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Remove rather than filling empty genes.

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This commit is contained in:
Lee Spector 2023-12-26 17:27:41 -05:00
parent feb5a52d25
commit d8402962f1
3 changed files with 8 additions and 12 deletions
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2
src/propeller/genome.cljc
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@ -12,7 +12,7 @@ They hold the genetic material for an `individual`. In the initial population, w
#(utils/random-instruction instructions))] #(utils/random-instruction instructions))]
(if bmx? (if bmx?
(-> plushy (-> plushy
(utils/fill-empty-genes instructions) (utils/remove-empty-genes)
(utils/enforce-gene-length-limit bmx-gene-length-limit)) (utils/enforce-gene-length-limit bmx-gene-length-limit))
plushy))) plushy)))

14
src/propeller/utils.cljc
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@ -198,17 +198,13 @@
(+ (* 0.5 (metrics/multiset-distance p1 p2)) (+ (* 0.5 (metrics/multiset-distance p1 p2))
(math/abs (- (count p1) (count p2))))) (math/abs (- (count p1) (count p2)))))
(defn fill-empty-genes (defn remove-empty-genes
"A utility function for bmx-related genetic operators. Returns the provided "A utility function for bmx-related genetic operators. Returns the provided
plushy with any empty genes (regions before/between/after instances of :gap) plushy with any empty genes (regions before/between/after instances of :gap)
filled with a new random instruction." removed."
[plushy instructions] [plushy]
(flatten (interpose :gap (vec (flatten (interpose :gap (filter #(not (empty? %))
(mapv (fn [gene] (extract-genes plushy))))))
(if (empty? gene)
(random-instruction instructions)
gene))
(extract-genes plushy)))))
(defn break-up (defn break-up
"A utility function for bmx-related genetic operators. Returns the provided "A utility function for bmx-related genetic operators. Returns the provided

4
src/propeller/variation.cljc
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@ -244,7 +244,7 @@ The function `new-individual` returns a new individual produced by selection and
(-> (bmx plushy1 plushy2 bmx-exchange-rate max-distance argmap) (-> (bmx plushy1 plushy2 bmx-exchange-rate max-distance argmap)
(uniform-gap-addition gap-change-prob) (uniform-gap-addition gap-change-prob)
(uniform-gap-deletion gap-change-prob) (uniform-gap-deletion gap-change-prob)
(utils/fill-empty-genes (:instructions argmap)) (utils/remove-empty-genes)
(utils/enforce-gene-length-limit (:bmx-gene-length-limit argmap)))) (utils/enforce-gene-length-limit (:bmx-gene-length-limit argmap))))
; ;
:umad ;; uniform mutation by addition and deletion, see uniform-deletion for the :umad ;; uniform mutation by addition and deletion, see uniform-deletion for the
@ -277,7 +277,7 @@ The function `new-individual` returns a new individual produced by selection and
(uniform-gap-deletion gap-change-prob) (uniform-gap-deletion gap-change-prob)
(uniform-addition (:instructions argmap) umad-rate) (uniform-addition (:instructions argmap) umad-rate)
(uniform-deletion umad-rate) (uniform-deletion umad-rate)
(utils/fill-empty-genes (:instructions argmap)) (utils/remove-empty-genes)
(utils/enforce-gene-length-limit (:bmx-gene-length-limit argmap)))) (utils/enforce-gene-length-limit (:bmx-gene-length-limit argmap))))
; ;
:rumad ;; responsive UMAD, uses a deletion rate computed from the actual :rumad ;; responsive UMAD, uses a deletion rate computed from the actual