Merge pull request #231 from thelmuth/experiment/epsilon-lexicase

Experiment/epsilon lexicase; lein release :minor

src/clojush/args.clj

@@ -1,6 +1,3 @@
-;; gorilla-repl.fileformat = 1
-
-;; @@
 (ns clojush.args
   (:require [clj-random.core :as random])
   (:use [clojush globals random util pushstate]
@@ -556,17 +553,3 @@
   ([argmap]
    (load-push-argmap argmap)
    (reset-globals)))
-
-
-
-
-
-
-
-
-
-
-
-
-
-;; @@

src/clojush/globals.clj

@@ -38,6 +38,7 @@
 (def timing-map (atom {:initialization 0 :reproduction 0 :report 0 :fitness 0 :other 0}))  ;; Used for timing of different parts of pushgp
 (def solution-rates (atom (repeat 0))) ;; Used in historically-assessed hardness
 (def elitegroups (atom ())) ;; Used for elitegroup lexicase selection (will only work if lexicase-selection is off)
+(def epsilons-for-epsilon-lexicase (atom ())) ;; Used in epsilon lexicase. Only calculated once per population
 (def population-behaviors (atom ())) ;; Used to store the behaviors of the population for use in tracking behavioral diversity
 (def selection-counts (atom {})) ;; Used to store the number of selections for each individual, indexed by UUIDs
 

src/clojush/pushgp/breed.clj

@@ -150,8 +150,3 @@
                 (<= prob (second (first vectored-go-probabilities))))
           (perform-genetic-operator (first (first vectored-go-probabilities)) population location rand-gen argmap)
           (recur (rest vectored-go-probabilities)))))))
-
-
-
-
-

src/clojush/pushgp/parent_selection.clj

@@ -1,4 +1,3 @@
-
 (ns clojush.pushgp.parent-selection
   (:use [clojush random globals util])
   (:require [clojure.set :as set]))
@@ -71,6 +70,9 @@
                          survivors)
                  (rest cases)))))))
 
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
+;; epsilon lexicase selection
+
 (defn mad
   "returns median absolute deviation (MAD)"
   [x]
@@ -81,8 +83,21 @@
                  x)]
     (median dev)))
 
+(defn calculate-epsilons-for-epsilon-lexicase
+  "Calculates the epsilon values for epsilon lexicase selection. Only runs once
+   per generation. "
+  [pop-agents {:keys [epsilon-lexicase-epsilon]}]
+  (when (not epsilon-lexicase-epsilon)
+    (let [pop (map deref pop-agents)
+          test-case-errors (apply map list (map :errors pop))
+          meta-case-errors (apply map list (map :meta-errors pop))
+          all-errors (concat test-case-errors meta-case-errors)
+          epsilons (map mad all-errors)]
+      (println "Epsilons for epsilon lexicase:" epsilons)
+      (reset! epsilons-for-epsilon-lexicase epsilons))))
+
 (defn epsilon-lexicase-selection
-    "Returns an individual that does within epsilon of the best on the fitness cases when considered one at a
+  "Returns an individual that does within epsilon of the best on the fitness cases when considered one at a
    time in random order.  If trivial-geography-radius is non-zero, selection is limited to parents within +/- r of location"
   [pop location {:keys [trivial-geography-radius epsilon-lexicase-epsilon]}]
   (let [lower (mod (- location trivial-geography-radius) (count pop))
@@ -100,12 +115,10 @@
               (empty? (rest survivors)))
         (lrand-nth survivors)
         (let [; If epsilon-lexicase-epsilon is set in the argmap, use it for epsilon.
-              ; Otherwise, use automatic epsilon selections. aka use MAD for epsilon.
+              ; Otherwise, use automatic epsilon selections, which are calculated once per generation.
               epsilon (if epsilon-lexicase-epsilon
                         epsilon-lexicase-epsilon
-                        (mad (map #(nth (:errors %)
-                                        (first cases))
-                                  survivors)))
+                        (nth @epsilons-for-epsilon-lexicase (first cases)))
               min-err-for-case (apply min (map #(nth % (first cases))
                                                (map #(:errors %) survivors)))]
         (recur (filter #(<= (nth (:errors %)
@@ -236,6 +249,3 @@
                                                                1
                                                                (inc sel-count)))))
     selected))
-
-
-

src/clojush/pushgp/pushgp.clj

@@ -1,4 +1,3 @@
-
 (ns clojush.pushgp.pushgp
   (:require [clojure.java.io :as io]
             [clj-random.core :as random]
@@ -170,6 +169,9 @@
           ;; calculate implicit fitness sharing fitness for population
           (when (= (:total-error-method @push-argmap) :ifs)
             (calculate-implicit-fitness-sharing pop-agents @push-argmap))
+          ;; calculate epsilons for epsilon lexicase selection
+          (when (= (:parent-selection @push-argmap) :epsilon-lexicase)
+            (calculate-epsilons-for-epsilon-lexicase pop-agents @push-argmap))
           (timer @push-argmap :other)
           ;; report and check for success
           (let [[outcome best] (report-and-check-for-success (vec (doall (map deref pop-agents)))
@@ -185,4 +187,3 @@
                                           (install-next-generation pop-agents child-agents @push-argmap)
                                           (recur (inc generation)))
                   :else  (final-report generation best @push-argmap))))))))
-