Merge remote-tracking branch 'upstream/master'

.gitignore

@@ -34,3 +34,4 @@ node_modules/
 /data
 **/.DS_Store
 *.edn
+/.cpcache/

deps.edn

@@ -0,0 +1,7 @@
+{:paths ["src" "target/classes"],
+ :deps
+ {org.clojure/clojure #:mvn{:version "1.10.0"},
+  org.clojure/clojurescript #:mvn{:version "1.9.946"},
+  org.clojure/test.check #:mvn{:version "1.1.0"},
+  net.clojars.schneau/psb2 #:mvn{:version "1.1.0"}},
+ :mvn/repos {}}

src/propeller/genome.cljc

@@ -3,7 +3,7 @@
             [propeller.utils :as utils]))
 
 (defn make-random-plushy
-  "Creates and returns a new plushy."
+  "Creates and returns a new plushy made of random instructions and of a maximum size of max-initial-plushy-size."
   [instructions max-initial-plushy-size]
   (repeatedly
     (rand-int max-initial-plushy-size)

src/propeller/gp.cljc

@@ -84,7 +84,7 @@
           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)]
+                   argmap)]                                 ;adds :epsilons if using epsilon-lexicase
       (if (:custom-report argmap)
         ((:custom-report argmap) evaluations evaluated-pop generation argmap)
         (report evaluations evaluated-pop generation argmap training-data))
@@ -128,4 +128,4 @@
                       (if (zero? (mod generation ds-parent-gens))
                         (downsample/update-case-distances rep-evaluated-pop indexed-training-data indexed-training-data ids-type (/ solution-error-threshold (count indexed-training-data))) ; update distances every ds-parent-gens generations
                         indexed-training-data)
-                       indexed-training-data))))))
+                       indexed-training-data))))))

src/propeller/selection.cljc

@@ -2,14 +2,18 @@
   (:require [propeller.tools.math :as math-tools]))
 
 (defn tournament-selection
-  "Selects an individual from the population using a tournament."
+  "Selects an individual from the population using tournaments of
+  tournament-size by taking the individual in the tournament with the lowest :total-error. "
   [pop argmap]
   (let [tournament-size (:tournament-size argmap)
         tournament-set (take tournament-size (shuffle pop))]
     (apply min-key :total-error tournament-set)))
 
 (defn lexicase-selection
-  "Selects an individual from the population using lexicase selection."
+  "Selects an individual from the population using lexicase selection.
+  Lexicase parent selection filters the population by considering one random training case at a time,
+  eliminating any individuals with errors for the current case that are worse than the best error in the selection pool,
+  until a single individual remains."
   [pop argmap]
   (loop [survivors (map rand-nth (vals (group-by :errors pop)))
          cases (shuffle (range (count (:errors (first pop)))))]
@@ -40,6 +44,7 @@
         (recur (+ tot (:fitness (first (rest individuals)))) (rest individuals))))))
 
 (defn epsilon-list
+  "List of epsilons for each training case based on median absolute deviation of errors."
   [pop]
   (let [error-list (map :errors pop)
         length (count (:errors (first pop)))]
@@ -52,7 +57,9 @@
                (inc i))))))
 
 (defn epsilon-lexicase-selection
-  "Selects an individual from the population using epsilon-lexicase selection."
+  "Selects an individual from the population using epsilon-lexicase selection.
+  Epsilon lexicase selection follows the same process as lexicase selection except,
+  for a test case, only individuals with an error outside of a predefined epsilon are filtered."
   [pop argmap]
   (let [epsilons (:epsilons argmap)]
     (loop [survivors pop

src/propeller/session.cljc

@@ -1,3 +1,10 @@
+; The "session" namespace is for trying things out interactively.
+; For example, you can use it to test a new Push instruction by running a program that uses it and seeing the result.
+; You might just want to do this interactively in the REPL, but the session file makes it a little easier since it alerady
+; requires most of the namespaces you'll want to refer to.
+; The commented-out stuff is a reminder of how to do some basic things.
+
+
 (ns propeller.session
   (:require [propeller.genome :as genome]
             [propeller.gp :as gp]

src/propeller/simplification.cljc

@@ -5,6 +5,7 @@
             [propeller.tools.math :as math]))
 
 (defn choose-random-k
+  "Takes k random indices"
   [k indices]
   (take k (shuffle indices)))
 
@@ -15,11 +16,12 @@
     (keep-indexed #(when (not (some #{%1} sorted-indices)) %2) plushy)))
 
 (defn delete-k-random
+  "Deletes k random instructions from the plushy"
   [k plushy]
   (delete-at-indices (choose-random-k k (range (count plushy))) plushy))
 
 (defn auto-simplify-plushy
-  "naive auto-simplification"
+  "simplifies plushy by deleting instructions that have no impact on errors. naive auto-simplification"
   [plushy error-function {:keys [simplification-steps training-data simplification-k simplification-verbose?] :as argmap}]
   (when simplification-verbose? (prn {:start-plushy-length (count plushy) :k simplification-k}))
   (let [initial-errors (:errors (error-function argmap training-data {:plushy plushy}))]

src/propeller/tools/math.cljc

@@ -10,14 +10,19 @@
   "returns 1 if number is nonzero, 0 otherwise"
   [x]
   (if (zero? x) 0 1))
-(defn mean [coll]
+
+(defn mean
+  "Returns the mean."
+  [coll]
   (let [sum (apply + coll)
         count (count coll)]
     (if (pos? count)
       (/ sum (float count))
       0.0)))
 
-(defn median [coll]
+(defn median
+  "Returns the median."
+  [coll]
   (let [sorted (sort coll)
         cnt (count sorted)
         halfway (quot cnt 2.0)]
@@ -29,6 +34,7 @@
         (mean [bottom-val top-val])))))
 
 (defn median-absolute-deviation
+  "Returns the median absolute deviation."
   [coll]
   (let [median-val (median coll)]
     (median (map #(Math/abs (- % median-val)) coll))))

src/propeller/utils.cljc

@@ -35,7 +35,7 @@
     lst))
 
 (defn ensure-list
-  "Returns a non-lazy list if passed a seq argument. Othwrwise, returns a list
+  "Returns a non-lazy list if passed a seq argument. Otherwise, returns a list
   containing the argument."
   [thing]
   (if (seq? thing)

src/propeller/variation.cljc

@@ -3,7 +3,8 @@
       [propeller.utils :as utils]))
 
 (defn crossover
-  "Crosses over two individuals using uniform crossover. Pads shorter one."
+  "Crosses over two individuals using uniform crossover, one Push instruction at a time.
+   Pads shorter one from the end of the list of instructions."
   [plushy-a plushy-b]
   (let [shorter (min-key count plushy-a plushy-b)
         longer (if (= shorter plushy-a)
@@ -17,7 +18,8 @@
                  longer))))
 
 (defn tail-aligned-crossover
-  "Crosses over two individuals using uniform crossover. Pads shorter one on the left."
+  "Crosses over two individuals using uniform crossover, one Push instruction at a time.
+   Pads shorter one from the beginning of the list of instructions."
   [plushy-a plushy-b]
   (let [shorter (min-key count plushy-a plushy-b)
         longer (if (= shorter plushy-a)
@@ -31,7 +33,8 @@
                  longer))))
 
 (defn diploid-crossover
-  "Crosses over two individuals using uniform crossover. Pads shorter one."
+  "Crosses over two individuals using uniform crossover with pairs of Push instructions.
+   Pads shorter one from the end of the list of instructions."
   [plushy-a plushy-b]
   (let [plushy-a (partition 2 plushy-a)
         plushy-b (partition 2 plushy-b)
@@ -47,7 +50,8 @@
                           longer)))))
 
 (defn tail-aligned-diploid-crossover
-  "Crosses over two individuals using uniform crossover. Pads shorter one on the left."
+  "Crosses over two individuals using uniform crossover with pairs of Push instructions.
+   Pads shorter one from the beginning of the list of instructions."
   [plushy-a plushy-b]
   (let [plushy-a (partition 2 plushy-a)
         plushy-b (partition 2 plushy-b)
@@ -158,7 +162,10 @@
        (-> (:plushy umad-parent)
            (uniform-addition (:instructions argmap) (:umad-rate argmap))
            (uniform-deletion (:umad-rate argmap)))
-       ;
+       ; uniform mutation by addition and deletion is a uniform mutation operator which
+       ;first adds genes with some probability before or after every existing gene and then
+       ;deletes random genes from the resulting genome
+
        :rumad
        (let [parent-genome (:plushy (selection/select-parent pop argmap))
              after-addition (uniform-addition parent-genome
@@ -168,7 +175,8 @@
                                            (count parent-genome))
                                         (count parent-genome))]
          (uniform-deletion after-addition effective-addition-rate))
-       ;
+       ; Adds and deletes instructions in the parent genome with the same rate
+
        :uniform-addition
        (-> (:plushy (selection/select-parent pop argmap))
            (uniform-addition (:instructions argmap) (:umad-rate argmap)))