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Add ExtensionMassDeduplication
1 parent 9af7006 commit 7b982c7

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+286
-19
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11 files changed

+286
-19
lines changed

‎README.md

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@@ -194,6 +194,10 @@ Find the flamegraph in: `./target/criterion/profile_evolve_binary/profile/flameg
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* Add simulated annealing strategy
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* Add Roulette selection with and without duplicates (with fitness ordering)
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* Add OrderOne crossover for UniqueGenotype?
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* Order Crossover (OX): Simple and works well for many permutation problems.
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* Partially Mapped Crossover (PMX): Preserves more of the parent's structure but is slightly more complex.
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* Cycle Crossover (CX): Ensures all genes come from one parent, useful for strict preservation of order.
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* Edge Crossover (EX): Preserves adjacency relationships, suitable for Traveling Salesman Problem or similar.
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* Add WholeArithmetic crossover for RangeGenotype?
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* Add CountTrueWithWork instead of CountTrueWithSleep for better benchmarks?
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* Explore more non-Vec genes: PackedSimd?

‎benches/extension.rs

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@@ -50,6 +50,7 @@ pub fn criterion_benchmark(c: &mut Criterion) {
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let extensions: Vec<ExtensionWrapper> = vec![
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ExtensionMassGenesis::new(population_size).into(),
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ExtensionMassExtinction::new(population_size, 0.10, 0.02).into(),
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ExtensionMassDeduplication::new(population_size).into(),
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ExtensionMassDegeneration::new(population_size, 10, 0.02).into(),
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];
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for mut extension in extensions {

‎src/extension.rs

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@@ -4,12 +4,14 @@
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//! selected for, killing of the offspring again. This reduces the efficiency, but also has the
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//! risk of local optimum lock-in. To increase the variation in the population, an
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//! [extension](crate::extension) mechanisms can optionally be used
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mod mass_deduplication;
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mod mass_degeneration;
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mod mass_extinction;
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mod mass_genesis;
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mod noop;
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mod wrapper;
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pub use self::mass_deduplication::MassDeduplication as ExtensionMassDeduplication;
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pub use self::mass_degeneration::MassDegeneration as ExtensionMassDegeneration;
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pub use self::mass_extinction::MassExtinction as ExtensionMassExtinction;
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pub use self::mass_genesis::MassGenesis as ExtensionMassGenesis;
@@ -53,6 +55,7 @@ pub trait Extension: Clone + Send + Sync + std::fmt::Debug {
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#[derive(Clone, Debug)]
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pub enum ExtensionEvent {
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MassDeduplication(String),
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MassDegeneration(String),
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MassExtinction(String),
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MassGenesis(String),

‎src/extension/mass_deduplication.rs

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@@ -0,0 +1,86 @@
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use super::{Extension, ExtensionEvent};
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use crate::chromosome::{Chromosome, GenesHash};
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use crate::genotype::EvolveGenotype;
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use crate::strategy::evolve::{EvolveConfig, EvolveState};
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use crate::strategy::{StrategyAction, StrategyReporter, StrategyState};
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use rand::Rng;
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use std::collections::hash_map::Entry;
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use std::collections::HashMap;
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use std::time::Instant;
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/// Simulates a cambrian explosion. The controlling metric is population cardinality in the
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/// population after selection. When this cardinality drops to the threshold, the population is
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/// reduced to only the unique individuals. Only works when genes_hash is stored on chromosome, as
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/// this is the uniqueness key, otherwise the extension is ignored.
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///
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/// Population will recover in the following generations
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#[derive(Debug, Clone)]
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pub struct MassDeduplication {
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pub cardinality_threshold: usize,
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}
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impl Extension for MassDeduplication {
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fn call<G: EvolveGenotype, R: Rng, SR: StrategyReporter<Genotype = G>>(
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&mut self,
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genotype: &mut G,
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state: &mut EvolveState<G>,
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config: &EvolveConfig,
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reporter: &mut SR,
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_rng: &mut R,
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) {
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if genotype.genes_hashing() && state.population.size() >= config.target_population_size {
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let now = Instant::now();
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// ensures min 1
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if let Some(cardinality) = state.population_cardinality() {
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if cardinality <= self.cardinality_threshold {
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reporter.on_extension_event(
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ExtensionEvent::MassDeduplication("".to_string()),
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genotype,
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state,
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config,
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);
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let mut selected_chromosomes: HashMap<GenesHash, G::Chromosome> =
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HashMap::new();
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state
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.population
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.chromosomes
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.drain(..)
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.for_each(|chromosome| {
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if let Some(genes_hash) = chromosome.genes_hash() {
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match selected_chromosomes.entry(genes_hash) {
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Entry::Occupied(_) => {
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genotype.chromosome_destructor(chromosome);
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}
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Entry::Vacant(entry) => {
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entry.insert(chromosome);
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}
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}
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} else {
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genotype.chromosome_destructor(chromosome);
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}
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});
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state
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.population
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.chromosomes
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.extend(selected_chromosomes.into_values());
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// ensures min 2
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if state.population.size() == 1 {
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genotype.chromosome_cloner_expand(&mut state.population.chromosomes, 1);
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}
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}
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}
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state.add_duration(StrategyAction::Extension, now.elapsed());
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}
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}
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}
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impl MassDeduplication {
81+
pub fn new(cardinality_threshold: usize) -> Self {
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Self {
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cardinality_threshold,
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}
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}
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}

‎src/extension/mass_degeneration.rs

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@@ -6,9 +6,9 @@ use rand::Rng;
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use std::time::Instant;
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/// Simulates a cambrian explosion. The controlling metric is population cardinality in the
9-
/// population after selection. When this cardinality drops to the threshold, the population
10-
/// (except for the two best chromosomes) is mutated the provided number of times, where the
11-
/// [Genotype](crate::genotype::Genotype) determines whether this is random, relative or scaled.
9+
/// population after selection. When this cardinality drops to the threshold, the population is
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/// mutated the provided number of times, where the [Genotype](crate::genotype::Genotype)
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/// determines whether this is random, relative or scaled.
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/// The elitism_rate ensures the passing of the best chromosomes before mutations are applied.
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///
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/// Duplicate mutations of the same gene are allowed. There is no change in population size.

‎src/extension/wrapper.rs

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@@ -1,3 +1,4 @@
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pub use super::mass_deduplication::MassDeduplication as ExtensionMassDeduplication;
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pub use super::mass_degeneration::MassDegeneration as ExtensionMassDegeneration;
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pub use super::mass_extinction::MassExtinction as ExtensionMassExtinction;
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pub use super::mass_genesis::MassGenesis as ExtensionMassGenesis;
@@ -11,10 +12,11 @@ use rand::Rng;
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#[derive(Clone, Debug)]
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pub enum Wrapper {
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Noop(ExtensionNoop),
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MassDeduplication(ExtensionMassDeduplication),
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MassDegeneration(ExtensionMassDegeneration),
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MassExtinction(ExtensionMassExtinction),
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MassGenesis(ExtensionMassGenesis),
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MassDegeneration(ExtensionMassDegeneration),
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Noop(ExtensionNoop),
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}
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2022
impl Extension for Wrapper {
@@ -27,23 +29,31 @@ impl Extension for Wrapper {
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rng: &mut R,
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) {
2931
match self {
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Wrapper::Noop(extension) => extension.call(genotype, state, config, reporter, rng),
31-
Wrapper::MassExtinction(extension) => {
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Wrapper::MassDeduplication(extension) => {
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extension.call(genotype, state, config, reporter, rng)
3334
}
34-
Wrapper::MassGenesis(extension) => {
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Wrapper::MassDegeneration(extension) => {
3536
extension.call(genotype, state, config, reporter, rng)
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}
37-
Wrapper::MassDegeneration(extension) => {
38+
Wrapper::MassExtinction(extension) => {
3839
extension.call(genotype, state, config, reporter, rng)
3940
}
41+
Wrapper::MassGenesis(extension) => {
42+
extension.call(genotype, state, config, reporter, rng)
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}
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Wrapper::Noop(extension) => extension.call(genotype, state, config, reporter, rng),
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}
4146
}
4247
}
4348

44-
impl From<ExtensionNoop> for Wrapper {
45-
fn from(extension: ExtensionNoop) -> Self {
46-
Wrapper::Noop(extension)
49+
impl From<ExtensionMassDeduplication> for Wrapper {
50+
fn from(extension: ExtensionMassDeduplication) -> Self {
51+
Wrapper::MassDeduplication(extension)
52+
}
53+
}
54+
impl From<ExtensionMassDegeneration> for Wrapper {
55+
fn from(extension: ExtensionMassDegeneration) -> Self {
56+
Wrapper::MassDegeneration(extension)
4757
}
4858
}
4959
impl From<ExtensionMassExtinction> for Wrapper {
@@ -56,8 +66,8 @@ impl From<ExtensionMassGenesis> for Wrapper {
5666
Wrapper::MassGenesis(extension)
5767
}
5868
}
59-
impl From<ExtensionMassDegeneration> for Wrapper {
60-
fn from(extension: ExtensionMassDegeneration) -> Self {
61-
Wrapper::MassDegeneration(extension)
69+
impl From<ExtensionNoop> for Wrapper {
70+
fn from(extension: ExtensionNoop) -> Self {
71+
Wrapper::Noop(extension)
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}
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}

‎src/strategy/evolve/prelude.rs

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@@ -11,8 +11,8 @@ pub use crate::crossover::{
1111
};
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#[doc(no_inline)]
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pub use crate::extension::{
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ExtensionEvent, ExtensionMassDegeneration, ExtensionMassExtinction, ExtensionMassGenesis,
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ExtensionNoop, ExtensionWrapper,
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ExtensionEvent, ExtensionMassDeduplication, ExtensionMassDegeneration, ExtensionMassExtinction,
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ExtensionMassGenesis, ExtensionNoop, ExtensionWrapper,
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};
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#[doc(no_inline)]
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pub use crate::fitness::{

‎src/strategy/evolve/reporter.rs

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@@ -260,6 +260,11 @@ impl<G: EvolveGenotype> StrategyReporter for Simple<G> {
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self.number_of_extension_events += 1;
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if self.show_extension_event {
262262
match event {
263+
ExtensionEvent::MassDeduplication(message) => self.writeln(format_args!(
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"extension event - mass deduplication - generation {} - {}",
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state.current_generation(),
266+
message
267+
)),
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ExtensionEvent::MassDegeneration(message) => self.writeln(format_args!(
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"extension event - mass degeneration - generation {} - {}",
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state.current_generation(),

‎src/strategy/prelude.rs

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@@ -11,8 +11,8 @@ pub use crate::crossover::{
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};
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#[doc(no_inline)]
1313
pub use crate::extension::{
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ExtensionEvent, ExtensionMassDegeneration, ExtensionMassExtinction, ExtensionMassGenesis,
15-
ExtensionNoop, ExtensionWrapper,
14+
ExtensionEvent, ExtensionMassDeduplication, ExtensionMassDegeneration, ExtensionMassExtinction,
15+
ExtensionMassGenesis, ExtensionNoop, ExtensionWrapper,
1616
};
1717
#[doc(no_inline)]
1818
pub use crate::fitness::{

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