From a7deb0361112173509e93e068c17568a77a0375c Mon Sep 17 00:00:00 2001
From: Shuzo Katayama
 <shuzokatayama@host-Shuzos-Air-mac-6476ba9b7300.eduroam.ssid.10net.amherst.edu>
Date: Tue, 13 Jul 2021 11:56:49 -0400
Subject: [PATCH] fixed argmap and levenshtein distance

---
 src/propeller/core.cljc                       | 10 ++++----
 src/propeller/gp.cljc                         | 24 +++++++++----------
 .../problems/PSB2/substitution_cipher.cljc    |  2 +-
 src/propeller/tools/metrics.cljc              |  2 +-
 4 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/src/propeller/core.cljc b/src/propeller/core.cljc
index 713fa41..e85cab7 100755
--- a/src/propeller/core.cljc
+++ b/src/propeller/core.cljc
@@ -27,14 +27,14 @@
       (merge
         {:instructions            (eval-problem-var (first args) "instructions")
          :error-function          (eval-problem-var (first args) "error-function")
-         :max-generations         300
-         :population-size         1000
-         :max-initial-plushy-size 250
-         :step-limit              2000
+         :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}
+         :variation               {:umad 0.5 :crossover 0.5}
          :elitism                 false
          :PSB2-path               ""
          :PSB2-problem            (clojure.string/replace (first args) #"PSB2." "")}
diff --git a/src/propeller/gp.cljc b/src/propeller/gp.cljc
index c151ecf..6774a3e 100755
--- a/src/propeller/gp.cljc
+++ b/src/propeller/gp.cljc
@@ -17,16 +17,16 @@
   "Reports information each generation."
   [pop generation argmap]
   (let [best (first pop)]
-    (println {:generation            generation
-              :best-plushy           (:plushy best)
-              :best-program          (genome/plushy->push (:plushy best) argmap)
-              :best-total-error      (:total-error best)
-              :best-errors           (:errors best)
-              :best-behaviors        (:behaviors best)
-              :genotypic-diversity   (float (/ (count (distinct (map :plushy pop))) (count pop)))
-              :behavioral-diversity  (float (/ (count (distinct (map :behaviors pop))) (count pop)))
-              :average-genome-length (float (/ (reduce + (map count (map :plushy pop))) (count pop)))
-              :average-total-error   (float (/ (reduce + (map :total-error pop)) (count pop)))})
+    (clojure.pprint/pprint {:generation            generation
+                            :best-plushy           (:plushy best)
+                            :best-program          (genome/plushy->push (:plushy best) argmap)
+                            :best-total-error      (:total-error best)
+                            :best-errors           (:errors best)
+                            :best-behaviors        (:behaviors best)
+                            :genotypic-diversity   (float (/ (count (distinct (map :plushy pop))) (count pop)))
+                            :behavioral-diversity  (float (/ (count (distinct (map :behaviors pop))) (count pop)))
+                            :average-genome-length (float (/ (reduce + (map count (map :plushy pop))) (count pop)))
+                            :average-total-error   (float (/ (reduce + (map :total-error pop)) (count pop)))})
     (println)))
 ;  (clojure.pprint/pprint
 
@@ -43,7 +43,7 @@
   (let [PSB2-data (if (= PSB2-path "")
                     #{}
                     (psb2/fetch-examples PSB2-path PSB2-problem 200 2000))
-        enhanced-argmap (assoc argmap :train-and-test-data PSB2-data)]
+        argmap (assoc argmap :train-and-test-data PSB2-data)]
 
     (loop [generation 0
            population (repeatedly
@@ -54,7 +54,7 @@
       (let [evaluated-pop (sort-by :total-error
                                    (#?(:clj  pmap
                                        :cljs map)
-                                     (partial error-function enhanced-argmap) population))
+                                     (partial error-function argmap) population))
             best-individual (first evaluated-pop)]
         (report evaluated-pop generation argmap)
         (cond
diff --git a/src/propeller/problems/PSB2/substitution_cipher.cljc b/src/propeller/problems/PSB2/substitution_cipher.cljc
index c29ef3f..83d96d2 100644
--- a/src/propeller/problems/PSB2/substitution_cipher.cljc
+++ b/src/propeller/problems/PSB2/substitution_cipher.cljc
@@ -68,7 +68,7 @@
          errors (map (fn [correct-output output]
                        (if (= output :no-stack-item)
                          10000
-                         (metrics/levenshtein-distance correct-output output)))
+                         (metrics/levenshtein-distance (str correct-output) (str output))))
                      correct-outputs
                      parsed-outputs)]
      (assoc individual
diff --git a/src/propeller/tools/metrics.cljc b/src/propeller/tools/metrics.cljc
index 156265f..bebd992 100755
--- a/src/propeller/tools/metrics.cljc
+++ b/src/propeller/tools/metrics.cljc
@@ -75,7 +75,7 @@
               ;; we need to initialize the prev-row with the edit distance
               ;; between the various prefixes of b and the empty string
               (range (inc (count (str b))))
-              (str a)))))
+              (str a))))
 
 (defn sequence-similarity
   "Returns a number between 0 and 1, indicating how similar the sequences are