Switch to normalized autoconstructive hypervariation; reformat
This commit is contained in:
Lee Spector
parent
adf039195c
commit
37df3432fb
@ -23,29 +23,18 @@
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[evaluations pop generation argmap training-data]
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(let [best (first pop)]
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(clojure.pprint/pprint
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(merge {:generation generation
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:best-plushy (:plushy best)
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:best-program (genome/plushy->push (:plushy best) argmap)
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:best-total-error (:total-error best)
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:evaluations evaluations
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:ds-indices (map #(:index %) training-data)
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:best-errors (:errors best)
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:best-behaviors (:behaviors best)
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:genotypic-diversity (float (/ (count (distinct (map :plushy pop))) (count pop)))
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:behavioral-diversity (float (/ (count (distinct (map :behaviors pop))) (count pop)))
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:average-genome-length (float (/ (reduce + (map count (map :plushy pop))) (count pop)))
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:average-total-error (float (/ (reduce + (map :total-error pop)) (count pop)))}
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(if (> (or (:ah-umad (:variation argmap)) 0) 0) ;; using autoconstructive hypervariability
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{:average-hypervariability
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(let [variabilities (map (fn [i]
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(let [p (:plushy i)]
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(if (empty? p)
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0
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(/ (reduce + (variation/ah-rates p 0 1))
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(count p)))))
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pop)]
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(float (/ (reduce + variabilities) (count variabilities))))}
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{})))
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{:generation generation
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:best-plushy (:plushy best)
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:best-program (genome/plushy->push (:plushy best) argmap)
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:best-total-error (:total-error best)
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:evaluations evaluations
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:ds-indices (map #(:index %) training-data)
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:best-errors (:errors best)
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:best-behaviors (:behaviors best)
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:genotypic-diversity (float (/ (count (distinct (map :plushy pop))) (count pop)))
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:behavioral-diversity (float (/ (count (distinct (map :behaviors pop))) (count pop)))
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:average-genome-length (float (/ (reduce + (map count (map :plushy pop))) (count pop)))
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:average-total-error (float (/ (reduce + (map :total-error pop)) (count pop)))})
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(println)))
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(defn gp
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@ -163,8 +163,8 @@
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:boolean_bufa
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^{:stacks #{:boolean}}
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(fn [state]
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(make-instruction state
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(fn [b1 b2] b1)
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(make-instruction state
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(fn [b1 b2] b1)
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[:boolean :boolean]
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:boolean)))
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@ -172,9 +172,9 @@
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:boolean_nota
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^{:stacks #{:boolean}}
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(fn [state]
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(make-instruction state
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(fn [b1 b2] (not b1))
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[:boolean :boolean]
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(make-instruction state
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(fn [b1 b2] (not b1))
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[:boolean :boolean]
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:boolean)))
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@ -184,7 +184,7 @@
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(fn [state]
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(make-instruction state
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(fn [b1 b2] (not (and b1 b2)))
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[:boolean :boolean]
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[:boolean :boolean]
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:boolean)))
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(def-instruction
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@ -224,7 +224,7 @@
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:c2 ;; defined here
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:c1 ;; defined here
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:c0 ;; defined here
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;; BOOLEAN TAGGING?
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;; Recommended by Kalkreuth et al: BUFa, NOTa, AND, OR, XOR, NAND, NOR, XNOR
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@ -303,21 +303,20 @@
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:training-data (:train train-and-test-data)
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:testing-data (:test train-and-test-data)
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:max-generations 1000
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:population-size 100
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:population-size 1000
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:max-initial-plushy-size 100
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:step-limit 1000
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:step-limit 10000
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:parent-selection :lexicase
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:downsample? true
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:ds-function :case-rand
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:downsample-rate 0.1
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:downsample-rate 0.5
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;:parent-selection :tournament
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;:parent-selection :motley-batch-lexicase
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;:max-batch-size [1 2 4 8 16 32 64 128 256]
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;:tournament-size 5
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;:umad-rate 0.09
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:ah-umad-protect-rate 0.001 ;; ah-umad
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:ah-umad-vary-rate 0.1 ;; ah-umad
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:ah-umad-tournament-size 1 ;; ah-umad
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:ah-umad-protection 10 ;; ah-umad
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:ah-umad-rate 0.1 ;; ah-umad
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;:umad-rate [1/2
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; 1/4 1/4
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; 1/8 1/8 1/8
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@ -202,16 +202,24 @@ The function `new-individual` returns a new individual produced by selection and
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%)
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(partition 2 plushy))))
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(defn with-mean
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"Returns numeric vector v scaled so that the mean value is m"
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[m v]
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(if (empty? v)
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v
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(let [initial-mean (/ (reduce + v) (count v))]
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(map #(* m (/ % initial-mean)) v))))
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(defn ah-rates
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"Returns the sequence of rates with which each element of plushy should
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be mutated when using autoconstructive hypervariability."
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[plushy protect-rate hypervariable-rate]
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be mutated when using autoconstructive hypervariability."
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[plushy protection rate]
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(loop [i 0
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protected true
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rates []
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remainder plushy]
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(if (empty? remainder)
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rates
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(with-mean rate rates)
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(if (and (not protected)
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(= (first remainder) :protect))
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(recur i
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@ -222,33 +230,33 @@ The function `new-individual` returns a new individual produced by selection and
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(if protected
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(not= (first remainder) :vary)
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false)
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(conj rates (if protected protect-rate hypervariable-rate))
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(conj rates (if protected (/ 1 protection) 1))
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(rest remainder))))))
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(defn ah-uniform-addition
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"Returns plushy with new instructions possibly added before or after each
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existing instruction. Rates are autoconstructively hypervariable."
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[plushy instructions protect-rate hypervariable-rate]
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[plushy instructions protection rate]
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(apply concat
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(map #(if (< (rand) %2)
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(shuffle [%1 (utils/random-instruction instructions)])
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[%1])
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plushy
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(ah-rates plushy protect-rate hypervariable-rate))))
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(mapv #(if (< (rand) %2)
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(shuffle [%1 (utils/random-instruction instructions)])
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[%1])
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plushy
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(ah-rates plushy protection rate))))
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(defn ah-uniform-deletion
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"Randomly deletes instructions from plushy at some rate.
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Rates are autoconstructively hypervariable."
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[plushy protect-rate hypervariable-rate]
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(map first
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(remove (fn [[_ rate]]
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(< (rand)
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(if (zero? rate)
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0
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(/ 1 (+ 1 (/ 1 rate))))))
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(map vector
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plushy
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(ah-rates plushy protect-rate hypervariable-rate)))))
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[plushy protection rate]
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(mapv first
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(remove (fn [[_ rate]]
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(< (rand)
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(if (zero? rate)
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0
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(/ 1 (+ 1 (/ 1 rate))))))
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(mapv vector
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plushy
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(ah-rates plushy protection rate)))))
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(defn new-individual
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"Returns a new individual produced by selection and variation of
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@ -256,131 +264,126 @@ The function `new-individual` returns a new individual produced by selection and
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[pop argmap]
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(let [umad-parent (selection/select-parent pop argmap)
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parent-ind (:index umad-parent)] ;this is a hack to log hyperselection, only works for umad
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{:plushy
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(let [r (rand)
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op (loop [accum 0.0
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ops-probs (vec (:variation argmap))]
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(if (empty? ops-probs)
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:reproduction
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(let [[op1 prob1] (first ops-probs)]
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(if (>= (+ accum prob1) r)
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op1
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(recur (+ accum prob1)
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(rest ops-probs))))))]
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(case op
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:crossover
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(crossover
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(:plushy (selection/select-parent pop argmap))
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(:plushy (selection/select-parent pop argmap)))
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{:plushy
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(let [r (rand)
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op (loop [accum 0.0
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ops-probs (vec (:variation argmap))]
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(if (empty? ops-probs)
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:reproduction
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(let [[op1 prob1] (first ops-probs)]
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(if (>= (+ accum prob1) r)
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op1
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(recur (+ accum prob1)
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(rest ops-probs))))))]
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(case op
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:crossover
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(crossover
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(:plushy (selection/select-parent pop argmap))
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(:plushy (selection/select-parent pop argmap)))
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;
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:tail-aligned-crossover
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(tail-aligned-crossover
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(:plushy (selection/select-parent pop argmap))
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(:plushy (selection/select-parent pop argmap)))
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:tail-aligned-crossover
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(tail-aligned-crossover
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(:plushy (selection/select-parent pop argmap))
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(:plushy (selection/select-parent pop argmap)))
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;
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:umad
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(let [rate (utils/onenum (:umad-rate argmap))]
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(-> (:plushy (selection/select-parent pop argmap))
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(uniform-addition (:instructions argmap) rate)
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(uniform-deletion rate)))
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:umad
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(let [rate (utils/onenum (:umad-rate argmap))]
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(-> (:plushy (selection/select-parent pop argmap))
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(uniform-addition (:instructions argmap) rate)
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(uniform-deletion rate)))
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; uniform mutation by addition and deletion is a uniform mutation operator which
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;first adds genes with some probability before or after every existing gene and then
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;deletes random genes from the resulting genome
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;
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:rumad
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(let [parent-genome (:plushy (selection/select-parent pop argmap))
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after-addition (uniform-addition parent-genome
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(:instructions argmap)
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(utils/onenum (:umad-rate argmap)))
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effective-addition-rate (/ (- (count after-addition)
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(count parent-genome))
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(count parent-genome))]
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(uniform-deletion after-addition effective-addition-rate))
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:rumad
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(let [parent-genome (:plushy (selection/select-parent pop argmap))
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after-addition (uniform-addition parent-genome
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(:instructions argmap)
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(utils/onenum (:umad-rate argmap)))
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effective-addition-rate (/ (- (count after-addition)
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(count parent-genome))
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(count parent-genome))]
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(uniform-deletion after-addition effective-addition-rate))
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; Adds and deletes instructions in the parent genome with the same rate
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;
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:vumad ;; variable umad: :umad-rate is interpreted as max, actual uniform 0-max
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(let [rate (rand (utils/onenum (:umad-rate argmap)))]
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:vumad ;; variable umad: :umad-rate is interpreted as max, actual uniform 0-max
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(let [rate (rand (utils/onenum (:umad-rate argmap)))]
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(-> (:plushy (selection/select-parent pop argmap))
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(uniform-addition (:instructions argmap) rate)
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(uniform-deletion rate)))
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;
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:ah-umad ;; autoconstructive hypervariability UMAD
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(let [protection (utils/onenum (:ah-umad-protection argmap))
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rate (utils/onenum (:ah-umad-rate argmap))
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parent-genome (:plushy (selection/select-parent pop argmap))]
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(-> parent-genome
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(ah-uniform-addition (:instructions argmap) protection rate)
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(ah-uniform-deletion protection rate)))
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;
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:uniform-addition
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(-> (:plushy (selection/select-parent pop argmap))
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(uniform-addition (:instructions argmap) rate)
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(uniform-deletion rate)))
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(uniform-addition (:instructions argmap)
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(utils/onenum (:umad-rate argmap))))
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;
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:ah-umad ;; autoconstructive hypervariability UMAD
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(let [protect-rate (utils/onenum (:ah-umad-protect-rate argmap))
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vary-rate (utils/onenum (:ah-umad-vary-rate argmap))
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tourn-size (utils/onenum (:ah-umad-tournament-size argmap))
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parent-genome (:plushy (selection/select-parent pop argmap))
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offspring (repeatedly
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tourn-size
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#(-> parent-genome
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(ah-uniform-addition (:instructions argmap) protect-rate vary-rate)
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(ah-uniform-deletion protect-rate vary-rate)))
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hypervariabilities (map #(reduce + (ah-rates % 0 1)) offspring)]
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(second (last (sort-by first (map vector hypervariabilities offspring)))))
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;
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:uniform-addition
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(-> (:plushy (selection/select-parent pop argmap))
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(uniform-addition (:instructions argmap)
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(utils/onenum (:umad-rate argmap))))
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;
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:uniform-replacement
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(-> (:plushy (selection/select-parent pop argmap))
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(uniform-replacement (:instructions argmap)
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(utils/onenum (:replacement-rate argmap))))
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;
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:diploid-uniform-silent-replacement
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(-> (:plushy (selection/select-parent pop argmap))
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(diploid-uniform-silent-replacement (:instructions argmap)
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(utils/onenum (:replacement-rate argmap))))
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;
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:uniform-deletion
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(-> (:plushy (selection/select-parent pop argmap))
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(uniform-deletion (utils/onenum (:umad-rate argmap))))
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;
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:diploid-crossover
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(diploid-crossover
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(:plushy (selection/select-parent pop argmap))
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(:plushy (selection/select-parent pop argmap)))
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;
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:tail-aligned-diploid-crossover
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(tail-aligned-diploid-crossover
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(:plushy (selection/select-parent pop argmap))
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(:plushy (selection/select-parent pop argmap)))
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;
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:diploid-umad
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(let [rate (utils/onenum (:umad-rate argmap))]
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:uniform-replacement
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(-> (:plushy (selection/select-parent pop argmap))
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(diploid-uniform-addition (:instructions argmap) rate)
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(diploid-uniform-deletion rate)))
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(uniform-replacement (:instructions argmap)
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(utils/onenum (:replacement-rate argmap))))
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;
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:diploid-vumad ;; variable umad: :umad-rate is interpreted as max, actual uniform 0-max
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(let [rate (rand (utils/onenum (:umad-rate argmap)))]
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:diploid-uniform-silent-replacement
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(-> (:plushy (selection/select-parent pop argmap))
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(diploid-uniform-addition (:instructions argmap) rate)
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(diploid-uniform-deletion rate)))
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(diploid-uniform-silent-replacement (:instructions argmap)
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(utils/onenum (:replacement-rate argmap))))
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;
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:diploid-uniform-addition
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(-> (:plushy (selection/select-parent pop argmap))
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(diploid-uniform-addition (:instructions argmap)
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(utils/onenum (:umad-rate argmap))))
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:uniform-deletion
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(-> (:plushy (selection/select-parent pop argmap))
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(uniform-deletion (utils/onenum (:umad-rate argmap))))
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;
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:diploid-uniform-deletion
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(-> (:plushy (selection/select-parent pop argmap))
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(diploid-uniform-deletion (utils/onenum (:umad-rate argmap))))
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:diploid-crossover
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(diploid-crossover
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(:plushy (selection/select-parent pop argmap))
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(:plushy (selection/select-parent pop argmap)))
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;
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:diploid-flip
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(-> (:plushy (selection/select-parent pop argmap))
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(diploid-flip (utils/onenum (:diploid-flip-rate argmap))))
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:tail-aligned-diploid-crossover
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(tail-aligned-diploid-crossover
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(:plushy (selection/select-parent pop argmap))
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(:plushy (selection/select-parent pop argmap)))
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;
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:alternation
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(alternation (:plushy (selection/select-parent pop argmap))
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(:plushy (selection/select-parent pop argmap))
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(utils/onenum (or (:alternation-rate argmap) 0))
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(utils/onenum (or (:alignment-deviation argmap) 0)))
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:diploid-umad
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(let [rate (utils/onenum (:umad-rate argmap))]
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(-> (:plushy (selection/select-parent pop argmap))
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(diploid-uniform-addition (:instructions argmap) rate)
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(diploid-uniform-deletion rate)))
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;
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:reproduction
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(:plushy (selection/select-parent pop argmap))
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:diploid-vumad ;; variable umad: :umad-rate is interpreted as max, actual uniform 0-max
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(let [rate (rand (utils/onenum (:umad-rate argmap)))]
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(-> (:plushy (selection/select-parent pop argmap))
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(diploid-uniform-addition (:instructions argmap) rate)
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(diploid-uniform-deletion rate)))
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;
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:else
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(throw #?(:clj (Exception. (str "No match in new-individual for " op))
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:cljs (js/Error
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(str "No match in new-individual for " op))))))}))
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:diploid-uniform-addition
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(-> (:plushy (selection/select-parent pop argmap))
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(diploid-uniform-addition (:instructions argmap)
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(utils/onenum (:umad-rate argmap))))
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;
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:diploid-uniform-deletion
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(-> (:plushy (selection/select-parent pop argmap))
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(diploid-uniform-deletion (utils/onenum (:umad-rate argmap))))
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;
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:diploid-flip
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(-> (:plushy (selection/select-parent pop argmap))
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(diploid-flip (utils/onenum (:diploid-flip-rate argmap))))
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;
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:alternation
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(alternation (:plushy (selection/select-parent pop argmap))
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(:plushy (selection/select-parent pop argmap))
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(utils/onenum (or (:alternation-rate argmap) 0))
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(utils/onenum (or (:alignment-deviation argmap) 0)))
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;
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:reproduction
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(:plushy (selection/select-parent pop argmap))
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;
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:else
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(throw #?(:clj (Exception. (str "No match in new-individual for " op))
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:cljs (js/Error
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(str "No match in new-individual for " op))))))}))
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