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Merge branch 'master' of github.com:dafg05/propeller

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Daniel Flores García 2021-07-14 20:39:56 -04:00
commit ffc218046c
27 changed files with 410 additions and 271 deletions
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# Default ignored files
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<?xml version="1.0" encoding="UTF-8"?>
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<module fileurl="file://$PROJECT_DIR$/propeller.iml" filepath="$PROJECT_DIR$/propeller.iml" />
</modules>
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64
README.md
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@ -4,16 +4,62 @@ Yet another Push-based genetic programming system in Clojure.
## Usage
To run PushGP from a REPL, load propel.core into your REPL (i.e. `lein repl`),
and run `-main` with arguments including, first, the problem name, for example:
`(-main 'simple-regression)` or `(-main 'simple-regression :population-size 100)`.
If you have installed [leiningen](https://leiningen.org), which is a tool
for running Clojure programs, then you can run Propeller on a genetic
programming problem that is defined within this project from the command
line with the command `lein run -m <namespace>`, replacing `<namespace>`
with the actual namespace that you will find at the top of the problem file.
For example, you can run the simple-regression genetic programming problem with:
```
lein run -m propeller.problems.simple-regression
```
Additional command-line arguments may
be provided to override the default key/value pairs specified in the
problem file, for example:
```
lein run -m propeller.problems.simple-regression :population-size 100
```
On Unix operating systems, including MacOS, you can use something
like the following to send output both to the terminal
and to a text file (called `outfile` in this example):
```
lein run -m propeller.problems.simple-regression | tee outfile
```
If you want to provide command line arguments that include
characters that may be interpreted by your command line shell
before they get to Clojure, then enclose those in double
quotes, like in this example that provides a non-default
value for the `:variation` argument, which is a clojure map
containing curly brackets that may confuse your shell:
```
lein run -m propeller.problems.simple-regression :variation "{:umad 1.0}"
```
To run a genetic programming problem from a REPL, start
your REPL for the project (e.g. with `lein repl` at the
command line when in the project directory, or through your
IDE) and then do something like the following (which in
this case runs the simple-regression problem with
`:population-size` 100):
```
(require 'propeller.problems.simple-regression)
(in-ns 'propeller.problems.simple-regression)
(-main :population-size 100 :variation {:umad 1.0})
```
If you want to run the problem with the default parameters,
then you should call `-main` without arguments, as `(-main)`.
To run PushGP on the genetic programming problem p from the
command line, execute `lein run p`. For example `lein run simple-regression`. Additional command-line arguments may
be provided to override the default key/value pairs specified in `-main`, for
example, `lein run simple-regression :population-size 100`. You can use something
like `lein run simple-regression | tee outfile` to send output both to the terminal
and to `outfile`.
## CLJS Usage

34
src/propeller/core.cljc
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@ -1,34 +1,10 @@
(ns propeller.core
#?(:clj (:gen-class))
(:require [propeller.gp :as gp]
#?(:cljs [cljs.reader :refer [read-string]])))
(defn eval-problem-var
[problem-name var-name]
(eval (symbol (str "propeller.problems." problem-name "/" var-name))))
#?(:clj (:gen-class)))
(defn -main
"Runs propel-gp, giving it a map of arguments."
"Not intended to be run; just print a message."
[& args]
;; Exception for when no args were passed
(when (empty? args)
(println "You must specify a problem to run.")
(println "Try, for example:")
(println " lein run software.smallest")
(System/exit 1))
(require (symbol (str "propeller.problems." (first args))))
(gp/gp
(merge
{: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 0.5 :crossover 0.5}
:elitism false}
(eval-problem-var (first args) "arglist")
(apply hash-map
(map #(if (and (string? %) (not (.contains % "/"))) (read-string %) %)
(rest args))))))
(println "To run a genetic programming problem, provide a the problem's")
(println "namespace as specified in the Propeller README file at")
(println "https://github.com/lspector/propeller/blob/master/README.md"))

22
src/propeller/problems/PSB2/basement.cljc
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@ -5,8 +5,8 @@
[propeller.utils :as utils]
[propeller.push.utils.helpers :refer [get-stack-instructions]]
[propeller.push.state :as state]
[clojure.pprint :as pprint]
[propeller.tools.math :as math]))
[propeller.tools.math :as math]
[propeller.gp :as gp]))
; =========== PROBLEM DESCRIPTION ============================
; BASEMENT from PSB2
@ -59,9 +59,23 @@
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors)))))
(def arglist
(defn -main
"Runs propel-gp, giving it a map of arguments."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)})
:testing-data (:test train-and-test-data)
: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 0.5 :crossover 0.5}
:elitism false}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))

21
src/propeller/problems/PSB2/bouncing_balls.cljc
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@ -6,7 +6,8 @@
[propeller.push.utils.helpers :refer [get-stack-instructions]]
[propeller.push.state :as state]
[clojure.pprint :as pprint]
[propeller.tools.math :as math]))
[propeller.tools.math :as math]
[propeller.gp :as gp]))
; =========== PROBLEM DESCRIPTION ===============================
; BOUNCING BALLS from PSB2
@ -70,8 +71,22 @@
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors)))))
(def arglist
(defn -main
"Runs propel-gp, giving it a map of arguments."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)})
:testing-data (:test train-and-test-data)
: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 0.5 :crossover 0.5}
:elitism false}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))

21
src/propeller/problems/PSB2/bowling.cljc
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@ -6,7 +6,8 @@
[propeller.push.utils.helpers :refer [get-stack-instructions]]
[propeller.push.state :as state]
[clojure.pprint :as pprint]
[propeller.tools.math :as math]))
[propeller.tools.math :as math]
[propeller.gp :as gp]))
; =========== PROBLEM DESCRIPTION ======================
; BOWLING from PSB2
@ -58,8 +59,22 @@
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors)))))
(def arglist
(defn -main
"Runs propel-gp, giving it a map of arguments."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)})
:testing-data (:test train-and-test-data)
: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 0.5 :crossover 0.5}
:elitism false}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))

21
src/propeller/problems/PSB2/camel_case.cljc
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@ -6,7 +6,8 @@
[propeller.push.utils.helpers :refer [get-stack-instructions]]
[propeller.push.state :as state]
[propeller.tools.math :as math]
[propeller.tools.metrics :as metrics]))
[propeller.tools.metrics :as metrics]
[propeller.gp :as gp]))
; =========== PROBLEM DESCRIPTION =====================================
; CAMEL CASE from PSB2
@ -94,8 +95,22 @@
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors)))))
(def arglist
(defn -main
"Runs propel-gp, giving it a map of arguments."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)})
:testing-data (:test train-and-test-data)
: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 0.5 :crossover 0.5}
:elitism false}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))

21
src/propeller/problems/PSB2/dice_game.cljc
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@ -6,7 +6,8 @@
[propeller.push.utils.helpers :refer [get-stack-instructions]]
[propeller.push.state :as state]
[clojure.pprint :as pprint]
[propeller.tools.math :as math]))
[propeller.tools.math :as math]
[propeller.gp :as gp]))
; =========== PROBLEM DESCRIPTION ===============================
; DICE GAME from PSB2
@ -67,8 +68,22 @@
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors)))))
(def arglist
(defn -main
"Runs propel-gp, giving it a map of arguments."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)})
:testing-data (:test train-and-test-data)
: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 0.5 :crossover 0.5}
:elitism false}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))

21
src/propeller/problems/PSB2/fuel_cost.cljc
View File

@ -6,7 +6,8 @@
[propeller.push.utils.helpers :refer [get-stack-instructions]]
[propeller.push.state :as state]
[clojure.pprint :as pprint]
[propeller.tools.math :as math]))
[propeller.tools.math :as math]
[propeller.gp :as gp]))
; =========== PROBLEM DESCRIPTION =========================
; FUEL COST from PSB2
@ -60,9 +61,23 @@
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors)))))
(def arglist
(defn -main
"Runs propel-gp, giving it a map of arguments."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)})
:testing-data (:test train-and-test-data)
: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 0.5 :crossover 0.5}
:elitism false}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))

21
src/propeller/problems/PSB2/middle_character.cljc
View File

@ -6,7 +6,8 @@
[propeller.push.utils.helpers :refer [get-stack-instructions]]
[propeller.push.state :as state]
[propeller.tools.math :as math]
[propeller.tools.metrics :as metrics]))
[propeller.tools.metrics :as metrics]
[propeller.gp :as gp]))
; =========== PROBLEM DESCRIPTION =============================
; MIDDLE CHARACTER from PSB2
@ -63,8 +64,22 @@
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors)))))
(def arglist
(defn -main
"Runs propel-gp, giving it a map of arguments."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)})
:testing-data (:test train-and-test-data)
: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 0.5 :crossover 0.5}
:elitism false}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))

21
src/propeller/problems/PSB2/substitution_cipher.cljc
View File

@ -6,7 +6,8 @@
[propeller.push.utils.helpers :refer [get-stack-instructions]]
[propeller.push.state :as state]
[propeller.tools.math :as math]
[propeller.tools.metrics :as metrics]))
[propeller.tools.metrics :as metrics]
[propeller.gp :as gp]))
; =========== PROBLEM DESCRIPTION =========================
; SUBSTITUTION CIPHER from PSB2
@ -75,8 +76,22 @@
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors)))))
(def arglist
(defn -main
"Runs propel-gp, giving it a map of arguments."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)})
:testing-data (:test train-and-test-data)
: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 0.5 :crossover 0.5}
:elitism false}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))

21
src/propeller/problems/PSB2/twitter.cljc
View File

@ -6,7 +6,8 @@
[propeller.push.utils.helpers :refer [get-stack-instructions]]
[propeller.push.state :as state]
[propeller.tools.math :as math]
[propeller.tools.metrics :as metrics]))
[propeller.tools.metrics :as metrics]
[propeller.gp :as gp]))
; =========== PROBLEM DESCRIPTION =============================
; TWITTER from PSB2
@ -66,8 +67,22 @@
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors)))))
(def arglist
(defn -main
"Runs propel-gp, giving it a map of arguments."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)})
:testing-data (:test train-and-test-data)
: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 0.5 :crossover 0.5}
:elitism false}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))

21
src/propeller/problems/simple_regression.cljc
View File

@ -2,7 +2,8 @@
(:require [propeller.genome :as genome]
[propeller.push.interpreter :as interpreter]
[propeller.push.state :as state]
[propeller.tools.math :as math]))
[propeller.tools.math :as math]
[propeller.gp :as gp]))
(defn- target-function
"Target function: f(x) = x^3 + x + 3"
@ -59,8 +60,22 @@
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors))))))
(def arglist
(defn -main
"Runs propel-gp, giving it a map of arguments."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)})
:testing-data (:test train-and-test-data)
: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 0.5 :crossover 0.5}
:elitism false}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))

28
src/propeller/problems/software/number_io.cljc
View File

@ -6,6 +6,7 @@
[propeller.utils :as utils]
[propeller.push.state :as state]
[propeller.tools.math :as math]
[propeller.gp :as gp]
#?(:cljs [cljs.reader :refer [read-string]])))
;; =============================================================================
@ -60,11 +61,8 @@
:test test-set}))
(defn error-function
([argmap individual]
(error-function argmap individual :train))
([argmap individual subset]
[argmap data individual]
(let [program (genome/plushy->push (:plushy individual) argmap)
data (get train-and-test-data subset)
inputs (:inputs data)
correct-outputs (:outputs data)
outputs (map (fn [input]
@ -90,4 +88,24 @@
:behaviors parsed-outputs
:errors errors
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors))))))
:cljs (apply + errors)))))
(defn -main
"Runs propel-gp, giving it a map of arguments."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)
: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 0.5 :crossover 0.5}
:elitism false}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))

28
src/propeller/problems/software/smallest.cljc
View File

@ -5,6 +5,7 @@
[propeller.push.utils.helpers :refer [get-stack-instructions]]
[propeller.utils :as utils]
[propeller.push.state :as state]
[propeller.gp :as gp]
#?(:cljs [cljs.reader :refer [read-string]])))
;; =============================================================================
@ -62,11 +63,8 @@
:test test-set}))
(defn error-function
([argmap individual]
(error-function argmap individual :train))
([argmap individual subset]
[argmap data individual]
(let [program (genome/plushy->push (:plushy individual) argmap)
data (get train-and-test-data subset)
inputs (:inputs data)
correct-outputs (:outputs data)
outputs (map (fn [input]
@ -92,4 +90,24 @@
:behaviors outputs
:errors errors
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors))))))
:cljs (apply + errors)))))
(defn -main
"Runs propel-gp, giving it a map of arguments."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)
: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 0.5 :crossover 0.5}
:elitism false}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))

21
src/propeller/problems/string_classification.cljc
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@ -1,7 +1,8 @@
(ns propeller.problems.string-classification
(:require [propeller.genome :as genome]
[propeller.push.interpreter :as interpreter]
[propeller.push.state :as state]))
[propeller.push.state :as state]
[propeller.gp :as gp]))
;; =============================================================================
;; String classification
@ -79,8 +80,22 @@
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors)))))
(def arglist
(defn -main
"Runs propel-gp, giving it a map of arguments."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)})
:testing-data (:test train-and-test-data)
: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 0.5 :crossover 0.5}
:elitism false}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))

21
src/propeller/problems/valiant.cljc
View File

@ -1,7 +1,8 @@
(ns propeller.problems.valiant
(:require [propeller.genome :as genome]
[propeller.push.interpreter :as interpreter]
[propeller.push.state :as state]))
[propeller.push.state :as state]
[propeller.gp :as gp]))
(def num-vars 100) ;10) ;100) ;1000)
(def num-inputs 50) ;5) ; 50) ;500)
@ -58,8 +59,22 @@
:total-error #?(:clj (apply +' errors)
:cljs (apply + errors)))))
(def arglist
(defn -main
"Runs propel-gp, giving it a map of arguments."
[& args]
(gp/gp
(merge
{:instructions instructions
:error-function error-function
:training-data (:train train-and-test-data)
:testing-data (:test train-and-test-data)})
:testing-data (:test train-and-test-data)
: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 0.5 :crossover 0.5}
:elitism false}
(apply hash-map (map #(if (string? %) (read-string %) %) args)))))