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Author
Last Commit
Sep. 18, 2018
Created
Apr. 13, 2018

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Evolute

Evolutionary algorithm toolbox

Documentation

Evolute is a simple tool for quick experimentation with evolutionary algorithms for numerical optimization.

It defines a population of individuals, represented as floating point vectors, and applies a configurable set of evolutionary operators to them in a predefined order.

The order is the following:

  1. Selection: a subset of individuals are discarded, depending on their fitness value
  2. Reproduction: the discarded individuals are replaced by new individuals, somehow generated from the survivors
  3. Mutation: mutate some of the individuals
  4. Update: update the fitnesses of the individuals

Some nomenclature:

  • individual: a single member of the population.
  • genotype: refers to an individual in the encoded state. Evolute encodes information in floating point vectors.
  • locus: a member of a genotype (a single scalar in the vector)
  • phenotype: refers to an individual in the decoded state. In the case of neuroevolution, this would be a neural network object, which is encoded as a genotype. Evolute is not doing any genotype - phenotype conversion, this has to be implemented by the user in the fitness calculation.

Module: population

Defines containers for individuals and aggregates the operators applied to them. Currently the following population types are defined:

  • GeneticPopulation: can be used for genetic algorithms, simply evaluates the fitnesses and applies the operators in the above specified order. Its constructor accepts the following arguments:
    • loci: number of elements in an individual's chromosome
    • fitness_wrapper: instance of a class in evolute.evaluation
    • limit: maximum number of individuals, defaults to 100
    • operators: an instance of evolute.operators.Operators, see operators later
    • initializer: instance of a class defined in evolute.initialization, optional

Will add support for MemeticPopulation, which allows for explicit modification of the individuals during fitness calculation

An evolutionary optimization can be run using the population.run() method, which accepts the following arguments:

  • epochs: how many iterations should be done
  • survival_rate: reset survival rate
  • mutation_rate: reset mutation rate
  • force_update_at_every: at every kth iteration, force a complete fitness-recalculation
  • verbosity: 0 is silent, > 0 is verbose.
  • history: evolute.utils.history.History object, in which runtime metrics can be recorded. If omitted, one is instantiated implicitly.

The run() method returns a history object with generation, best_grade, mean_grade and grade_stdev recorded by default.

A population can be saved and loaded with the save() and load() methods, which produces a gzip-compressed pickle of the Population object.

Single epoch can be also run with the epoch() method and an update can be forced with the update() method.

For convenience, these methods are defined:

  • epoch(): use this to evaluate a single epoch
  • update(): forces a fitness update
  • simple_fitness(): class factory method, which takes a nude fitness function and wraps it implicitly with SimpleFitness (see below).
  • get_individual(index)
  • set_indivudual(index, individual)
  • get_best(): the current best individual with the lowest fitness/grade
  • get_champion: the all-time best individual is alway stored implicitly, and can be accessed here.

Module: evaluation

Defines different wrappers for fitness functions. Fitness is a scalar value assigned to every individual. Currently in Evolute, the lower fitness is the better.

Since a fitness function can be any kind of logic, fitness wrappers expect a function pointer or some kind of callable. Some advanced wrappers are there to support possibly multiple fitness functions or functions with multiple return values. In the end, the fitness has to be reduced to a single scalar.

The process of combining multiple fitnesses to a single scalar is termed grading in Evolute.

Fitness wrappers

Currently the following fitness wappers are defined in evolute.evaluation:

  • SimpleFitness: wraps a simple function with a single scalar return value. Its constructor expects the following arguments:
    • fitness_function: a function reference or callable object
    • constants: optional dictionary of constants to be passed by name

Variables may be passed to the fitness function during the running of the algorithm.

  • MultipleFitnesses: wraps multiple fitness functions. The constructor expects the following arguments:

    • functions_by_name: dictionary of fitness function references or callable objects. They need to be identified by a unique name or ID
    • contants_by_function_name: optional dictionary of arguments (as dicts as well). They have to be referenced by the same name or ID.
    • order_by_name: optional, an ordered iterable of the IDs if call order matters.
    • grader: grader object or any callable which takes the array of fitnesses and produces a single scalar grade from them. Defaults to simple summation.
  • MultiReturnFitness: wrapper for a single fitness function which returns multiple fitness values. The constructor expects the following arguments:

    • number_of_return_values
    • constants: optional
    • grader: optional, defaults to simple summation

Graders

More advanced fitness wrappers expect a Grader instance defined in evolute.evaluation.grade or any callable which accepts a NumPy array and returns a single scalar.

Some graders are available in evolute.evaluation:

  • SumGrader: simply sums the fitness values
  • WeightedSumGrader: accepts a set of weights in its constructor and produces a weighted sum (dot product) with the fitness values.

Module: initialization

This module defines initializers: objects for random population initialization strategies. Currently the following distributions are available in evolute.initialization:

  • NormalRandom: with customizable mean and stdev
  • UniformRandom: with customizable low and high
  • OrthogonalNormal: produces a diagonal random matrix

Module: operators

Evolutionary operators are defined here. This module defines an Operators class, which aggregates all the operators needed to run an evolutionary optimization. Operators' constructor takes the following arguments:

  • selection_op
  • mutate_op
  • mate_op

Submodules define the particular operator types, which are the following:

Selection

During selection, a subset of individuals are discarded. The logic by which these are specified depends on the actual implementation:

  • Elitism: selects the top m% of individuals. Its constructor accepts the following arguments:
    • selection_rate: scalar between 0 and 1 to specify the rate of discarded individuals
    • mate_op: a mate operator, which is used to fill up the slots where individuals are missing (applies reproduction). Details on these later.
    • exclude_self_mating: bool, whether to disallow mating an individual with itself

If no selection operator is defined, every selection-using class defaults to Elitism.

Mate

Mating is defined as some kind of combination of two individuals to reproduce a new individual. Currently the following mate operators are defined:

  • LambdaMate: wraps a user-defined function, which takes two individuals and produces a single individual
  • RandomPickMate: randomly pics loci from the two genotypes
  • SmoothMate: takes the mean of the two genotypes
  • ScatterMateWrapper: wrapper for any mate operator. When applied, it adds gaussian noise to the new individual. Its constructor expects the following parameters:
    • base: reference to the base mate operator object
    • stdev: standard deviation of the additive gaussian noise

If no mate operator is defined, every mate-using class defaults to RandomPickMate.

Mutate

This operator takes the whole population and mutates its individuals by perturbing them with some kind of noise. The following mutation operators are available:

  • UniformLocuswiseMutation: adds uniform distributed noise to individuals. Mutants are determined on the locus level, and mutation rate (see below) is adjusted for this. Its constructor takes the following arguments:
    • rate: rate by which mutations occur in the population. It has to be given as a rate of individuals but it is implicitly corrected for loci.
    • low and high: parameters of the uniform distribution
  • NormalIndividualwiseMutation: adds normal random noise to individuals. Mutants are determined on the individuals' level. Its constructor takes the following arguments:
    • rate
    • stdev

If no mutate operator is defined, every mutate-using class defaults to UniformLocuswiseMutation.

Module: utility

Some useful stuff here. Maybe the most interesting is the evolute.keras_utility module, which defines some helpers to interface with Keras and do some Neuroevolution on the weights of a network.