interface.clj

;; gorilla-repl.fileformat = 1

;; **
;;; # Gorilla REPL
;; **

;; **
;;; Load in libraries and core functions.
;; **

;; @@
(use '[clojure repl pprint walk])
(use '[clojure.zip :as zip])
(use 'gorilla-plot.core)
(use '[gorilla-repl table html])
(use 'sym-regression-project.render :reload)
(use 'sym-regression-project.core :reload)
(require '[clojure.java.io :as io])
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-nil'>nil</span>","value":"nil"}
;; <=

;; @@
(defn read-from-file [filename]
  "Function that reads from a file specified by filename"
	  (with-open [r (java.io.PushbackReader.
	                 (clojure.java.io/reader filename))]
	    (binding [*read-eval* false]
	      (read r))))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;user/read-from-file</span>","value":"#'user/read-from-file"}
;; <=

;; @@
(io/delete-file "data.txt")
;; @@

;; **
;;; Define a test function.
;; **

;; @@
(def domain-step 1)

;(def data (doall (map (fn [x] [x (+ (* 3 x) (* 2 x x))]) (range 0 10 0.5))))
;(def data (doall (map (fn [x] [x (Math/sin x)]) (range 0 10 domain-step))))
(def data (doall (map (fn [x] [x (* (+ x 3) (+ x 3) (- x 3))]) (range -10 10 domain-step))))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;user/data</span>","value":"#'user/data"}
;; <=

;; @@
(list-plot data)
;; @@
;; =>
;;; {"type":"vega","content":{"axes":[{"type":"x","scale":"x"},{"type":"y","scale":"y"}],"scales":[{"name":"x","type":"linear","range":"width","zero":false,"domain":{"data":"219a04d2-2ca7-4c78-ae8b-f2ba173568dc","field":"data.x"}},{"name":"y","type":"linear","range":"height","nice":true,"zero":false,"domain":{"data":"219a04d2-2ca7-4c78-ae8b-f2ba173568dc","field":"data.y"}}],"marks":[{"type":"symbol","from":{"data":"219a04d2-2ca7-4c78-ae8b-f2ba173568dc"},"properties":{"enter":{"x":{"field":"data.x","scale":"x"},"y":{"field":"data.y","scale":"y"},"fill":{"value":"steelblue"},"fillOpacity":{"value":1}},"update":{"shape":"circle","size":{"value":70},"stroke":{"value":"transparent"}},"hover":{"size":{"value":210},"stroke":{"value":"white"}}}}],"data":[{"name":"219a04d2-2ca7-4c78-ae8b-f2ba173568dc","values":[{"x":-10,"y":-637},{"x":-9,"y":-432},{"x":-8,"y":-275},{"x":-7,"y":-160},{"x":-6,"y":-81},{"x":-5,"y":-32},{"x":-4,"y":-7},{"x":-3,"y":0},{"x":-2,"y":-5},{"x":-1,"y":-16},{"x":0,"y":-27},{"x":1,"y":-32},{"x":2,"y":-25},{"x":3,"y":0},{"x":4,"y":49},{"x":5,"y":128},{"x":6,"y":243},{"x":7,"y":400},{"x":8,"y":605},{"x":9,"y":864}]}],"width":400,"height":247.2187957763672,"padding":{"bottom":20,"top":10,"right":10,"left":50}},"value":"#gorilla_repl.vega.VegaView{:content {:axes [{:type \"x\", :scale \"x\"} {:type \"y\", :scale \"y\"}], :scales [{:name \"x\", :type \"linear\", :range \"width\", :zero false, :domain {:data \"219a04d2-2ca7-4c78-ae8b-f2ba173568dc\", :field \"data.x\"}} {:name \"y\", :type \"linear\", :range \"height\", :nice true, :zero false, :domain {:data \"219a04d2-2ca7-4c78-ae8b-f2ba173568dc\", :field \"data.y\"}}], :marks [{:type \"symbol\", :from {:data \"219a04d2-2ca7-4c78-ae8b-f2ba173568dc\"}, :properties {:enter {:x {:field \"data.x\", :scale \"x\"}, :y {:field \"data.y\", :scale \"y\"}, :fill {:value \"steelblue\"}, :fillOpacity {:value 1}}, :update {:shape \"circle\", :size {:value 70}, :stroke {:value \"transparent\"}}, :hover {:size {:value 210}, :stroke {:value \"white\"}}}}], :data [{:name \"219a04d2-2ca7-4c78-ae8b-f2ba173568dc\", :values ({:x -10, :y -637} {:x -9, :y -432} {:x -8, :y -275} {:x -7, :y -160} {:x -6, :y -81} {:x -5, :y -32} {:x -4, :y -7} {:x -3, :y 0} {:x -2, :y -5} {:x -1, :y -16} {:x 0, :y -27} {:x 1, :y -32} {:x 2, :y -25} {:x 3, :y 0} {:x 4, :y 49} {:x 5, :y 128} {:x 6, :y 243} {:x 7, :y 400} {:x 8, :y 605} {:x 9, :y 864})}], :width 400, :height 247.2188, :padding {:bottom 20, :top 10, :right 10, :left 50}}}"}
;; <=

;; **
;;; Program configuration.
;; **

;; @@
(defn evolve
  [population config]
  (let [{:keys [score-1-func score-2-func mutation-new-tree-func tournament-size clone-n mutate-n crossover-n max-archive-size
                report-num]} config
       
        generation-number (inc (:gen-num (first population))) 
        generation {:gen-num generation-number}
        
        popu-without-gen (if (not (nil? (:gen-num (first population)))) (drop 1 population) population)
        previous-archive (filter #(true? (:archived %)) popu-without-gen)
        
        objective-scored-popn (score-population (filter #(nil? (:archived %)) popu-without-gen) score-1-func score-2-func)
        archive (flatten (cons previous-archive (map #(merge  {:archived true} %) (flatten (into-archive should-be-archived is-dominated objective-scored-popn objective-scored-popn)))))
        c-archive (into () (distinct (flatten (into-archive should-be-archived is-dominated archive archive))))
       
        ; insert function that removes different expressions with same score...
        archive-coords (distinct (map #(extract-coords %) c-archive))
        checked-archive (map #(remove-repeats c-archive %) archive-coords)
        
        
        archive-size (count checked-archive)
        thinned-archive (thinning-done thin-archive find-min-distance distance-calcs checked-archive archive-size max-archive-size)
        
        
        
        scored-archive (map #(strength-func % objective-scored-popn) thinned-archive)
        scored-true-popn (map #(fitness-population % scored-archive) objective-scored-popn)
        population-for-selection (flatten (cons scored-archive scored-true-popn))
       
        clones (repeatedly clone-n #(tournament-selector population-for-selection tournament-size))
        mutations (repeatedly mutate-n 
                              #(mutate-expr 
                                (tournament-selector population-for-selection tournament-size)
                                mutation-new-tree-func))
        crossovers (reduce into (repeatedly crossover-n
                               #(crossover-expr
                                 (tournament-selector population-for-selection tournament-size)
                                 (tournament-selector population-for-selection tournament-size))))]
    
     (if (= (rem generation-number report-num) 0) (println generation) ())
     
    ; uncomment for indication of thinning time.
    ;(time (thinning-done thin-archive find-min-distance distance-calcs checked-archive archive-size max-archive-size))
    
    (spit "data.txt" population)
    
    (cons generation (into thinned-archive (into clones (into mutations crossovers))))))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;user/evolve</span>","value":"#'user/evolve"}
;; <=

;; @@
(def config {
             :score-1-func (memoize #(score-1 data %))
             :score-2-func (memoize #(score-2 count-nodes %))
             :mutation-new-tree-func #(random-full-tree functions terminals 3)
             :tournament-size 2
             :clone-n 40
             :crossover-n 25
             :mutate-n 10
             :max-archive-size 20
             :report-num 5})
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;user/config</span>","value":"#'user/config"}
;; <=

;; @@
;; Generate an initial population (default size 100).
;(def init-pop (read-from-file "data.txt"))
(def init-pop (cons {:gen-num 1} (repeatedly 100 #(random-full-tree functions terminals 3))))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;user/init-pop</span>","value":"#'user/init-pop"}
;; <=

;; @@
;; Run algorithm and time (default loop 20 times).
(time (def run-data (doall (take 1000 (iterate #(evolve % config) init-pop)))))
;; @@
;; ->
;;; {:gen-num 5}
;;; {:gen-num 10}
;;; {:gen-num 15}
;;; {:gen-num 20}
;;; {:gen-num 25}
;;; {:gen-num 30}
;;; {:gen-num 35}
;;; {:gen-num 40}
;;; {:gen-num 45}
;;; {:gen-num 50}
;;; {:gen-num 55}
;;; {:gen-num 60}
;;; {:gen-num 65}
;;; {:gen-num 70}
;;; {:gen-num 75}
;;; {:gen-num 80}
;;; {:gen-num 85}
;;; {:gen-num 90}
;;; {:gen-num 95}
;;; {:gen-num 100}
;;; {:gen-num 105}
;;; {:gen-num 110}
;;; {:gen-num 115}
;;; {:gen-num 120}
;;; {:gen-num 125}
;;; {:gen-num 130}
;;; {:gen-num 135}
;;; {:gen-num 140}
;;; {:gen-num 145}
;;; {:gen-num 150}
;;; {:gen-num 155}
;;; {:gen-num 160}
;;; {:gen-num 165}
;;; {:gen-num 170}
;;; {:gen-num 175}
;;; {:gen-num 180}
;;; {:gen-num 185}
;;; {:gen-num 190}
;;; {:gen-num 195}
;;; {:gen-num 200}
;;; {:gen-num 205}
;;; {:gen-num 210}
;;; {:gen-num 215}
;;; {:gen-num 220}
;;; {:gen-num 225}
;;; {:gen-num 230}
;;; {:gen-num 235}
;;; {:gen-num 240}
;;; {:gen-num 245}
;;; {:gen-num 250}
;;; {:gen-num 255}
;;; {:gen-num 260}
;;; {:gen-num 265}
;;; {:gen-num 270}
;;; {:gen-num 275}
;;; {:gen-num 280}
;;; {:gen-num 285}
;;; {:gen-num 290}
;;; {:gen-num 295}
;;; {:gen-num 300}
;;; {:gen-num 305}
;;; {:gen-num 310}
;;; {:gen-num 315}
;;; {:gen-num 320}
;;; {:gen-num 325}
;;; {:gen-num 330}
;;; {:gen-num 335}
;;; {:gen-num 340}
;;; {:gen-num 345}
;;; {:gen-num 350}
;;; {:gen-num 355}
;;; {:gen-num 360}
;;; {:gen-num 365}
;;; {:gen-num 370}
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;;; {:gen-num 385}
;;; {:gen-num 390}
;;; {:gen-num 395}
;;; {:gen-num 400}
;;; {:gen-num 405}
;;; {:gen-num 410}
;;; {:gen-num 415}
;;; {:gen-num 420}
;;; {:gen-num 425}
;;; {:gen-num 430}
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;;; {:gen-num 440}
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;;; {:gen-num 475}
;;; {:gen-num 480}
;;; {:gen-num 485}
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;;; {:gen-num 495}
;;; {:gen-num 500}
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;;; {:gen-num 530}
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;;; {:gen-num 545}
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;;; {:gen-num 555}
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;;; {:gen-num 565}
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;;; {:gen-num 620}
;;; {:gen-num 625}
;;; {:gen-num 630}
;;; {:gen-num 635}
;;; {:gen-num 640}
;;; {:gen-num 645}
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;;; {:gen-num 655}
;;; {:gen-num 660}
;;; {:gen-num 665}
;;; {:gen-num 670}
;;; {:gen-num 675}
;;; {:gen-num 680}
;;; {:gen-num 685}
;;; {:gen-num 690}
;;; {:gen-num 695}
;;; {:gen-num 700}
;;; {:gen-num 705}
;;; {:gen-num 710}
;;; {:gen-num 715}
;;; {:gen-num 720}
;;; {:gen-num 725}
;;; {:gen-num 730}
;;; {:gen-num 735}
;;; {:gen-num 740}
;;; {:gen-num 745}
;;; {:gen-num 750}
;;; {:gen-num 755}
;;; {:gen-num 760}
;;; {:gen-num 765}
;;; {:gen-num 770}
;;; {:gen-num 775}
;;; {:gen-num 780}
;;; {:gen-num 785}
;;; {:gen-num 790}
;;; {:gen-num 795}
;;; {:gen-num 800}
;;; {:gen-num 805}
;;; {:gen-num 810}
;;; {:gen-num 815}
;;; {:gen-num 820}
;;; {:gen-num 825}
;;; {:gen-num 830}
;;; {:gen-num 835}
;;; {:gen-num 840}
;;; {:gen-num 845}
;;; {:gen-num 850}
;;; {:gen-num 855}
;;; {:gen-num 860}
;;; {:gen-num 865}
;;; {:gen-num 870}
;;; {:gen-num 875}
;;; {:gen-num 880}
;;; {:gen-num 885}
;;; {:gen-num 890}
;;; {:gen-num 895}
;;; {:gen-num 900}
;;; {:gen-num 905}
;;; {:gen-num 910}
;;; {:gen-num 915}
;;; {:gen-num 920}
;;; {:gen-num 925}
;;; {:gen-num 930}
;;; {:gen-num 935}
;;; {:gen-num 940}
;;; {:gen-num 945}
;;; {:gen-num 950}
;;; {:gen-num 955}
;;; {:gen-num 960}
;;; {:gen-num 965}
;;; {:gen-num 970}
;;; {:gen-num 975}
;;; {:gen-num 980}
;;; {:gen-num 985}
;;; {:gen-num 990}
;;; {:gen-num 995}
;;; {:gen-num 1000}
;;; &quot;Elapsed time: 159214.774171 msecs&quot;
;;; 
;; <-
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;user/run-data</span>","value":"#'user/run-data"}
;; <=

;; **
;;; Analyse results of symbolic regression.
;; **

;; @@

;; Remove generation numbers from each generation
(defn filter-out-generation-num
  [generation]
(filter #(nil? (:gen-num %)) generation))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;user/filter-out-generation-num</span>","value":"#'user/filter-out-generation-num"}
;; <=

;; @@
;; Remove all archived expressions from each generation.
(defn filter-out-archive
  [generation]
  (filter #(nil? (:archived %)) generation))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;user/filter-out-archive</span>","value":"#'user/filter-out-archive"}
;; <=

;; @@
(defn best-in-generation-1
  [popn score-1-func score-2-func]
  (apply max-key :score-1 (score-population popn score-1-func score-2-func)))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;user/best-in-generation-1</span>","value":"#'user/best-in-generation-1"}
;; <=

;; @@
(defn best-in-generation-2
  [popn score-1-func score-2-func]
  (apply max-key :score-2 (score-population popn score-1-func score-2-func)))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;user/best-in-generation-2</span>","value":"#'user/best-in-generation-2"}
;; <=

;; @@
(def individuals (map #(filter-out-generation-num %) run-data))
(def all-individuals (map #(filter-out-archive %) individuals))
(def final-archive (filter #(true? (:archived %)) (last individuals)))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;user/final-archive</span>","value":"#'user/final-archive"}
;; <=

;; @@
(def bests-1 (doall (map #(best-in-generation-1 % (:score-1-func config) (:score-2-func config)) all-individuals)))
(list-plot (map :score-1 bests-1) :joined true)
;; @@
;; =>
;;; 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;; <=

;; @@
;; scored-generations maps the score-population function over every generation.
(def scored-generations (doall (map #(score-population % (:score-1-func config) (:score-2-func config)) all-individuals)))

;; final-generation outputs the scored expressions from the very last iteration.
(def final-generation (last scored-generations))

;; scored-individuals returns a sequence of every scored individual.
(def scored-individuals (flatten scored-generations))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;user/scored-individuals</span>","value":"#'user/scored-individuals"}
;; <=

;; @@
(def unarchived (map #(merge % {:archived false}) final-archive))

(def pareto-front-gen (map #(merge % {:archived false}) (into () (set (flatten (into-archive should-be-archived is-dominated final-generation final-generation))))))


(def pareto-front-individuals (distinct (into () (set (flatten (into-archive should-be-archived is-dominated unarchived pareto-front-gen))))))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;user/pareto-front-individuals</span>","value":"#'user/pareto-front-individuals"}
;; <=

;; @@
;; Generate a graph showing the individual from the final generation that has the highest score-1 value.
(compose
 (list-plot data)
 (plot (functionalise (:expr (apply max-key :score-1 pareto-front-individuals))) [-10 10]))
;; @@
;; =>
;;; 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;; <=

;; @@
;; Apply extract-coords to every individual.
(def points (map #(extract-coords %) scored-individuals))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;user/points</span>","value":"#'user/points"}
;; <=

;; @@
;; Generate a set of coordinates for every individual from the final generation that lies on the Pareto front.
(def pareto-front-points (distinct (map #(extract-coords %) pareto-front-individuals)))
;; @@
;; =>
;;; {"type":"html","content":"<span class='clj-var'>#&#x27;user/pareto-front-points</span>","value":"#'user/pareto-front-points"}
;; <=

;; @@
(list-plot pareto-front-points)
;; @@
;; =>
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;; <=

;; @@
(def sorted-pareto-front-individuals
(sort-by (juxt :score-2 :score-1) pareto-front-individuals))
(apply max-key :score-1 pareto-front-individuals)

;note need to remove indistinct expressions!!!
       
;; @@
;; =>
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;; <=

;; @@
(plot (functionalise (:expr (nth  sorted-pareto-front-individuals 11))) [-5 7])
;; @@
;; =>
;;; 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;; <=

;; @@
pareto-front-points
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;; <=

;; @@
(mathematician-view (:expr (nth sorted-pareto-front-individuals 11)))
;; @@
;; =>
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;; <=

;; @@

;; @@

;; @@

;; @@