Remove diploidy
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Lee Spector
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5fd533c24f
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54b9897803
@ -21,8 +21,7 @@ They hold the genetic material for an `individual`. In the initial population, w
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"
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([plushy] (plushy->push plushy {}))
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([plushy argmap]
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(let [plushy (if (:diploid argmap) (map first (partition 2 plushy)) plushy)
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plushy (if (or (> (or (:ah-umad (:variation argmap)) 0) 0) ;; must strip :vary and :protect
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(let [plushy (if (or (> (or (:ah-umad (:variation argmap)) 0) 0) ;; must strip :vary and :protect
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(> (or (:autoconstructive-crossover (:variation argmap)) 0) 0)) ;; must strip :gene
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(filter (complement #{:vary :protect :gene}) plushy)
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plushy)
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@ -60,10 +60,9 @@
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(loop [generation 0
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evaluations 0
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population (utils/pmapallv
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(fn [_] {:plushy (let [plushy (genome/make-random-plushy instructions max-initial-plushy-size)]
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(if (:diploid argmap)
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(interleave plushy plushy)
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plushy))}) (range population-size) argmap)
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(fn [_] {:plushy (genome/make-random-plushy instructions max-initial-plushy-size)})
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(range population-size)
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argmap)
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indexed-training-data (if downsample? (downsample/assign-indices-to-data (downsample/initialize-case-distances argmap) argmap) (:training-data argmap))]
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(let [training-data (if downsample?
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(case (:ds-function argmap)
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@ -334,12 +334,7 @@
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:alternation 0
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:reproduction 0
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:tail-aligned-crossover 0}
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;:diploid true
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;:variation {:diploid-vumad 0.8
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; :diploid-uniform-silent-replacement 0.1
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; :diploid-flip 0.1}
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;:replacement-rate 0.01
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;:diploid-flip-rate 0.01
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:elitism false
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:single-thread-mode false}
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(apply hash-map (map #(if (string? %) (read-string %) %) args)))))
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@ -7,6 +7,12 @@
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Propeller includes many kinds of genetic operators to create variation within the population.
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You can specify the rate of the variation genetic operators with the `:variation` map.
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***Some*** of the available genetic operators are described in this documentation. See the code
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for others and for details.
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To add a new genetic operator you must add a case for the operator's keyword in new-individual,
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calling existing or new utility functions that should be included earlier in this file.
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## Crossover
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Crossover genetic operators take two `plushy` representations of Push programs
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@ -16,8 +22,6 @@ and exchange genetic material to create a new `plushy`.
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|----------------------------------|------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------|
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| `crossover` | `plushy-a` `plushy-b` | Crosses over two individuals using uniform crossover, one Push instruction at a time. Pads shorter one from the end of the list of instructions. |
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| `tail-aligned-crossover` | `plushy-a` `plushy-b` | Crosses over two individuals using uniform crossover, one Push instruction at a time. Pads shorter one from the beginning of the list of instructions. |
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| `diploid-crossover` | `plushy-a` `plushy-b` | Crosses over two individuals using uniform crossover with pairs of Push instructions. Pads shorter one from the end of the list of instructions. |
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| `tail-aligned-diploid-crossover` | `plushy-a` `plushy-b` | Crosses over two individuals using uniform crossover with pairs of Push instructions. Pads shorter one from the beginning of the list of instructions. |
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## Addition, Deletion, Replacement, Flip
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@ -27,10 +31,7 @@ Addition, deletion, replacement, and flip genetic operators take a `plushy` and
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|-------------------------------------------|--------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------|
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| `uniform-addition` | `plushy` `instructions` `umad-rate` | Returns a plushy with new instructions possibly added before or after each existing instruction. |
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| `uniform-replacement` | `plushy` `instructions` `replacement-rate` | Returns a plushy with new instructions possibly replacing existing instructions. |
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| `diploid-uniform-silent-replacement` | `plushy` `instructions` `replacement-rate` | Returns a plushy with new instructions possibly replacing existing instructions, but only among the silent member of each pair. |
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| `diploid-uniform-addition` | `plushy` `instructions` `umad-rate` | Returns a plushy with new instructions possibly added before or after each existing pair of instructions. |
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| `uniform-deletion` | `plushy` `umad-rate` | Randomly deletes instructions from plushy at some rate. |
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| `diploid-uniform-deletion` | `plushy` `flip-rate` | Randomly flips pairs in a diploid plushy at some rate. |
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## Uniform Mutation by Addition and Deletion
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@ -104,40 +105,6 @@ The function `new-individual` returns a new individual produced by selection and
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shorter-padded
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longer))))
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(defn diploid-crossover
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"Crosses over two individuals using uniform crossover with pairs of Push instructions.
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Pads shorter one from the end of the list of instructions."
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[plushy-a plushy-b]
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(let [plushy-a (partition 2 plushy-a)
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plushy-b (partition 2 plushy-b)
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shorter (min-key count plushy-a plushy-b)
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longer (if (= shorter plushy-a)
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plushy-b
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plushy-a)
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length-diff (- (count longer) (count shorter))
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shorter-padded (concat shorter (repeat length-diff :crossover-padding))]
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(flatten (remove #(= % :crossover-padding)
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(map #(if (< (rand) 0.5) %1 %2)
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shorter-padded
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longer)))))
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(defn tail-aligned-diploid-crossover
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"Crosses over two individuals using uniform crossover with pairs of Push instructions.
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Pads shorter one from the beginning of the list of instructions."
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[plushy-a plushy-b]
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(let [plushy-a (partition 2 plushy-a)
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plushy-b (partition 2 plushy-b)
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shorter (min-key count plushy-a plushy-b)
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longer (if (= shorter plushy-a)
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plushy-b
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plushy-a)
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length-diff (- (count longer) (count shorter))
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shorter-padded (concat (repeat length-diff :crossover-padding) shorter)]
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(flatten (remove #(= % :crossover-padding)
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(map #(if (< (rand) 0.5) %1 %2)
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shorter-padded
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longer)))))
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(defn uniform-addition
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"Returns plushy with new instructions possibly added before or after each
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existing instruction."
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@ -157,27 +124,6 @@ The function `new-individual` returns a new individual produced by selection and
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%)
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plushy))
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(defn diploid-uniform-silent-replacement
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"Returns plushy with new instructions possibly replacing existing
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instructions, but only among the silent member of each pair."
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[plushy instructions replacement-rate]
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(interleave (map first (partition 2 plushy))
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(map #(if (< (rand) replacement-rate)
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(utils/random-instruction instructions)
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%)
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(map second (partition 2 plushy)))))
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(defn diploid-uniform-addition
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"Returns plushy with new instructions possibly added before or after each
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existing instruction."
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[plushy instructions umad-rate]
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(flatten
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(map (fn [pair]
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(if (< (rand) umad-rate)
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(shuffle [pair (repeatedly 2 #(utils/random-instruction instructions))])
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[pair]))
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(partition 2 plushy))))
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(defn uniform-deletion
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"Randomly deletes instructions from plushy at some rate."
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[plushy umad-rate]
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@ -187,23 +133,9 @@ The function `new-individual` returns a new individual produced by selection and
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(/ 1 (+ 1 (/ 1 umad-rate)))))
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plushy)))
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(defn diploid-uniform-deletion
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"Randomly deletes instructions from plushy at some rate."
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[plushy umad-rate]
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(flatten (remove (fn [_] (< (rand)
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(/ 1 (+ 1 (/ 1 umad-rate)))))
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(partition 2 plushy))))
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(defn diploid-flip
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"Randomly flips pairs in a diploid plushy at some rate."
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[plushy flip-rate]
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(flatten (map #(if (< (rand) flip-rate)
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(reverse %)
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%)
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(partition 2 plushy))))
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(defn ah-normalize
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"Takes a vector of :protect and :vary and returns a numeric vector
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"A utility for autoconstructive hypervariability mutation.
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Takes a vector of :protect and :vary and returns a numeric vector
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that conforms to the specified min, max, and mean."
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[v ah-min ah-max ah-mean]
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(let [c (count v)
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@ -232,7 +164,8 @@ The function `new-individual` returns a new individual produced by selection and
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extremes)))
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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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"A utility for autoconstructive hypervariability mutation.
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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 ah-min ah-max ah-mean]
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(loop [i 0
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@ -280,11 +213,14 @@ The function `new-individual` returns a new individual produced by selection and
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(ah-rates plushy ah-min ah-max ah-mean)))))
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(defn count-genes
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"Returns the number of segments between (and before and after) instances of :gene."
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"A utility for autoconstructive crossover. Returns the number of segments
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between (and before and after) instances of :gene."
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[plushy]
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(inc (count (filter #(= % :gene) plushy))))
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(defn extract-genes
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"A utility for autoconstructive crossover. Returns the segments of the plushy
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before/between/after instances of :gene."
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[plushy]
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(loop [genes []
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current-gene []
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@ -302,11 +238,6 @@ The function `new-individual` returns a new individual produced by selection and
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(conj current-gene (first remainder))
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(rest remainder)))))
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#_(extract-genes [:add :x :y :gene :z :gene :gene :gene :w :gene])
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#_(extract-genes [:gene :z :gene :gene :gene :w :gene])
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#_(extract-genes [:gene])
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#_(extract-genes [])
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(defn autoconstructive-crossover
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"Crosses over two plushies using autoconstructive crossover, one Push instruction at a time.
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Assumes the plushies have the same number of genes."
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@ -318,9 +249,6 @@ The function `new-individual` returns a new individual produced by selection and
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a-genes
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b-genes)))))
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#_(autoconstructive-crossover [:add :x :y :gene :z :gene :gene :gene :w :gene]
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[1 :gene 2 3 :gene 4 :gene 5 :gene :gene])
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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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individuals in the population."
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@ -359,16 +287,15 @@ The function `new-individual` returns a new individual produced by selection and
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argmap))]
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(autoconstructive-crossover plushy1 plushy2))
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;
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:umad
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:umad ;; uniform mutation by addition and deleted, see uniform-deletion for the
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;; adjustment that makes this size neutral on average
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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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:rumad ;; responsive UMAD, uses a deletion rate computed from the actual
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;; number of additions made
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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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@ -377,9 +304,9 @@ The function `new-individual` returns a new individual produced by selection and
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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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:vumad ;; variable umad: :umad-rate is interpreted as the max, and the
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;; actual rate is chosen uniformly from the range [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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@ -403,50 +330,10 @@ The function `new-individual` returns a new individual produced by selection and
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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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(-> (: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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: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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: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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