From c5dd9701497601c207c73afef54e4532fc2f6688 Mon Sep 17 00:00:00 2001
From: dndang23 <dndang23@amherst.edu>
Date: Wed, 28 Dec 2022 17:14:54 -0500
Subject: [PATCH 1/3] Implemented epsilon-lexicase selection into propeller
---
src/propeller/gp.cljc | 38 +++++++++++++++++++++++++++++++++++-
src/propeller/selection.cljc | 21 +++++++++++++++++++-
2 files changed, 57 insertions(+), 2 deletions(-)
diff --git a/src/propeller/gp.cljc b/src/propeller/gp.cljc
index 72ec5af..8d291ae 100644
--- a/src/propeller/gp.cljc
+++ b/src/propeller/gp.cljc
@@ -13,6 +13,38 @@
[propeller.push.instructions.string]
[propeller.push.instructions.vector]))
+(defn mean [coll]
+ (let [sum (apply + coll)
+ count (count coll)]
+ (if (pos? count)
+ (/ sum (float count))
+ 0)))
+
+(defn median [coll]
+ (let [sorted (sort coll)
+ cnt (count sorted)
+ halfway (quot cnt 2.0)]
+ (if (odd? cnt)
+ (nth sorted halfway)
+ (let [bottom (dec halfway)
+ bottom-val (nth sorted bottom)
+ top-val (nth sorted halfway)]
+ (mean [bottom-val top-val])))))
+
+(defn median-absolute-deviation
+ [coll]
+ (let [median-val (median coll)]
+ (median (map #(Math/abs (- % median-val)) coll))))
+
+(defn epsilon-list
+ [pop]
+ (let [error-list (map :errors pop)
+ length (count (:errors (first pop)))]
+ (loop [epsilons [] i 0]
+ (if (= i length)
+ epsilons
+ (recur (conj epsilons (median-absolute-deviation (map #(nth % i) error-list))) (inc i))))))
+
(defn report
"Reports information each generation."
[pop generation argmap]
@@ -50,7 +82,11 @@
(mapper
(partial error-function argmap (:training-data argmap))
population))
- best-individual (first evaluated-pop)]
+ best-individual (first evaluated-pop)
+ argmap (if (= (:parent-selection argmap) :epsilon-lexicase)
+ (assoc argmap :epsilons (epsilon-list evaluated-pop))
+ argmap)]
+ (prn argmap)
(if (:custom-report argmap)
((:custom-report argmap) evaluated-pop generation argmap)
(report evaluated-pop generation argmap))
diff --git a/src/propeller/selection.cljc b/src/propeller/selection.cljc
index 487ecf2..2ab96d9 100755
--- a/src/propeller/selection.cljc
+++ b/src/propeller/selection.cljc
@@ -21,9 +21,28 @@
survivors)
(rest cases))))))
+(defn epsilon-lexicase-selection
+ "Selects an individual from the population using epsilon-lexicase selection."
+ [pop argmap]
+ (let [epsilons (:epsilons argmap)]
+ (loop [survivors pop
+ cases (shuffle (range (count (:errors (first pop)))))]
+ (if (or (empty? cases)
+ (empty? (rest survivors)))
+ (rand-nth survivors)
+
+ (let [min-err-for-case (apply min (map #(nth % (first cases))
+ (map :errors survivors)))
+ epsilon (nth epsilons (first cases))]
+
+ (recur (filter #(<= (Math/abs (- (nth (:errors %) (first cases)) min-err-for-case)) epsilon)
+ survivors)
+ (rest cases)))))))
+
(defn select-parent
"Selects a parent from the population using the specified method."
[pop argmap]
(case (:parent-selection argmap)
:tournament (tournament-selection pop argmap)
- :lexicase (lexicase-selection pop argmap)))
+ :lexicase (lexicase-selection pop argmap)
+ :epsilon-lexicase (epsilon-lexicase-selection pop argmap)))
From 072b8af06195154bfa27168cffa1491aa4bfd0cf Mon Sep 17 00:00:00 2001
From: dndang23 <dndang23@amherst.edu>
Date: Thu, 29 Dec 2022 18:22:02 -0500
Subject: [PATCH 2/3] Added comments
---
src/propeller/gp.cljc | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/propeller/gp.cljc b/src/propeller/gp.cljc
index 8d291ae..bc1d990 100644
--- a/src/propeller/gp.cljc
+++ b/src/propeller/gp.cljc
@@ -37,6 +37,7 @@
(median (map #(Math/abs (- % median-val)) coll))))
(defn epsilon-list
+ "Calculates the median absolute deviation of the population."
[pop]
(let [error-list (map :errors pop)
length (count (:errors (first pop)))]
@@ -86,7 +87,6 @@
argmap (if (= (:parent-selection argmap) :epsilon-lexicase)
(assoc argmap :epsilons (epsilon-list evaluated-pop))
argmap)]
- (prn argmap)
(if (:custom-report argmap)
((:custom-report argmap) evaluated-pop generation argmap)
(report evaluated-pop generation argmap))
From bff4da69752945cc1bfe1a85e2ed76ca4c255a85 Mon Sep 17 00:00:00 2001
From: dndang23 <dndang23@amherst.edu>
Date: Thu, 5 Jan 2023 16:21:21 -0800
Subject: [PATCH 3/3] Made organizational changes suggested by Ryan
---
src/propeller/gp.cljc | 38 +++--------------------------
src/propeller/selection.cljc | 12 ++++++++-
src/propeller/tools/math.cljc | 23 +++++++++++++++++
test/propeller/tools/math_test.cljc | 12 +++++++++
4 files changed, 49 insertions(+), 36 deletions(-)
diff --git a/src/propeller/gp.cljc b/src/propeller/gp.cljc
index bc1d990..9df6d01 100644
--- a/src/propeller/gp.cljc
+++ b/src/propeller/gp.cljc
@@ -11,40 +11,8 @@
[propeller.push.instructions.numeric]
[propeller.push.instructions.polymorphic]
[propeller.push.instructions.string]
- [propeller.push.instructions.vector]))
-
-(defn mean [coll]
- (let [sum (apply + coll)
- count (count coll)]
- (if (pos? count)
- (/ sum (float count))
- 0)))
-
-(defn median [coll]
- (let [sorted (sort coll)
- cnt (count sorted)
- halfway (quot cnt 2.0)]
- (if (odd? cnt)
- (nth sorted halfway)
- (let [bottom (dec halfway)
- bottom-val (nth sorted bottom)
- top-val (nth sorted halfway)]
- (mean [bottom-val top-val])))))
-
-(defn median-absolute-deviation
- [coll]
- (let [median-val (median coll)]
- (median (map #(Math/abs (- % median-val)) coll))))
-
-(defn epsilon-list
- "Calculates the median absolute deviation of the population."
- [pop]
- (let [error-list (map :errors pop)
- length (count (:errors (first pop)))]
- (loop [epsilons [] i 0]
- (if (= i length)
- epsilons
- (recur (conj epsilons (median-absolute-deviation (map #(nth % i) error-list))) (inc i))))))
+ [propeller.push.instructions.vector]
+ [propeller.selection :as selection]))
(defn report
"Reports information each generation."
@@ -85,7 +53,7 @@
population))
best-individual (first evaluated-pop)
argmap (if (= (:parent-selection argmap) :epsilon-lexicase)
- (assoc argmap :epsilons (epsilon-list evaluated-pop))
+ (assoc argmap :epsilons (selection/epsilon-list evaluated-pop))
argmap)]
(if (:custom-report argmap)
((:custom-report argmap) evaluated-pop generation argmap)
diff --git a/src/propeller/selection.cljc b/src/propeller/selection.cljc
index 2ab96d9..f6b2932 100755
--- a/src/propeller/selection.cljc
+++ b/src/propeller/selection.cljc
@@ -1,4 +1,5 @@
-(ns propeller.selection)
+(ns propeller.selection
+ (:require [propeller.tools.math :as math-tools]))
(defn tournament-selection
"Selects an individual from the population using a tournament."
@@ -21,6 +22,15 @@
survivors)
(rest cases))))))
+(defn epsilon-list
+ [pop]
+ (let [error-list (map :errors pop)
+ length (count (:errors (first pop)))]
+ (loop [epsilons [] i 0]
+ (if (= i length)
+ epsilons
+ (recur (conj epsilons (math-tools/median-absolute-deviation (map #(nth % i) error-list))) (inc i))))))
+
(defn epsilon-lexicase-selection
"Selects an individual from the population using epsilon-lexicase selection."
[pop argmap]
diff --git a/src/propeller/tools/math.cljc b/src/propeller/tools/math.cljc
index 03ed549..574dd18 100755
--- a/src/propeller/tools/math.cljc
+++ b/src/propeller/tools/math.cljc
@@ -6,6 +6,29 @@
(defonce E #?(:clj Math/E
:cljs js/Math.PI))
+(defn mean [coll]
+ (let [sum (apply + coll)
+ count (count coll)]
+ (if (pos? count)
+ (/ sum (float count))
+ 0)))
+
+(defn median [coll]
+ (let [sorted (sort coll)
+ cnt (count sorted)
+ halfway (quot cnt 2.0)]
+ (if (odd? cnt)
+ (nth sorted halfway)
+ (let [bottom (dec halfway)
+ bottom-val (nth sorted bottom)
+ top-val (nth sorted halfway)]
+ (mean [bottom-val top-val])))))
+
+(defn median-absolute-deviation
+ [coll]
+ (let [median-val (median coll)]
+ (median (map #(Math/abs (- % median-val)) coll))))
+
(defn abs
"Returns the absolute value of a number."
[x]
diff --git a/test/propeller/tools/math_test.cljc b/test/propeller/tools/math_test.cljc
index c189536..541fb9a 100644
--- a/test/propeller/tools/math_test.cljc
+++ b/test/propeller/tools/math_test.cljc
@@ -60,4 +60,16 @@
(t/is (m/approx= (m/tan (/ m/PI 4)) 1.0 0.00001))
(t/is (= (m/tan 0) 0.0)))
+(t/deftest mean-test
+ (t/is (= (m/mean []) 0.0))
+ (t/is (= (m/mean [1 2 3 4 5]) 3.0))
+ (t/is (= (m/mean '(6 7 8 9 10)) 8.0) 8.0))
+
+(t/deftest median-test
+ (t/is (= (m/median [1 2 3 4 5]) 3))
+ (t/is (= (m/median '(1 2 3 4 5 6)) 3.5)))
+
+(t/deftest median-absolute-deviation-test
+ (t/is (= (m/median-absolute-deviation [1 2 3 4 5]) 1))
+ (t/is (= (m/median-absolute-deviation '(1 2 3 4 5 6)) 1.5)))