nature.core — org.clojars.btezergil/nature 1.3.0

evolve clj/s

(evolve allele-set
        genome-length
        population-size
        generations
        fitness-function
        binary-operators
        unary-operators)

(evolve allele-set
        genome-length
        population-size
        generations
        fitness-function
        binary-operators
        unary-operators
        options)

Create and evolve a population under the specified conditions until a termination criteria is reached allele-set is a collection of legal genome values genome-length is the enforced size of each genetic sequence population-size is the enforced number of individuals that will be created generations is the number of iterations the algorithm will cycle through fitness-function is a partial function accepting generated sequences to evaluate solution qualities binary-operators is a collection of partial functions accepting and returning 1 or more individuals unary-operators is a collection of partial functions accepting and returning exactly 1 individual options an optional map of pre-specified keywords to values that further tune the behavior of nature. Current examples follow: :carry-over an integer representing the top n individuals to be carried over between each generation. Default is 1 :solutions an integer representing the top n individuals to return after evolution completes. Default is 1 :monitors a sequence of functions, assumed to be side-effectful, to be executed against population and current-genration for run-time stats. Default is nil

evolve-cooperatively clj/s

(evolve-cooperatively species-a species-b generations collaboration-fitness-fn)

(evolve-cooperatively species-a
                      species-b
                      generations
                      collaboration-fitness-fn
                      options)

Evolve two populations whose contextual fitness comes from collaboration.

Each species configuration contains :species-id, :population-size, :genome-generator, :binary-operators, and :unary-operators; optional :carry-over and :insert-new values default to 1 and 0. Binary operators accept two genomes and return one or more child genomes. Unary operators accept and return one genome. collaboration-fitness-fn accepts one genome from each species (in argument order) and returns a finite numeric score.

Options are :collaboration-mode (:balanced, the default, :cartesian, or :panel), :opponents (K for balanced scheduling, default 1), :final-ratio (default 1.0), :final-evaluation-fn, and :monitors. Final evaluators accept the two genomes and may return any value. Each monitor accepts the complete state map.

All collaboration modes accept :credit-policy (default :mean): :maximum, :top-two-mean, :weighted (with :credit-weights), or a custom context-to-finite-scalar callback. See nature.credit and README for the contract.

Panel mode accepts a non-empty :panel-selection-fns sequence, defaulting when omitted to one random member. Generation zero uses random bootstrap panels; selectors use each completed scored population and bounded historical champions to build the next panels. See nature.panel-selectors for selector functions and README for context keys.

evolve-with-sequence-generator clj/s

(evolve-with-sequence-generator generator-function
                                population-size
                                generations
                                fitness-function
                                binary-operators
                                unary-operators)

(evolve-with-sequence-generator generator-function
                                population-size
                                generations
                                fitness-function
                                binary-operators
                                unary-operators
                                options)

Same with evolve method, but takes a sequence generator function instead of an allele set and genome length. This method uses the sequence generator function to generate sequences for the initial population. :initial-population-retries optionally rebuilds the initial population when every fitness score is zero. Default is 0.