NeatSelection.java

package net.bmahe.genetics4j.neat.spec.selection;

import java.util.function.BiPredicate;

import org.apache.commons.lang3.Validate;

import org.immutables.value.Value;

import net.bmahe.genetics4j.core.Individual;

import net.bmahe.genetics4j.core.spec.selection.SelectionPolicy;

import net.bmahe.genetics4j.core.spec.selection.Tournament;

import net.bmahe.genetics4j.neat.NeatUtils;

/**

 * Selection policy for NEAT (NeuroEvolution of Augmenting Topologies) species-based selection.

 * 

 * <p>NeatSelection implements the species-based selection mechanism that is fundamental to NEAT's ability to maintain

 * population diversity and protect structural innovations. It organizes the population into species based on genetic

 * compatibility, applies fitness sharing within species, and manages reproduction allocation to prevent dominant

 * topologies from eliminating exploration.

 * 

 * <p>Key features:

 * <ul>

 * <li><strong>Species formation</strong>: Groups genetically similar individuals using compatibility predicates</li>

 * <li><strong>Fitness sharing</strong>: Reduces fitness pressure within species to promote diversity</li>

 * <li><strong>Species preservation</strong>: Maintains minimum viable species sizes</li>

 * <li><strong>Reproduction allocation</strong>: Distributes offspring based on species average fitness</li>

 * </ul>

 * 

 * <p>NEAT species-based selection process:

 * <ol>

 * <li><strong>Compatibility testing</strong>: Apply species predicate to group similar individuals</li>

 * <li><strong>Species assignment</strong>: Assign individuals to species based on genetic distance</li>

 * <li><strong>Fitness adjustment</strong>: Apply fitness sharing within each species</li>

 * <li><strong>Species filtering</strong>: Remove species below minimum size threshold</li>

 * <li><strong>Reproduction allocation</strong>: Determine offspring count per species</li>

 * <li><strong>Within-species selection</strong>: Select parents using specified selection policy</li>

 * </ol>

 * 

 * <p>Species management parameters:

 * <ul>

 * <li><strong>Keep ratio</strong>: Proportion of each species to preserve for reproduction</li>

 * <li><strong>Minimum size</strong>: Smallest viable species size to prevent extinction</li>

 * <li><strong>Compatibility predicate</strong>: Function determining species membership</li>

 * <li><strong>Selection policy</strong>: Within-species selection strategy</li>

 * </ul>

 * 

 * <p>Common usage patterns:

 * 

 * <pre>{@code

 * // Default NEAT selection with standard parameters

 * NeatSelection<Double> defaultSelection = NeatSelection.ofDefault();

 * 

 * // Custom compatibility threshold

 * BiPredicate<Individual<Double>, Individual<Double>> compatibilityPredicate = (i1,

 * 		i2) -> NeatUtils.compatibilityDistance(i1.genotype(), i2.genotype(), 0, 2, 2, 1.0f) < 3.0; // Higher threshold

 * 																																	// = fewer, larger

 * 																																	// species

 * 

 * NeatSelection<Double> customSelection = NeatSelection.<Double>builder()

 * 		.perSpeciesKeepRatio(0.8f) // Keep top 80% of each species

 * 		.minSpeciesSize(3) // Minimum 3 individuals per species

 * 		.speciesPredicate(compatibilityPredicate)

 * 		.speciesSelection(Tournament.of(5)) // Tournament size 5 within species

 * 		.build();

 * 

 * // Aggressive diversity preservation

 * NeatSelection<Double> diverseSelection = NeatSelection.of(

 * 		0.95f, // Keep 95% of each species

 * 			compatibilityPredicate,

 * 			new ProportionalSelection() // Proportional selection within species

 * );

 * }</pre>

 * 

 * <p>Compatibility distance calculation:

 * <ul>

 * <li><strong>Matching genes</strong>: Genes with same innovation numbers in both individuals</li>

 * <li><strong>Disjoint genes</strong>: Genes in one individual within the other's innovation range</li>

 * <li><strong>Excess genes</strong>: Genes beyond the other individual's highest innovation number</li>

 * <li><strong>Weight differences</strong>: Average difference in matching gene weights</li>

 * </ul>

 * 

 * <p>Species preservation strategies:

 * <ul>

 * <li><strong>Keep ratio</strong>: Ensures a proportion of each species survives selection pressure</li>

 * <li><strong>Minimum size</strong>: Prevents viable species from going extinct due to random drift</li>

 * <li><strong>Fitness sharing</strong>: Reduces competition between similar individuals</li>

 * <li><strong>Innovation protection</strong>: Gives new topologies time to optimize</li>

 * </ul>

 * 

 * <p>Integration with genetic operators:

 * <ul>

 * <li><strong>Crossover compatibility</strong>: Species ensure genetic similarity for meaningful recombination</li>

 * <li><strong>Mutation guidance</strong>: Species composition can influence mutation rates</li>

 * <li><strong>Structural innovation</strong>: Protected evolution of different network topologies</li>

 * <li><strong>Population dynamics</strong>: Species formation and extinction drive exploration</li>

 * </ul>

 * 

 * <p>Performance considerations:

 * <ul>

 * <li><strong>Compatibility caching</strong>: Distance calculations cached for efficiency</li>

 * <li><strong>Species reuse</strong>: Species structures maintained across generations</li>

 * <li><strong>Parallel evaluation</strong>: Species-based organization enables concurrent processing</li>

 * <li><strong>Memory efficiency</strong>: Efficient species membership tracking</li>

 * </ul>

 * 

 * @param <T> the fitness value type (typically Double)

 * @see SelectionPolicy

 * @see NeatUtils#compatibilityDistance

 * @see net.bmahe.genetics4j.neat.selection.NeatSelectionPolicyHandler

 * @see net.bmahe.genetics4j.neat.Species

 */

@Value.Immutable

	/**

	 * Returns the proportion of each species to preserve for reproduction.

	 * 

	 * <p>This ratio determines what fraction of each species will be retained after fitness-based culling. Higher values

	 * preserve more diversity within species but may slow convergence, while lower values increase selection pressure

	 * but may lose beneficial genetic variations.

	 * 

	 * <p>Typical values:

	 * <ul>

	 * <li><strong>0.9 (default)</strong>: Preserve top 90% of each species</li>

	 * <li><strong>0.8-0.95</strong>: Balanced diversity preservation</li>

	 * <li><strong>&lt; 0.8</strong>: Aggressive selection pressure</li>

	 * <li><strong>&gt; 0.95</strong>: Minimal selection pressure, maximum diversity</li>

	 * </ul>

	 * 

	 * @return keep ratio between 0.0 and 1.0 (exclusive of 0.0, inclusive of 1.0)

	 */

	@Value.Default

	public float perSpeciesKeepRatio() {

	}

	/**

	 * Returns the minimum number of individuals required to maintain a species.

	 * 

	 * <p>Species with fewer members than this threshold will be eliminated to prevent resource waste on non-viable

	 * populations. This helps focus evolutionary resources on species with sufficient genetic diversity to explore their

	 * local fitness landscape effectively.

	 * 

	 * <p>Typical values:

	 * <ul>

	 * <li><strong>5 (default)</strong>: Balanced viability threshold</li>

	 * <li><strong>3-10</strong>: Reasonable range for most problems</li>

	 * <li><strong>&lt; 3</strong>: Very permissive, allows small species to survive</li>

	 * <li><strong>&gt; 10</strong>: Strict threshold, eliminates marginal species</li>

	 * </ul>

	 * 

	 * @return minimum species size (must be positive)

	 */

	@Value.Default

	public int minSpeciesSize() {

	}

	/**

	 * Returns the predicate used to determine species membership.

	 * 

	 * <p>This bi-predicate takes two individuals and returns true if they should belong to the same species based on

	 * their genetic compatibility. Typically implemented using NEAT compatibility distance with a threshold value.

	 * 

	 * <p>Common implementations:

	 * <ul>

	 * <li><strong>Compatibility distance</strong>: Based on matching, disjoint, excess genes and weight differences</li>

	 * <li><strong>Topological similarity</strong>: Based on network structure similarity</li>

	 * <li><strong>Behavioral similarity</strong>: Based on network output patterns</li>

	 * <li><strong>Custom metrics</strong>: Domain-specific similarity measures</li>

	 * </ul>

	 * 

	 * @return bi-predicate for determining species membership

	 */

	public abstract BiPredicate<Individual<T>, Individual<T>> speciesPredicate();

	/**

	 * Returns the selection policy used within each species.

	 * 

	 * <p>After individuals are organized into species, this policy determines how parents are selected within each

	 * species for reproduction. Common choices include tournament selection, proportional selection, or rank-based

	 * selection.

	 * 

	 * <p>Selection policy considerations:

	 * <ul>

	 * <li><strong>Tournament selection</strong>: Good balance of selection pressure and diversity</li>

	 * <li><strong>Proportional selection</strong>: Fitness-proportionate selection within species</li>

	 * <li><strong>Rank selection</strong>: Rank-based selection to avoid fitness scaling issues</li>

	 * <li><strong>Elite selection</strong>: Always select best individuals within species</li>

	 * </ul>

	 * 

	 * @return selection policy for within-species parent selection

	 */

	public abstract SelectionPolicy speciesSelection();

	@Value.Check

	public void check() {

	}

	public static <U extends Comparable<U>> Builder<U> builder() {

	}

	/**

	 * Creates a NEAT selection policy with custom keep ratio and specified parameters.

	 * 

	 * @param <U>                 the fitness value type

	 * @param perSpeciesKeepRatio proportion of each species to preserve (0.0 < ratio <= 1.0)

	 * @param speciesPredicate    predicate for determining species membership

	 * @param speciesSelection    selection policy for within-species parent selection

	 * @return a new NEAT selection policy with the specified parameters

	 */

	public static <U extends Comparable<U>> NeatSelection<U> of(final float perSpeciesKeepRatio,

			final BiPredicate<Individual<U>, Individual<U>> speciesPredicate, final SelectionPolicy speciesSelection) {

	}

	/**

	 * Creates a NEAT selection policy with default keep ratio and specified parameters.

	 * 

	 * @param <U>              the fitness value type

	 * @param speciesPredicate predicate for determining species membership

	 * @param speciesSelection selection policy for within-species parent selection

	 * @return a new NEAT selection policy with default keep ratio (0.9)

	 */

	public static <U extends Comparable<U>> NeatSelection<U> of(

			final BiPredicate<Individual<U>, Individual<U>> speciesPredicate, final SelectionPolicy speciesSelection) {

	}

	/**

	 * Creates a NEAT selection policy with standard default parameters.

	 * 

	 * <p>Default configuration:

	 * <ul>

	 * <li><strong>Keep ratio</strong>: 0.9 (preserve top 90% of each species)</li>

	 * <li><strong>Minimum species size</strong>: 5 individuals</li>

	 * <li><strong>Compatibility distance</strong>: Threshold of 1.0 with standard coefficients</li>

	 * <li><strong>Species selection</strong>: Tournament selection with size 3</li>

	 * </ul>

	 * 

	 * <p>Compatibility distance uses:

	 * <ul>

	 * <li>Weight coefficient: 1.0</li>

	 * <li>Excess gene coefficient: 2.0</li>

	 * <li>Disjoint gene coefficient: 2.0</li>

	 * <li>Distance threshold: 1.0</li>

	 * </ul>

	 * 

	 * @param <U> the fitness value type

	 * @return a new NEAT selection policy with standard default parameters

	 */

	public static <U extends Comparable<U>> NeatSelection<U> ofDefault() {

	}

}

Mutations

1.1
Location : minSpeciesSize
Killed by : none Substituted 5 with 6 → SURVIVED Covering tests

2.2
Location : minSpeciesSize
Killed by : net.bmahe.genetics4j.neat.selection.NeatSelectorImplTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.selection.NeatSelectorImplTest]/[method:simple()] replaced int return with 0 for net/bmahe/genetics4j/neat/spec/selection/NeatSelection::minSpeciesSize → KILLED

2.2
Location : ofDefault
Killed by : none Substituted 3 with 4 → SURVIVED Covering tests

3.3
Location : ofDefault
Killed by : net.bmahe.genetics4j.neat.selection.NeatSelectorImplTest.[engine:junit-jupiter]/[class:net.bmahe.genetics4j.neat.selection.NeatSelectorImplTest]/[method:constructor()] removed call to net/bmahe/genetics4j/neat/spec/selection/NeatSelection$Builder::speciesPredicate → KILLED