genetic-algorithm

A genetic algorithm implementation for Rust. Inspired by the book Genetic Algorithms in Elixir

There are three main elements to this approach:

• The Genotype (the search space)
• The Fitness function (the search goal)
• The strategy (the search strategy)
  • Evolve (evolution strategy)
  • Permutate (for small search spaces, with a 100% guarantee)
  • HillClimb (when search space is convex with little local optima or when crossover is impossible/inefficient)

Terminology:

• Population: a population has population_size number of individuals (called chromosomes).
• Chromosome: a chromosome has genes_size number of genes
• Allele: alleles are the possible values of the genes
• Gene: a gene is a combination of position in the chromosome and value of the gene (allele)
• Genes: storage trait of the genes for a chromosome, always Vec<Allele>
• Genotype: Knows how to generate, mutate and crossover chromosomes efficiently
• Fitness: knows how to determine the fitness of a chromosome

All multithreading mechanisms are implemented using rayon::iter and std::sync::mpsc.

Documentation

See docs.rs

Quick Usage

use genetic_algorithm::strategy::evolve::prelude::*;

// the search space
let genotype = BinaryGenotype::builder() // boolean alleles
    .with_genes_size(100)                // 100 genes per chromosome
    .build()
    .unwrap();

println!("{}", genotype);

// the search goal to optimize towards (maximize or minimize)
#[derive(Clone, Debug)]
pub struct CountTrue;
impl Fitness for CountTrue {
    type Genotype = BinaryGenotype; // Genes = Vec<bool>
    fn calculate_for_chromosome(
        &mut self, 
        chromosome: &FitnessChromosome<Self>, 
        _genotype: &FitnessGenotype<Self>
    ) -> Option<FitnessValue> {
        Some(chromosome.genes.iter().filter(|&value| *value).count() as FitnessValue)
    }
}

// the search strategy
let evolve = Evolve::builder()
    .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_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
    .with_fitness_ordering(FitnessOrdering::Maximize) // optional, default is Maximize, aim towards the most true values
    .with_target_population_size(100)                 // evolve with 100 chromosomes
    .with_target_fitness_score(100)                   // goal is 100 times true in the best chromosome
    .with_reporter(EvolveReporterSimple::new(100))    // optional builder step, report every 100 generations
    .call();
    .unwrap()

println!("{}", evolve);

// it's all about the best genes after all
let (best_genes, best_fitness_score) = evolve.best_genes_and_fitness_score().unwrap();
assert_eq!(best_genes, vec![true; 100]);
assert_eq!(best_fitness_score, 100);

Examples

Run with cargo run --example [EXAMPLE_BASENAME] --release

• N-Queens puzzle https://en.wikipedia.org/wiki/Eight_queens_puzzle.
  • See examples/evolve_nqueens
  • See examples/hill_climb_nqueens
  • UniqueGenotype<u8> with a 64x64 chess board setup
  • custom NQueensFitness fitness
• Knapsack problem: https://en.wikipedia.org/wiki/Knapsack_problem
  • See examples/evolve_knapsack
  • See examples/permutate_knapsack
  • BinaryGenotype<Item(weight, value)> each gene encodes presence in the knapsack
  • custom KnapsackFitness(&items, weight_limit) fitness
• Infinite Monkey theorem: https://en.wikipedia.org/wiki/Infinite_monkey_theorem
  • See examples/evolve_monkeys
  • ListGenotype<char> 100 monkeys randomly typing characters in a loop
  • custom fitness using hamming distance
• Permutation strategy instead of Evolve strategy for small search spaces, with a 100% guarantee
  • See examples/permutate_knapsack
• HillClimb strategy instead of Evolve strategy, when crossover is impossible or inefficient
  • See examples/hill_climb_nqueens
  • See examples/hill_climb_table_seating
• Explore internal and external multithreading options
  • See examples/explore_multithreading
• Use superset StrategyBuilder for easier switching in implementation
  • See examples/explore_strategies
• Use fitness LRU cache
  • See examples/evolve_binary_cache_fitness
  • Note: doesn't help performance much in this case... or any case, better fix your population diversity
• Custom Reporting implementation
  • See examples/permutate_scrabble
• Custom Mutate implementation
  • See examples/evolve_milp_custom_mutate

Performance considerations

For the Evolve strategy:

• Reporting: start with EvolveReporterSimple for basic understanding of:
  • fitness v. framework overhead
  • staleness and population characteristics (cardinality etc.)
• Select: no considerations. All selects are basically some form of in-place sorting of some kind based on chromosome metadata. This is relatively fast compared to the rest of the operations.
• Crossover: the workhorse of internal parts. Crossover touches most genes each generation, calculates genes hashes and clones up to the whole population to produce offspring (depending on selection-rate).
• Mutate: no considerations. It touches genes like crossover does, but should be used sparingly anyway; with low gene counts (<10%) and low probability (5-20%)
• Fitness: can be anything, but usually very dominant (>80% total time). This fully depends on the user domain. Parallelize it using with_par_fitness() in the Builder. But beware that parallelization has it's own overhead and is not always faster.

So framework overhead is mostly Crossover. Practical overhead is mostly Fitness.

Regarding the optionality of genes hashing and chromosomes recycling: For large chromosomes, disabling chromosome recycling and enabling genes hashing leads to a 3x factor in framework overhead. For small chromosomes, neither feature has overhead effects. But do keep in mind that for large chromosomes the Fitness calculation will be even more dominant with regards to the framework overhead as it already is. See examples/evolve_large_genotype

Default configuration for correctness AND performance

• .with_genes_hashing(true) // Required for proper GA dynamics
• .with_chromosome_recycling(true) // Still worth it for large chromosomes, maybe disable for easier custom implementations

Tests

Run tests with cargo test

Use .with_rng_seed_from_u64(0) builder step to create deterministic tests results.

Benchmarks

Implemented using criterion. Run benchmarks with cargo bench

Profiling

Implemented using criterion and pprof.

Uncomment in Cargo.toml

[profile.release]
debug = 1

Run with cargo run --example profile_evolve_binary --release -- --bench --profile-time 5

Find the flamegraph in: ./target/criterion/profile_evolve_binary/profile/flamegraph.svg

TODO

MAYBE

• Consider dropping .with_genes_hashing() and always set to true, because it is needed for proper GA functionality regardless the overhead
• Consider dropping .with_chromosome_recycling() and always set to false (stripping the recycling completely), because it is complicated and risky for custom Crossover implementations and maybe framework overhead simply doesn't matter as much with regards to Fitness overhead
• Target cardinality range for Mutate Dynamic to avoid constant switching (noisy in reporting events)
• Add scaling helper function
• Add simulated annealing strategy
• Add Roulette selection with and without duplicates (with fitness ordering)
• Add OrderOne crossover for UniqueGenotype?
  • Order Crossover (OX): Simple and works well for many permutation problems.
  • Partially Mapped Crossover (PMX): Preserves more of the parent's structure but is slightly more complex.
  • Cycle Crossover (CX): Ensures all genes come from one parent, useful for strict preservation of order.
  • Edge Crossover (EX): Preserves adjacency relationships, suitable for Traveling Salesman Problem or similar.
• Add WholeArithmetic crossover for RangeGenotype?
• Add CountTrueWithWork instead of CountTrueWithSleep for better benchmarks?
• StrategyBuilder, with_par_fitness_threshold, with_permutate_threshold?
• Add target fitness score to Permutate? Seems illogical, but would be symmetrical. Don't know yet
• Add negative selection-rate to encode in-place crossover? But do keep the old extend with best-parents with the pre v0.20 selection-rate behaviour which was crucial for evolve_nqueens

ISSUES

ARCHIVE

• archive/centralized-gpu-experiment branch is archived for now, as zero-copy transfer of genes to GPU proved impractical in practice