for (var rule : transformationRules) {
-                        rule.prepare(model, queryEngine);
-                }
-                objectives = storeAdapter.getObjectives();
-                statesAndTraversedActivations = new HashMap<>();
-                strategy = storeAdapter.getStrategy();
-                strategy.initialize(this);
-                modelVisualizerAdapter = model.tryGetAdapter(ModelVisualizerAdapter.class).orElse(null);
-                isVisualizationEnabled = modelVisualizerAdapter != null;
-        }
-        @Override
-        public void addTransformationRule(TransformationRule rule) {
-                transformationRules.add(rule);
-                rule.prepare(model, queryEngine);
-        }
-        public List<Version> getTrajectory() {
-                return new ArrayList<>(trajectory);
-        }
-        @Override
-        public Model getModel() {
-                return model;
-        }
-        @Override
-        public DesignSpaceExplorationStoreAdapter getStoreAdapter() {
-                return storeAdapter;
-        }
-        @Override
-        public List<Version> explore() {
-                var state = model.commit();
-                trajectory.add(state);
-                strategy.explore();
-                if (isVisualizationEnabled) {
-                        modelVisualizerAdapter.visualize();
-                }
-                return solutions;
-        }
-        @Override
-        public int getModelSize() {
-                return sizeInterpretation.get(Tuple.of());
-        }
-        @Override
-        public Tuple1 createObject() {
-                var newNodeId =  getModelSize();
-                sizeInterpretation.put(Tuple.of(), newNodeId + 1);
-                return Tuple.of(newNodeId);
-        }
-        @Override
-        public Tuple deleteObject(Tuple tuple) {
-                if (tuple.getSize() != 1) {
-                        throw new IllegalArgumentException("Tuple size must be 1");
-                }
-//              TODO: implement more efficient deletion
-//              if (tuple.get(0) == getModelSize() - 1) {
-//                      sizeInterpretation.put(Tuple.of(), getModelSize() - 1);
-//              }
-                return tuple;
-        }
-        @Override
-        public boolean checkGlobalConstraints() {
-                for (var resultSet : globalConstraintResultSets) {
-                        if (resultSet.size() > 0) {
-                                return false;
-                        }
-                }
-                return true;
-        }
-        @Override
-        public boolean backtrack() {
-                return backtrack("");
-        }
-        @Override
-        public boolean backtrack(String reason) {
-                if (trajectory.size() < 2) {
-                        return false;
-                }
-                var currentState = model.getState();
-                if (!parents.containsKey(currentState)) {
-                        return false;
-                }
-                if (isVisualizationEnabled) {
-                        modelVisualizerAdapter.addTransition(trajectory.get(trajectory.size() - 1),
-                                        trajectory.get(trajectory.size() - 2), "backtrack(" + reason + ")");
-                }
-                model.restore(parents.get(model.getState()));
-                trajectory.remove(trajectory.size() - 1);
-                return true;
-        }
-        @Override
-        public void restoreTrajectory(List<Version> trajectory) {
-                model.restore(trajectory.get(trajectory.size() - 1));
-//              if (isVisualizationEnabled) {
-//                      modelVisualizerAdapter.addTransition(this.trajectory.get(trajectory.size() - 1),
-//                                      trajectory.get(trajectory.size() - 1), "restore");
-//              }
-                this.trajectory = new ArrayList<>(trajectory);
-        }
-        @Override
-        public void setRandom(Random random) {
-                this.random = random;
-        }
-        @Override
-        @SuppressWarnings("squid:S2245")
-        public void setRandom(long seed) {
-                this.random = new Random(seed);
-        }
-        @Override
-        public List<Version> getSolutions() {
-                return solutions;
-        }
-        @Override
-        public Fitness getFitness() {
-        return fitnessCache.computeIfAbsent(model.getState(), s -> calculateFitness());
-        }
-        private Fitness calculateFitness() {
-                Fitness result = new Fitness();
-                boolean satisfiesHardObjectives = true;
-                for (Objective objective : objectives) {
-                        var fitness = objective.getFitness(this);
-                        result.put(objective.getName(), fitness);
-                        if (objective.isHardObjective() && !objective.satisfiesHardObjective(fitness)) {
-                                satisfiesHardObjectives = false;
-                        }
-                }
-                result.setSatisfiesHardObjectives(satisfiesHardObjectives);
-                return result;
-        }
-        @Override
-        public void newSolution() {
-                var state = model.getState();
-                solutions.add(state);
-                if (isVisualizationEnabled) {
-                        modelVisualizerAdapter.addSolution(state);
-                }
-        }
-        @Override
-        public int getDepth() {
-                return trajectory.size() - 1;
-        }
-        public LinkedHashSet<Activation> getUntraversedActivations() {
-                var traversedActivations = statesAndTraversedActivations.get(model.getState());
-                if (traversedActivations == null) {
-                        return new LinkedHashSet<>(getAllActivations());
-                }
-                else {
-                        LinkedHashSet<Activation> untraversedActivations = new LinkedHashSet<>();
-                        for (Activation activation : getAllActivations()) {
-                                if (!traversedActivations.contains(activation)) {
-                                        untraversedActivations.add(activation);
-                                }
-                        }
-                        return untraversedActivations;
-                }
-        }
-        @Override
-        public boolean fireActivation(Activation activation) {
-                if (activation == null) {
-                        return false;
-                }
-                var previousState = model.getState();
-                if (!activation.fire()) {
-                        return false;
-                }
-                statesAndTraversedActivations.computeIfAbsent(previousState, s -> new ArrayList<>()).add(activation);
-                var newState = model.commit();
-                trajectory.add(newState);
-                parents.put(newState, previousState);
-                isNewState = !statesAndTraversedActivations.containsKey(newState);
-                if (isVisualizationEnabled) {
-                        if (isNewState) {
-                                modelVisualizerAdapter.addState(newState, getFitness().values());
-                        }
-                        modelVisualizerAdapter.addTransition(previousState, newState, activation.transformationRule().getName(),
-                                        activation.activation());
-                }
-                return true;
-        }
-        @Override
-        public boolean fireRandomActivation() {
-                var activations = getUntraversedActivations();
-                if (activations.isEmpty()) {
-                        return false;
-                }
-                int index = random.nextInt(activations.size());
-                var iterator = activations.iterator();
-                while (index-- > 0) {
-                        iterator.next();
-                }
-                var activationId = iterator.next();
-                return fireActivation(activationId);
-        }
-        public List<Activation> getAllActivations() {
-                List<Activation> result = new LinkedList<>();
-                for (var rule : transformationRules) {
-                        result.addAll(rule.getAllActivationsAsList());
-                }
-                return result;
-        }
-        public boolean isCurrentStateAlreadyTraversed() {
-                return !isNewState;
-        }
-        public ObjectiveComparatorHelper getObjectiveComparatorHelper() {
-                if (objectiveComparatorHelper == null) {
-                        objectiveComparatorHelper = new ObjectiveComparatorHelper(objectives);
-                }
-                return objectiveComparatorHelper;
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/DesignSpaceExplorationBuilderImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/DesignSpaceExplorationBuilderImpl.java
deleted file mode 100644
index 8f7056f2..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/DesignSpaceExplorationBuilderImpl.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse.internal;
-import tools.refinery.store.adapter.AbstractModelAdapterBuilder;
-import tools.refinery.store.model.ModelStore;
-import tools.refinery.store.model.ModelStoreBuilder;
-import tools.refinery.store.query.dnf.RelationalQuery;
-import tools.refinery.store.dse.DesignSpaceExplorationBuilder;
-import tools.refinery.store.dse.Strategy;
-import tools.refinery.store.dse.objectives.Objective;
-import java.util.LinkedHashSet;
-import java.util.LinkedList;
-import java.util.List;
-public class DesignSpaceExplorationBuilderImpl
-                extends AbstractModelAdapterBuilder<DesignSpaceExplorationStoreAdapterImpl>
-                implements DesignSpaceExplorationBuilder {
-        private final LinkedHashSet<TransformationRule> transformationSpecifications = new LinkedHashSet<>();
-        private final LinkedHashSet<RelationalQuery> globalConstraints = new LinkedHashSet<>();
-        private final List<Objective> objectives = new LinkedList<>();
-        private Strategy strategy;
-        @Override
-        protected DesignSpaceExplorationStoreAdapterImpl doBuild(ModelStore store) {
-                return new DesignSpaceExplorationStoreAdapterImpl(store, transformationSpecifications, globalConstraints,
-                                objectives, strategy);
-        }
-        @Override
-        public DesignSpaceExplorationBuilder transformation(TransformationRule transformationRule) {
-                checkNotConfigured();
-                transformationSpecifications.add(transformationRule);
-                return this;
-        }
-        @Override
-        public DesignSpaceExplorationBuilder globalConstraint(RelationalQuery globalConstraint) {
-                checkNotConfigured();
-                globalConstraints.add(globalConstraint);
-                return this;
-        }
-        @Override
-        public DesignSpaceExplorationBuilder objective(Objective objective) {
-                checkNotConfigured();
-                objectives.add(objective);
-                return this;
-        }
-        @Override
-        public DesignSpaceExplorationBuilder strategy(Strategy strategy) {
-                checkNotConfigured();
-                this.strategy = strategy;
-                return this;
-        }
-        @Override
-        protected void doConfigure(ModelStoreBuilder storeBuilder) {
-                storeBuilder.symbols(DesignSpaceExplorationAdapterImpl.NODE_COUNT_SYMBOL);
-                super.doConfigure(storeBuilder);
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/DesignSpaceExplorationStoreAdapterImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/DesignSpaceExplorationStoreAdapterImpl.java
deleted file mode 100644
index fea39886..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/DesignSpaceExplorationStoreAdapterImpl.java
+++ /dev/null
@@ -1,65 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse.internal;
-import tools.refinery.store.dse.DesignSpaceExplorationStoreAdapter;
-import tools.refinery.store.dse.Strategy;
-import tools.refinery.store.dse.objectives.Objective;
-import tools.refinery.store.model.Model;
-import tools.refinery.store.model.ModelStore;
-import tools.refinery.store.query.dnf.RelationalQuery;
-import java.util.List;
-import java.util.Set;
-public class DesignSpaceExplorationStoreAdapterImpl implements DesignSpaceExplorationStoreAdapter {
-        private final ModelStore store;
-        private final Set<TransformationRule> transformationSpecifications;
-        private final Set<RelationalQuery> globalConstraints;
-        private final List<Objective> objectives;
-        private final Strategy strategy;
-        public DesignSpaceExplorationStoreAdapterImpl(ModelStore store,
-                                                                                                  Set<TransformationRule> transformationSpecifications,
-                                                                                                  Set<RelationalQuery> globalConstraints,
-                                                                                                  List<Objective> objectives, Strategy strategy) {
-                        this.store = store;
-                        this.transformationSpecifications = transformationSpecifications;
-                        this.globalConstraints = globalConstraints;
-                        this.objectives = objectives;
-                        this.strategy = strategy;
-        }
-        @Override
-        public ModelStore getStore() {
-                return store;
-        }
-        @Override
-        public DesignSpaceExplorationAdapterImpl createModelAdapter(Model model) {
-                return new DesignSpaceExplorationAdapterImpl(model, this);
-        }
-        @Override
-        public Set<TransformationRule> getTransformationSpecifications() {
-                return transformationSpecifications;
-        }
-        @Override
-        public Set<RelationalQuery> getGlobalConstraints() {
-                return globalConstraints;
-        }
-        @Override
-        public List<Objective> getObjectives() {
-                return objectives;
-        }
-        @Override
-        public Strategy getStrategy() {
-                return strategy;
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/TransformationRule.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/TransformationRule.java
deleted file mode 100644
index 37117164..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/TransformationRule.java
+++ /dev/null
@@ -1,99 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse.internal;
-import org.eclipse.collections.api.block.procedure.Procedure;
-import tools.refinery.store.model.Model;
-import tools.refinery.store.query.ModelQueryAdapter;
-import tools.refinery.store.query.dnf.RelationalQuery;
-import tools.refinery.store.dse.ActionFactory;
-import tools.refinery.store.query.resultset.OrderedResultSet;
-import tools.refinery.store.query.resultset.ResultSet;
-import tools.refinery.store.tuple.Tuple;
-import java.util.*;
-public class TransformationRule {
-        private final String name;
-        private final RelationalQuery precondition;
-        private final ActionFactory actionFactory;
-        private Procedure<Tuple> action;
-        private OrderedResultSet<Boolean> activations;
-        private Random random;
-        private ModelQueryAdapter queryEngine;
-        @SuppressWarnings("squid:S2245")
-        public TransformationRule(String name, RelationalQuery precondition, ActionFactory actionFactory) {
-                this(name, precondition, actionFactory, new Random());
-        }
-        @SuppressWarnings("squid:S2245")
-        public TransformationRule(String name, RelationalQuery precondition, ActionFactory actionFactory, long seed) {
-                this(name, precondition, actionFactory, new Random(seed));
-        }
-        public TransformationRule(String name, RelationalQuery precondition, ActionFactory actionFactory, Random random) {
-                this.name = name;
-                this.precondition = precondition;
-                this.actionFactory = actionFactory;
-                this.random = random;
-        }
-        public boolean prepare(Model model, ModelQueryAdapter queryEngine) {
-                action = actionFactory.prepare(model);
-                this.queryEngine = queryEngine;
-                activations = new OrderedResultSet<>(queryEngine.getResultSet(precondition));
-                return true;
-        }
-        public boolean fireActivation(Tuple activation) {
-                action.accept(activation);
-                queryEngine.flushChanges();
-                return true;
-        }
-        public boolean fireRandomActivation() {
-                return getRandomActivation().fire();
-        }
-        public String getName() {
-                return name;
-        }
-        public RelationalQuery getPrecondition() {
-                return precondition;
-        }
-        public ResultSet<Boolean> getAllActivationsAsResultSet() {
-                return activations;
-        }
-        public Set<Activation> getAllActivations() {
-                var result = new LinkedHashSet<Activation>();
-                var cursor = activations.getAll();
-                while (cursor.move()) {
-                        result.add(new Activation(this, cursor.getKey()));
-                }
-                return result;
-        }
-        public List<Activation> getAllActivationsAsList() {
-                var result = new ArrayList<Activation>();
-                var cursor = activations.getAll();
-                while (cursor.move()) {
-                        result.add(new Activation(this, cursor.getKey()));
-                }
-                return result;
-        }
-        public Activation getRandomActivation() {
-                return new Activation(this, activations.getKey(random.nextInt(activations.size())));
-        }
-        public Activation getActivation(int index) {
-                return new Activation(this, activations.getKey(index));
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/ActionVariable.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/ActionVariable.java
deleted file mode 100644
index 92de565d..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/ActionVariable.java
+++ /dev/null
@@ -1,12 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse.internal.action;
-import tools.refinery.store.tuple.Tuple;
-public interface ActionVariable extends AtomicAction {
-        Tuple getValue();
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/ActivationVariable.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/ActivationVariable.java
deleted file mode 100644
index 6b4c6340..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/ActivationVariable.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse.internal.action;
-import tools.refinery.store.model.Model;
-import tools.refinery.store.tuple.Tuple;
-public class ActivationVariable implements ActionVariable {
-        private final int index;
-        private Tuple value;
-        public ActivationVariable() {
-                this(0);
-        }
-        public ActivationVariable(int index) {
-                this.index = index;
-        }
-        @Override
-        public void fire(Tuple activation) {
-                value = Tuple.of(activation.get(index));
-        }
-        @Override
-        public ActivationVariable prepare(Model model) {
-                return this;
-        }
-        @Override
-        public Tuple getValue() {
-                return value;
-        }
-        @Override
-        public boolean equalsWithSubstitution(AtomicAction other) {
-                if (other == null || getClass() != other.getClass()) {
-                        return false;
-                }
-                var otherAction = (ActivationVariable) other;
-                if (index != otherAction.index) {
-                        return false;
-                }
-                if (value == null) {
-                        return otherAction.value == null;
-                }
-                return value.equals(otherAction.value);
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/AtomicAction.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/AtomicAction.java
deleted file mode 100644
index a8f10bca..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/AtomicAction.java
+++ /dev/null
@@ -1,18 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse.internal.action;
-import tools.refinery.store.model.Model;
-import tools.refinery.store.tuple.Tuple;
-public interface AtomicAction {
-        void fire(Tuple activation);
-        AtomicAction prepare(Model model);
-        boolean equalsWithSubstitution(AtomicAction other);
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/DeleteAction.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/DeleteAction.java
deleted file mode 100644
index 9900390f..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/DeleteAction.java
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse.internal.action;
-import tools.refinery.store.dse.DesignSpaceExplorationAdapter;
-import tools.refinery.store.model.Model;
-import tools.refinery.store.tuple.Tuple;
-public class DeleteAction implements AtomicAction {
-        private final ActionVariable variable;
-        private DesignSpaceExplorationAdapter dseAdapter;
-        public DeleteAction(ActionVariable variable) {
-                this.variable = variable;
-        }
-        @Override
-        public void fire(Tuple activation) {
-                dseAdapter.deleteObject(variable.getValue());
-        }
-        @Override
-        public DeleteAction prepare(Model model) {
-                dseAdapter = model.getAdapter(DesignSpaceExplorationAdapter.class);
-                return this;
-        }
-        @Override
-        public boolean equalsWithSubstitution(AtomicAction other) {
-                if (other == null || getClass() != other.getClass()) {
-                        return false;
-                }
-                var otherAction = (DeleteAction) other;
-                return this.variable.getClass() == otherAction.variable.getClass();
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/InsertAction.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/InsertAction.java
deleted file mode 100644
index 90fcc5ac..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/InsertAction.java
+++ /dev/null
@@ -1,94 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse.internal.action;
-import tools.refinery.store.model.Interpretation;
-import tools.refinery.store.model.Model;
-import tools.refinery.store.tuple.Tuple;
-import tools.refinery.store.tuple.Tuple0;
-import java.util.Arrays;
-public class InsertAction<T> implements AtomicAction {
-        private final Interpretation<T> interpretation;
-        private final T value;
-        private final int arity;
-        private final ActionVariable[] variables;
-        public InsertAction(Interpretation<T> interpretation, T value, ActionVariable... variables) {
-                this.interpretation = interpretation;
-                this.value = value;
-                this.variables = variables;
-                this.arity = interpretation.getSymbol().arity();
-                if (variables.length != arity) {
-                        throw new IllegalArgumentException("Expected " + arity + " variables, but got " + variables.length);
-                }
-        }
-        @Override
-        public void fire(Tuple activation) {
-                Tuple tuple;
-                if (arity == 0) {
-                        tuple = Tuple0.INSTANCE;
-                }
-                else if (arity == 1) {
-                        tuple = variables[0].getValue();
-                }
-                else if (arity == 2) {
-                        tuple = Tuple.of(variables[0].getValue().get(0), variables[1].getValue().get(0));
-                }
-                else if (arity == 3) {
-                        tuple = Tuple.of(variables[0].getValue().get(0), variables[1].getValue().get(0), variables[2].getValue().get(0));
-                }
-                else {
-                        tuple = Tuple.of(Arrays.stream(variables).map(variable -> variable.getValue().get(0))
-                                        .mapToInt(Integer::intValue).toArray());
-                }
-                interpretation.put(tuple, value);
-        }
-        public void put(Tuple tuple) {
-                interpretation.put(tuple, value);
-        }
-        @Override
-        public InsertAction<T> prepare(Model model) {
-                return this;
-        }
-        public ActionVariable[] getVariables() {
-                return variables;
-        }
-        @Override
-        public boolean equalsWithSubstitution(AtomicAction other) {
-                if (other == null || getClass() != other.getClass()) {
-                        return false;
-                }
-                var otherAction = (InsertAction<?>) other;
-                if (variables.length != otherAction.variables.length) {
-                        return false;
-                }
-                if (!interpretation.equals(otherAction.interpretation)) {
-                        return false;
-                }
-                if (value == null) {
-                        if (otherAction.value != null) {
-                                return false;
-                        }
-                }
-        else if (!value.equals(otherAction.value)) {
-                        return false;
-                }
-                for (var i = 0; i < variables.length; i++) {
-                        if (!variables[i].equalsWithSubstitution(otherAction.variables[i])) {
-                                return false;
-                        }
-                }
-                return true;
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/NewItemVariable.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/NewItemVariable.java
deleted file mode 100644
index cbb9697e..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/NewItemVariable.java
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse.internal.action;
-import tools.refinery.store.dse.DesignSpaceExplorationAdapter;
-import tools.refinery.store.model.Model;
-import tools.refinery.store.tuple.Tuple;
-import tools.refinery.store.tuple.Tuple1;
-public class NewItemVariable implements ActionVariable {
-        private DesignSpaceExplorationAdapter dseAdapter;
-        private Tuple1 value;
-        @Override
-        public void fire(Tuple activation) {
-                value = dseAdapter.createObject();
-        }
-        @Override
-        public NewItemVariable prepare(Model model) {
-                dseAdapter = model.getAdapter(DesignSpaceExplorationAdapter.class);
-                return this;
-        }
-        @Override
-        public Tuple1 getValue() {
-                return value;
-        }
-        @Override
-        public boolean equalsWithSubstitution(AtomicAction other) {
-                if (other == null || getClass() != other.getClass()) {
-                        return false;
-                }
-                var otherAction = (NewItemVariable) other;
-                if (value == null) {
-                        return otherAction.value == null;
-                }
-                return value.equals(otherAction.value);
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/TransformationAction.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/TransformationAction.java
deleted file mode 100644
index adc4df9e..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/internal/action/TransformationAction.java
+++ /dev/null
@@ -1,129 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse.internal.action;
-import tools.refinery.store.model.Model;
-import tools.refinery.store.tuple.Tuple;
-import tools.refinery.store.tuple.Tuple2;
-import java.util.*;
-public class TransformationAction {
-        private final List<ActionVariable> actionVariables = new ArrayList<>();
-        private final List<InsertAction<?>> insertActions = new ArrayList<>();
-        private final List<DeleteAction> deleteActions = new ArrayList<>();
-        private boolean configured = false;
-        private final Map<Integer, List<Tuple2>> actionVariableUsageMap = new LinkedHashMap<>();
-        public TransformationAction add(ActionVariable action) {
-                checkConfigured();
-                actionVariables.add(action);
-                return this;
-        }
-        public TransformationAction add(InsertAction<?> action) {
-                checkConfigured();
-                insertActions.add(action);
-                return this;
-        }
-        public TransformationAction add(DeleteAction action) {
-                checkConfigured();
-                deleteActions.add(action);
-                return this;
-        }
-        private void checkConfigured() {
-                if (configured) {
-                        throw new IllegalStateException("Action already configured.");
-                }
-        }
-        public TransformationAction prepare(Model model) {
-                for (ActionVariable action : actionVariables) {
-                        action.prepare(model);
-                }
-                for (InsertAction<?> action : insertActions) {
-                        action.prepare(model);
-                }
-                for (DeleteAction action : deleteActions) {
-                        action.prepare(model);
-                }
-                for (var insertAction : insertActions) {
-                        var actionIndex = insertActions.indexOf(insertAction);
-                        var variables = insertAction.getVariables();
-                        for (var i = 0; i < variables.length; i++) {
-                                var variablelGlobalIndex = actionVariables.indexOf(variables[i]);
-                                actionVariableUsageMap.computeIfAbsent(variablelGlobalIndex, k -> new ArrayList<>());
-                                actionVariableUsageMap.get(variablelGlobalIndex).add(Tuple.of(actionIndex, i));
-                        }
-                }
-                configured = true;
-                return this;
-        }
-        public boolean fire(Tuple activation) {
-                for (ActionVariable action : actionVariables) {
-                        action.fire(activation);
-                }
-                for (InsertAction<?> action : insertActions) {
-                        action.fire(activation);
-                }
-                for (DeleteAction action : deleteActions) {
-                        action.fire(activation);
-                }
-                return true;
-        }
-        // Returns true if ActionVariables and InsertActions are inserted in same order, ActionVariables are equal (they
-        // have the same index for getting the value from the activation Tuple) and InsertActions are equal (they have
-        // the same arity and value to be set).
-        public boolean equalsWithSubstitution(TransformationAction other) {
-                if (other == this) {
-                        return true;
-                }
-                if (actionVariables.size() != other.actionVariables.size()) {
-                        return false;
-                }
-                if (insertActions.size() != other.insertActions.size()) {
-                        return false;
-                }
-                if (deleteActions.size() != other.deleteActions.size()) {
-                        return false;
-                }
-                for (var i = 0; i < actionVariables.size(); i++) {
-                        var variable = actionVariables.get(i);
-                        var otherVariable = other.actionVariables.get(i);
-                        if (!variable.equalsWithSubstitution(otherVariable)) {
-                                return false;
-                        }
-                }
-                for (var i = 0; i < insertActions.size(); i++) {
-                        var insertAction = insertActions.get(i);
-                        var otherInsertAction = other.insertActions.get(i);
-                        if (!insertAction.equalsWithSubstitution(otherInsertAction)) {
-                                return false;
-                        }
-                }
-                for (var i = 0; i < deleteActions.size(); i++) {
-                        var deleteAction = deleteActions.get(i);
-                        var otherDeleteAction = other.deleteActions.get(i);
-                        if (!deleteAction.equalsWithSubstitution(otherDeleteAction)) {
-                                return false;
-                        }
-                }
-                return this.actionVariableUsageMap.equals(other.actionVariableUsageMap);
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/DanglingEdges.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/DanglingEdges.java
new file mode 100644
index 00000000..ac9d125b
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/DanglingEdges.java
@@ -0,0 +1,12 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification;
+public enum DanglingEdges {
+        IGNORE,
+        DELETE,
+        FAIL
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationAdapter.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationAdapter.java
new file mode 100644
index 00000000..58b60499
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationAdapter.java
@@ -0,0 +1,24 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification;
+import tools.refinery.store.adapter.ModelAdapter;
+import tools.refinery.store.dse.modification.internal.ModificationBuilderImpl;
+import tools.refinery.store.tuple.Tuple;
+import tools.refinery.store.tuple.Tuple1;
+public interface ModificationAdapter extends ModelAdapter {
+        int getModelSize();
+        Tuple1 createObject();
+        boolean deleteObject(Tuple tuple, DanglingEdges danglingEdges);
+        static ModificationBuilder builder() {
+                return new ModificationBuilderImpl();
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationBuilder.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationBuilder.java
new file mode 100644
index 00000000..48c22bdf
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationBuilder.java
@@ -0,0 +1,11 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification;
+import tools.refinery.store.adapter.ModelAdapterBuilder;
+public interface ModificationBuilder extends ModelAdapterBuilder {
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationStoreAdapter.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationStoreAdapter.java
new file mode 100644
index 00000000..144c4d05
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationStoreAdapter.java
@@ -0,0 +1,11 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification;
+import tools.refinery.store.adapter.ModelStoreAdapter;
+public interface ModificationStoreAdapter extends ModelStoreAdapter {
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/CreateActionLiteral.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/CreateActionLiteral.java
new file mode 100644
index 00000000..5b86a5e1
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/CreateActionLiteral.java
@@ -0,0 +1,43 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification.actions;
+import tools.refinery.store.dse.modification.ModificationAdapter;
+import tools.refinery.store.dse.transition.actions.AbstractActionLiteral;
+import tools.refinery.store.dse.transition.actions.BoundActionLiteral;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.term.NodeVariable;
+import java.util.List;
+public class CreateActionLiteral extends AbstractActionLiteral {
+        private final NodeVariable variable;
+        public CreateActionLiteral(NodeVariable variable) {
+                this.variable = variable;
+        }
+        public NodeVariable getVariable() {
+                return variable;
+        }
+        @Override
+        public List<NodeVariable> getInputVariables() {
+                return List.of();
+        }
+        @Override
+        public List<NodeVariable> getOutputVariables() {
+                return List.of(variable);
+        }
+        @Override
+        public BoundActionLiteral bindToModel(Model model) {
+                var adapter = model.getAdapter(ModificationAdapter.class);
+                return ignoredTuple -> adapter.createObject();
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/DeleteActionLiteral.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/DeleteActionLiteral.java
new file mode 100644
index 00000000..18ad2b9d
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/DeleteActionLiteral.java
@@ -0,0 +1,51 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification.actions;
+import tools.refinery.store.dse.modification.DanglingEdges;
+import tools.refinery.store.dse.modification.ModificationAdapter;
+import tools.refinery.store.dse.transition.actions.AbstractActionLiteral;
+import tools.refinery.store.dse.transition.actions.BoundActionLiteral;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.tuple.Tuple;
+import java.util.List;
+public class DeleteActionLiteral extends AbstractActionLiteral {
+        private final NodeVariable variable;
+        private final DanglingEdges danglingEdges;
+        public DeleteActionLiteral(NodeVariable variable, DanglingEdges danglingEdges) {
+                this.variable = variable;
+                this.danglingEdges = danglingEdges;
+        }
+        public NodeVariable getVariable() {
+                return variable;
+        }
+        public DanglingEdges getDanglingEdges() {
+                return danglingEdges;
+        }
+        @Override
+        public List<NodeVariable> getInputVariables() {
+                return List.of(variable);
+        }
+        @Override
+        public List<NodeVariable> getOutputVariables() {
+                return List.of();
+        }
+        @Override
+        public BoundActionLiteral bindToModel(Model model) {
+                var adapter = model.getAdapter(ModificationAdapter.class);
+                return tuple -> adapter.deleteObject(tuple, danglingEdges) ? Tuple.of() : null;
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/ModificationActionLiterals.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/ModificationActionLiterals.java
new file mode 100644
index 00000000..31f50ac7
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/ModificationActionLiterals.java
@@ -0,0 +1,23 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification.actions;
+import tools.refinery.store.dse.modification.DanglingEdges;
+import tools.refinery.store.query.term.NodeVariable;
+public class ModificationActionLiterals {
+        private ModificationActionLiterals() {
+                throw new IllegalArgumentException("This is a static utility class and should not be instantiated directly");
+        }
+        public static CreateActionLiteral create(NodeVariable variable) {
+                return new CreateActionLiteral(variable);
+        }
+        public static DeleteActionLiteral delete(NodeVariable variable, DanglingEdges danglingEdges) {
+                return new DeleteActionLiteral(variable, danglingEdges);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationAdapterImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationAdapterImpl.java
new file mode 100644
index 00000000..4e77c462
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationAdapterImpl.java
@@ -0,0 +1,107 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification.internal;
+import tools.refinery.store.adapter.ModelStoreAdapter;
+import tools.refinery.store.dse.modification.DanglingEdges;
+import tools.refinery.store.dse.modification.ModificationAdapter;
+import tools.refinery.store.model.Interpretation;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.representation.Symbol;
+import tools.refinery.store.tuple.Tuple;
+import tools.refinery.store.tuple.Tuple1;
+import java.util.HashSet;
+public class ModificationAdapterImpl implements ModificationAdapter {
+        static final Symbol<Integer> NEXT_ID = Symbol.of("NEXT_ID", 0, Integer.class, 0);
+        final ModelStoreAdapter storeAdapter;
+        final Model model;
+        Interpretation<Integer> nodeCountInterpretation;
+        ModificationAdapterImpl(ModelStoreAdapter storeAdapter, Model model) {
+                this.storeAdapter = storeAdapter;
+                this.model = model;
+                this.nodeCountInterpretation = model.getInterpretation(NEXT_ID);
+        }
+        @Override
+        public Model getModel() {
+                return model;
+        }
+        @Override
+        public ModelStoreAdapter getStoreAdapter() {
+                return storeAdapter;
+        }
+        @Override
+        public int getModelSize() {
+                return nodeCountInterpretation.get(Tuple.of());
+        }
+        @Override
+        public Tuple1 createObject() {
+                var newNodeId = getModelSize();
+                nodeCountInterpretation.put(Tuple.of(), newNodeId + 1);
+                return Tuple.of(newNodeId);
+        }
+        @Override
+        public boolean deleteObject(Tuple tuple, DanglingEdges danglingEdges) {
+                if (tuple.getSize() != 1) {
+                        throw new IllegalArgumentException("Tuple size must be 1");
+                }
+                int objectId = tuple.get(0);
+                if (danglingEdges == DanglingEdges.DELETE) {
+                        deleteDanglingEdges(objectId);
+                } else if (danglingEdges == DanglingEdges.FAIL && hasDanglingEdges(objectId)) {
+                        return false;
+                }
+                int modelSize = getModelSize();
+                if (objectId == modelSize - 1) {
+                        nodeCountInterpretation.put(Tuple.of(), modelSize - 1);
+                }
+                return true;
+        }
+        private void deleteDanglingEdges(int objectId) {
+                for (var symbol : model.getStore().getSymbols()) {
+                        deleteDanglingEdges(objectId, (Symbol<?>) symbol);
+                }
+        }
+        private <T> void deleteDanglingEdges(int objectId, Symbol<T> symbol) {
+                var interpretation = model.getInterpretation(symbol);
+                var toDelete = new HashSet<Tuple>();
+                int arity = symbol.arity();
+                for (int i = 0; i < arity; i++) {
+                        var cursor = interpretation.getAdjacent(i, objectId);
+                        while (cursor.move()) {
+                                toDelete.add(cursor.getKey());
+                        }
+                }
+                var defaultValue = symbol.defaultValue();
+                for (var tuple : toDelete) {
+                        interpretation.put(tuple, defaultValue);
+                }
+        }
+        private boolean hasDanglingEdges(int objectId) {
+                for (var symbol : model.getStore().getSymbols()) {
+                        var interpretation = model.getInterpretation(symbol);
+                        int arity = symbol.arity();
+                        for (int i = 0; i < arity; i++) {
+                                if (interpretation.getAdjacentSize(i, objectId) > 0) {
+                                        return true;
+                                }
+                        }
+                }
+                return false;
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationBuilderImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationBuilderImpl.java
new file mode 100644
index 00000000..c4d38d22
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationBuilderImpl.java
@@ -0,0 +1,29 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification.internal;
+import tools.refinery.store.adapter.AbstractModelAdapterBuilder;
+import tools.refinery.store.dse.modification.ModificationBuilder;
+import tools.refinery.store.dse.modification.ModificationStoreAdapter;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.model.ModelStoreBuilder;
+import tools.refinery.store.statecoding.StateCoderBuilder;
+public class ModificationBuilderImpl extends AbstractModelAdapterBuilder<ModificationStoreAdapter> implements ModificationBuilder {
+        @Override
+        protected void doConfigure(ModelStoreBuilder storeBuilder) {
+                storeBuilder.symbols(ModificationAdapterImpl.NEXT_ID);
+                storeBuilder.tryGetAdapter(StateCoderBuilder.class).ifPresent(
+                                coderBuilder -> coderBuilder.exclude(ModificationAdapterImpl.NEXT_ID));
+                super.doConfigure(storeBuilder);
+        }
+        @Override
+        protected ModificationStoreAdapter doBuild(ModelStore store) {
+                return new ModificationStoreAdapterImpl(store);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationStoreAdapterImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationStoreAdapterImpl.java
new file mode 100644
index 00000000..62e4227b
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationStoreAdapterImpl.java
@@ -0,0 +1,29 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification.internal;
+import tools.refinery.store.adapter.ModelAdapter;
+import tools.refinery.store.dse.modification.ModificationStoreAdapter;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.model.ModelStore;
+public class ModificationStoreAdapterImpl implements ModificationStoreAdapter {
+        ModelStore store;
+        ModificationStoreAdapterImpl(ModelStore store) {
+                this.store = store;
+        }
+        @Override
+        public ModelStore getStore() {
+                return store;
+        }
+        @Override
+        public ModelAdapter createModelAdapter(Model model) {
+                return new ModificationAdapterImpl(this, model);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/AlwaysSatisfiedDummyHardObjective.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/AlwaysSatisfiedDummyHardObjective.java
deleted file mode 100644
index afed75fd..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/AlwaysSatisfiedDummyHardObjective.java
+++ /dev/null
@@ -1,52 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2010-2016, Andras Szabolcs Nagy, Zoltan Ujhelyi and Daniel Varro
- * Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
- * This program and the accompanying materials are made available under the
- * terms of the Eclipse Public License v. 2.0 which is available at
- * http://www.eclipse.org/legal/epl-v20.html.
- *
- * SPDX-License-Identifier: EPL-2.0
- *******************************************************************************/
-package tools.refinery.store.dse.objectives;
-import tools.refinery.store.dse.DesignSpaceExplorationAdapter;
-/**
- * This hard objective is fulfilled in any circumstances. Use it if all states should be regarded as a valid solution.
- *
- * @author Andras Szabolcs Nagy
- *
- */
-public class AlwaysSatisfiedDummyHardObjective extends BaseObjective {
-        private static final String DEFAULT_NAME = "AlwaysSatisfiedDummyHardObjective";
-        public AlwaysSatisfiedDummyHardObjective() {
-                super(DEFAULT_NAME);
-        }
-        public AlwaysSatisfiedDummyHardObjective(String name) {
-                super(name);
-        }
-        @Override
-        public Double getFitness(DesignSpaceExplorationAdapter context) {
-                return 0d;
-        }
-        @Override
-        public boolean isHardObjective() {
-                return true;
-        }
-        @Override
-        public boolean satisfiesHardObjective(Double fitness) {
-                return true;
-        }
-        @Override
-        public Objective createNew() {
-                return this;
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/AlwaysSatisfiedRandomHardObjective.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/AlwaysSatisfiedRandomHardObjective.java
deleted file mode 100644
index cdd1754f..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/AlwaysSatisfiedRandomHardObjective.java
+++ /dev/null
@@ -1,57 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2010-2016, Andras Szabolcs Nagy, Zoltan Ujhelyi and Daniel Varro
- * Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
- * This program and the accompanying materials are made available under the
- * terms of the Eclipse Public License v. 2.0 which is available at
- * http://www.eclipse.org/legal/epl-v20.html.
- *
- * SPDX-License-Identifier: EPL-2.0
- *******************************************************************************/
-package tools.refinery.store.dse.objectives;
-import tools.refinery.store.dse.DesignSpaceExplorationAdapter;
-import java.util.Random;
-/**
- * This hard objective is fulfilled in any circumstances. Use it if all states should be regarded as a valid solution.
- *
- * @author Andras Szabolcs Nagy
- *
- */
-public class AlwaysSatisfiedRandomHardObjective extends BaseObjective {
-        private static final String DEFAULT_NAME = "AlwaysSatisfiedDummyHardObjective";
-        @SuppressWarnings("squid:S2245")
-        private static final Random random = new Random(0);
-        public AlwaysSatisfiedRandomHardObjective() {
-                super(DEFAULT_NAME);
-        }
-        public AlwaysSatisfiedRandomHardObjective(String name) {
-                super(name);
-        }
-        @Override
-        public Double getFitness(DesignSpaceExplorationAdapter context) {
-//              return 0d;
-                return random.nextDouble();
-        }
-        @Override
-        public boolean isHardObjective() {
-                return true;
-        }
-        @Override
-        public boolean satisfiesHardObjective(Double fitness) {
-                return true;
-        }
-        @Override
-        public Objective createNew() {
-                return this;
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/BaseObjective.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/BaseObjective.java
deleted file mode 100644
index b76598fb..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/BaseObjective.java
+++ /dev/null
@@ -1,132 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2010-2015, Andras Szabolcs Nagy, Abel Hegedus, Akos Horvath, Zoltan Ujhelyi and Daniel Varro
- * Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
- * This program and the accompanying materials are made available under the
- * terms of the Eclipse Public License v. 2.0 which is available at
- * http://www.eclipse.org/legal/epl-v20.html.
- *
- * SPDX-License-Identifier: EPL-2.0
- *******************************************************************************/
-package tools.refinery.store.dse.objectives;
-import tools.refinery.store.dse.DesignSpaceExplorationAdapter;
-import java.util.Comparator;
-import java.util.Objects;
-/**
- * This abstract class implements the basic functionality of an objective ({@link Objective} namely its name,
- * comparator, level and fitness hard constraint.
- *
- * @author Andras Szabolcs Nagy
- *
- */
-public abstract class BaseObjective implements Objective {
-        protected final String name;
-        protected Comparator<Double> comparator = Comparators.HIGHER_IS_BETTER;
-        protected double fitnessConstraint;
-        protected boolean isThereFitnessConstraint = false;
-        protected Comparator<Double> fitnessConstraintComparator;
-        protected BaseObjective(String name) {
-                Objects.requireNonNull(name, "Name of the objective cannot be null.");
-                this.name = name;
-        }
-        @Override
-        public String getName() {
-                return name;
-        }
-        @Override
-        public void setComparator(Comparator<Double> comparator) {
-                this.comparator = comparator;
-        }
-        @Override
-        public Comparator<Double> getComparator() {
-                return comparator;
-        }
-        public BaseObjective withComparator(Comparator<Double> comparator) {
-                setComparator(comparator);
-                return this;
-        }
-        /**
-         * Adds a hard constraint on the fitness value. For example, the fitness value must be better than 10 to accept the
-         * current state as a solution.
-         *
-         * @param fitnessConstraint
-         *            Solutions should be better than this value.
-         * @param fitnessConstraintComparator
-         *            {@link Comparator} to determine if the current state is better than the given value.
-         * @return The actual instance to enable builder pattern like usage.
-         */
-        public BaseObjective withHardConstraintOnFitness(double fitnessConstraint,
-                                                                                                         Comparator<Double> fitnessConstraintComparator) {
-                this.fitnessConstraint = fitnessConstraint;
-                this.fitnessConstraintComparator = fitnessConstraintComparator;
-                this.isThereFitnessConstraint = true;
-                return this;
-        }
-        /**
-         * Adds a hard constraint on the fitness value. For example, the fitness value must be better than 10 to accept the
-         * current state as a solution. The provided comparator will be used.
-         *
-         * @param fitnessConstraint
-         *            Solutions should be better than this value.
-         * @return The actual instance to enable builder pattern like usage.
-         */
-        public BaseObjective withHardConstraintOnFitness(double fitnessConstraint) {
-                return withHardConstraintOnFitness(fitnessConstraint, null);
-        }
-        @Override
-        public void init(DesignSpaceExplorationAdapter context) {
-                if (fitnessConstraintComparator == null) {
-                        fitnessConstraintComparator = comparator;
-                }
-        }
-        @Override
-        public boolean isHardObjective() {
-                return isThereFitnessConstraint;
-        }
-        @Override
-        public boolean satisfiesHardObjective(Double fitness) {
-                if (isThereFitnessConstraint) {
-                        int compare = fitnessConstraintComparator.compare(fitness, fitnessConstraint);
-                        if (compare < 0) {
-                                return false;
-                        }
-                }
-                return true;
-        }
-        @Override
-        public int hashCode() {
-                return name.hashCode();
-        }
-        @Override
-        public boolean equals(Object obj) {
-                if (this == obj) {
-                        return true;
-                }
-                if (obj instanceof BaseObjective baseObjective) {
-                        return name.equals(baseObjective.getName());
-                }
-                return false;
-        }
-        @Override
-        public String toString() {
-                return name;
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/Comparators.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/Comparators.java
deleted file mode 100644
index 181397b3..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/Comparators.java
+++ /dev/null
@@ -1,26 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2010-2015, Andras Szabolcs Nagy, Abel Hegedus, Akos Horvath, Zoltan Ujhelyi and Daniel Varro
- * Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
- * This program and the accompanying materials are made available under the
- * terms of the Eclipse Public License v. 2.0 which is available at
- * http://www.eclipse.org/legal/epl-v20.html.
- *
- * SPDX-License-Identifier: EPL-2.0
- *******************************************************************************/
-package tools.refinery.store.dse.objectives;
-import java.util.Comparator;
-public class Comparators {
-        private Comparators() { /*Utility class constructor*/ }
-        public static final Comparator<Double> HIGHER_IS_BETTER = Double::compareTo;
-        public static final Comparator<Double> LOWER_IS_BETTER = (o1, o2) -> o2.compareTo(o1);
-        private static final Double ZERO = (double) 0;
-        public static final Comparator<Double> DIFFERENCE_TO_ZERO_IS_BETTER = (o1, o2) -> ZERO.compareTo(Math.abs(o1)-Math.abs(o2));
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/Fitness.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/Fitness.java
deleted file mode 100644
index b1dc4442..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/Fitness.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2010-2014, Miklos Foldenyi, Andras Szabolcs Nagy, Abel Hegedus, Akos Horvath, Zoltan Ujhelyi and Daniel Varro
- * Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
- * This program and the accompanying materials are made available under the
- * terms of the Eclipse Public License v. 2.0 which is available at
- * http://www.eclipse.org/legal/epl-v20.html.
- *
- * SPDX-License-Identifier: EPL-2.0
- *******************************************************************************/
-package tools.refinery.store.dse.objectives;
-import java.util.HashMap;
-public class Fitness extends HashMap<String, Double> {
-        private boolean satisfiesHardObjectives;
-        public boolean isSatisfiesHardObjectives() {
-                return satisfiesHardObjectives;
-        }
-        public void setSatisfiesHardObjectives(boolean satisfiesHardObjectives) {
-                this.satisfiesHardObjectives = satisfiesHardObjectives;
-        }
-        @Override
-        public String toString() {
-                return super.toString() + " hardObjectives=" + satisfiesHardObjectives;
-        }
-        @Override
-        public boolean equals(Object other) {
-                if (other == null) return false;
-                if (getClass() != other.getClass()) return false;
-                if (!super.equals(other)) return false;
-                return satisfiesHardObjectives == ((Fitness) other).satisfiesHardObjectives;
-        }
-        @Override
-        public int hashCode() {
-                int h = super.hashCode();
-                h = h * 31 + (satisfiesHardObjectives ? 1 : 0);
-                return h;
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/Objective.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/Objective.java
deleted file mode 100644
index c7313622..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/Objective.java
+++ /dev/null
@@ -1,101 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2010-2014, Miklos Foldenyi, Andras Szabolcs Nagy, Abel Hegedus, Akos Horvath, Zoltan Ujhelyi and Daniel Varro
- * Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
- * This program and the accompanying materials are made available under the
- * terms of the Eclipse Public License v. 2.0 which is available at
- * http://www.eclipse.org/legal/epl-v20.html.
- *
- * SPDX-License-Identifier: EPL-2.0
- *******************************************************************************/
-package tools.refinery.store.dse.objectives;
-import tools.refinery.store.dse.DesignSpaceExplorationAdapter;
-import java.util.Comparator;
-/**
- *
- * Implementation of this interface represents a single objective of the DSE problem, which can assess a solution
- * (trajectory) in a single number. It has a name and a comparator which orders two solution based on the calculated
- * value.
- * <p>
- * Objectives can be either hard or soft objectives. Hard objectives can be satisfied or unsatisfied. If all of the hard
- * objectives are satisfied on a single solution, then it is considered to be a valid (or goal) solution.
- * <p>
- * Certain objectives can have inner state for calculating the fitness value. In this case a new instance is necessary
- * for every new thread, and the {@code createNew} method should not return the same instance more than once.
- *
- * @author Andras Szabolcs Nagy
- *
- */
-public interface Objective {
-        /**
-         * Returns the name of the objective.
-         *
-         * @return The name of the objective.
-         */
-        String getName();
-        /**
-         * Sets the {@link Comparator} which is used to compare fitness (doubles). It determines whether the objective is to
-         * minimize or maximize (or minimize or maximize a delta from a given number).
-         *
-         * @param comparator The comparator.
-         */
-        void setComparator(Comparator<Double> comparator);
-        /**
-         * Returns a {@link Comparator} which is used to compare fitness (doubles). It determines whether the objective is
-         * to minimize or maximize (or minimize or maximize a delta from a given number).
-         *
-         * @return The comparator.
-         */
-        Comparator<Double> getComparator();
-        /**
-         * Calculates the value of the objective on a given solution (trajectory).
-         *
-         * @param context
-         *            The {@link DesignSpaceExplorationAdapter}
-         * @return The objective value in double.
-         */
-        Double getFitness(DesignSpaceExplorationAdapter context);
-        /**
-         * Initializes the objective. It is called exactly once for every thread starts.
-         *
-         * @param context
-         *            The {@link DesignSpaceExplorationAdapter}.
-         */
-        void init(DesignSpaceExplorationAdapter context);
-        /**
-         * Returns an instance of the {@link Objective}. If it returns the same instance, all the methods has to be thread
-         * save as they are called concurrently.
-         *
-         * @return An instance of the objective.
-         */
-        Objective createNew();
-        /**
-         * Returns true if the objective is a hard objective. In such a case the method
-         * {@link Objective#satisfiesHardObjective(Double)} is called.
-         *
-         * @return True if the objective is a hard objective.
-         * @see Objective#satisfiesHardObjective(Double)
-         * @see Objective
-         */
-        boolean isHardObjective();
-        /**
-         * Determines if the given fitness value satisfies the hard objective.
-         *
-         * @param fitness
-         *            The fitness value of a solution.
-         * @return True if it satisfies the hard objective or it is a soft constraint.
-         * @see Objective
-         */
-        boolean satisfiesHardObjective(Double fitness);
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/ObjectiveComparatorHelper.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/ObjectiveComparatorHelper.java
deleted file mode 100644
index eb03eeaf..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/objectives/ObjectiveComparatorHelper.java
+++ /dev/null
@@ -1,60 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2010-2015, Andras Szabolcs Nagy, Abel Hegedus, Akos Horvath, Zoltan Ujhelyi and Daniel Varro
- * Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
- * This program and the accompanying materials are made available under the
- * terms of the Eclipse Public License v. 2.0 which is available at
- * http://www.eclipse.org/legal/epl-v20.html.
- *
- * SPDX-License-Identifier: EPL-2.0
- *******************************************************************************/
-package tools.refinery.store.dse.objectives;
-import java.util.List;
-/**
- * This class is responsible to compare and sort fitness values.
- *
- * @author András Szabolcs Nagy
- */
-public class ObjectiveComparatorHelper {
-        private final List<Objective> objectives;
-        public ObjectiveComparatorHelper(List<Objective> objectives) {
-                this.objectives = objectives;
-        }
-        /**
-         * Compares two fitnesses based on dominance. Returns -1 if the second parameter {@code o2} is a better
-         * solution ({@code o2} dominates {@code o1}), 1 if the first parameter {@code o1} is better ({@code o1} dominates
-         * {@code o2}) and returns 0 if they are non-dominating each other.
-         */
-        public int compare(Fitness o1, Fitness o2) {
-                boolean o1HasBetterFitness = false;
-                boolean o2HasBetterFitness = false;
-                for (Objective objective : objectives) {
-                        String objectiveName = objective.getName();
-                        int sgn = objective.getComparator().compare(o1.get(objectiveName), o2.get(objectiveName));
-                        if (sgn < 0) {
-                                o2HasBetterFitness = true;
-                        }
-                        if (sgn > 0) {
-                                o1HasBetterFitness = true;
-                        }
-                        if (o1HasBetterFitness && o2HasBetterFitness) {
-                                break;
-                        }
-                }
-                if (o2HasBetterFitness) {
-                        return -1;
-                } else if (o1HasBetterFitness) {
-                        return 1;
-                }
-                return 0;
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/BoundPropagator.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/BoundPropagator.java
new file mode 100644
index 00000000..5ad61463
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/BoundPropagator.java
@@ -0,0 +1,11 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.propagation;
+@FunctionalInterface
+public interface BoundPropagator {
+        PropagationResult propagateOne();
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/PropagationAdapter.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/PropagationAdapter.java
new file mode 100644
index 00000000..3ea5a75f
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/PropagationAdapter.java
@@ -0,0 +1,20 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.propagation;
+import tools.refinery.store.adapter.ModelAdapter;
+import tools.refinery.store.dse.propagation.impl.PropagationBuilderImpl;
+public interface PropagationAdapter extends ModelAdapter {
+        @Override
+        PropagationStoreAdapter getStoreAdapter();
+        PropagationResult propagate();
+        static PropagationBuilder builder() {
+                return new PropagationBuilderImpl();
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/PropagationBuilder.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/PropagationBuilder.java
new file mode 100644
index 00000000..f8a89b30
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/PropagationBuilder.java
@@ -0,0 +1,32 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.propagation;
+import tools.refinery.store.adapter.ModelAdapterBuilder;
+import tools.refinery.store.dse.transition.Rule;
+import tools.refinery.store.model.ModelStore;
+import java.util.Collection;
+import java.util.List;
+@SuppressWarnings("UnusedReturnValue")
+public interface PropagationBuilder extends ModelAdapterBuilder {
+        PropagationBuilder rule(Rule propagationRule);
+        default PropagationBuilder rules(Rule... propagationRules) {
+                return rules(List.of(propagationRules));
+        }
+        default PropagationBuilder rules(Collection<Rule> propagationRules) {
+                propagationRules.forEach(this::rule);
+                return this;
+        }
+        PropagationBuilder propagator(Propagator propagator);
+        @Override
+        PropagationStoreAdapter build(ModelStore store);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/PropagationResult.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/PropagationResult.java
new file mode 100644
index 00000000..ea56653a
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/PropagationResult.java
@@ -0,0 +1,28 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.propagation;
+public enum PropagationResult {
+        UNCHANGED,
+        PROPAGATED,
+        REJECTED;
+        public PropagationResult andThen(PropagationResult next) {
+                return switch (this) {
+                        case UNCHANGED -> next;
+                        case PROPAGATED -> next == REJECTED ? REJECTED : PROPAGATED;
+                        case REJECTED -> REJECTED;
+                };
+        }
+        public boolean isRejected() {
+                return this == REJECTED;
+        }
+        public boolean isChanged() {
+                return this == PROPAGATED;
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/PropagationStoreAdapter.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/PropagationStoreAdapter.java
new file mode 100644
index 00000000..82cba909
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/PropagationStoreAdapter.java
@@ -0,0 +1,14 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.propagation;
+import tools.refinery.store.adapter.ModelStoreAdapter;
+import tools.refinery.store.model.Model;
+public interface PropagationStoreAdapter extends ModelStoreAdapter {
+        @Override
+        PropagationAdapter createModelAdapter(Model model);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/Propagator.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/Propagator.java
new file mode 100644
index 00000000..c6b4e1c9
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/Propagator.java
@@ -0,0 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.propagation;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.model.ModelStoreBuilder;
+@FunctionalInterface
+public interface Propagator {
+        default void configure(ModelStoreBuilder storeBuilder) {
+        }
+        BoundPropagator bindToModel(Model model);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/PropagationAdapterImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/PropagationAdapterImpl.java
new file mode 100644
index 00000000..fdd19217
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/PropagationAdapterImpl.java
@@ -0,0 +1,75 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.propagation.impl;
+import tools.refinery.store.dse.propagation.BoundPropagator;
+import tools.refinery.store.dse.propagation.PropagationAdapter;
+import tools.refinery.store.dse.propagation.PropagationResult;
+import tools.refinery.store.dse.propagation.PropagationStoreAdapter;
+import tools.refinery.store.model.Model;
+class PropagationAdapterImpl implements PropagationAdapter {
+        private final Model model;
+        private final PropagationStoreAdapterImpl storeAdapter;
+        private final BoundPropagator[] boundPropagators;
+        public PropagationAdapterImpl(Model model, PropagationStoreAdapterImpl storeAdapter) {
+                this.model = model;
+                this.storeAdapter = storeAdapter;
+                var propagators = storeAdapter.getPropagators();
+                boundPropagators = new BoundPropagator[propagators.size()];
+                for (int i = 0; i < boundPropagators.length; i++) {
+                        boundPropagators[i] = propagators.get(i).bindToModel(model);
+                }
+        }
+        @Override
+        public PropagationResult propagate() {
+                PropagationResult result = PropagationResult.UNCHANGED;
+                PropagationResult lastResult;
+                do {
+                        model.checkCancelled();
+                        lastResult = propagateOne();
+                        result = result.andThen(lastResult);
+                } while (lastResult.isChanged());
+                return result;
+        }
+        private PropagationResult propagateOne() {
+                PropagationResult result = PropagationResult.UNCHANGED;
+                for (int i = 0; i < boundPropagators.length; i++) {
+                        model.checkCancelled();
+                        var lastResult = propagateUntilFixedPoint(i);
+                        result = result.andThen(lastResult);
+                        if (result.isRejected()) {
+                                break;
+                        }
+                }
+                return result;
+        }
+        private PropagationResult propagateUntilFixedPoint(int propagatorIndex) {
+                var propagator = boundPropagators[propagatorIndex];
+                PropagationResult result = PropagationResult.UNCHANGED;
+                PropagationResult lastResult;
+                do {
+                        model.checkCancelled();
+                        lastResult = propagator.propagateOne();
+                        result = result.andThen(lastResult);
+                } while (lastResult.isChanged());
+                return result;
+        }
+        @Override
+        public Model getModel() {
+                return model;
+        }
+        @Override
+        public PropagationStoreAdapter getStoreAdapter() {
+                return storeAdapter;
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/PropagationBuilderImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/PropagationBuilderImpl.java
new file mode 100644
index 00000000..c844a89f
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/PropagationBuilderImpl.java
@@ -0,0 +1,53 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.propagation.impl;
+import tools.refinery.store.adapter.AbstractModelAdapterBuilder;
+import tools.refinery.store.dse.propagation.PropagationBuilder;
+import tools.refinery.store.dse.propagation.PropagationStoreAdapter;
+import tools.refinery.store.dse.propagation.Propagator;
+import tools.refinery.store.dse.propagation.impl.rule.RuleBasedPropagator;
+import tools.refinery.store.dse.transition.Rule;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.model.ModelStoreBuilder;
+import java.util.*;
+public class PropagationBuilderImpl extends AbstractModelAdapterBuilder<PropagationStoreAdapter>
+                implements PropagationBuilder {
+        private final Set<Rule> propagationRules = new LinkedHashSet<>();
+        private final Deque<Propagator> propagators = new ArrayDeque<>();
+        @Override
+        public PropagationBuilder rule(Rule propagationRule) {
+                checkNotConfigured();
+                propagationRules.add(propagationRule);
+                return this;
+        }
+        @Override
+        public PropagationBuilder propagator(Propagator propagator) {
+                checkNotConfigured();
+                propagators.addFirst(propagator);
+                return this;
+        }
+        @Override
+        protected void doConfigure(ModelStoreBuilder storeBuilder) {
+                super.doConfigure(storeBuilder);
+                if (!propagationRules.isEmpty()) {
+                        propagators.addFirst(new RuleBasedPropagator(List.copyOf(propagationRules)));
+                }
+                for (var propagator : propagators) {
+                        propagator.configure(storeBuilder);
+                }
+        }
+        @Override
+        protected PropagationStoreAdapter doBuild(ModelStore store) {
+                return new PropagationStoreAdapterImpl(store, List.copyOf(propagators));
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/PropagationStoreAdapterImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/PropagationStoreAdapterImpl.java
new file mode 100644
index 00000000..a223caed
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/PropagationStoreAdapterImpl.java
@@ -0,0 +1,38 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.propagation.impl;
+import tools.refinery.store.dse.propagation.PropagationAdapter;
+import tools.refinery.store.dse.propagation.PropagationStoreAdapter;
+import tools.refinery.store.dse.propagation.Propagator;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.model.ModelStore;
+import java.util.List;
+class PropagationStoreAdapterImpl implements PropagationStoreAdapter {
+        private final ModelStore store;
+        private final List<Propagator> propagators;
+        PropagationStoreAdapterImpl(ModelStore store, List<Propagator> propagators) {
+                this.store = store;
+                this.propagators = propagators;
+        }
+        @Override
+        public ModelStore getStore() {
+                return store;
+        }
+        @Override
+        public PropagationAdapter createModelAdapter(Model model) {
+                return new PropagationAdapterImpl(model, this);
+        }
+        List<Propagator> getPropagators() {
+                return propagators;
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/rule/BoundPropagationRule.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/rule/BoundPropagationRule.java
new file mode 100644
index 00000000..a70292ad
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/rule/BoundPropagationRule.java
@@ -0,0 +1,40 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.propagation.impl.rule;
+import tools.refinery.store.dse.propagation.PropagationResult;
+import tools.refinery.store.dse.transition.Rule;
+import tools.refinery.store.dse.transition.actions.BoundAction;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.query.resultset.ResultSet;
+class BoundPropagationRule {
+        private final Model model;
+        private final ResultSet<Boolean> resultSet;
+        private final BoundAction action;
+        public BoundPropagationRule(Model model, Rule rule) {
+                this.model = model;
+                resultSet = model.getAdapter(ModelQueryAdapter.class).getResultSet(rule.getPrecondition());
+                action = rule.createAction(model);
+        }
+        public PropagationResult fireAll() {
+                if (resultSet.size() == 0) {
+                        return PropagationResult.UNCHANGED;
+                }
+                var cursor = resultSet.getAll();
+                while (cursor.move()) {
+                        model.checkCancelled();
+                        var result = action.fire(cursor.getKey());
+                        if (!result) {
+                                return PropagationResult.REJECTED;
+                        }
+                }
+                return PropagationResult.PROPAGATED;
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/rule/BoundRuleBasedPropagator.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/rule/BoundRuleBasedPropagator.java
new file mode 100644
index 00000000..bd03f923
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/rule/BoundRuleBasedPropagator.java
@@ -0,0 +1,43 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.propagation.impl.rule;
+import tools.refinery.store.dse.propagation.BoundPropagator;
+import tools.refinery.store.dse.propagation.PropagationResult;
+import tools.refinery.store.dse.transition.Rule;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.ModelQueryAdapter;
+import java.util.List;
+public class BoundRuleBasedPropagator implements BoundPropagator {
+        private final ModelQueryAdapter queryEngine;
+        private final BoundPropagationRule[] boundRules;
+        public BoundRuleBasedPropagator(Model model, List<Rule> propagationRules) {
+                queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                boundRules = new BoundPropagationRule[propagationRules.size()];
+                for (int i = 0; i < boundRules.length; i++) {
+                        boundRules[i] = new BoundPropagationRule(model, propagationRules.get(i));
+                }
+        }
+        @Override
+        public PropagationResult propagateOne() {
+                queryEngine.flushChanges();
+                PropagationResult result = PropagationResult.UNCHANGED;
+                // Use a classic for loop to avoid allocating an iterator.
+                //noinspection ForLoopReplaceableByForEach
+                for (int i = 0; i < boundRules.length; i++) {
+                        var lastResult = boundRules[i].fireAll();
+                        result = result.andThen(lastResult);
+                        if (result.isRejected()) {
+                                break;
+                        }
+                }
+                return result;
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/rule/RuleBasedPropagator.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/rule/RuleBasedPropagator.java
new file mode 100644
index 00000000..709b2416
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/propagation/impl/rule/RuleBasedPropagator.java
@@ -0,0 +1,36 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.propagation.impl.rule;
+import tools.refinery.store.dse.propagation.BoundPropagator;
+import tools.refinery.store.dse.propagation.Propagator;
+import tools.refinery.store.dse.transition.Rule;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.model.ModelStoreBuilder;
+import tools.refinery.store.query.ModelQueryBuilder;
+import java.util.List;
+public class RuleBasedPropagator implements Propagator {
+        private final List<Rule> propagationRules;
+        public RuleBasedPropagator(List<Rule> propagationRules) {
+                this.propagationRules = propagationRules;
+        }
+        @Override
+        public void configure(ModelStoreBuilder storeBuilder) {
+                var queryBuilder = storeBuilder.getAdapter(ModelQueryBuilder.class);
+                for (var propagationRule : propagationRules) {
+                        queryBuilder.query(propagationRule.getPrecondition());
+                }
+        }
+        @Override
+        public BoundPropagator bindToModel(Model model) {
+                return new BoundRuleBasedPropagator(model, propagationRules);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstExplorer.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstExplorer.java
new file mode 100644
index 00000000..5e2f8fa9
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstExplorer.java
@@ -0,0 +1,65 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.strategy;
+import tools.refinery.store.model.Model;
+import java.util.Random;
+public class BestFirstExplorer extends BestFirstWorker {
+        final int id;
+        Random random;
+        public BestFirstExplorer(BestFirstStoreManager storeManager, Model model, int id) {
+                super(storeManager, model);
+                this.id = id;
+                this.random = new Random(id);
+        }
+        private boolean shouldRun() {
+                model.checkCancelled();
+                return !hasEnoughSolution();
+        }
+        public void explore() {
+                var lastBest = submit().newVersion();
+                while (shouldRun()) {
+                        if (lastBest == null) {
+                                if (random.nextInt(10) == 0) {
+                                        lastBest = restoreToRandom(random);
+                                } else {
+                                        lastBest = restoreToBest();
+                                }
+                                if (lastBest == null) {
+                                        return;
+                                }
+                        }
+                        boolean tryActivation = true;
+                        while (tryActivation && shouldRun()) {
+                                var randomVisitResult = this.visitRandomUnvisited(random);
+                                tryActivation = randomVisitResult.shouldRetry();
+                                var newSubmit = randomVisitResult.submitResult();
+                                if (newSubmit != null) {
+                                        if (!newSubmit.include()) {
+                                                restoreToLast();
+                                        } else {
+                                                var newVisit = newSubmit.newVersion();
+                                                int compareResult = compare(lastBest, newVisit);
+                                                if (compareResult >= 0)  {
+                                                        lastBest = newVisit;
+                                                } else {
+                                                        lastBest = null;
+                                                }
+                                                break;
+                                        }
+                                } else {
+                                        lastBest = null;
+                                        break;
+                                }
+                        }
+                }
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstStoreManager.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstStoreManager.java
new file mode 100644
index 00000000..3d32f84c
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstStoreManager.java
@@ -0,0 +1,87 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.strategy;
+import tools.refinery.store.dse.transition.DesignSpaceExplorationStoreAdapter;
+import tools.refinery.store.dse.transition.VersionWithObjectiveValue;
+import tools.refinery.store.dse.transition.statespace.ActivationStore;
+import tools.refinery.store.dse.transition.statespace.EquivalenceClassStore;
+import tools.refinery.store.dse.transition.statespace.ObjectivePriorityQueue;
+import tools.refinery.store.dse.transition.statespace.SolutionStore;
+import tools.refinery.store.dse.transition.statespace.internal.ActivationStoreImpl;
+import tools.refinery.store.dse.transition.statespace.internal.FastEquivalenceClassStore;
+import tools.refinery.store.dse.transition.statespace.internal.ObjectivePriorityQueueImpl;
+import tools.refinery.store.dse.transition.statespace.internal.SolutionStoreImpl;
+import tools.refinery.store.map.Version;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.statecoding.StateCoderStoreAdapter;
+import tools.refinery.visualization.statespace.VisualizationStore;
+import tools.refinery.visualization.statespace.internal.VisualizationStoreImpl;
+import java.util.function.Consumer;
+public class BestFirstStoreManager {
+        ModelStore modelStore;
+        ObjectivePriorityQueue objectiveStore;
+        ActivationStore activationStore;
+        SolutionStore solutionStore;
+        EquivalenceClassStore equivalenceClassStore;
+        VisualizationStore visualizationStore;
+        public BestFirstStoreManager(ModelStore modelStore, int maxNumberOfSolutions) {
+                this.modelStore = modelStore;
+                DesignSpaceExplorationStoreAdapter storeAdapter =
+                                modelStore.getAdapter(DesignSpaceExplorationStoreAdapter.class);
+                objectiveStore = new ObjectivePriorityQueueImpl(storeAdapter.getObjectives());
+                Consumer<VersionWithObjectiveValue> whenAllActivationsVisited = x -> objectiveStore.remove(x);
+                activationStore = new ActivationStoreImpl(storeAdapter.getTransformations().size(), whenAllActivationsVisited);
+                solutionStore = new SolutionStoreImpl(maxNumberOfSolutions);
+                equivalenceClassStore = new FastEquivalenceClassStore(modelStore.getAdapter(StateCoderStoreAdapter.class)) {
+                        @Override
+                        protected void delegate(VersionWithObjectiveValue version, int[] emptyActivations, boolean accept) {
+                                throw new UnsupportedOperationException("This equivalence storage is not prepared to resolve " +
+                                                "symmetries!");
+                        }
+                };
+                visualizationStore = new VisualizationStoreImpl();
+        }
+        public ModelStore getModelStore() {
+                return modelStore;
+        }
+        ObjectivePriorityQueue getObjectiveStore() {
+                return objectiveStore;
+        }
+        ActivationStore getActivationStore() {
+                return activationStore;
+        }
+        public SolutionStore getSolutionStore() {
+                return solutionStore;
+        }
+        EquivalenceClassStore getEquivalenceClassStore() {
+                return equivalenceClassStore;
+        }
+        public VisualizationStore getVisualizationStore() {
+                return visualizationStore;
+        }
+        public void startExploration(Version initial) {
+                startExploration(initial, 1);
+        }
+        public void startExploration(Version initial, int randomSeed) {
+                BestFirstExplorer bestFirstExplorer = new BestFirstExplorer(this, modelStore.createModelForState(initial),
+                                randomSeed);
+                bestFirstExplorer.explore();
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstStrategy.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstStrategy.java
deleted file mode 100644
index 92d878ce..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstStrategy.java
+++ /dev/null
@@ -1,203 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2010-2016, Andras Szabolcs Nagy, Zoltan Ujhelyi and Daniel Varro
- * Copyright (c) 2023 The Refinery Authors <https://refinery.tools/>
- * This program and the accompanying materials are made available under the
- * terms of the Eclipse Public License v. 2.0 which is available at
- * http://www.eclipse.org/legal/epl-v20.html.
- *
- * SPDX-License-Identifier: EPL-2.0
- *******************************************************************************/
-package tools.refinery.store.dse.strategy;
-import tools.refinery.store.map.Version;
-import tools.refinery.store.dse.DesignSpaceExplorationAdapter;
-import tools.refinery.store.dse.Strategy;
-import tools.refinery.store.dse.internal.Activation;
-import tools.refinery.store.dse.objectives.Fitness;
-import tools.refinery.store.dse.objectives.ObjectiveComparatorHelper;
-import java.util.*;
-public class BestFirstStrategy implements Strategy {
-        private DesignSpaceExplorationAdapter dseAdapter;
-        private int maxDepth = Integer.MAX_VALUE;
-        private int maxSolutions = Integer.MAX_VALUE;
-        private boolean backTrackIfSolution = true;
-        private boolean onlyBetterFirst = false;
-        private PriorityQueue<TrajectoryWithFitness> trajectoriesToExplore;
-        private record TrajectoryWithFitness(List<Version> trajectory, Fitness fitness) {
-                @Override
-                public String toString() {
-                                return trajectory.toString() + fitness.toString();
-                        }
-                @Override
-                public int hashCode() {
-                        return trajectory.get(trajectory.size() - 1).hashCode();
-                }
-                @Override
-                public boolean equals(Object obj) {
-                        if (obj instanceof TrajectoryWithFitness other) {
-                                return Objects.equals(trajectory.get(trajectory.size() - 1), other.trajectory.get(other.trajectory.size() - 1));
-//                              return trajectory.equals(((TrajectoryWithFitness) obj).trajectory);
-                        }
-                        return false;
-                }
-        }
-        public BestFirstStrategy withDepthLimit(int maxDepth) {
-                if (maxDepth >= 0) {
-                        this.maxDepth = maxDepth;
-                }
-                return this;
-        }
-        public BestFirstStrategy withSolutionLimit(int maxSolutions) {
-                if (maxSolutions >= 0) {
-                        this.maxSolutions = maxSolutions;
-                }
-                return this;
-        }
-        public BestFirstStrategy continueIfHardObjectivesFulfilled() {
-                backTrackIfSolution = false;
-                return this;
-        }
-        public BestFirstStrategy goOnOnlyIfFitnessIsBetter() {
-                onlyBetterFirst = true;
-                return this;
-        }
-        @Override
-        public void initialize(DesignSpaceExplorationAdapter designSpaceExplorationAdapter) {
-                this.dseAdapter = designSpaceExplorationAdapter;
-                final ObjectiveComparatorHelper objectiveComparatorHelper = dseAdapter.getObjectiveComparatorHelper();
-                trajectoriesToExplore = new PriorityQueue<>(11,
-                                (o1, o2) -> objectiveComparatorHelper.compare(o2.fitness, o1.fitness));
-        }
-        @Override
-        public void explore() {
-                if (maxSolutions == 0) {
-                        return;
-                }
-                final ObjectiveComparatorHelper objectiveComparatorHelper = dseAdapter.getObjectiveComparatorHelper();
-                boolean globalConstraintsAreSatisfied = dseAdapter.checkGlobalConstraints();
-                if (!globalConstraintsAreSatisfied) {
-                        // Global constraint is not satisfied in the first state. Terminate.
-                        return;
-                }
-                final Fitness firstFitness = dseAdapter.getFitness();
-                if (firstFitness.isSatisfiesHardObjectives()) {
-                        dseAdapter.newSolution();
-                        // First state is a solution. Terminate.
-                        if (backTrackIfSolution) {
-                                return;
-                        }
-                }
-                if (maxDepth == 0) {
-                        return;
-                }
-                var firstTrajectoryWithFitness = new TrajectoryWithFitness(dseAdapter.getTrajectory(), firstFitness);
-                trajectoriesToExplore.add(firstTrajectoryWithFitness);
-                TrajectoryWithFitness currentTrajectoryWithFitness = null;
-                mainLoop: while (true) {
-                        if (currentTrajectoryWithFitness == null) {
-                                if (trajectoriesToExplore.isEmpty()) {
-                                        // State space is fully traversed.
-                                        return;
-                                } else {
-                                        currentTrajectoryWithFitness = trajectoriesToExplore.element();
-                                        // New trajectory is chosen: " + currentTrajectoryWithFitness
-                                        dseAdapter.restoreTrajectory(currentTrajectoryWithFitness.trajectory);
-                                }
-                        }
-                        Collection<Activation> activations = dseAdapter.getUntraversedActivations();
-                        Iterator<Activation> iterator = activations.iterator();
-                        while (iterator.hasNext()) {
-                                final Activation nextActivation = iterator.next();
-                                if (!iterator.hasNext()) {
-                                        // Last untraversed activation of the state.
-                                        trajectoriesToExplore.remove(currentTrajectoryWithFitness);
-                                }
-                                // Executing new activation
-                                dseAdapter.fireActivation(nextActivation);
-                                if (dseAdapter.isCurrentStateAlreadyTraversed()) {
-                                        // The new state is already visited.
-                                        dseAdapter.backtrack();
-                                } else if (!dseAdapter.checkGlobalConstraints()) {
-                                        // Global constraint is not satisfied.
-                                        dseAdapter.backtrack();
-                                } else {
-                                        final Fitness nextFitness = dseAdapter.getFitness();
-                                        if (nextFitness.isSatisfiesHardObjectives()) {
-                                                dseAdapter.newSolution();
-                                                var solutions = dseAdapter.getSolutions().size();
-                                                if (solutions >= maxSolutions) {
-                                                        return;
-                                                }
-                                                // Found a solution.
-                                                if (backTrackIfSolution) {
-                                                        dseAdapter.backtrack();
-                                                        continue;
-                                                }
-                                        }
-                                        if (dseAdapter.getDepth() >= maxDepth) {
-                                                // Reached max depth.
-                                                dseAdapter.backtrack();
-                                                continue;
-                                        }
-                                        TrajectoryWithFitness nextTrajectoryWithFitness = new TrajectoryWithFitness(
-                                                        dseAdapter.getTrajectory(), nextFitness);
-                                        trajectoriesToExplore.add(nextTrajectoryWithFitness);
-                                        int compare = objectiveComparatorHelper.compare(currentTrajectoryWithFitness.fitness,
-                                                        nextTrajectoryWithFitness.fitness);
-                                        if (compare < 0) {
-                                                // Better fitness, moving on
-                                                currentTrajectoryWithFitness = nextTrajectoryWithFitness;
-                                                continue mainLoop;
-                                        } else if (compare == 0) {
-                                                if (onlyBetterFirst) {
-                                                        // Equally good fitness, backtrack
-                                                        dseAdapter.backtrack();
-                                                } else {
-                                                        // Equally good fitness, moving on
-                                                        currentTrajectoryWithFitness = nextTrajectoryWithFitness;
-                                                        continue mainLoop;
-                                                }
-                                        } else {
-                                                //"Worse fitness
-                                                currentTrajectoryWithFitness = null;
-                                                continue mainLoop;
-                                        }
-                                }
-                        }
-                        // State is fully traversed.
-                        currentTrajectoryWithFitness = null;
-                }
-                // Interrupted.
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstWorker.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstWorker.java
new file mode 100644
index 00000000..aca800a3
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/BestFirstWorker.java
@@ -0,0 +1,164 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.strategy;
+import org.jetbrains.annotations.Nullable;
+import tools.refinery.store.dse.propagation.PropagationAdapter;
+import tools.refinery.store.dse.transition.DesignSpaceExplorationAdapter;
+import tools.refinery.store.dse.transition.ObjectiveValue;
+import tools.refinery.store.dse.transition.VersionWithObjectiveValue;
+import tools.refinery.store.dse.transition.statespace.internal.ActivationStoreWorker;
+import tools.refinery.store.map.Version;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.statecoding.StateCoderAdapter;
+import tools.refinery.visualization.statespace.VisualizationStore;
+import java.util.Random;
+public class BestFirstWorker {
+        final BestFirstStoreManager storeManager;
+        final Model model;
+        final ActivationStoreWorker activationStoreWorker;
+        final StateCoderAdapter stateCoderAdapter;
+        final DesignSpaceExplorationAdapter explorationAdapter;
+        final ModelQueryAdapter queryAdapter;
+        final @Nullable PropagationAdapter propagationAdapter;
+        final VisualizationStore visualizationStore;
+        final boolean isVisualizationEnabled;
+        public BestFirstWorker(BestFirstStoreManager storeManager, Model model) {
+                this.storeManager = storeManager;
+                this.model = model;
+                explorationAdapter = model.getAdapter(DesignSpaceExplorationAdapter.class);
+                stateCoderAdapter = model.getAdapter(StateCoderAdapter.class);
+                queryAdapter = model.getAdapter(ModelQueryAdapter.class);
+                propagationAdapter = model.tryGetAdapter(PropagationAdapter.class).orElse(null);
+                activationStoreWorker = new ActivationStoreWorker(storeManager.getActivationStore(),
+                                explorationAdapter.getTransformations());
+                visualizationStore = storeManager.getVisualizationStore();
+                isVisualizationEnabled = visualizationStore != null;
+        }
+        protected VersionWithObjectiveValue last = null;
+        public SubmitResult submit() {
+                checkSynchronized();
+                if (queryAdapter.hasPendingChanges()) {
+                        throw new AssertionError("Pending changes detected before model submission");
+                }
+                if (explorationAdapter.checkExclude()) {
+                        return new SubmitResult(false, false, null, null);
+                }
+                var code = stateCoderAdapter.calculateStateCode();
+                boolean isNew = storeManager.getEquivalenceClassStore().submit(code);
+                if (isNew) {
+                        Version version = model.commit();
+                        ObjectiveValue objectiveValue = explorationAdapter.getObjectiveValue();
+                        var versionWithObjectiveValue = new VersionWithObjectiveValue(version, objectiveValue);
+                        last = versionWithObjectiveValue;
+                        var accepted = explorationAdapter.checkAccept();
+                        storeManager.getObjectiveStore().submit(versionWithObjectiveValue);
+                        storeManager.getActivationStore().markNewAsVisited(versionWithObjectiveValue, activationStoreWorker.calculateEmptyActivationSize());
+                        if(accepted) {
+                                storeManager.solutionStore.submit(versionWithObjectiveValue);
+                        }
+                        if (isVisualizationEnabled) {
+                                visualizationStore.addState(last.version(), last.objectiveValue().toString());
+                                if (accepted) {
+                                        visualizationStore.addSolution(last.version());
+                                }
+                        }
+                        return new SubmitResult(true, accepted, objectiveValue, last);
+                }
+                return new SubmitResult(false, false, null, null);
+        }
+        public void restoreToLast() {
+                if (explorationAdapter.getModel().hasUncommittedChanges()) {
+                        explorationAdapter.getModel().restore(last.version());
+                }
+        }
+        public VersionWithObjectiveValue restoreToBest() {
+                var bestVersion = storeManager.getObjectiveStore().getBest();
+                last = bestVersion;
+                if (bestVersion != null) {
+                        this.model.restore(bestVersion.version());
+                }
+                return last;
+        }
+        public VersionWithObjectiveValue restoreToRandom(Random random) {
+                var objectiveStore = storeManager.getObjectiveStore();
+                if (objectiveStore.getSize() == 0) {
+                        return null;
+                }
+                var randomVersion = objectiveStore.getRandom(random);
+                last = randomVersion;
+                if (randomVersion != null) {
+                        this.model.restore(randomVersion.version());
+                }
+                return last;
+        }
+        public int compare(VersionWithObjectiveValue s1, VersionWithObjectiveValue s2) {
+                return storeManager.getObjectiveStore().getComparator().compare(s1, s2);
+        }
+        public record RandomVisitResult(SubmitResult submitResult, boolean shouldRetry) {
+        }
+        public RandomVisitResult visitRandomUnvisited(Random random) {
+                checkSynchronized();
+                if (model.hasUncommittedChanges()) {
+                        throw new IllegalStateException("The model has uncommitted changes!");
+                }
+                var visitResult = activationStoreWorker.fireRandomActivation(this.last, random);
+                if (!visitResult.successfulVisit()) {
+                        return new RandomVisitResult(null, visitResult.mayHaveMore());
+                }
+                if (propagationAdapter != null) {
+                        var propagationResult = propagationAdapter.propagate();
+                        if (propagationResult.isRejected()) {
+                                return new RandomVisitResult(null, visitResult.mayHaveMore());
+                        }
+                }
+                queryAdapter.flushChanges();
+                Version oldVersion = null;
+                if (isVisualizationEnabled) {
+                        oldVersion = last.version();
+                }
+                var submitResult = submit();
+                if (isVisualizationEnabled && submitResult.newVersion() != null) {
+                        var newVersion = submitResult.newVersion().version();
+                        visualizationStore.addTransition(oldVersion, newVersion,
+                                        "fire: " + visitResult.transformation() + ", " + visitResult.activation());
+                }
+                return new RandomVisitResult(submitResult, visitResult.mayHaveMore());
+        }
+        public boolean hasEnoughSolution() {
+                return storeManager.solutionStore.hasEnoughSolution();
+        }
+        private void checkSynchronized() {
+                if (last != null && !last.version().equals(model.getState())) {
+                        throw new AssertionError("Worker is not synchronized with model state");
+                }
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/DepthFirstStrategy.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/DepthFirstStrategy.java
deleted file mode 100644
index 0a0caa7e..00000000
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/DepthFirstStrategy.java
+++ /dev/null
@@ -1,92 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.dse.strategy;
-import tools.refinery.store.dse.DesignSpaceExplorationAdapter;
-import tools.refinery.store.dse.Strategy;
-import tools.refinery.store.dse.objectives.Fitness;
-public class DepthFirstStrategy implements Strategy {
-        private DesignSpaceExplorationAdapter dseAdapter;
-        private int maxDepth = Integer.MAX_VALUE;
-        private int maxSolutions = Integer.MAX_VALUE;
-        private boolean backtrackFromSolution = true;
-        public DepthFirstStrategy withDepthLimit(int maxDepth) {
-                if (maxDepth >= 0) {
-                        this.maxDepth = maxDepth;
-                }
-                return this;
-        }
-        public DepthFirstStrategy withSolutionLimit(int maxSolutions) {
-                if (maxSolutions >= 0) {
-                        this.maxSolutions = maxSolutions;
-                }
-                return this;
-        }
-        public DepthFirstStrategy continueIfHardObjectivesFulfilled() {
-                backtrackFromSolution = false;
-                return this;
-        }
-        @Override
-        public void initialize(DesignSpaceExplorationAdapter designSpaceExplorationAdapter) {
-                this.dseAdapter = designSpaceExplorationAdapter;
-        }
-        @Override
-        public void explore() {
-                if (maxSolutions == 0) {
-                        return;
-                }
-                while (dseAdapter.getSolutions().size() < maxSolutions) {
-                        if (!checkAndHandleGlobalConstraints()) {
-                                return;
-                        }
-                        Fitness fitness = dseAdapter.getFitness();
-                        if (fitness.isSatisfiesHardObjectives()) {
-                                dseAdapter.newSolution();
-                                if (backtrackFromSolution && !dseAdapter.backtrack()) {
-                                        return;
-                                }
-                        }
-                        if (!checkAndHandleDepth()) {
-                                return;
-                        }
-                        if (!backtrackToLastUntraversed()) {
-                                return;
-                        }
-                        if (!dseAdapter.fireRandomActivation()) {
-                                return;
-                        }
-                }
-        }
-        private boolean checkAndHandleGlobalConstraints() {
-                return dseAdapter.checkGlobalConstraints() || dseAdapter.backtrack();
-        }
-        private boolean checkAndHandleDepth() {
-                return dseAdapter.getDepth() < maxDepth || dseAdapter.backtrack();
-        }
-        private boolean backtrackToLastUntraversed() {
-                while (dseAdapter.getUntraversedActivations().isEmpty()) {
-                        if (!dseAdapter.backtrack()) {
-                                return false;
-                        }
-                }
-                return true;
-        }
-}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/SubmitResult.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/SubmitResult.java
new file mode 100644
index 00000000..37d548d7
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/strategy/SubmitResult.java
@@ -0,0 +1,14 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.strategy;
+import tools.refinery.store.dse.transition.ObjectiveValue;
+import tools.refinery.store.dse.transition.VersionWithObjectiveValue;
+import tools.refinery.store.map.Version;
+public record SubmitResult(boolean include, boolean accepted, ObjectiveValue objective, VersionWithObjectiveValue newVersion) {
+        }
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/DesignSpaceExplorationAdapter.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/DesignSpaceExplorationAdapter.java
new file mode 100644
index 00000000..d326f1dd
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/DesignSpaceExplorationAdapter.java
@@ -0,0 +1,28 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition;
+import tools.refinery.store.adapter.ModelAdapter;
+import tools.refinery.store.dse.transition.internal.DesignSpaceExplorationBuilderImpl;
+import java.util.List;
+public interface DesignSpaceExplorationAdapter extends ModelAdapter {
+        @Override
+        DesignSpaceExplorationStoreAdapter getStoreAdapter();
+        static DesignSpaceExplorationBuilder builder() {
+                return new DesignSpaceExplorationBuilderImpl();
+        }
+        List<Transformation> getTransformations();
+        boolean checkAccept();
+        boolean checkExclude();
+        ObjectiveValue getObjectiveValue();
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/DesignSpaceExplorationBuilder.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/DesignSpaceExplorationBuilder.java
new file mode 100644
index 00000000..800cf8f7
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/DesignSpaceExplorationBuilder.java
@@ -0,0 +1,61 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition;
+import tools.refinery.store.adapter.ModelAdapterBuilder;
+import tools.refinery.store.dse.transition.objectives.Criterion;
+import tools.refinery.store.dse.transition.objectives.Objective;
+import java.util.Collection;
+import java.util.List;
+// Builder pattern with methods returning {@code this} for convenience.
+@SuppressWarnings("UnusedReturnValue")
+public interface DesignSpaceExplorationBuilder extends ModelAdapterBuilder {
+        DesignSpaceExplorationBuilder transformation(Rule transformationRuleDefinition);
+        default DesignSpaceExplorationBuilder transformations(Rule... transformationRuleDefinitions) {
+                return transformations(List.of(transformationRuleDefinitions));
+        }
+        default DesignSpaceExplorationBuilder transformations(Collection<? extends Rule> transformationRules) {
+                transformationRules.forEach(this::transformation);
+                return this;
+        }
+        DesignSpaceExplorationBuilder accept(Criterion criteria);
+        default DesignSpaceExplorationBuilder accept(Criterion... criteria) {
+                return accept(List.of(criteria));
+        }
+        default DesignSpaceExplorationBuilder accept(Collection<Criterion> criteria) {
+                criteria.forEach(this::accept);
+                return this;
+        }
+        DesignSpaceExplorationBuilder exclude(Criterion criteria);
+        default DesignSpaceExplorationBuilder exclude(Criterion... criteria) {
+                return exclude(List.of(criteria));
+        }
+        default DesignSpaceExplorationBuilder exclude(Collection<Criterion> criteria) {
+                criteria.forEach(this::exclude);
+                return this;
+        }
+        DesignSpaceExplorationBuilder objective(Objective objective);
+        default DesignSpaceExplorationBuilder objectives(Objective... objectives) {
+                return objectives(List.of(objectives));
+        }
+        default DesignSpaceExplorationBuilder objectives(Collection<? extends Objective> objectives) {
+                objectives.forEach(this::objective);
+                return this;
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/DesignSpaceExplorationStoreAdapter.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/DesignSpaceExplorationStoreAdapter.java
new file mode 100644
index 00000000..fb082fae
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/DesignSpaceExplorationStoreAdapter.java
@@ -0,0 +1,27 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition;
+import tools.refinery.store.adapter.ModelStoreAdapter;
+import tools.refinery.store.dse.transition.objectives.Criterion;
+import tools.refinery.store.dse.transition.objectives.Objective;
+import tools.refinery.store.model.Model;
+import java.util.List;
+public interface DesignSpaceExplorationStoreAdapter extends ModelStoreAdapter
+{
+        @Override
+        DesignSpaceExplorationAdapter createModelAdapter(Model model);
+        List<Rule> getTransformations();
+        List<Criterion> getAccepts();
+        List<Criterion> getExcludes();
+        List<Objective> getObjectives();
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/ObjectiveValue.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/ObjectiveValue.java
new file mode 100644
index 00000000..89ee61c8
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/ObjectiveValue.java
@@ -0,0 +1,24 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition;
+public interface ObjectiveValue {
+        double get(int index);
+        int getSize();
+        static ObjectiveValue of(double v1) {
+                return new ObjectiveValues.ObjectiveValue1(v1);
+        }
+        static ObjectiveValue of(double v1, double v2) {
+                return new ObjectiveValues.ObjectiveValue2(v1,v2);
+        }
+        static ObjectiveValue of(double[] v) {
+                return new ObjectiveValues.ObjectiveValueN(v);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/ObjectiveValues.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/ObjectiveValues.java
new file mode 100644
index 00000000..60913ff3
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/ObjectiveValues.java
@@ -0,0 +1,69 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition;
+import java.util.Arrays;
+public interface ObjectiveValues {
+        public record ObjectiveValue1(double value0) implements ObjectiveValue {
+                @Override
+                public double get(int index) {
+                        if(index == 0) return value0;
+                        else throw new IllegalArgumentException("No value at " + index);
+                }
+                @Override
+                public int getSize() {
+                        return 1;
+                }
+        }
+        public record ObjectiveValue2(double value0, double value1) implements ObjectiveValue {
+                @Override
+                public double get(int index) {
+                        if(index == 0) return value0;
+                        else if(index == 1) return value1;
+                        else throw new IllegalArgumentException("No value at " + index);
+                }
+                @Override
+                public int getSize() {
+                        return 2;
+                }
+        }
+        public record ObjectiveValueN(double[] values) implements ObjectiveValue {
+                @Override
+                public double get(int index) {
+                        return values[index];
+                }
+                @Override
+                public int getSize() {
+                        return values().length;
+                }
+                @Override
+                public boolean equals(Object o) {
+                        if (this == o) return true;
+                        if (o == null || getClass() != o.getClass()) return false;
+                        ObjectiveValueN that = (ObjectiveValueN) o;
+                        return Arrays.equals(values, that.values);
+                }
+                @Override
+                public int hashCode() {
+                        return Arrays.hashCode(values);
+                }
+                @Override
+                public String toString() {
+                        return "ObjectiveValueN{" +
+                                        "values=" + Arrays.toString(values) +
+                                        '}';
+                }
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/Rule.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/Rule.java
new file mode 100644
index 00000000..ff45ed3e
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/Rule.java
@@ -0,0 +1,99 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition;
+import tools.refinery.store.dse.transition.actions.Action;
+import tools.refinery.store.dse.transition.actions.BoundAction;
+import tools.refinery.store.dse.transition.callback.*;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.dnf.RelationalQuery;
+public class Rule {
+        private final String name;
+        private final RelationalQuery precondition;
+        private final Action action;
+        public Rule(String name, RelationalQuery precondition, Action action) {
+                if (precondition.arity() != action.getArity()) {
+                        throw new IllegalArgumentException("Expected an action clause with %d parameters, got %d instead"
+                                        .formatted(precondition.arity(), action.getArity()));
+                }
+                this.name = name;
+                this.precondition = precondition;
+                this.action = action;
+        }
+        public String getName() {
+                return name;
+        }
+        public RelationalQuery getPrecondition() {
+                return precondition;
+        }
+        public BoundAction createAction(Model model) {
+                return action.bindToModel(model);
+        }
+        public static RuleBuilder builder(String name) {
+                return new RuleBuilder(name);
+        }
+        public static RuleBuilder builder() {
+                return builder(null);
+        }
+        public static Rule of(String name, RuleCallback0 callback) {
+                var builder = builder(name);
+                callback.accept(builder);
+                return builder.build();
+        }
+        public static Rule of(RuleCallback0 callback) {
+                return of(null, callback);
+        }
+        public static Rule of(String name, RuleCallback1 callback) {
+                var builder = builder(name);
+                callback.accept(builder, builder.parameter("p1"));
+                return builder.build();
+        }
+        public static Rule of(RuleCallback1 callback) {
+                return of(null, callback);
+        }
+        public static Rule of(String name, RuleCallback2 callback) {
+                var builder = builder(name);
+                callback.accept(builder, builder.parameter("p1"), builder.parameter("p2"));
+                return builder.build();
+        }
+        public static Rule of(RuleCallback2 callback) {
+                return of(null, callback);
+        }
+        public static Rule of(String name, RuleCallback3 callback) {
+                var builder = builder(name);
+                callback.accept(builder, builder.parameter("p1"), builder.parameter("p2"), builder.parameter("p3"));
+                return builder.build();
+        }
+        public static Rule of(RuleCallback3 callback) {
+                return of(null, callback);
+        }
+        public static Rule of(String name, RuleCallback4 callback) {
+                var builder = builder(name);
+                callback.accept(builder, builder.parameter("p1"), builder.parameter("p2"), builder.parameter("p3"),
+                                builder.parameter("p4"));
+                return builder.build();
+        }
+        public static Rule of(RuleCallback4 callback) {
+                return of(null, callback);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/RuleBuilder.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/RuleBuilder.java
new file mode 100644
index 00000000..865ac369
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/RuleBuilder.java
@@ -0,0 +1,71 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition;
+import tools.refinery.store.dse.transition.actions.Action;
+import tools.refinery.store.dse.transition.actions.ActionLiteral;
+import tools.refinery.store.dse.transition.callback.*;
+import tools.refinery.store.query.dnf.AbstractQueryBuilder;
+import tools.refinery.store.query.dnf.Dnf;
+import tools.refinery.store.query.term.Variable;
+import java.util.List;
+public class RuleBuilder extends AbstractQueryBuilder<RuleBuilder> {
+        private final String name;
+        private List<ActionLiteral> action;
+        RuleBuilder(String name) {
+                super(Dnf.builder(name == null ? null : name + "#precondition"));
+                this.name = name;
+        }
+        @Override
+        protected RuleBuilder self() {
+                return this;
+        }
+        public RuleBuilder action(ActionLiteral... literals) {
+                return action(List.of(literals));
+        }
+        public RuleBuilder action(List<? extends ActionLiteral> literals) {
+                if (this.action != null) {
+                        throw new IllegalStateException("Actions have already been set");
+                }
+                this.action = List.copyOf(literals);
+                return this;
+        }
+        public RuleBuilder action(Action action) {
+                return action(action.getActionLiterals());
+        }
+        public RuleBuilder action(ActionCallback0 callback) {
+                return action(callback.toLiterals());
+        }
+        public RuleBuilder action(ActionCallback1 callback) {
+                return action(callback.toLiterals(Variable.of("v1")));
+        }
+        public RuleBuilder action(ActionCallback2 callback) {
+                return action(callback.toLiterals(Variable.of("v1"), Variable.of("v2")));
+        }
+        public RuleBuilder action(ActionCallback3 callback) {
+                return action(callback.toLiterals(Variable.of("v1"), Variable.of("v2"), Variable.of("v3")));
+        }
+        public RuleBuilder action(ActionCallback4 callback) {
+                return action(callback.toLiterals(Variable.of("v1"), Variable.of("v2"), Variable.of("v3"), Variable.of("v4")));
+        }
+        public Rule build() {
+                var precondition = dnfBuilder.build().asRelation();
+                return new Rule(name, precondition, Action.ofPrecondition(precondition, action));
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/Transformation.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/Transformation.java
new file mode 100644
index 00000000..0eeccbdf
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/Transformation.java
@@ -0,0 +1,43 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition;
+import tools.refinery.store.dse.transition.actions.BoundAction;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.query.resultset.OrderedResultSet;
+import tools.refinery.store.query.resultset.ResultSet;
+import tools.refinery.store.tuple.Tuple;
+public class Transformation {
+        private final Rule definition;
+        private final OrderedResultSet<Boolean> activations;
+        private final BoundAction action;
+        public Transformation(Model model, Rule definition) {
+                this.definition = definition;
+                var precondition = definition.getPrecondition();
+                var queryEngine = model.getAdapter(ModelQueryAdapter.class);
+                activations = new OrderedResultSet<>(queryEngine.getResultSet(precondition));
+                action = definition.createAction(model);
+        }
+        public Rule getDefinition() {
+                return definition;
+        }
+        public ResultSet<Boolean> getAllActivationsAsResultSet() {
+                return activations;
+        }
+        public Tuple getActivation(int index) {
+                return activations.getKey(index);
+        }
+        public boolean fireActivation(Tuple activation) {
+                return action.fire(activation);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/VersionWithObjectiveValue.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/VersionWithObjectiveValue.java
new file mode 100644
index 00000000..ca28e27f
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/VersionWithObjectiveValue.java
@@ -0,0 +1,11 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition;
+import tools.refinery.store.map.Version;
+public record VersionWithObjectiveValue(Version version, ObjectiveValue objectiveValue) {
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/AbstractActionLiteral.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/AbstractActionLiteral.java
new file mode 100644
index 00000000..e30f06bb
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/AbstractActionLiteral.java
@@ -0,0 +1,9 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.actions;
+public abstract class AbstractActionLiteral implements ActionLiteral {
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/Action.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/Action.java
new file mode 100644
index 00000000..d63ddfdd
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/Action.java
@@ -0,0 +1,132 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.actions;
+import org.eclipse.collections.api.factory.primitive.ObjectIntMaps;
+import org.eclipse.collections.api.map.primitive.MutableObjectIntMap;
+import org.jetbrains.annotations.Nullable;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.dnf.RelationalQuery;
+import tools.refinery.store.query.dnf.SymbolicParameter;
+import tools.refinery.store.query.term.NodeVariable;
+import java.util.*;
+public class Action {
+        private final List<NodeVariable> parameters;
+        private final Set<NodeVariable> localVariables;
+        private final List<ActionLiteral> actionLiterals;
+        private final int[] @Nullable [] inputAllocations;
+        private final int[] @Nullable [] outputAllocations;
+        public Action(List<NodeVariable> parameters, List<? extends ActionLiteral> actionLiterals) {
+                this.parameters = List.copyOf(parameters);
+                this.actionLiterals = List.copyOf(actionLiterals);
+                var allocation = ObjectIntMaps.mutable.<NodeVariable>empty();
+                int arity = parameters.size();
+                for (int i = 0; i < arity; i++) {
+                        allocation.put(parameters.get(i), i);
+                }
+                var mutableLocalVariables = new LinkedHashSet<NodeVariable>();
+                int size = actionLiterals.size();
+                inputAllocations = new int[size][];
+                outputAllocations = new int[size][];
+                for (int i = 0; i < size; i++) {
+                        computeInputAllocation(i, parameters, allocation);
+                        computeOutputAllocation(i, mutableLocalVariables, allocation);
+                }
+                this.localVariables = Collections.unmodifiableSet(mutableLocalVariables);
+        }
+        private void computeInputAllocation(int actionIndex, List<NodeVariable> parameters,
+                                                                                MutableObjectIntMap<NodeVariable> allocation) {
+                var actionLiteral = actionLiterals.get(actionIndex);
+                var inputVariables = actionLiteral.getInputVariables();
+                if (inputVariables.equals(parameters)) {
+                        // Identity mappings use a {@code null} allocation to pass the activation tuple unchanged.
+                        return;
+                }
+                var inputs = new int[inputVariables.size()];
+                for (int i = 0; i < inputs.length; i++) {
+                        var variable = inputVariables.get(i);
+                        if (!allocation.containsKey(variable)) {
+                                throw new IllegalArgumentException("Unbound input variable %s of action literal %s"
+                                                .formatted(variable, actionLiteral));
+                        }
+                        inputs[i] = allocation.get(variable);
+                }
+                inputAllocations[actionIndex] = inputs;
+        }
+        private void computeOutputAllocation(int actionIndex, Set<NodeVariable> mutableLocalVariable,
+                                                                                 MutableObjectIntMap<NodeVariable> allocation) {
+                var actionLiteral = actionLiterals.get(actionIndex);
+                var outputVariables = actionLiteral.getOutputVariables();
+                int size = outputVariables.size();
+                if (size == 0) {
+                        // Identity mappings use a {@code null} allocation to avoid iterating over the output tuple.
+                        return;
+                }
+                if (size >= 2 && new HashSet<>(outputVariables).size() != size) {
+                        throw new IllegalArgumentException("Action literal %s has duplicate output variables %s"
+                                        .formatted(actionLiteral, outputVariables));
+                }
+                int arity = parameters.size();
+                var outputs = new int[size];
+                for (int i = 0; i < size; i++) {
+                        var variable = outputVariables.get(i);
+                        if (allocation.containsKey(variable)) {
+                                throw new IllegalArgumentException("Output variable %s of action literal %s was already assigned"
+                                                .formatted(variable, actionLiteral));
+                        }
+                        int variableId = mutableLocalVariable.size();
+                        allocation.put(variable, arity + variableId);
+                        outputs[i] = variableId;
+                        mutableLocalVariable.add(variable);
+                }
+                outputAllocations[actionIndex] = outputs;
+        }
+        public List<NodeVariable> getParameters() {
+                return parameters;
+        }
+        public int getArity() {
+                return parameters.size();
+        }
+        public Set<NodeVariable> getLocalVariables() {
+                return localVariables;
+        }
+        public List<ActionLiteral> getActionLiterals() {
+                return actionLiterals;
+        }
+        int @Nullable [] getInputAllocation(int actionIndex) {
+                return inputAllocations[actionIndex];
+        }
+        int @Nullable [] getOutputAllocation(int actionIndex) {
+                return outputAllocations[actionIndex];
+        }
+        public BoundAction bindToModel(Model model) {
+                return new BoundAction(this, model);
+        }
+        public static Action ofSymbolicParameters(List<SymbolicParameter> symbolicParameters,
+                                                                                          List<? extends ActionLiteral> actionLiterals) {
+                var nodeVariables = symbolicParameters.stream()
+                                .map(symbolicParameter -> symbolicParameter.getVariable().asNodeVariable())
+                                .toList();
+                return new Action(nodeVariables, actionLiterals);
+        }
+        public static Action ofPrecondition(RelationalQuery precondition, List<? extends ActionLiteral> actionLiterals) {
+                return ofSymbolicParameters(precondition.getDnf().getSymbolicParameters(), actionLiterals);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/ActionLiteral.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/ActionLiteral.java
new file mode 100644
index 00000000..a721ef73
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/ActionLiteral.java
@@ -0,0 +1,19 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.actions;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.term.NodeVariable;
+import java.util.List;
+public interface ActionLiteral {
+        List<NodeVariable> getInputVariables();
+        List<NodeVariable> getOutputVariables();
+        BoundActionLiteral bindToModel(Model model);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/ActionLiterals.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/ActionLiterals.java
new file mode 100644
index 00000000..275e1e25
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/ActionLiterals.java
@@ -0,0 +1,33 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.actions;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.representation.Symbol;
+import java.util.List;
+import java.util.Objects;
+public final class ActionLiterals {
+        private ActionLiterals() {
+                throw new IllegalArgumentException("This is a static utility class and should not be instantiated directly");
+        }
+        public static <T> PutActionLiteral<T> put(Symbol<T> symbol, T value, NodeVariable... parameters) {
+                return new PutActionLiteral<>(symbol, value, List.of(parameters));
+        }
+        public static PutActionLiteral<Boolean> add(Symbol<Boolean> symbol, NodeVariable... parameters) {
+                if (!Objects.equals(symbol.defaultValue(), false)) {
+                        throw new IllegalArgumentException("Use put to add a value to symbols other than two-valued logic");
+                }
+                return put(symbol, true, parameters);
+        }
+        public static <T> PutActionLiteral<T> remove(Symbol<T> symbol, NodeVariable... parameters) {
+                return put(symbol, symbol.defaultValue(), parameters);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/BoundAction.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/BoundAction.java
new file mode 100644
index 00000000..4da609fa
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/BoundAction.java
@@ -0,0 +1,119 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.actions;
+import org.jetbrains.annotations.Nullable;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.tuple.Tuple;
+public class BoundAction {
+        private final Action action;
+        private final Model model;
+        private BoundActionLiteral @Nullable [] boundLiterals;
+        private Tuple activation;
+        private final int[] localVariables;
+        BoundAction(Action action, Model model) {
+                this.action = action;
+                this.model = model;
+                localVariables = new int[action.getLocalVariables().size()];
+        }
+        public boolean fire(Tuple activation) {
+                model.checkCancelled();
+                if (this.activation != null) {
+                        throw new IllegalStateException("Reentrant firing is not allowed");
+                }
+                this.activation = activation;
+                if (boundLiterals == null) {
+                        boundLiterals = bindLiterals();
+                }
+                try {
+                        int size = boundLiterals.length;
+                        for (int i = 0; i < size; i++) {
+                                var inputAllocation = action.getInputAllocation(i);
+                                var boundLiteral = boundLiterals[i];
+                                var input = getInputTuple(inputAllocation);
+                                var output = boundLiteral.fire(input);
+                                if (output == null) {
+                                        return false;
+                                }
+                                var outputAllocation = this.action.getOutputAllocation(i);
+                                setOutputTuple(outputAllocation, output);
+                        }
+                } finally {
+                        this.activation = null;
+                }
+                return true;
+        }
+        private BoundActionLiteral[] bindLiterals() {
+                var actionLiterals = action.getActionLiterals();
+                int size = actionLiterals.size();
+                var boundLiteralsArray = new BoundActionLiteral[size];
+                for (int i = 0; i < size; i++) {
+                        boundLiteralsArray[i] = actionLiterals.get(i).bindToModel(model);
+                }
+                return boundLiteralsArray;
+        }
+        private Tuple getInputTuple(int @Nullable [] inputAllocation) {
+                if (inputAllocation == null) {
+                        // Identity allocation.
+                        return activation;
+                }
+                return switch (inputAllocation.length) {
+                        case 0 -> Tuple.of();
+                        case 1 -> Tuple.of(getInput(inputAllocation[0]));
+                        case 2 -> Tuple.of(getInput(inputAllocation[0]), getInput(inputAllocation[1]));
+                        case 3 -> Tuple.of(getInput(inputAllocation[0]), getInput(inputAllocation[1]),
+                                        getInput(inputAllocation[2]));
+                        case 4 -> Tuple.of(getInput(inputAllocation[0]), getInput(inputAllocation[1]),
+                                        getInput(inputAllocation[2]), getInput(inputAllocation[3]));
+                        default -> {
+                                var elements = new int[inputAllocation.length];
+                                for (var i = 0; i < inputAllocation.length; i++) {
+                                        elements[i] = getInput(inputAllocation[i]);
+                                }
+                                yield Tuple.of(elements);
+                        }
+                };
+        }
+        private int getInput(int index) {
+                int arity = action.getArity();
+                return index < arity ? activation.get(index) : localVariables[index - arity];
+        }
+        private void setOutputTuple(int @Nullable [] outputAllocation, Tuple output) {
+                if (outputAllocation == null || outputAllocation.length == 0) {
+                        return;
+                }
+                switch (outputAllocation.length) {
+                case 1 -> localVariables[outputAllocation[0]] = output.get(0);
+                case 2 -> {
+                        localVariables[outputAllocation[0]] = output.get(0);
+                        localVariables[outputAllocation[1]] = output.get(1);
+                }
+                case 3 -> {
+                        localVariables[outputAllocation[0]] = output.get(0);
+                        localVariables[outputAllocation[1]] = output.get(1);
+                        localVariables[outputAllocation[2]] = output.get(2);
+                }
+                case 4 -> {
+                        localVariables[outputAllocation[0]] = output.get(0);
+                        localVariables[outputAllocation[1]] = output.get(1);
+                        localVariables[outputAllocation[2]] = output.get(2);
+                        localVariables[outputAllocation[3]] = output.get(3);
+                }
+                default -> {
+                        for (int i = 0; i < outputAllocation.length; i++) {
+                                localVariables[outputAllocation[i]] = output.get(i);
+                        }
+                }
+                }
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/BoundActionLiteral.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/BoundActionLiteral.java
new file mode 100644
index 00000000..09c3c58c
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/BoundActionLiteral.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.actions;
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
+import tools.refinery.store.tuple.Tuple;
+@FunctionalInterface
+public interface BoundActionLiteral {
+        @Nullable
+        Tuple fire(@NotNull Tuple tuple);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/PutActionLiteral.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/PutActionLiteral.java
new file mode 100644
index 00000000..86288921
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/PutActionLiteral.java
@@ -0,0 +1,64 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.actions;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.store.representation.Symbol;
+import tools.refinery.store.tuple.Tuple;
+import java.util.List;
+public class PutActionLiteral<T> extends AbstractActionLiteral {
+        private final Symbol<T> symbol;
+        private final List<NodeVariable> parameters;
+        private final T value;
+        public PutActionLiteral(Symbol<T> symbol, T value, List<NodeVariable> parameters) {
+                if (symbol.arity() != parameters.size()) {
+                        throw new IllegalArgumentException("Expected %d parameters for symbol %s, got %d instead"
+                                        .formatted(symbol.arity(), symbol, parameters.size()));
+                }
+                if (value != null && !symbol.valueType().isInstance(value)) {
+                        throw new IllegalArgumentException("Expected value of type %s for symbol %s, got %s of type %s instead"
+                                        .formatted(symbol.valueType().getName(), symbol, value, value.getClass().getName()));
+                }
+                this.symbol = symbol;
+                this.parameters = List.copyOf(parameters);
+                this.value = value;
+        }
+        public Symbol<T> getSymbol() {
+                return symbol;
+        }
+        public List<NodeVariable> getParameters() {
+                return parameters;
+        }
+        public T getValue() {
+                return value;
+        }
+        @Override
+        public List<NodeVariable> getInputVariables() {
+                return getParameters();
+        }
+        @Override
+        public List<NodeVariable> getOutputVariables() {
+                return List.of();
+        }
+        @Override
+        public BoundActionLiteral bindToModel(Model model) {
+                var interpretation = model.getInterpretation(symbol);
+                return tuple -> {
+                        interpretation.put(tuple, value);
+                        return Tuple.of();
+                };
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback0.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback0.java
new file mode 100644
index 00000000..1190fdeb
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback0.java
@@ -0,0 +1,15 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.callback;
+import tools.refinery.store.dse.transition.actions.ActionLiteral;
+import java.util.List;
+@FunctionalInterface
+public interface ActionCallback0 {
+        List<ActionLiteral> toLiterals();
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback1.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback1.java
new file mode 100644
index 00000000..869f1a96
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback1.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.callback;
+import tools.refinery.store.dse.transition.actions.ActionLiteral;
+import tools.refinery.store.query.term.NodeVariable;
+import java.util.List;
+@FunctionalInterface
+public interface ActionCallback1 {
+        List<ActionLiteral> toLiterals(NodeVariable v1);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback2.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback2.java
new file mode 100644
index 00000000..a648fc93
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback2.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.callback;
+import tools.refinery.store.dse.transition.actions.ActionLiteral;
+import tools.refinery.store.query.term.NodeVariable;
+import java.util.List;
+@FunctionalInterface
+public interface ActionCallback2 {
+        List<ActionLiteral> toLiterals(NodeVariable v1, NodeVariable v2);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback3.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback3.java
new file mode 100644
index 00000000..a9b1d334
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback3.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.callback;
+import tools.refinery.store.dse.transition.actions.ActionLiteral;
+import tools.refinery.store.query.term.NodeVariable;
+import java.util.List;
+@FunctionalInterface
+public interface ActionCallback3 {
+        List<ActionLiteral> toLiterals(NodeVariable v1, NodeVariable v2, NodeVariable v3);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback4.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback4.java
new file mode 100644
index 00000000..aef1351c
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback4.java
@@ -0,0 +1,16 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.callback;
+import tools.refinery.store.dse.transition.actions.ActionLiteral;
+import tools.refinery.store.query.term.NodeVariable;
+import java.util.List;
+@FunctionalInterface
+public interface ActionCallback4 {
+        List<ActionLiteral> toLiterals(NodeVariable v1, NodeVariable v2, NodeVariable v3, NodeVariable v4);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback0.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback0.java
new file mode 100644
index 00000000..538c23ba
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback0.java
@@ -0,0 +1,13 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.callback;
+import tools.refinery.store.dse.transition.RuleBuilder;
+@FunctionalInterface
+public interface RuleCallback0 {
+        void accept(RuleBuilder builder);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback1.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback1.java
new file mode 100644
index 00000000..bd7bf4f5
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback1.java
@@ -0,0 +1,14 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.callback;
+import tools.refinery.store.dse.transition.RuleBuilder;
+import tools.refinery.store.query.term.NodeVariable;
+@FunctionalInterface
+public interface RuleCallback1 {
+        void accept(RuleBuilder builder, NodeVariable p1);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback2.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback2.java
new file mode 100644
index 00000000..7b02b68a
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback2.java
@@ -0,0 +1,14 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.callback;
+import tools.refinery.store.dse.transition.RuleBuilder;
+import tools.refinery.store.query.term.NodeVariable;
+@FunctionalInterface
+public interface RuleCallback2 {
+        void accept(RuleBuilder builder, NodeVariable p1, NodeVariable p2);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback3.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback3.java
new file mode 100644
index 00000000..6f112d48
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback3.java
@@ -0,0 +1,14 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.callback;
+import tools.refinery.store.dse.transition.RuleBuilder;
+import tools.refinery.store.query.term.NodeVariable;
+@FunctionalInterface
+public interface RuleCallback3 {
+        void accept(RuleBuilder builder, NodeVariable p1, NodeVariable p2, NodeVariable p3);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback4.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback4.java
new file mode 100644
index 00000000..dbcf8567
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback4.java
@@ -0,0 +1,14 @@
+/*
+ * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.callback;
+import tools.refinery.store.dse.transition.RuleBuilder;
+import tools.refinery.store.query.term.NodeVariable;
+@FunctionalInterface
+public interface RuleCallback4 {
+        void accept(RuleBuilder builder, NodeVariable p1, NodeVariable p2, NodeVariable p3, NodeVariable p4);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/internal/DesignSpaceExplorationAdapterImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/internal/DesignSpaceExplorationAdapterImpl.java
new file mode 100644
index 00000000..23325a1f
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/internal/DesignSpaceExplorationAdapterImpl.java
@@ -0,0 +1,94 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.internal;
+import tools.refinery.store.dse.transition.DesignSpaceExplorationAdapter;
+import tools.refinery.store.dse.transition.DesignSpaceExplorationStoreAdapter;
+import tools.refinery.store.dse.transition.ObjectiveValue;
+import tools.refinery.store.dse.transition.Transformation;
+import tools.refinery.store.dse.transition.objectives.CriterionCalculator;
+import tools.refinery.store.dse.transition.objectives.ObjectiveCalculator;
+import tools.refinery.store.model.Model;
+import java.util.List;
+public class DesignSpaceExplorationAdapterImpl implements DesignSpaceExplorationAdapter {
+        final Model model;
+        final DesignSpaceExplorationStoreAdapter designSpaceExplorationStoreAdapter;
+        final List<Transformation> transformations;
+        final List<CriterionCalculator> accepts;
+        final List<CriterionCalculator> excludes;
+        final List<ObjectiveCalculator> objectives;
+        public DesignSpaceExplorationAdapterImpl(Model model,
+                                                                                         DesignSpaceExplorationStoreAdapter designSpaceExplorationStoreAdapter,
+                                                                                         List<Transformation> transformations,
+                                                                                         List<CriterionCalculator> accepts,
+                                                                                         List<CriterionCalculator> excludes,
+                                                                                         List<ObjectiveCalculator> objectives) {
+                this.model = model;
+                this.designSpaceExplorationStoreAdapter = designSpaceExplorationStoreAdapter;
+                this.transformations = transformations;
+                this.accepts = accepts;
+                this.excludes = excludes;
+                this.objectives = objectives;
+        }
+        @Override
+        public Model getModel() {
+                return model;
+        }
+        @Override
+        public DesignSpaceExplorationStoreAdapter getStoreAdapter() {
+                return designSpaceExplorationStoreAdapter;
+        }
+        public List<Transformation> getTransformations() {
+                return transformations;
+        }
+        @Override
+        public boolean checkAccept() {
+                for (var accept : this.accepts) {
+                        model.checkCancelled();
+                        if (!accept.isSatisfied()) {
+                                return false;
+                        }
+                }
+                return true;
+        }
+        @Override
+        public boolean checkExclude() {
+                for (var exclude : this.excludes) {
+                        model.checkCancelled();
+                        if (exclude.isSatisfied()) {
+                                return true;
+                        }
+                }
+                return false;
+        }
+        @Override
+        public ObjectiveValue getObjectiveValue() {
+                model.checkCancelled();
+                if (objectives.size() == 1) {
+                        return ObjectiveValue.of(objectives.get(0).getValue());
+                } else if (objectives.size() == 2) {
+                        return ObjectiveValue.of(objectives.get(0).getValue(), objectives.get(1).getValue());
+                } else {
+                        double[] res = new double[objectives.size()];
+                        for (int i = 0; i < objectives.size(); i++) {
+                                model.checkCancelled();
+                                res[i] = objectives.get(i).getValue();
+                        }
+                        return ObjectiveValue.of(res);
+                }
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/internal/DesignSpaceExplorationBuilderImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/internal/DesignSpaceExplorationBuilderImpl.java
new file mode 100644
index 00000000..a91f6870
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/internal/DesignSpaceExplorationBuilderImpl.java
@@ -0,0 +1,75 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.internal;
+import tools.refinery.store.adapter.AbstractModelAdapterBuilder;
+import tools.refinery.store.dse.transition.DesignSpaceExplorationBuilder;
+import tools.refinery.store.dse.transition.Rule;
+import tools.refinery.store.dse.transition.objectives.Criterion;
+import tools.refinery.store.dse.transition.objectives.Objective;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.model.ModelStoreBuilder;
+import tools.refinery.store.query.ModelQueryBuilder;
+import java.util.LinkedHashSet;
+import java.util.List;
+public class DesignSpaceExplorationBuilderImpl
+                extends AbstractModelAdapterBuilder<DesignSpaceExplorationStoreAdapterImpl>
+                implements DesignSpaceExplorationBuilder {
+        LinkedHashSet<Rule> transformationRuleDefinitions = new LinkedHashSet<>();
+        LinkedHashSet<Criterion> accepts = new LinkedHashSet<>();
+        LinkedHashSet<Criterion> excludes = new LinkedHashSet<>();
+        LinkedHashSet<Objective> objectives = new LinkedHashSet<>();
+        @Override
+        public DesignSpaceExplorationBuilder transformation(Rule transformationRuleDefinition) {
+                transformationRuleDefinitions.add(transformationRuleDefinition);
+                return this;
+        }
+        @Override
+        public DesignSpaceExplorationBuilder accept(Criterion criteria) {
+                accepts.add(criteria);
+                return this;
+        }
+        @Override
+        public DesignSpaceExplorationBuilder exclude(Criterion criteria) {
+                excludes.add(criteria);
+                return this;
+        }
+        @Override
+        public DesignSpaceExplorationBuilder objective(Objective objective) {
+                objectives.add(objective);
+                return this;
+        }
+        @Override
+        protected void doConfigure(ModelStoreBuilder storeBuilder) {
+                var queryEngine = storeBuilder.getAdapter(ModelQueryBuilder.class);
+                transformationRuleDefinitions.forEach(x -> queryEngine.query(x.getPrecondition()));
+                accepts.forEach(x -> x.configure(storeBuilder));
+                excludes.forEach(x -> x.configure(storeBuilder));
+                objectives.forEach(x -> x.configure(storeBuilder));
+                super.doConfigure(storeBuilder);
+        }
+        @Override
+        protected DesignSpaceExplorationStoreAdapterImpl doBuild(ModelStore store) {
+                List<Rule> transformationRuleDefinitionsList = List.copyOf(transformationRuleDefinitions);
+                List<Criterion> acceptsList = List.copyOf(accepts);
+                List<Criterion> excludesList = List.copyOf(excludes);
+                List<Objective> objectivesList = List.copyOf(objectives);
+                return new DesignSpaceExplorationStoreAdapterImpl(store, transformationRuleDefinitionsList, acceptsList,
+                                excludesList, objectivesList);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/internal/DesignSpaceExplorationStoreAdapterImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/internal/DesignSpaceExplorationStoreAdapterImpl.java
new file mode 100644
index 00000000..bd85e7a6
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/internal/DesignSpaceExplorationStoreAdapterImpl.java
@@ -0,0 +1,74 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.internal;
+import tools.refinery.store.dse.transition.DesignSpaceExplorationStoreAdapter;
+import tools.refinery.store.dse.transition.Transformation;
+import tools.refinery.store.dse.transition.Rule;
+import tools.refinery.store.dse.transition.objectives.Criterion;
+import tools.refinery.store.dse.transition.objectives.CriterionCalculator;
+import tools.refinery.store.dse.transition.objectives.Objective;
+import tools.refinery.store.dse.transition.objectives.ObjectiveCalculator;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.model.ModelStore;
+import java.util.List;
+public class DesignSpaceExplorationStoreAdapterImpl implements DesignSpaceExplorationStoreAdapter {
+        protected final ModelStore store;
+        protected final List<Rule> ruleDefinitions;
+        protected final List<Criterion> accepts;
+        protected final List<Criterion> excludes;
+        protected final List<Objective> objectives;
+        public DesignSpaceExplorationStoreAdapterImpl(
+                        ModelStore store, List<Rule> ruleDefinitions, List<Criterion> accepts, List<Criterion> excludes,
+                        List<Objective> objectives) {
+                this.store = store;
+                this.ruleDefinitions = ruleDefinitions;
+                this.accepts = accepts;
+                this.excludes = excludes;
+                this.objectives = objectives;
+        }
+        @Override
+        public ModelStore getStore() {
+                return store;
+        }
+        @Override
+        public DesignSpaceExplorationAdapterImpl createModelAdapter(Model model) {
+                final List<Transformation> t = this.ruleDefinitions.stream()
+                                .map(x -> new Transformation(model, x))
+                                .toList();
+                final List<CriterionCalculator> a = this.accepts.stream().map(x -> x.createCalculator(model)).toList();
+                final List<CriterionCalculator> e = this.excludes.stream().map(x -> x.createCalculator(model)).toList();
+                final List<ObjectiveCalculator> o = this.objectives.stream().map(x -> x.createCalculator(model)).toList();
+                return new DesignSpaceExplorationAdapterImpl(model, this, t, a, e, o);
+        }
+        @Override
+        public List<Rule> getTransformations() {
+                return ruleDefinitions;
+        }
+        @Override
+        public List<Criterion> getAccepts() {
+                return accepts;
+        }
+        @Override
+        public List<Criterion> getExcludes() {
+                return excludes;
+        }
+        @Override
+        public List<Objective> getObjectives() {
+                return objectives;
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/AndCriterion.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/AndCriterion.java
new file mode 100644
index 00000000..0ad2b7a4
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/AndCriterion.java
@@ -0,0 +1,53 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.objectives;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.query.literal.Reduction;
+import java.util.ArrayList;
+import java.util.Collection;
+public final class AndCriterion extends CompositeCriterion {
+        AndCriterion(Collection<? extends Criterion> criteria) {
+                super(criteria);
+        }
+        @Override
+        public Reduction getReduction(ModelStore store) {
+                for (var criterion : getCriteria()) {
+                        var reduction = criterion.getReduction(store);
+                        if (reduction == Reduction.ALWAYS_FALSE) {
+                                return Reduction.ALWAYS_FALSE;
+                        } else if (reduction == Reduction.NOT_REDUCIBLE) {
+                                return Reduction.NOT_REDUCIBLE;
+                        }
+                }
+                return Reduction.ALWAYS_TRUE;
+        }
+        @Override
+        public CriterionCalculator createCalculator(Model model) {
+                var calculators = new ArrayList<CriterionCalculator>();
+                for (var criterion : getCriteria()) {
+                        var reduction = criterion.getReduction(model.getStore());
+                        if (reduction == Reduction.ALWAYS_FALSE) {
+                                return () -> false;
+                        } else if (reduction == Reduction.NOT_REDUCIBLE) {
+                                calculators.add(criterion.createCalculator(model));
+                        }
+                }
+                return () -> {
+                        for (var calculator : calculators) {
+                                if (!calculator.isSatisfied()) {
+                                        return false;
+                                }
+                        }
+                        return true;
+                };
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CompositeCriterion.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CompositeCriterion.java
new file mode 100644
index 00000000..5746cc7e
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CompositeCriterion.java
@@ -0,0 +1,43 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.objectives;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.model.ModelStoreBuilder;
+import tools.refinery.store.query.literal.Reduction;
+import java.util.*;
+public abstract sealed class CompositeCriterion implements Criterion permits AndCriterion, OrCriterion {
+        private final List<Criterion> criteria;
+        protected CompositeCriterion(Collection<? extends Criterion> criteria) {
+                var deDuplicatedCriteria = new LinkedHashSet<Criterion>();
+                for (var criterion : criteria) {
+                        if (criterion.getClass() == this.getClass()) {
+                                var childCriteria = ((CompositeCriterion) criterion).getCriteria();
+                                deDuplicatedCriteria.addAll(childCriteria);
+                        } else {
+                                deDuplicatedCriteria.add(criterion);
+                        }
+                }
+                this.criteria = List.copyOf(deDuplicatedCriteria);
+        }
+        public List<Criterion> getCriteria() {
+                return criteria;
+        }
+        @Override
+        public abstract Reduction getReduction(ModelStore store);
+        @Override
+        public void configure(ModelStoreBuilder storeBuilder) {
+                for (var criterion : criteria) {
+                        criterion.configure(storeBuilder);
+                }
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CompositeObjective.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CompositeObjective.java
new file mode 100644
index 00000000..192a824b
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CompositeObjective.java
@@ -0,0 +1,69 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.objectives;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.model.ModelStoreBuilder;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+public class CompositeObjective implements Objective {
+        private final List<Objective> objectives;
+        CompositeObjective(Collection<? extends Objective> objectives) {
+                var unwrappedObjectives = new ArrayList<Objective>();
+                for (var objective : objectives) {
+                        if (objective instanceof CompositeObjective compositeObjective) {
+                                unwrappedObjectives.addAll(compositeObjective.getObjectives());
+                        } else {
+                                unwrappedObjectives.add(objective);
+                        }
+                }
+                this.objectives = Collections.unmodifiableList(unwrappedObjectives);
+        }
+        public List<Objective> getObjectives() {
+                return objectives;
+        }
+        @Override
+        public boolean isAlwaysZero(ModelStore store) {
+                for (var objective : objectives) {
+                        if (!objective.isAlwaysZero(store)) {
+                                return false;
+                        }
+                }
+                return true;
+        }
+        @Override
+        public ObjectiveCalculator createCalculator(Model model) {
+                var calculators = new ArrayList<ObjectiveCalculator>();
+                for (var objective : objectives) {
+                        if (!objective.isAlwaysZero(model.getStore())) {
+                                calculators.add(objective.createCalculator(model));
+                        }
+                }
+                return () -> {
+                        double value = 0;
+                        for (var calculator : calculators) {
+                                value += calculator.getValue();
+                        }
+                        return value;
+                };
+        }
+        @Override
+        public void configure(ModelStoreBuilder storeBuilder) {
+                for (var objective : objectives) {
+                        objective.configure(storeBuilder);
+                }
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CountObjective.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CountObjective.java
new file mode 100644
index 00000000..fbd05ded
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CountObjective.java
@@ -0,0 +1,47 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.objectives;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.model.ModelStoreBuilder;
+import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.query.ModelQueryBuilder;
+import tools.refinery.store.query.ModelQueryStoreAdapter;
+import tools.refinery.store.query.dnf.RelationalQuery;
+import tools.refinery.store.query.literal.Reduction;
+public class CountObjective implements Objective {
+        private final RelationalQuery query;
+        private final double weight;
+        public CountObjective(RelationalQuery query) {
+                this(query, 1);
+        }
+        public CountObjective(RelationalQuery query, double weight) {
+                this.query = query;
+                this.weight = weight;
+        }
+        @Override
+        public boolean isAlwaysZero(ModelStore store) {
+                var queryStore = store.getAdapter(ModelQueryStoreAdapter.class);
+                var canonicalQuery = queryStore.getCanonicalQuery(query);
+                return canonicalQuery.getDnf().getReduction() == Reduction.ALWAYS_FALSE;
+        }
+        @Override
+        public ObjectiveCalculator createCalculator(Model model) {
+                var resultSet = model.getAdapter(ModelQueryAdapter.class).getResultSet(query);
+                return () -> resultSet.size() * weight;
+        }
+        @Override
+        public void configure(ModelStoreBuilder storeBuilder) {
+                storeBuilder.getAdapter(ModelQueryBuilder.class).query(query);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Criteria.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Criteria.java
new file mode 100644
index 00000000..0e4ec5c9
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Criteria.java
@@ -0,0 +1,47 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.objectives;
+import tools.refinery.store.query.dnf.AnyQuery;
+import java.util.Collection;
+import java.util.List;
+public final class Criteria {
+        private Criteria() {
+                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
+        }
+        public static QueryCriterion whenHasMatch(AnyQuery query) {
+                return new QueryCriterion(query, true);
+        }
+        public static QueryCriterion whenNoMatch(AnyQuery query) {
+                return new QueryCriterion(query, false);
+        }
+        public static Criterion and(Criterion... criteria) {
+                return and(List.of(criteria));
+        }
+        public static Criterion and(Collection<? extends Criterion> criteria) {
+                if (criteria.size() == 1) {
+                        return criteria.iterator().next();
+                }
+                return new AndCriterion(criteria);
+        }
+        public static Criterion or(Criterion... criteria) {
+                return or(List.of(criteria));
+        }
+        public static Criterion or(Collection<? extends Criterion> criteria) {
+                if (criteria.size() == 1) {
+                        return criteria.iterator().next();
+                }
+                return new OrCriterion(criteria);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Criterion.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Criterion.java
new file mode 100644
index 00000000..c827f20e
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Criterion.java
@@ -0,0 +1,22 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.objectives;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.model.ModelStoreBuilder;
+import tools.refinery.store.query.literal.Reduction;
+public interface Criterion {
+        default void configure(ModelStoreBuilder storeBuilder) {
+        }
+        default Reduction getReduction(ModelStore store) {
+                return Reduction.NOT_REDUCIBLE;
+        }
+        CriterionCalculator createCalculator(Model model);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CriterionCalculator.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CriterionCalculator.java
new file mode 100644
index 00000000..944ffed6
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CriterionCalculator.java
@@ -0,0 +1,10 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.objectives;
+public interface CriterionCalculator {
+        boolean isSatisfied();
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Objective.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Objective.java
new file mode 100644
index 00000000..49c34d87
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Objective.java
@@ -0,0 +1,23 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.objectives;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.model.ModelStoreBuilder;
+public interface Objective {
+        default void configure(ModelStoreBuilder storeBuilder) {
+        }
+        // The name {@code isAlwaysZero} is more straightforward than something like {@code canBeNonZero}.
+        @SuppressWarnings("BooleanMethodIsAlwaysInverted")
+        default boolean isAlwaysZero(ModelStore store) {
+                return false;
+        }
+        ObjectiveCalculator createCalculator(Model model);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/ObjectiveCalculator.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/ObjectiveCalculator.java
new file mode 100644
index 00000000..f01b8de9
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/ObjectiveCalculator.java
@@ -0,0 +1,10 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.objectives;
+public interface ObjectiveCalculator {
+        double getValue();
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Objectives.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Objectives.java
new file mode 100644
index 00000000..e552d14c
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Objectives.java
@@ -0,0 +1,41 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.objectives;
+import tools.refinery.store.query.dnf.FunctionalQuery;
+import tools.refinery.store.query.dnf.RelationalQuery;
+import java.util.Collection;
+import java.util.List;
+public final class Objectives {
+        private Objectives() {
+                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
+        }
+        public static CountObjective count(RelationalQuery query, double weight) {
+                return new CountObjective(query, weight);
+        }
+        public static CountObjective count(RelationalQuery query) {
+                return new CountObjective(query);
+        }
+        public static QueryObjective value(FunctionalQuery<? extends Number> query) {
+                return new QueryObjective(query);
+        }
+        public static Objective sum(Objective... objectives) {
+                return sum(List.of(objectives));
+        }
+        public static Objective sum(Collection<? extends Objective> objectives) {
+                if (objectives.size() == 1) {
+                        return objectives.iterator().next();
+                }
+                return new CompositeObjective(objectives);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/OrCriterion.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/OrCriterion.java
new file mode 100644
index 00000000..7a8d7778
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/OrCriterion.java
@@ -0,0 +1,53 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.objectives;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.query.literal.Reduction;
+import java.util.ArrayList;
+import java.util.Collection;
+public final class OrCriterion extends CompositeCriterion {
+        OrCriterion(Collection<? extends Criterion> criteria) {
+                super(criteria);
+        }
+        @Override
+        public Reduction getReduction(ModelStore store) {
+                for (var criterion : getCriteria()) {
+                        var reduction = criterion.getReduction(store);
+                        if (reduction == Reduction.ALWAYS_TRUE) {
+                                return Reduction.ALWAYS_TRUE;
+                        } else if (reduction == Reduction.NOT_REDUCIBLE) {
+                                return Reduction.NOT_REDUCIBLE;
+                        }
+                }
+                return Reduction.ALWAYS_FALSE;
+        }
+        @Override
+        public CriterionCalculator createCalculator(Model model) {
+                var calculators = new ArrayList<CriterionCalculator>();
+                for (var criterion : getCriteria()) {
+                        var reduction = criterion.getReduction(model.getStore());
+                        if (reduction == Reduction.ALWAYS_TRUE) {
+                                return () -> true;
+                        } else if (reduction == Reduction.NOT_REDUCIBLE) {
+                                calculators.add(criterion.createCalculator(model));
+                        }
+                }
+                return () -> {
+                        for (var calculator : calculators) {
+                                if (calculator.isSatisfied()) {
+                                        return true;
+                                }
+                        }
+                        return false;
+                };
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/QueryCriterion.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/QueryCriterion.java
new file mode 100644
index 00000000..e15e4e41
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/QueryCriterion.java
@@ -0,0 +1,59 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.objectives;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.model.ModelStoreBuilder;
+import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.query.ModelQueryBuilder;
+import tools.refinery.store.query.ModelQueryStoreAdapter;
+import tools.refinery.store.query.dnf.AnyQuery;
+import tools.refinery.store.query.literal.Reduction;
+public class QueryCriterion implements Criterion {
+        protected final boolean satisfiedIfHasMatch;
+        protected final AnyQuery query;
+        /**
+         * Criteria based on the existence of matches evaluated on the model.
+         *
+         * @param query               The query evaluated on the model.
+         * @param satisfiedIfHasMatch If true, the criteria satisfied if the query has any match on the model. Otherwise,
+         *                            the criteria satisfied if the query has no match on the model.
+         */
+        public QueryCriterion(AnyQuery query, boolean satisfiedIfHasMatch) {
+                this.query = query;
+                this.satisfiedIfHasMatch = satisfiedIfHasMatch;
+        }
+        @Override
+        public Reduction getReduction(ModelStore store) {
+                var queryStore = store.getAdapter(ModelQueryStoreAdapter.class);
+                var canonicalQuery = queryStore.getCanonicalQuery(query);
+                var reduction = canonicalQuery.getDnf().getReduction();
+                if (satisfiedIfHasMatch) {
+                        return reduction;
+                }
+                return reduction.negate();
+        }
+        @Override
+        public CriterionCalculator createCalculator(Model model) {
+                var resultSet = model.getAdapter(ModelQueryAdapter.class).getResultSet(query);
+                if (satisfiedIfHasMatch) {
+                        return () -> resultSet.size() > 0;
+                } else {
+                        return () -> resultSet.size() == 0;
+                }
+        }
+        @Override
+        public void configure(ModelStoreBuilder storeBuilder) {
+                Criterion.super.configure(storeBuilder);
+                storeBuilder.getAdapter(ModelQueryBuilder.class).query(query);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/QueryObjective.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/QueryObjective.java
new file mode 100644
index 00000000..5a7ba8f4
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/QueryObjective.java
@@ -0,0 +1,41 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.objectives;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.model.ModelStoreBuilder;
+import tools.refinery.store.query.ModelQueryAdapter;
+import tools.refinery.store.query.ModelQueryBuilder;
+import tools.refinery.store.query.dnf.FunctionalQuery;
+public class QueryObjective implements Objective {
+        protected final FunctionalQuery<? extends Number> objectiveFunction;
+        public QueryObjective(FunctionalQuery<? extends Number> objectiveFunction) {
+                if (objectiveFunction.arity() != 0) {
+                        throw new IllegalArgumentException("Objective functions must have 0 parameters, got %d instead"
+                                        .formatted(objectiveFunction.arity()));
+                }
+                this.objectiveFunction = objectiveFunction;
+        }
+        @Override
+        public ObjectiveCalculator createCalculator(Model model) {
+                var resultSet = model.getAdapter(ModelQueryAdapter.class).getResultSet(objectiveFunction);
+                return () -> {
+                        var cursor = resultSet.getAll();
+                        if (!cursor.move()) {
+                                return 0;
+                        }
+                        return Math.max(cursor.getValue().doubleValue(), 0);
+                };
+        }
+        @Override
+        public void configure(ModelStoreBuilder storeBuilder) {
+                storeBuilder.getAdapter(ModelQueryBuilder.class).query(objectiveFunction);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/ActivationStore.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/ActivationStore.java
new file mode 100644
index 00000000..52e0611d
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/ActivationStore.java
@@ -0,0 +1,18 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.statespace;
+import tools.refinery.store.dse.transition.VersionWithObjectiveValue;
+import tools.refinery.store.map.Version;
+import java.util.Random;
+public interface ActivationStore {
+        record VisitResult(boolean successfulVisit, boolean mayHaveMore, int transformation, int activation) { }
+        VisitResult markNewAsVisited(VersionWithObjectiveValue to, int[] emptyEntrySizes);
+        boolean hasUnmarkedActivation(VersionWithObjectiveValue version);
+        VisitResult getRandomAndMarkAsVisited(VersionWithObjectiveValue version, Random random);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/EquivalenceClassStore.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/EquivalenceClassStore.java
new file mode 100644
index 00000000..28d1488b
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/EquivalenceClassStore.java
@@ -0,0 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.statespace;
+import tools.refinery.store.dse.transition.VersionWithObjectiveValue;
+import tools.refinery.store.statecoding.StateCoderResult;
+public interface EquivalenceClassStore {
+        boolean submit(VersionWithObjectiveValue version, StateCoderResult stateCoderResult, int[] emptyActivations, boolean accept);
+        boolean submit(StateCoderResult stateCoderResult);
+        boolean hasUnresolvedSymmetry();
+        void resolveOneSymmetry();
+        int getNumberOfUnresolvedSymmetries();
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/ObjectivePriorityQueue.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/ObjectivePriorityQueue.java
new file mode 100644
index 00000000..df72c343
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/ObjectivePriorityQueue.java
@@ -0,0 +1,21 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.statespace;
+import tools.refinery.store.dse.transition.VersionWithObjectiveValue;
+import tools.refinery.store.map.Version;
+import java.util.Comparator;
+import java.util.Random;
+public interface ObjectivePriorityQueue {
+        Comparator<VersionWithObjectiveValue> getComparator();
+        void submit(VersionWithObjectiveValue versionWithObjectiveValue);
+        void remove(VersionWithObjectiveValue versionWithObjectiveValue);
+        int getSize();
+        VersionWithObjectiveValue getBest();
+        VersionWithObjectiveValue getRandom(Random random);
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/SolutionStore.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/SolutionStore.java
new file mode 100644
index 00000000..d1bfaa79
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/SolutionStore.java
@@ -0,0 +1,17 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.statespace;
+import tools.refinery.store.dse.transition.VersionWithObjectiveValue;
+import java.util.List;
+import java.util.concurrent.Future;
+public interface SolutionStore {
+        boolean submit(VersionWithObjectiveValue version);
+        List<VersionWithObjectiveValue> getSolutions();
+        boolean hasEnoughSolution();
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/AbstractEquivalenceClassStore.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/AbstractEquivalenceClassStore.java
new file mode 100644
index 00000000..b5087e86
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/AbstractEquivalenceClassStore.java
@@ -0,0 +1,54 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.statespace.internal;
+import tools.refinery.store.dse.transition.VersionWithObjectiveValue;
+import tools.refinery.store.dse.transition.statespace.EquivalenceClassStore;
+import tools.refinery.store.statecoding.StateCoderResult;
+import tools.refinery.store.statecoding.StateCoderStoreAdapter;
+public abstract class AbstractEquivalenceClassStore implements EquivalenceClassStore {
+        protected final StateCoderStoreAdapter stateCoderStoreAdapter;
+        AbstractEquivalenceClassStore(StateCoderStoreAdapter stateCoderStoreAdapter) {
+                this.stateCoderStoreAdapter = stateCoderStoreAdapter;
+        }
+        protected int numberOfUnresolvedSymmetries = 0;
+        protected abstract void delegate(VersionWithObjectiveValue version, int[] emptyActivations, boolean accept);
+        protected abstract boolean tryToAdd(StateCoderResult stateCoderResult, VersionWithObjectiveValue newVersion,
+                                                           int[] emptyActivations, boolean accept);
+        public abstract boolean tryToAdd(StateCoderResult stateCoderResult);
+        @Override
+        public boolean submit(StateCoderResult stateCoderResult) {
+                return tryToAdd(stateCoderResult);
+        }
+        @Override
+        public synchronized boolean submit(VersionWithObjectiveValue version, StateCoderResult stateCoderResult,
+                                                                           int[] emptyActivations, boolean accept) {
+                boolean hasNewVersion = tryToAdd(stateCoderResult, version, emptyActivations, accept);
+                if (hasNewVersion) {
+                        delegate(version, emptyActivations, accept);
+                        return true;
+                } else {
+                        numberOfUnresolvedSymmetries++;
+                        return false;
+                }
+        }
+        @Override
+        public boolean hasUnresolvedSymmetry() {
+                return numberOfUnresolvedSymmetries > 0;
+        }
+        @Override
+        public int getNumberOfUnresolvedSymmetries() {
+                return numberOfUnresolvedSymmetries;
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ActivationStoreBitVectorEntry.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ActivationStoreBitVectorEntry.java
new file mode 100644
index 00000000..c204ae35
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ActivationStoreBitVectorEntry.java
@@ -0,0 +1,50 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.statespace.internal;
+public class ActivationStoreBitVectorEntry extends ActivationStoreEntry {
+        final int[] selected;
+        ActivationStoreBitVectorEntry(int numberOfActivations) {
+                super(numberOfActivations);
+                this.selected = new int[(numberOfActivations / Integer.SIZE) + 1];
+        }
+        @Override
+        public int getNumberOfVisitedActivations() {
+                int visited = 0;
+                // Use indexed for loop to avoid allocating an iterator.
+                //noinspection ForLoopReplaceableByForEach
+                for (int i = 0; i < selected.length; i++) {
+                        visited += Integer.bitCount(selected[i]);
+                }
+                return visited;
+        }
+        private static final int ELEMENT_POSITION = 5; // size of Integer.SIZE
+        private static final int ELEMENT_BITMASK = (1 << ELEMENT_POSITION) - 1;
+        @Override
+        public int getAndAddActivationAfter(int index) {
+                int position = index;
+                do {
+                        final int selectedElement = position >> ELEMENT_POSITION;
+                        final int selectedBit = 1 << (position & ELEMENT_BITMASK);
+                        if ((selected[selectedElement] & selectedBit) == 0) {
+                                selected[selectedElement] |= selectedBit;
+                                return position;
+                        } else {
+                                if (position < this.numberOfActivations - 1) {
+                                        position++;
+                                } else {
+                                        position = 0;
+                                }
+                        }
+                } while (position != index);
+                throw new IllegalArgumentException("There is are no unvisited activations!");
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ActivationStoreEntry.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ActivationStoreEntry.java
new file mode 100644
index 00000000..7249751c
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ActivationStoreEntry.java
@@ -0,0 +1,37 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.statespace.internal;
+public abstract class ActivationStoreEntry {
+        protected final int numberOfActivations;
+        ActivationStoreEntry(int numberOfActivations) {
+                this.numberOfActivations = numberOfActivations;
+        }
+        public abstract int getNumberOfVisitedActivations();
+        public int getNumberOfUnvisitedActivations() {
+                return numberOfActivations - getNumberOfVisitedActivations();
+        }
+        public int getNumberOfActivations() {
+                return numberOfActivations;
+        }
+        public abstract int getAndAddActivationAfter(int index);
+        //      public abstract boolean contains(int activation)
+        //      public abstract boolean add(int activation)
+        public static ActivationStoreEntry create(int size) {
+                if(size <= Integer.SIZE*6) {
+                        return new ActivationStoreBitVectorEntry(size);
+                } else {
+                        return new ActivationStoreListEntry(size);
+                }
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ActivationStoreImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ActivationStoreImpl.java
new file mode 100644
index 00000000..82f89db7
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ActivationStoreImpl.java
@@ -0,0 +1,138 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.statespace.internal;
+import tools.refinery.store.dse.transition.VersionWithObjectiveValue;
+import tools.refinery.store.dse.transition.statespace.ActivationStore;
+import java.util.*;
+import java.util.function.Consumer;
+public class ActivationStoreImpl implements ActivationStore {
+        final int numberOfTransformations;
+        final Consumer<VersionWithObjectiveValue> actionWhenAllActivationVisited;
+        final Map<VersionWithObjectiveValue, List<ActivationStoreEntry>> versionToActivations;
+        public ActivationStoreImpl(final int numberOfTransformations,
+                                                           Consumer<VersionWithObjectiveValue> actionWhenAllActivationVisited) {
+                this.numberOfTransformations = numberOfTransformations;
+                this.actionWhenAllActivationVisited = actionWhenAllActivationVisited;
+                versionToActivations = new HashMap<>();
+        }
+        public synchronized VisitResult markNewAsVisited(VersionWithObjectiveValue to, int[] emptyEntrySizes) {
+                boolean[] successful = new boolean[]{false};
+                var entries = versionToActivations.computeIfAbsent(to, x -> {
+                        successful[0] = true;
+                        List<ActivationStoreEntry> result = new ArrayList<>(emptyEntrySizes.length);
+                        for (int emptyEntrySize : emptyEntrySizes) {
+                                result.add(ActivationStoreEntry.create(emptyEntrySize));
+                        }
+                        return result;
+                });
+                boolean hasMore = false;
+                for (var entry : entries) {
+                        if (entry.getNumberOfUnvisitedActivations() > 0) {
+                                hasMore = true;
+                                break;
+                        }
+                }
+                if (!hasMore) {
+                        actionWhenAllActivationVisited.accept(to);
+                }
+                return new VisitResult(successful[0], hasMore, -1, -1);
+        }
+        public synchronized VisitResult visitActivation(VersionWithObjectiveValue from, int transformationIndex,
+                                                                                                        int activationIndex) {
+                var entries = versionToActivations.get(from);
+                var entry = entries.get(transformationIndex);
+                final int unvisited = entry.getNumberOfUnvisitedActivations();
+                final boolean successfulVisit = unvisited > 0;
+                final boolean hasMoreInActivation = unvisited > 1;
+                final boolean hasMore;
+                final int transformation;
+                final int activation;
+                if (successfulVisit) {
+                        transformation = transformationIndex;
+                        activation = entry.getAndAddActivationAfter(activationIndex);
+                } else {
+                        transformation = -1;
+                        activation = -1;
+                }
+                if (!hasMoreInActivation) {
+                        boolean hasMoreInOtherTransformation = false;
+                        for (var e : entries) {
+                                if (e != entry && e.getNumberOfUnvisitedActivations() > 0) {
+                                        hasMoreInOtherTransformation = true;
+                                        break;
+                                }
+                        }
+                        hasMore = hasMoreInOtherTransformation;
+                } else {
+                        hasMore = true;
+                }
+                if (!hasMore) {
+                        actionWhenAllActivationVisited.accept(from);
+                }
+                return new VisitResult(successfulVisit, hasMore, transformation, activation);
+        }
+        @Override
+        public synchronized boolean hasUnmarkedActivation(VersionWithObjectiveValue version) {
+                var entries = versionToActivations.get(version);
+                boolean hasMore = false;
+                for (var entry : entries) {
+                        if (entry.getNumberOfUnvisitedActivations() > 0) {
+                                hasMore = true;
+                                break;
+                        }
+                }
+                return hasMore;
+        }
+        @Override
+        public synchronized VisitResult getRandomAndMarkAsVisited(VersionWithObjectiveValue version, Random random) {
+                var entries = versionToActivations.get(version);
+                var weights = new double[entries.size()];
+                double totalWeight = 0;
+                int numberOfAllUnvisitedActivations = 0;
+                for (int i = 0; i < weights.length; i++) {
+                        var entry = entries.get(i);
+                        int unvisited = entry.getNumberOfUnvisitedActivations();
+                        double weight = unvisited == 0 ? 0 : unvisited; //(Math.log(unvisited) + 1.0);
+                        weights[i] = weight;
+                        totalWeight += weight;
+                        numberOfAllUnvisitedActivations += unvisited;
+                }
+                if (numberOfAllUnvisitedActivations == 0) {
+                        this.actionWhenAllActivationVisited.accept(version);
+                        return new VisitResult(false, false, -1, -1);
+                }
+                double offset = random.nextDouble(totalWeight);
+                int transformation = 0;
+                for (; transformation < entries.size(); transformation++) {
+                        double weight = weights[transformation];
+                        if (weight > 0 && offset < weight) {
+                                var entry = entries.get(transformation);
+                                int activation = random.nextInt(entry.getNumberOfActivations());
+                                return this.visitActivation(version, transformation, activation);
+                        }
+                        offset -= weight;
+                }
+                throw new AssertionError("Unvisited activation %f not found".formatted(offset));
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ActivationStoreListEntry.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ActivationStoreListEntry.java
new file mode 100644
index 00000000..14298bee
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ActivationStoreListEntry.java
@@ -0,0 +1,104 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.statespace.internal;
+import org.eclipse.collections.api.factory.primitive.IntLists;
+import org.eclipse.collections.api.list.primitive.MutableIntList;
+public class ActivationStoreListEntry extends ActivationStoreEntry {
+        private final MutableIntList visitedActivations = IntLists.mutable.empty();
+        ActivationStoreListEntry(int numberOfActivations) {
+                super(numberOfActivations);
+        }
+        @Override
+        public int getNumberOfVisitedActivations() {
+                return visitedActivations.size();
+        }
+        @Override
+        public int getAndAddActivationAfter(int index) {
+                // If it is empty, just add it.
+                if(this.visitedActivations.isEmpty()) {
+                        this.visitedActivations.add(index);
+                        return index;
+                }
+                final int positionInSearch = getPosition(index);
+                int position = positionInSearch;
+                // if the position is after the last, we can insert it at the end of the list
+                if(position == this.visitedActivations.size()) {
+                        this.visitedActivations.add(index);
+                        return index;
+                } else if(this.visitedActivations.get(position) != index) {
+                        // If the index is not in the position, one can insert it
+                        this.visitedActivations.addAtIndex(position,index);
+                        return index;
+                }
+                // Otherwise, get the next empty space between two elements
+                while(position + 1 < this.visitedActivations.size()) {
+                        if(this.visitedActivations.get(position+1)-this.visitedActivations.get(position) > 1) {
+                                int newElement = this.visitedActivations.get(position)+1;
+                                this.visitedActivations.addAtIndex(position+1, newElement);
+                                return newElement;
+                        }
+                        position++;
+                }
+                // Otherwise, try to add to the last space
+                int last = this.visitedActivations.get(this.visitedActivations.size()-1);
+                if(last<this.numberOfActivations-1) {
+                        this.visitedActivations.add(last+1);
+                        return last+1;
+                }
+                // Otherwise, try to put to the beginning
+                if(this.visitedActivations.get(0) > 0) {
+                        this.visitedActivations.addAtIndex(0,0);
+                        return 0;
+                }
+                // Otherwise, get the next empty space between two elements
+                position = 0;
+                while(position < positionInSearch) {
+                        if(this.visitedActivations.get(position+1)-this.visitedActivations.get(position) > 1) {
+                                int newElement = this.visitedActivations.get(position)+1;
+                                this.visitedActivations.addAtIndex(position+1, newElement);
+                                return newElement;
+                        }
+                        position++;
+                }
+                throw new IllegalArgumentException("There is are no unvisited activations!");
+        }
+        /**
+         * Returns the position of an index in the {@code visitedActivations}. If the collection contains the index, in
+         * returns its position, otherwise, it  returns the position where the index need to be put.
+         *
+         * @param index Index of an activation.
+         * @return The position of the index.
+         */
+        private int getPosition(int index) {
+                int left = 0;
+                int right = this.visitedActivations.size() - 1;
+                while (left <= right) {
+                        final int middle = (right - left) / 2 + left;
+                        final int middleElement = visitedActivations.get(middle);
+                        if(middleElement == index) {
+                                return middle;
+                        } else if(middleElement < index) {
+                                left = middle +1;
+                        } else{
+                                right = middle-1;
+                        }
+                }
+                return right+1;
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ActivationStoreWorker.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ActivationStoreWorker.java
new file mode 100644
index 00000000..1d7c5ce5
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ActivationStoreWorker.java
@@ -0,0 +1,55 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.statespace.internal;
+import tools.refinery.store.dse.transition.Transformation;
+import tools.refinery.store.dse.transition.VersionWithObjectiveValue;
+import tools.refinery.store.dse.transition.statespace.ActivationStore;
+import java.util.List;
+import java.util.Random;
+public class ActivationStoreWorker {
+        final ActivationStore store;
+        final List<Transformation> transformations;
+        public ActivationStoreWorker(ActivationStore store, List<Transformation> transformations) {
+                this.store = store;
+                this.transformations = transformations;
+        }
+        public int[] calculateEmptyActivationSize() {
+                int[] result = new int[transformations.size()];
+                for (int i = 0; i < result.length; i++) {
+                        result[i] = transformations.get(i).getAllActivationsAsResultSet().size();
+                }
+                return result;
+        }
+        public ActivationStore.VisitResult fireRandomActivation(VersionWithObjectiveValue thisVersion, Random random) {
+                var result = store.getRandomAndMarkAsVisited(thisVersion, random);
+                if (result.successfulVisit()) {
+                        int selectedTransformation = result.transformation();
+                        int selectedActivation = result.activation();
+                        Transformation transformation = transformations.get(selectedTransformation);
+                        var tuple = transformation.getActivation(selectedActivation);
+                        boolean success = transformation.fireActivation(tuple);
+                        if (success) {
+                                return result;
+                        } else {
+                                return new ActivationStore.VisitResult(
+                                                false,
+                                                result.mayHaveMore(),
+                                                selectedTransformation,
+                                                selectedActivation);
+                        }
+                }
+                return result;
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/CompleteEquivalenceClassStore.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/CompleteEquivalenceClassStore.java
new file mode 100644
index 00000000..20a026b6
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/CompleteEquivalenceClassStore.java
@@ -0,0 +1,104 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.statespace.internal;
+import org.eclipse.collections.api.factory.primitive.IntObjectMaps;
+import org.eclipse.collections.api.map.primitive.MutableIntObjectMap;
+import tools.refinery.store.dse.transition.VersionWithObjectiveValue;
+import tools.refinery.store.dse.transition.statespace.EquivalenceClassStore;
+import tools.refinery.store.statecoding.StateCoderResult;
+import tools.refinery.store.statecoding.StateCoderStoreAdapter;
+import tools.refinery.store.statecoding.StateEquivalenceChecker;
+import java.util.ArrayList;
+public abstract class CompleteEquivalenceClassStore extends AbstractEquivalenceClassStore implements EquivalenceClassStore {
+        static class SymmetryStoreArray extends ArrayList<VersionWithObjectiveValue> {
+                final int[] activationSizes;
+                final boolean accept;
+                SymmetryStoreArray(int[] activationSizes, boolean accept) {
+                        super();
+                        this.activationSizes = activationSizes;
+                        this.accept = accept;
+                }
+        }
+        private final MutableIntObjectMap<Object> modelCode2Versions = IntObjectMaps.mutable.empty();
+        protected CompleteEquivalenceClassStore(StateCoderStoreAdapter stateCoderStoreAdapter) {
+                super(stateCoderStoreAdapter);
+        }
+        @Override
+        protected boolean tryToAdd(StateCoderResult stateCoderResult, VersionWithObjectiveValue newVersion,
+                                           int[] emptyActivations, boolean accept) {
+                int modelCode = stateCoderResult.modelCode();
+                Object old = modelCode2Versions.updateValue(
+                                modelCode,
+                                () -> newVersion,
+                                x -> {
+                                        if (x instanceof SymmetryStoreArray array) {
+                                                if(array.accept != accept || array.activationSizes != emptyActivations) {
+                                                        this.delegate(newVersion,emptyActivations,accept);
+                                                        return x;
+                                                }
+                                                array.add(newVersion);
+                                                return array;
+                                        } else {
+                                                SymmetryStoreArray result = new SymmetryStoreArray(emptyActivations, accept);
+                                                result.add((VersionWithObjectiveValue) x);
+                                                result.add(newVersion);
+                                                return result;
+                                        }
+                                });
+                return old == null;
+        }
+        @Override
+        public void resolveOneSymmetry() {
+                var unresolvedSimilarity = getOneUnresolvedSymmetry();
+                if (unresolvedSimilarity == null) {
+                        return;
+                }
+                var outcome = this.stateCoderStoreAdapter.checkEquivalence(unresolvedSimilarity.get(0).version(),
+                                unresolvedSimilarity.get(1).version());
+                if (outcome != StateEquivalenceChecker.EquivalenceResult.ISOMORPHIC) {
+                        delegate(unresolvedSimilarity.get(1), unresolvedSimilarity.activationSizes, unresolvedSimilarity.accept);
+                }
+        }
+        //record  UnresolvedSymmetryResult
+        private synchronized SymmetryStoreArray getOneUnresolvedSymmetry() {
+                if (numberOfUnresolvedSymmetries <= 0) {
+                        return null;
+                }
+                for (var entry : modelCode2Versions.keyValuesView()) {
+                        int hash = entry.getOne();
+                        var value = entry.getTwo();
+                        if (value instanceof SymmetryStoreArray array) {
+                                int size = array.size();
+                                var representative = array.get(0);
+                                var similar = array.get(size - 1);
+                                array.remove(size - 1);
+                                if (size <= 2) {
+                                        modelCode2Versions.put(hash, representative);
+                                }
+                                var result = new SymmetryStoreArray(array.activationSizes, array.accept);
+                                result.add(representative);
+                                result.add(similar);
+                                return result;
+                        }
+                }
+                return null;
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/FastEquivalenceClassStore.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/FastEquivalenceClassStore.java
new file mode 100644
index 00000000..6d028124
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/FastEquivalenceClassStore.java
@@ -0,0 +1,37 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.statespace.internal;
+import org.eclipse.collections.api.factory.primitive.IntSets;
+import org.eclipse.collections.api.set.primitive.MutableIntSet;
+import tools.refinery.store.dse.transition.VersionWithObjectiveValue;
+import tools.refinery.store.dse.transition.statespace.EquivalenceClassStore;
+import tools.refinery.store.statecoding.StateCoderResult;
+import tools.refinery.store.statecoding.StateCoderStoreAdapter;
+public abstract class FastEquivalenceClassStore extends AbstractEquivalenceClassStore implements EquivalenceClassStore {
+        private final MutableIntSet codes = IntSets.mutable.empty();
+        protected FastEquivalenceClassStore(StateCoderStoreAdapter stateCoderStoreAdapter) {
+                super(stateCoderStoreAdapter);
+        }
+        @Override
+        protected synchronized boolean tryToAdd(StateCoderResult stateCoderResult, VersionWithObjectiveValue newVersion,
+                                                                int[] emptyActivations, boolean accept) {
+                return this.codes.add(stateCoderResult.modelCode());
+        }
+        public synchronized boolean tryToAdd(StateCoderResult stateCoderResult) {
+                return this.codes.add(stateCoderResult.modelCode());
+        }
+        @Override
+        public void resolveOneSymmetry() {
+                throw new IllegalArgumentException("This equivalence storage is not prepared to resolve symmetries!");
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ObjectivePriorityQueueImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ObjectivePriorityQueueImpl.java
new file mode 100644
index 00000000..2f3e142a
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/ObjectivePriorityQueueImpl.java
@@ -0,0 +1,68 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.statespace.internal;
+import tools.refinery.store.dse.transition.ObjectiveValues;
+import tools.refinery.store.dse.transition.VersionWithObjectiveValue;
+import tools.refinery.store.dse.transition.objectives.Objective;
+import tools.refinery.store.dse.transition.statespace.ObjectivePriorityQueue;
+import java.util.Comparator;
+import java.util.List;
+import java.util.PriorityQueue;
+import java.util.Random;
+public class ObjectivePriorityQueueImpl implements ObjectivePriorityQueue {
+        public static final Comparator<VersionWithObjectiveValue> c1 = (o1, o2) -> Double.compare(
+                        ((ObjectiveValues.ObjectiveValue1) o1.objectiveValue()).value0(),
+                        ((ObjectiveValues.ObjectiveValue1) o2.objectiveValue()).value0());
+        // TODO: support multi objective!
+        final PriorityQueue<VersionWithObjectiveValue> priorityQueue;
+        public ObjectivePriorityQueueImpl(List<Objective> objectives) {
+                if(objectives.size() == 1) {
+                        this.priorityQueue = new PriorityQueue<>(c1);
+                } else {
+                        throw new UnsupportedOperationException("Only single objective comparator is implemented currently!");
+                }
+        }
+        @Override
+        public Comparator<VersionWithObjectiveValue> getComparator() {
+                return c1;
+        }
+        @Override
+        public synchronized void submit(VersionWithObjectiveValue versionWithObjectiveValue) {
+                priorityQueue.add(versionWithObjectiveValue);
+        }
+        @Override
+        public synchronized void remove(VersionWithObjectiveValue versionWithObjectiveValue) {
+                priorityQueue.remove(versionWithObjectiveValue);
+        }
+        @Override
+        public synchronized int getSize() {
+                return priorityQueue.size();
+        }
+        @Override
+        public synchronized VersionWithObjectiveValue getBest() {
+                return priorityQueue.peek();
+        }
+        @Override
+        public synchronized VersionWithObjectiveValue getRandom(Random random) {
+                int randomPosition = random.nextInt(getSize());
+                for (VersionWithObjectiveValue entry : this.priorityQueue) {
+                        if (randomPosition-- == 0) {
+                                return entry;
+                        }
+                }
+                throw new IllegalStateException("The priority queue is inconsistent!");
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/SolutionStoreImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/SolutionStoreImpl.java
new file mode 100644
index 00000000..43548eaa
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/statespace/internal/SolutionStoreImpl.java
@@ -0,0 +1,52 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.transition.statespace.internal;
+import tools.refinery.store.dse.transition.VersionWithObjectiveValue;
+import tools.refinery.store.dse.transition.statespace.SolutionStore;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.PriorityQueue;
+public class SolutionStoreImpl implements SolutionStore {
+        final int maxNumberSolutions;
+        public static final int UNLIMITED = -1;
+        final PriorityQueue<VersionWithObjectiveValue> solutions;
+        public SolutionStoreImpl(int maxNumberSolutions) {
+                this.maxNumberSolutions = maxNumberSolutions;
+                solutions = new PriorityQueue<>(ObjectivePriorityQueueImpl.c1.reversed());
+        }
+        @Override
+        public synchronized boolean submit(VersionWithObjectiveValue version) {
+                boolean removeLast = hasEnoughSolution();
+                solutions.add(version);
+                if(removeLast) {
+                        var last = solutions.poll();
+                        return last != version;
+                } else {
+                        return true;
+                }
+        }
+        @Override
+        public List<VersionWithObjectiveValue> getSolutions() {
+                return new ArrayList<>(solutions);
+        }
+        @Override
+        public boolean hasEnoughSolution() {
+                if (maxNumberSolutions == UNLIMITED) {
+                        return false;
+                } else {
+                        return solutions.size() >= maxNumberSolutions;
+                }
+        }
+}