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Ryan Boldi 2023-01-07 22:54:37 +01:00
commit 43752ed6e0
8 changed files with 144 additions and 156 deletions
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16
package-lock.json generated
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@ -61,9 +61,9 @@
} }
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@ -1368,9 +1368,9 @@
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"dev": true, "dev": true,
"requires": { "requires": {
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@ -1499,6 +1499,7 @@
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@ -2279,10 +2280,12 @@
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@ -2415,6 +2418,7 @@
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2
project.clj
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@ -1,4 +1,4 @@
(defproject net.clojars.lspector/propeller "0.2.3" (defproject net.clojars.lspector/propeller "0.3.0"
:description "Yet another Push-based genetic programming system in Clojure." :description "Yet another Push-based genetic programming system in Clojure."
:url "https://github.com/lspector/propeller" :url "https://github.com/lspector/propeller"
:license {:name "EPL-2.0 OR GPL-2.0-or-later WITH Classpath-exception-2.0" :license {:name "EPL-2.0 OR GPL-2.0-or-later WITH Classpath-exception-2.0"

8
src/propeller/gp.cljc
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@ -13,7 +13,8 @@
[propeller.push.instructions.numeric] [propeller.push.instructions.numeric]
[propeller.push.instructions.polymorphic] [propeller.push.instructions.polymorphic]
[propeller.push.instructions.string] [propeller.push.instructions.string]
[propeller.push.instructions.vector])) [propeller.push.instructions.vector]
[propeller.selection :as selection]))
(defn report (defn report
"Reports information each generation." "Reports information each generation."
@ -80,7 +81,10 @@
(partial error-function argmap training-data) (partial error-function argmap training-data)
population)) population))
best-individual (first evaluated-pop) best-individual (first evaluated-pop)
best-individual-passes-ds (and downsample? (<= (:total-error best-individual) solution-error-threshold))] best-individual-passes-ds (and downsample? (<= (:total-error best-individual) solution-error-threshold))
argmap (if (= (:parent-selection argmap) :epsilon-lexicase)
(assoc argmap :epsilons (selection/epsilon-list evaluated-pop))
argmap)]
(if (:custom-report argmap) (if (:custom-report argmap)
((:custom-report argmap) evaluations evaluated-pop generation argmap) ((:custom-report argmap) evaluations evaluated-pop generation argmap)
(report evaluations evaluated-pop generation argmap training-data)) (report evaluations evaluated-pop generation argmap training-data))

37
src/propeller/selection.cljc Executable file → Normal file
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@ -1,4 +1,5 @@
(ns propeller.selection) (ns propeller.selection
(:require [propeller.tools.math :as math-tools]))
(defn tournament-selection (defn tournament-selection
"Selects an individual from the population using a tournament." "Selects an individual from the population using a tournament."
@ -38,10 +39,42 @@
(first individuals) (first individuals)
(recur (+ tot (:fitness (first (rest individuals)))) (rest individuals)))))) (recur (+ tot (:fitness (first (rest individuals)))) (rest individuals))))))
(defn epsilon-list
[pop]
(let [error-list (map :errors pop)
length (count (:errors (first pop)))]
(loop [epsilons [] i 0]
(if (= i length)
epsilons
(recur (conj epsilons
(math-tools/median-absolute-deviation
(map #(nth % i) error-list)))
(inc i))))))
(defn epsilon-lexicase-selection
"Selects an individual from the population using epsilon-lexicase selection."
[pop argmap]
(let [epsilons (:epsilons argmap)]
(loop [survivors pop
cases (shuffle (range (count (:errors (first pop)))))]
(if (or (empty? cases)
(empty? (rest survivors)))
(rand-nth survivors)
(let [min-err-for-case (apply min (map #(nth % (first cases))
(map :errors survivors)))
epsilon (nth epsilons (first cases))]
(recur (filter #(<= (Math/abs (- (nth (:errors %)
(first cases))
min-err-for-case))
epsilon)
survivors)
(rest cases)))))))
(defn select-parent (defn select-parent
"Selects a parent from the population using the specified method." "Selects a parent from the population using the specified method."
[pop argmap] [pop argmap]
(case (:parent-selection argmap) (case (:parent-selection argmap)
:tournament (tournament-selection pop argmap) :tournament (tournament-selection pop argmap)
:lexicase (lexicase-selection pop argmap) :lexicase (lexicase-selection pop argmap)
:roulette (fitness-proportionate-selection pop argmap))) :roulette (fitness-proportionate-selection pop argmap)
:epsilon-lexicase (epsilon-lexicase-selection pop argmap)))

197
src/propeller/session.cljc
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@ -3,8 +3,6 @@
[propeller.gp :as gp] [propeller.gp :as gp]
[propeller.selection :as selection] [propeller.selection :as selection]
[propeller.variation :as variation] [propeller.variation :as variation]
[propeller.problems.simple-regression :as regression]
[propeller.problems.string-classification :as string-classif]
[propeller.push.instructions :as instructions] [propeller.push.instructions :as instructions]
[propeller.push.interpreter :as interpreter] [propeller.push.interpreter :as interpreter]
[propeller.push.state :as state])) [propeller.push.state :as state]))
@ -15,143 +13,58 @@
#_(interpreter/interpret-program #_(interpreter/interpret-program
'(1 2 :integer_add) (assoc state/empty-state :keep-history true) 1000) '(1 2 :integer_add) (assoc state/empty-state :keep-history true) 1000)
;#_(interpreter/interpret-program #_(interpreter/interpret-program
; '(3 3 :integer_eq :exec_if (1 "yes") (2 "no")) '(3 3 :integer_eq :exec_if (1 "yes") (2 "no"))
; state/empty-state state/empty-state
; 1000) 1000)
;
;#_(interpreter/interpret-program #_(interpreter/interpret-program
; '(:in1 :string_reverse 1 :string_take "?" :string_eq :exec_if '(:in1 :string_reverse 1 :string_take "?" :string_eq :exec_if
; (:in1 " I am asking." :string_concat) (:in1 " I am asking." :string_concat)
; (:in1 " I am saying." :string_concat)) (:in1 " I am saying." :string_concat))
; (assoc state/empty-state :input {:in1 "Can you hear me?"}) (assoc state/empty-state :input {:in1 "Can you hear me?"})
; 1000) 1000)
;
;#_(interpreter/interpret-program #_(interpreter/interpret-program
; '(:in1 :string_reverse 1 :string_take "?" :string_eq :exec_if '(:in1 :string_reverse 1 :string_take "?" :string_eq :exec_if
; (:in1 " I am asking." :string_concat) (:in1 " I am asking." :string_concat)
; (:in1 " I am saying." :string_concat)) (:in1 " I am saying." :string_concat))
; (assoc state/empty-state :input {:in1 "I can hear you."}) (assoc state/empty-state :input {:in1 "I can hear you."})
; 1000) 1000)
;
;#_(genome/plushy->push #_(genome/plushy->push
; (genome/make-random-plushy (instructions/get-stack-instructions #{:float :integer :exec :boolean}) 20)) (genome/make-random-plushy (instructions/get-stack-instructions #{:float :integer :exec :boolean}) 20))
;
;#_(gp/gp {:instructions propeller.problems.software.number-io/instructions #_(require '[propeller.problems.simple-regression :as regression])
; :error-function propeller.problems.software.number-io/error-function
; :max-generations 500 #_(gp/gp {:instructions regression/instructions
; :population-size 500 :error-function regression/error-function
; :max-initial-plushy-size 100 :training-data (:train regression/train-and-test-data)
; :step-limit 200 :testing-data (:test regression/train-and-test-data)
; :parent-selection :lexicase :max-generations 500
; :tournament-size 5 :population-size 500
; :umad-rate 0.1 :max-initial-plushy-size 100
; :variation {:umad 0.5 :crossover 0.5} :step-limit 200
; :elitism false}) :parent-selection :tournament
; :tournament-size 5
;#_(gp/gp {:instructions propeller.problems.simple-regression/instructions :umad-rate 0.01
; :error-function propeller.problems.simple-regression/error-function :variation {:umad 1.0
; :max-generations 500 :crossover 0.0}
; :population-size 500 :elitism false})
; :max-initial-plushy-size 100
; :step-limit 200 #_(require '[propeller.problems.string-classification :as sc])
; :parent-selection :tournament
; :tournament-size 5 #_(gp/gp {:instructions sc/instructions
; :umad-rate 0.01 :error-function sc/error-function
; :variation {:umad 1.0 :training-data (:train sc/train-and-test-data)
; :crossover 0.0} :testing-data (:test sc/train-and-test-data)
; :elitism false}) :max-generations 500
; :population-size 500
;#_(gp/gp {:instructions propeller.problems.simple-regression/instructions :max-initial-plushy-size 100
; :error-function propeller.problems.simple-regression/error-function :step-limit 200
; :max-generations 500 :parent-selection :lexicase
; :population-size 500 :tournament-size 5
; :max-initial-plushy-size 100 :umad-rate 0.1
; :step-limit 200 :variation {:umad 0.5 :crossover 0.5}
; :parent-selection :tournament :elitism false})
; :tournament-size 5
; :umad-rate 0.1
; :variation {:umad 1.0
; :crossover 0.0}
; :elitism false})
;
;
;#_(gp/gp {:instructions propeller.problems.simple-regression/instructions
; :error-function propeller.problems.simple-regression/error-function
; :max-generations 500
; :population-size 500
; :max-initial-plushy-size 100
; :step-limit 200
; :parent-selection :lexicase
; :tournament-size 5
; :umad-rate 0.1
; :variation {:umad 1.0
; :crossover 0.0}
; :elitism false})
;
;#_(gp/gp {:instructions propeller.problems.simple-regression/instructions
; :error-function propeller.problems.simple-regression/error-function
; :max-generations 500
; :population-size 500
; :max-initial-plushy-size 100
; :step-limit 200
; :parent-selection :lexicase
; :tournament-size 5
; :umad-rate 0.1
; :diploid-flip-rate 0.1
; :variation {:umad 0.8
; :diploid-flip 0.2}
; :elitism false
; :diploid true})
;
;
;#_(gp/gp {:instructions propeller.problems.software.smallest/instructions
; :error-function propeller.problems.software.smallest/error-function
; :max-generations 500
; :population-size 500
; :max-initial-plushy-size 100
; :step-limit 200
; :parent-selection :lexicase
; :tournament-size 5
; :umad-rate 0.1
; :diploid-flip-rate 0.1
; :variation {;:umad 0.8
; ;:diploid-flip 0.2
; :umad 1
; }
; :elitism false
; :diploid false})
;
;#_(gp/gp {:instructions propeller.problems.software.smallest/instructions
; :error-function propeller.problems.software.smallest/error-function
; :max-generations 500
; :population-size 500
; :max-initial-plushy-size 200 ;100
; :step-limit 200
; :parent-selection :lexicase
; :tournament-size 5
; :umad-rate 0.1
; :diploid-flip-rate 0.1
; :variation {:umad 0.8
; :diploid-flip 0.2
; ;:umad 1
; }
; :elitism false
; :diploid true})
;
;
;(gp/gp {:instructions propeller.problems.string-classification/instructions
; :error-function propeller.problems.string-classification/error-function
; :max-generations 500
; :population-size 500
; :max-initial-plushy-size 100
; :step-limit 200
; :parent-selection :lexicase
; :tournament-size 5
; :umad-rate 0.1
; :diploid-flip-rate 0.1
; :variation {:umad 0.8
; :diploid-flip 0.2
; }
; :elitism false
; :diploid true})

22
src/propeller/tools/math.cljc Executable file → Normal file
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@ -10,6 +10,28 @@
"returns 1 if number is nonzero, 0 otherwise" "returns 1 if number is nonzero, 0 otherwise"
[x] [x]
(if (zero? x) 0 1)) (if (zero? x) 0 1))
(defn mean [coll]
(let [sum (apply + coll)
count (count coll)]
(if (pos? count)
(/ sum (float count))
0.0)))
(defn median [coll]
(let [sorted (sort coll)
cnt (count sorted)
halfway (quot cnt 2.0)]
(if (odd? cnt)
(nth sorted halfway)
(let [bottom (dec halfway)
bottom-val (nth sorted bottom)
top-val (nth sorted halfway)]
(mean [bottom-val top-val])))))
(defn median-absolute-deviation
[coll]
(let [median-val (median coll)]
(median (map #(Math/abs (- % median-val)) coll))))
(defn abs (defn abs
"Returns the absolute value of a number." "Returns the absolute value of a number."

12
test/propeller/tools/math_test.cljc
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@ -60,4 +60,16 @@
(t/is (m/approx= (m/tan (/ m/PI 4)) 1.0 0.00001)) (t/is (m/approx= (m/tan (/ m/PI 4)) 1.0 0.00001))
(t/is (= (m/tan 0) 0.0))) (t/is (= (m/tan 0) 0.0)))
(t/deftest mean-test
(t/is (= (m/mean []) 0.0))
(t/is (= (m/mean [1 2 3 4 5]) 3.0))
(t/is (= (m/mean '(6 7 8 9 10)) 8.0) 8.0))
(t/deftest median-test
(t/is (= (m/median [1 2 3 4 5]) 3))
(t/is (= (m/median '(1 2 3 4 5 6)) 3.5)))
(t/deftest median-absolute-deviation-test
(t/is (= (m/median-absolute-deviation [1 2 3 4 5]) 1))
(t/is (= (m/median-absolute-deviation '(1 2 3 4 5 6)) 1.5)))

6
yarn.lock
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@ -21,9 +21,9 @@ assert@^1.1.1:
util "0.10.3" util "0.10.3"
async@^2.6.2: async@^2.6.2:
version "2.6.3" version "2.6.4"
resolved "https://registry.yarnpkg.com/async/-/async-2.6.3.tgz#d72625e2344a3656e3a3ad4fa749fa83299d82ff" resolved "https://registry.yarnpkg.com/async/-/async-2.6.4.tgz#706b7ff6084664cd7eae713f6f965433b5504221"
integrity sha512-zflvls11DCy+dQWzTW2dzuilv8Z5X/pjfmZOWba6TNIVDm+2UDaJmXSOXlasHKfNBs8oo3M0aT50fDEWfKZjXg== integrity sha512-mzo5dfJYwAn29PeiJ0zvwTo04zj8HDJj0Mn8TD7sno7q12prdbnasKJHhkm2c1LgrhlJ0teaea8860oxi51mGA==
dependencies: dependencies:
lodash "^4.17.14" lodash "^4.17.14"