Add elitism_rate to ExtensionMassExtinction and ExtensionMassDegeneration

Fix best_chromosome_indices for all None fitness

Author: basvanwesting

CHANGELOG.md

@@ -4,6 +4,16 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.20.1] - 2025-05-08
+### Added
+* Add `elitism_rate` to `ExtensionMassExtinction` and
+  `ExtensionMassDegeneration`. The `elitism_rate` ensures the passing of the best
+  chromosomes before extinction or degeneration is applied
+
+### Fixed
+* Fix `best_chromosome_indices()` on `Population` in case where there are no
+  fitness values other than None
+
 ## [0.20.0] - 2025-05-08
 
 ### Changed

benches/extension.rs

@@ -49,8 +49,8 @@ pub fn criterion_benchmark(c: &mut Criterion) {
     for genes_size in &genes_sizes {
         let extensions: Vec<ExtensionWrapper> = vec![
             ExtensionMassGenesis::new(population_size).into(),
-            ExtensionMassExtinction::new(population_size, 0.10).into(),
-            ExtensionMassDegeneration::new(population_size, 10).into(),
+            ExtensionMassExtinction::new(population_size, 0.10, 0.02).into(),
+            ExtensionMassDegeneration::new(population_size, 10, 0.02).into(),
         ];
         for mut extension in extensions {
             group.throughput(Throughput::Elements(population_size as u64));

examples/evolve_scrabble.rs

@@ -279,9 +279,9 @@ fn main() {
         .with_crossover(CrossoverUniform::new(0.7, 0.8))
         // .with_select(SelectTournament::new(0.5, 0.02, 4))
         .with_select(SelectElite::new(0.5, 0.02))
-        .with_extension(ExtensionMassDegeneration::new(2, 10))
+        .with_extension(ExtensionMassDegeneration::new(2, 10, 0.02))
         // .with_extension(ExtensionMassGenesis::new(2))
-        // .with_extension(ExtensionMassExtinction::new(2, 0.1))
+        // .with_extension(ExtensionMassExtinction::new(2, 0.1, 0.02))
         // .with_reporter(EvolveReporterSimple::default())
         // .with_reporter(EvolveReporterSimple::new_with_flags(
         //     100, false, false, false, true,

src/extension.rs

@@ -30,6 +30,25 @@ pub trait Extension: Clone + Send + Sync + std::fmt::Debug {
         reporter: &mut SR,
         rng: &mut R,
     );
+
+    fn extract_elite_chromosomes<G: EvolveGenotype>(
+        &self,
+        state: &mut EvolveState<G>,
+        config: &EvolveConfig,
+        elitism_size: usize,
+    ) -> Vec<G::Chromosome> {
+        let mut elite_chromosomes: Vec<G::Chromosome> = Vec::with_capacity(elitism_size);
+        for index in state
+            .population
+            .best_chromosome_indices(elitism_size, config.fitness_ordering)
+            .into_iter()
+            .rev()
+        {
+            let chromosome = state.population.chromosomes.swap_remove(index);
+            elite_chromosomes.push(chromosome);
+        }
+        elite_chromosomes
+    }
 }
 
 #[derive(Clone, Debug)]

src/extension/mass_degeneration.rs

@@ -6,15 +6,17 @@ use rand::Rng;
 use std::time::Instant;
 
 /// Simulates a cambrian explosion. The controlling metric is population cardinality in the
-/// population after selection. When this cardinality drops to the threshold, the full population
-/// is mutated the provided number of times, where the [Genotype](crate::genotype::Genotype)
-/// determines whether this is random, relative or scaled.
+/// population after selection. When this cardinality drops to the threshold, the population
+/// (except for the two best chromosomes) is mutated the provided number of times, where the
+/// [Genotype](crate::genotype::Genotype) determines whether this is random, relative or scaled.
+/// The elitism_rate ensures the passing of the best chromosomes before mutations are applied.
 ///
 /// Duplicate mutations of the same gene are allowed. There is no change in population size.
 #[derive(Debug, Clone)]
 pub struct MassDegeneration {
     pub cardinality_threshold: usize,
     pub number_of_mutations: usize,
+    pub elitism_rate: f32,
 }
 
 impl Extension for MassDegeneration {
@@ -36,6 +38,15 @@ impl Extension for MassDegeneration {
                         state,
                         config,
                     );
+                    let population_size = state.population.size();
+
+                    let elitism_size = ((population_size as f32 * self.elitism_rate).ceil()
+                        as usize)
+                        .min(population_size);
+                    let mut elite_chromosomes =
+                        self.extract_elite_chromosomes(state, config, elitism_size);
+                    let elitism_size = elite_chromosomes.len();
+
                     for chromosome in state.population.chromosomes.iter_mut() {
                         genotype.mutate_chromosome_genes(
                             self.number_of_mutations,
@@ -45,6 +56,15 @@ impl Extension for MassDegeneration {
                             rng,
                         );
                     }
+
+                    state.population.chromosomes.append(&mut elite_chromosomes);
+                    // move back to front, elite_chromosomes internally unordered
+                    for i in 0..elitism_size {
+                        state
+                            .population
+                            .chromosomes
+                            .swap(i, population_size - 1 - i);
+                    }
                 }
             }
             state.add_duration(StrategyAction::Extension, now.elapsed());
@@ -53,10 +73,11 @@ impl Extension for MassDegeneration {
 }
 
 impl MassDegeneration {
-    pub fn new(cardinality_threshold: usize, number_of_rounds: usize) -> Self {
+    pub fn new(cardinality_threshold: usize, number_of_rounds: usize, elitism_rate: f32) -> Self {
         Self {
             cardinality_threshold,
             number_of_mutations: number_of_rounds,
+            elitism_rate,
         }
     }
 }

src/extension/mass_extinction.rs

@@ -8,12 +8,14 @@ use std::time::Instant;
 /// Simulates a cambrian explosion. The controlling metric is population cardinality in the
 /// population after selection. When this cardinality drops to the threshold, the population is
 /// randomly reduced regardless of fitness using the survival_rate (fraction of population).
+/// The elitism_rate ensures the passing of the best chromosomes before random reduction starts.
 ///
 /// Population will recover in the following generations
 #[derive(Debug, Clone)]
 pub struct MassExtinction {
     pub cardinality_threshold: usize,
     pub survival_rate: f32,
+    pub elitism_rate: f32,
 }
 
 impl Extension for MassExtinction {
@@ -35,16 +37,37 @@ impl Extension for MassExtinction {
                         state,
                         config,
                     );
+                    let population_size = state.population.size();
+
+                    let elitism_size = ((population_size as f32 * self.elitism_rate).ceil()
+                        as usize)
+                        .min(population_size);
+                    let mut elite_chromosomes =
+                        self.extract_elite_chromosomes(state, config, elitism_size);
+                    let elitism_size = elite_chromosomes.len();
+
+                    let remaining_size: usize = ((population_size as f32 * self.survival_rate)
+                        .ceil() as usize)
+                        .min(population_size)
+                        .max(2);
+
+                    let remaining_size = remaining_size.saturating_sub(elitism_size);
 
-                    let remaining_size: usize = std::cmp::max(
-                        (state.population.size() as f32 * self.survival_rate).ceil() as usize,
-                        2,
-                    );
                     state.population.shuffle(rng);
                     genotype.chromosome_destructor_truncate(
                         &mut state.population.chromosomes,
                         remaining_size,
                     );
+
+                    state.population.chromosomes.append(&mut elite_chromosomes);
+                    let population_size = state.population.size();
+                    // move back to front, elite_chromosomes internally unordered
+                    for i in 0..elitism_size {
+                        state
+                            .population
+                            .chromosomes
+                            .swap(i, population_size - 1 - i);
+                    }
                 }
             }
             state.add_duration(StrategyAction::Extension, now.elapsed());
@@ -53,10 +76,11 @@ impl Extension for MassExtinction {
 }
 
 impl MassExtinction {
-    pub fn new(cardinality_threshold: usize, survival_rate: f32) -> Self {
+    pub fn new(cardinality_threshold: usize, survival_rate: f32, elitism_rate: f32) -> Self {
         Self {
             cardinality_threshold,
             survival_rate,
+            elitism_rate,
         }
     }
 }

src/extension/mass_genesis.rs

@@ -34,22 +34,17 @@ impl Extension for MassGenesis {
                         state,
                         config,
                     );
-                    if let Some(best_chromosome_index) = state
-                        .population
-                        .best_chromosome_index(config.fitness_ordering)
-                    {
-                        let best_chromosome = state
-                            .population
-                            .chromosomes
-                            .swap_remove(best_chromosome_index);
-                        genotype
-                            .chromosome_destructor_truncate(&mut state.population.chromosomes, 0);
-                        state
-                            .population
-                            .chromosomes
-                            .push(genotype.chromosome_cloner(&best_chromosome));
-                        state.population.chromosomes.push(best_chromosome);
-                    }
+
+                    let mut elite_chromosomes = self.extract_elite_chromosomes(state, config, 2);
+                    let elitism_size = elite_chromosomes.len();
+
+                    let remaining_size = 2usize.saturating_sub(elitism_size);
+
+                    genotype.chromosome_destructor_truncate(
+                        &mut state.population.chromosomes,
+                        remaining_size,
+                    );
+                    state.population.chromosomes.append(&mut elite_chromosomes);
                 }
             }
             state.add_duration(StrategyAction::Extension, now.elapsed());

src/population.rs

@@ -77,18 +77,22 @@ impl<C: Chromosome> Population<C> {
             .enumerate()
             .collect();
 
-        let index = amount.min(data.len().saturating_sub(1));
-        let (lesser, _median, _greater) = match fitness_ordering {
-            FitnessOrdering::Maximize => {
-                data.select_nth_unstable_by_key(index, |(_, score)| Reverse(*score))
-            }
-            FitnessOrdering::Minimize => {
-                data.select_nth_unstable_by_key(index, |(_, score)| *score)
-            }
-        };
-        let mut result: Vec<usize> = lesser.iter().map(|(idx, _)| *idx).collect();
-        result.sort_unstable();
-        result
+        if data.is_empty() {
+            Vec::new()
+        } else {
+            let index = amount.min(data.len().saturating_sub(1));
+            let (lesser, _median, _greater) = match fitness_ordering {
+                FitnessOrdering::Maximize => {
+                    data.select_nth_unstable_by_key(index, |(_, score)| Reverse(*score))
+                }
+                FitnessOrdering::Minimize => {
+                    data.select_nth_unstable_by_key(index, |(_, score)| *score)
+                }
+            };
+            let mut result: Vec<usize> = lesser.iter().map(|(idx, _)| *idx).collect();
+            result.sort_unstable();
+            result
+        }
     }
 
     pub fn age_mean(&self) -> f32 {

src/strategy.rs

@@ -41,7 +41,7 @@
 //! let builder = StrategyBuilder::new()
 //!     .with_genotype(genotype)                                // (E,H,P) the genotype
 //!     .with_select(SelectElite::new(0.5, 0.02))               // (E) sort the chromosomes by fitness to determine crossover order. Strive to replace 50% of the population with offspring. Allow 2% through the non-generational best chromosomes gate before selection and replacement
-//!     .with_extension(ExtensionMassExtinction::new(10, 0.1))  // (E) optional builder step, simulate cambrian explosion by mass extinction, when population cardinality drops to 10 after the selection, trim to 10% of population
+//!     .with_extension(ExtensionMassExtinction::new(10, 0.1, 0.02))  // (E) optional builder step, simulate cambrian explosion by mass extinction, when population cardinality drops to 10 after the selection, trim to 10% of population
 //!     .with_crossover(CrossoverUniform::new(0.7, 0.8))        // (E) crossover all individual genes between 2 chromosomes for offspring with 70% parent selection (30% do not produce offspring) and 80% chance of crossover (20% of parents just clone)
 //!     .with_mutate(MutateSingleGene::new(0.2))                // (E) mutate offspring for a single gene with a 20% probability per chromosome
 //!     .with_fitness(CountTrue)                                // (E,H,P) count the number of true values in the chromosomes

src/strategy/evolve.rs

@@ -146,7 +146,7 @@ pub enum EvolveVariant {
 ///     .with_genotype(genotype)
 ///
 ///     .with_select(SelectElite::new(0.5, 0.02))               // sort the chromosomes by fitness to determine crossover order. Strive to replace 50% of the population with offspring. Allow 2% through the non-generational best chromosomes gate before selection and replacement
-///     .with_extension(ExtensionMassExtinction::new(10, 0.1))  // optional builder step, simulate cambrian explosion by mass extinction, when population cardinality drops to 10 after the selection, trim to 10% of population
+///     .with_extension(ExtensionMassExtinction::new(10, 0.1, 0.02))  // optional builder step, simulate cambrian explosion by mass extinction, when population cardinality drops to 10 after the selection, trim to 10% of population
 ///     .with_crossover(CrossoverUniform::new(0.7, 0.8))        // crossover all individual genes between 2 chromosomes for offspring with 70% parent selection (30% do not produce offspring) and 80% chance of crossover (20% of parents just clone)
 ///     .with_mutate(MutateSingleGene::new(0.2))                // mutate offspring for a single gene with a 20% probability per chromosome
 ///     .with_fitness(CountTrue)                                // count the number of true values in the chromosomes