From 3ca6d4175f4c743713aa8fdc95c4f078f1140944 Mon Sep 17 00:00:00 2001
From: Lee Spector <lspector@amherst.edu>
Date: Thu, 31 Aug 2023 17:17:33 -0400
Subject: [PATCH] Initialize diploid genomes to pairs of same; implement
 diploid vumad; mess around with mul3

---
 src/propeller/gp.cljc                    |  5 ++++-
 src/propeller/problems/boolean/mul3.cljc | 28 +++++++++++++++++-------
 src/propeller/variation.cljc             |  6 +++++
 3 files changed, 30 insertions(+), 9 deletions(-)

diff --git a/src/propeller/gp.cljc b/src/propeller/gp.cljc
index f7d3ff9..adfe378 100644
--- a/src/propeller/gp.cljc
+++ b/src/propeller/gp.cljc
@@ -44,7 +44,10 @@
   ;;
   (loop [generation 0
          population (utils/pmapallv
-                     (fn [_] {:plushy (genome/make-random-plushy instructions max-initial-plushy-size)})
+                     (fn [_] {:plushy (let [plushy  (genome/make-random-plushy instructions max-initial-plushy-size)]
+                                        (if (:diploid argmap)
+                                          (interleave plushy plushy)
+                                          plushy))})
                      (range population-size)
                      argmap)]             ;creates population of random plushys
     (let [evaluated-pop (sort-by :total-error
diff --git a/src/propeller/problems/boolean/mul3.cljc b/src/propeller/problems/boolean/mul3.cljc
index 677ba73..6537d16 100644
--- a/src/propeller/problems/boolean/mul3.cljc
+++ b/src/propeller/problems/boolean/mul3.cljc
@@ -164,6 +164,9 @@
         :set-c2 ;; defined here
         :set-c1 ;; defined here
         :set-c0 ;; defined here
+;; PROVIDE ACCESS ALSO TO c0-c5?
+        ;; AND/OR BOOLEAN TAGGING?
+
         ;; Recommended by Kalkreuth et al: BUFa, NOTa, AND, OR, XOR, NAND, NOR, XNOR
         :boolean_bufa ;; defined here
         :boolean_nota ;; defined here
@@ -173,15 +176,21 @@
         :boolean_nand ;; defined here
         :boolean_nor ;; defined here
         :boolean_xnor ;; defined here
+
+        ;:boolean_pop
         ;:boolean_dup
         ;:boolean_swap
         ;:boolean_rot
-        ;:boolean_pop
+
         ;:exec_pop
         ;:exec_dup
+        ;:exec_swap
+        ;:exec_rot
         ;'close
-        true
-        false))
+
+        ;true
+        ;false
+        ))
 
 
 
@@ -231,7 +240,7 @@
      :error-function           error-function
      :training-data            (:train train-and-test-data)
      :testing-data             (:test train-and-test-data)
-     :max-generations          100
+     :max-generations          1000
      :population-size          1000
      :max-initial-plushy-size  100
      :step-limit               1000
@@ -239,12 +248,15 @@
      ;:parent-selection         :tournament
      :tournament-size          5
      :umad-rate                0.01
-     :variation                {:vumad 1}
+     :variation                {:umad 1
+                                :reproduction 0
+                                :tail-aligned-crossover 0
+                                }
      ;:diploid                  true
-     ;:variation                {:diploid-umad 0.8
+     ;:variation                {:diploid-vumad 0.8
      ;                           :diploid-uniform-silent-replacement 0.1
      ;                           :diploid-flip 0.1}
-     ;:replacement-rate         0.1
-     ;:diploid-flip-rate        0.1
+     ;:replacement-rate         0.01
+     ;:diploid-flip-rate        0.01
      :elitism                  false}
     (apply hash-map (map #(if (string? %) (read-string %) %) args)))))
diff --git a/src/propeller/variation.cljc b/src/propeller/variation.cljc
index 5b1c08f..36d8321 100755
--- a/src/propeller/variation.cljc
+++ b/src/propeller/variation.cljc
@@ -266,6 +266,12 @@ The function `new-individual` returns a new individual produced by selection and
            (diploid-uniform-addition (:instructions argmap) (:umad-rate argmap))
            (diploid-uniform-deletion (:umad-rate argmap)))
        ;
+       :diploid-vumad ;; variable umad: :umad-rate is interpreted as max, actual uniform 0-max
+       (let [rate (rand (:umad-rate argmap))]
+         (-> (:plushy (selection/select-parent pop argmap))
+             (diploid-uniform-addition (:instructions argmap) rate)
+             (diploid-uniform-deletion rate)))
+       ;
        :diploid-uniform-addition
        (-> (:plushy (selection/select-parent pop argmap))
            (diploid-uniform-addition (:instructions argmap) (:umad-rate argmap)))