diff --git a/doc/Intro.md b/doc/Intro.md new file mode 100644 index 0000000..e77f306 --- /dev/null +++ b/doc/Intro.md @@ -0,0 +1,201 @@ +# Introduction to Propeller + +**Propeller** is an implementation of the Push programming language and the PushGP genetic programming system in Clojure. + +For more information on Push and PushGP see http://pushlanguage.org. + +## Overview + +**Propeller** is a Push-based genetic programming system in Clojure. + + +* [Introduction to Propeller](#introduction-to-propeller) + * [Overview](#overview) + * [What can you do with propeller?](#what-can-you-do-with-propeller) + * [Installation](#installation) + * [How do I run a problem in propeller?](#how-do-i-run-a-problem-in-propeller) + * [An Example](#an-example) + * [Can you use a REPL?](#can-you-use-a-repl) + * [Tutorials](#tutorials) + * [Contributing](#contributing) + * [License](#license) + * [Citation](#citation) + * [About Propeller](#about-propeller) + * [Contact](#contact) + * [Library Reference](#library-reference) + + +### What can you do with Propeller? + +You can evolve a program made of Push instructions to solve a problem. + +## Installation + +You can use either leiningen or deps.edn to run Propeller. + +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 `, replacing `` +with the actual namespace that you will find at the top of the problem file. + +If you have installed [Clojure](https://clojure.org/guides/install_clojure#java), +you can run Propeller on a genetic programming problem with the command `clj -m `, +replacing `` with the actual namespace that you will find at the top of the problem file. +The examples below use leiningen, but you can replace `lein run` with `clj` to run the same problem. + +## How do I run a problem in propeller? + +To run a problem in propeller, you want to call the `-main` function in the problem file using leiningen. +The `-main` function will create a map of arguments from the input and run the main genetic programming loop. + +Below is the general format to run a problem through the command-line: + +``` +lein run -m +``` + +Additional command-line arguments may +be provided to override the default key/value pairs specified in the +problem file, + +``` +lein run -m ... +``` + +The possible keys come from the table below: + +| Key | Description | +|----------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| `:instructions` | List of possible Push instructions used to create a plushy | +| `:error-function` | The error function used to evaluate individuals, specified in the given problem's namespace | +| `:training-data` | Map of inputs and desired outputs used to evaluate individuals of the form: {:input1 first-input :input2 second-input ... :output1 first-output ...} | +| `:testing-data` | Map of inputs and desired outputs not in the training-data to test generalizability of a program that fits the `training-data`. The map is of the form: {:input1 first-input :input2 second-input ... :output1 first-output ...} | +| `:max-generations` | Maximum number of generations | +| `:population-size` | Size of population in a generation | +| `:max-initial-plushy-size` | Maximum number of Push instructions in the initial plushy | +| `:step-limit` | The maximum number of steps that a Push program will be executed by `interpret-program` | +| `:parent-selection` | Function from `propeller.selection` that determines method of parent selection method. Propeller includes `:tournament-selection`, `:lexicase-selection`, and `:epsilon-lexicase-selection`. | +| `:tournament-size` | If using a tournament selection method, the number of individuals in each tournaments used to determine parents | +| `:umad-rate` | Rate (decimal between 0 and 1) of uniform mutation by addition and deletion (UMAD) genetic operator | +| `:variation` | Map with genetic operators as keys and probabilities as values. For example, {:umad 0.3 :crossover 0.7}. This would mean that when the system needs to generate a child, it will use UMAD 30% of the time and crossover 70% of the time. The probabilities should sum to 1. | +| `:elitism` | When true, will cause the individual with the lowest error in the population to survive, without variation, into the next generation. | + +When you run a problem, you will get a report each generation with the following information: + +``` +:generation + :best-plushy + :best-program + :best-total-error + :best-errors + :best-behaviors + :genotypic-diversity + :behavioral-diversity + :average-genome-length + :average-total-error +``` + +### An Example + +For example, you can run the simple-regression genetic programming problem with: + +``` +lein run -m propeller.problems.simple-regression +``` + +This will run simple-regression with the default set of arguments in the `simple-regression` problem file. + +``` +{: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} +``` + +You can override the default key/value pairs with additional arguments. 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}" +``` + +### Can you use a REPL? + +Yes! + +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). + +## Tutorials + +- Adding genetic operators +- Adding selection methods +- Adding a new problem +- How to use simplification +- Experimentation Guide + +## Contributing + +You can report a bug on the [GitHub issues page](https://github.com/lspector/propeller/issues). + +The best way to contribute to propeller is to fork the [main GitHub repository](https://github.com/lspector/propeller) and submit a pull request. + +## License + +Eclipse Public License 2.0 +This commercially-friendly copyleft license provides the ability to commercially license binaries; +a modern royalty-free patent license grant; and the ability for linked works to use other licenses, including commercial ones. + +## Citation + +We are in the process of creating a DOI, but in the meantime, we ask +that you cite the [link to the repository](https://github.com/lspector/propeller) if you use Propeller. + +## About Propeller + +https://deap.readthedocs.io/en/master/about.html + +## Contact + +## Library Reference \ No newline at end of file diff --git a/doc/Tutorials/Adding_Genetic_Operators.md b/doc/Tutorials/Adding_Genetic_Operators.md new file mode 100644 index 0000000..0265aa2 --- /dev/null +++ b/doc/Tutorials/Adding_Genetic_Operators.md @@ -0,0 +1,62 @@ +# Adding Genetic Operators + +In addition to the already-included genetic operators, you can add your own! + +## Variation Genetic Operators + +1. Go to `propeller.variation.cljc` +2. Define a genetic operator function +3. In `propeller.variation/new-individual`, add the new genetic operator in the `new-individual` function under the `case` call + +```clojure +(defn new-individual + "Returns a new individual produced by selection and variation of + individuals in the population." + [pop argmap] + ... + (case op + ... + + :new-genetic-operator + (-> (:plushy (selection/select-parent pop argmap)) + (new-genetic-operator )) + ... + :else + (throw #?(:clj (Exception. (str "No match in new-individual for " op)) + :cljs (js/Error + (str "No match in new-individual for " op))))))}) +``` + +4. When running a problem, specify the genetic operator in `:variation`. +For example: +``` +lein run -m propeller.problems.simple-regression :variation "{:new-genetic-operator 1.0}" + +``` + +## Selection Genetic Operators + +1. Go to `propeller.selection.cljc` +2. Define a genetic operator function +3. In `propeller.selection.cljc`, add the new genetic operator in the `select-parent` function under the `case` call. + +```clojure +(defn select-parent + "Selects a parent from the population using the specified method." + [pop argmap] + (case (:parent-selection argmap) + ... + :new-genetic-operator (:new-genetic-operator ) + ... + )) +``` + +4. When running a problem, specify the selection method in `:parent-selection` + +For example: + +``` +lein run -m propeller.problems.simple-regression :parent-selection :new-genetic-operator + +``` + diff --git a/doc/Tutorials/Adding_Problem.md b/doc/Tutorials/Adding_Problem.md new file mode 100644 index 0000000..f85ad74 --- /dev/null +++ b/doc/Tutorials/Adding_Problem.md @@ -0,0 +1,122 @@ +# Adding a Problem + +In general, a problem file has 3 components: `train-and-test-data`, `instructions`, `error-function`, and `-main`. + +1. To add a new problem, you need training and test data. For Problem Synthesis Benchmark Problems (PSB2), +you can fetch datasets using `psb2.core/fetch-examples`. + +```clojure +(defn fetch-examples + "Fetches and returns training and test data from a PSB2 problem. + Returns a map of the form {:train training-examples :test testing-examples} + where training-examples and testing-examples are lists of training and test + data. The elements of these lists are maps of the form: + {:input1 first-input :input2 second-input ... :output1 first-output ...} + The training examples will include all hard-coded edge cases included in the suite, + along with enough random cases to include `n-train` cases. + Note that this function loads large datasets and can be slow, 30-120 seconds. + Parameters: + `datasets-directory` - Location of the PSB2 datasets as downloaded from https://zenodo.org/record/4678739 + `problem-name` - Name of the PSB2 problem, lowercase and seperated by dashes. + - Ex: indices-of-substring + `n-train` - Number of training cases to return + `n-test` - Number of test cases to return" + [datasets-directory problem-name n-train n-test] + ) +``` +2. Define the possible Push instructions to be used to create plushys. It should be a non-lazy list of +instructions from `push/instructions` +3. Define an error function that will evaluate plushys and add `:behaviors parsed-outputs`, + `:errors`, and `:total-error` to the individual +4. Define the function `-main` with a map of default arguments. + +## Example of a Problem + +```clojure +(ns propeller.problems.PSB2.solve-boolean + (:require [psb2.core :as psb2] + [propeller.genome :as genome] + [propeller.push.interpreter :as interpreter] + [propeller.utils :as utils] + [propeller.push.instructions :refer [get-stack-instructions]] + [propeller.push.state :as state] + [propeller.gp :as gp] + #?(:cljs [cljs.reader :refer [read-string]]))) + +; =========== PROBLEM DESCRIPTION ================================ +; SOLVE BOOLEAN from PSB2 +; Given a string representing a Boolean +; expression consisting of T, F, |, and &, evaluate it and return +; the resulting Boolean. +; +; Source: https://arxiv.org/pdf/2106.06086.pdf +; ================================================================== + +(def train-and-test-data (psb2/fetch-examples "data" "solve-boolean" 200 2000)) + +(def instructions + (utils/not-lazy + (concat + ;;; stack-specific instructions + (get-stack-instructions #{:exec :integer :boolean :char :string :print}) + ;;; input instructions + (list :in1) + ;;; close + (list 'close) + ;;; ERCs (constants) + (list true false \t \f \& \|)))) + +(defn error-function + [argmap data individual] + (let [program (genome/plushy->push (:plushy individual) argmap) + inputs (map (fn [i] (get i :input1)) data) + correct-outputs (map (fn [i] (get i :output1)) data) + outputs (map (fn [input] + (state/peek-stack + (interpreter/interpret-program + program + (assoc state/empty-state :input {:in1 input}) + (:step-limit argmap)) + :boolean)) + inputs) + parsed-outputs (map (fn [output] + (try (read-string output) + #?(:clj (catch Exception e 1000.0) + :cljs (catch js/Error. e 1000.0)))) + outputs) + errors (map (fn [correct-output output] + (if (= output :no-stack-item) + 10000 + (if (= correct-output output) + 0 + 1))) + correct-outputs + parsed-outputs)] + (assoc individual + :behaviors parsed-outputs + :errors errors + :total-error #?(:clj (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 300 + :population-size 1000 + :max-initial-plushy-size 250 + :step-limit 2000 + :parent-selection :lexicase + :tournament-size 5 + :umad-rate 0.1 + :variation {:umad 1.0 :crossover 0.0} + :elitism false} + (apply hash-map (map #(if (string? %) (read-string %) %) args)))) + (#?(:clj shutdown-agents))) + +``` \ No newline at end of file diff --git a/doc/Tutorials/Adding_Selection_Method.md b/doc/Tutorials/Adding_Selection_Method.md new file mode 100644 index 0000000..8c57b01 --- /dev/null +++ b/doc/Tutorials/Adding_Selection_Method.md @@ -0,0 +1,20 @@ +# Adding a Selection Method + +1. Define a selection method function in `propeller.selection` that selects an individual from the population +2. Add the selection method in `propeller.selection/select-parent` under the `case` call: + +```clojure +(defn select-parent + "Selects a parent from the population using the specified method." + [pop argmap] + (case (:parent-selection argmap) + :new-selection-method (new-selection-method ))) +``` + +3. When runnning a problem, specify the selection method in `:parent-selection`. +For example: +``` +lein run -m propeller.problems.simple-regression :parent-selection :new-selection-method" +``` + + diff --git a/doc/Tutorials/Experimentation.md b/doc/Tutorials/Experimentation.md new file mode 100644 index 0000000..1313b05 --- /dev/null +++ b/doc/Tutorials/Experimentation.md @@ -0,0 +1,5 @@ +# A Guide to Experimentation + +You can use Propeller to run experiments either on + +## \ No newline at end of file diff --git a/doc/intro.md b/doc/Tutorials/Simplification.md similarity index 67% rename from doc/intro.md rename to doc/Tutorials/Simplification.md index 0e67dcf..0c390af 100644 --- a/doc/intro.md +++ b/doc/Tutorials/Simplification.md @@ -1,12 +1,7 @@ -# Introduction to Propeller - -TODO: write [great documentation](http://jacobian.org/writing/what-to-write/) - - - - # Simplification +Propeller allows you to automatically simplify plushys by removing instructions that have no impact on the error values +when evaluating the individual on test cases. To use Propeller's auto-simplification system, simply include the following four command line arguments when running a problem: ```clojure @@ -16,7 +11,7 @@ Toggle auto-simplification ```clojure :simplification-k 4 ``` -This is the upper bound for elements deleted from the plushy every step. Every step, a number in $[1, k]$ of elements is deleted from the plushy representation of the solution. +This is the upper bound for elements deleted from the plushy every step. Every step, a number in [1, k] of elements is deleted from the plushy representation of the solution. ```clojure :simplification-steps 1000 ``` @@ -24,7 +19,7 @@ Number of simplification steps to perform ```clojure :simplification-verbose? true ``` -whether or not to output simplification info into the output of the evolutionary run. +Whether or not to output simplification info into the output of the evolutionary run. The output with verbose adds the following lines to the output: ```clojure {:start-plushy-length 42, :k 4} diff --git a/doc/doc/codox/Adding_Genetic_Operators.html b/doc/doc/codox/Adding_Genetic_Operators.html new file mode 100644 index 0000000..3ab38b2 --- /dev/null +++ b/doc/doc/codox/Adding_Genetic_Operators.html @@ -0,0 +1,56 @@ + +Adding Genetic Operators

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Adding Genetic Operators

+

In addition to the already-included genetic operators, you can add your own!

+

Variation Genetic Operators

+
    +
  1. Go to propeller.variation.cljc
    2. +
  2. Define a genetic operator function
    3. +
  3. In propeller.variation/new-individual, add the new genetic operator in the new-individual function under the case call
    4. +
+
(defn new-individual
+  "Returns a new individual produced by selection and variation of
+  individuals in the population."
+  [pop argmap]
+  ...
+     (case op
+       ...
+       
+       :new-genetic-operator
+       (-> (:plushy (selection/select-parent pop argmap))
+           (new-genetic-operator ))
+       ...
+       :else
+       (throw #?(:clj  (Exception. (str "No match in new-individual for " op))
+                 :cljs (js/Error
+                         (str "No match in new-individual for " op))))))})
+
+
    +
  1. When running a problem, specify the genetic operator in :variation. For example:
    2. +
+
lein run -m propeller.problems.simple-regression :variation "{:new-genetic-operator 1.0}"
+
+
+

Selection Genetic Operators

+
    +
  1. Go to propeller.selection.cljc
    2. +
  2. Define a genetic operator function
    3. +
  3. In propeller.selection.cljc, add the new genetic operator in the select-parent function under the case call.
    4. +
+
(defn select-parent
+  "Selects a parent from the population using the specified method."
+  [pop argmap]
+  (case (:parent-selection argmap)
+    ...
+    :new-genetic-operator (:new-genetic-operator )
+    ...
+    ))
+
+
    +
  1. When running a problem, specify the selection method in :parent-selection
    2. +
+

For example:

+
lein run -m propeller.problems.simple-regression :parent-selection :new-genetic-operator
+
+
+
\ No newline at end of file diff --git a/doc/doc/codox/Adding_Problem.html b/doc/doc/codox/Adding_Problem.html new file mode 100644 index 0000000..112ca54 --- /dev/null +++ b/doc/doc/codox/Adding_Problem.html @@ -0,0 +1,119 @@ + +Adding a Problem

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Adding a Problem

+

In general, a problem file has 3 components: train-and-test-data, instructions, error-function, and -main.

+
    +
  1. To add a new problem, you need training and test data. For Problem Synthesis Benchmark Problems (PSB2), you can fetch datasets using psb2.core/fetch-examples.
    2. +
+
(defn fetch-examples
+   "Fetches and returns training and test data from a PSB2 problem.
+    Returns a map of the form {:train training-examples :test testing-examples}
+    where training-examples and testing-examples are lists of training and test
+    data. The elements of these lists are maps of the form:
+    {:input1 first-input :input2 second-input ... :output1 first-output ...}
+    The training examples will include all hard-coded edge cases included in the suite,
+    along with enough random cases to include `n-train` cases.
+    Note that this function loads large datasets and can be slow, 30-120 seconds.
+    Parameters:
+      `datasets-directory` - Location of the PSB2 datasets as downloaded from https://zenodo.org/record/4678739
+      `problem-name` - Name of the PSB2 problem, lowercase and seperated by dashes.
+          - Ex: indices-of-substring
+      `n-train` - Number of training cases to return
+      `n-test` - Number of test cases to return"
+   [datasets-directory problem-name n-train n-test]
+   )
+
+
    +
  1. Define the possible Push instructions to be used to create plushys. It should be a non-lazy list of instructions from push/instructions
    2. +
  2. Define an error function that will evaluate plushys and add :behaviors parsed-outputs, :errors, and :total-error to the individual
    3. +
  3. Define the function -main with a map of default arguments.
    4. +
+

Example of a Problem

+
(ns propeller.problems.PSB2.solve-boolean
+  (:require [psb2.core :as psb2]
+            [propeller.genome :as genome]
+            [propeller.push.interpreter :as interpreter]
+            [propeller.utils :as utils]
+            [propeller.push.instructions :refer [get-stack-instructions]]
+            [propeller.push.state :as state]
+            [propeller.gp :as gp]
+            #?(:cljs [cljs.reader :refer [read-string]])))
+
+; ===========  PROBLEM DESCRIPTION  ================================
+; SOLVE BOOLEAN from PSB2
+; Given a string representing a Boolean
+; expression consisting of T, F, |, and &, evaluate it and return
+; the resulting Boolean.
+;
+; Source: https://arxiv.org/pdf/2106.06086.pdf
+; ==================================================================
+
+(def train-and-test-data (psb2/fetch-examples "data" "solve-boolean" 200 2000))
+
+(def instructions
+  (utils/not-lazy
+    (concat
+      ;;; stack-specific instructions
+      (get-stack-instructions #{:exec :integer :boolean :char :string :print})
+      ;;; input instructions
+      (list :in1)
+      ;;; close
+      (list 'close)
+      ;;; ERCs (constants)
+      (list true false \t \f \& \|))))
+
+(defn error-function
+  [argmap data individual]
+  (let [program (genome/plushy->push (:plushy individual) argmap)
+        inputs (map (fn [i] (get i :input1)) data)
+        correct-outputs (map (fn [i] (get i :output1)) data)
+        outputs (map (fn [input]
+                       (state/peek-stack
+                         (interpreter/interpret-program
+                           program
+                           (assoc state/empty-state :input {:in1 input})
+                           (:step-limit argmap))
+                         :boolean))
+                     inputs)
+        parsed-outputs (map (fn [output]
+                              (try (read-string output)
+                                   #?(:clj  (catch Exception e 1000.0)
+                                      :cljs (catch js/Error. e 1000.0))))
+                            outputs)
+        errors (map (fn [correct-output output]
+                      (if (= output :no-stack-item)
+                        10000
+                        (if (= correct-output output)
+                           0
+                           1)))
+                    correct-outputs
+                    parsed-outputs)]
+    (assoc individual
+      :behaviors parsed-outputs
+      :errors errors
+      :total-error #?(:clj  (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         300
+       :population-size         1000
+       :max-initial-plushy-size 250
+       :step-limit              2000
+       :parent-selection        :lexicase
+       :tournament-size         5
+       :umad-rate               0.1
+       :variation               {:umad 1.0 :crossover 0.0}
+       :elitism                 false}
+      (apply hash-map (map #(if (string? %) (read-string %) %) args))))
+  (#?(:clj shutdown-agents)))
+
+
+
\ No newline at end of file diff --git a/doc/doc/codox/Adding_Selection_Method.html b/doc/doc/codox/Adding_Selection_Method.html new file mode 100644 index 0000000..25309b6 --- /dev/null +++ b/doc/doc/codox/Adding_Selection_Method.html @@ -0,0 +1,19 @@ + +Adding a Selection Method

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Adding a Selection Method

+
    +
  1. Define a selection method function in propeller.selection that selects an individual from the population
    2. +
  2. Add the selection method in propeller.selection/select-parent under the case call:
    3. +
+
(defn select-parent
+  "Selects a parent from the population using the specified method."
+  [pop argmap]
+  (case (:parent-selection argmap)
+    :new-selection-method (new-selection-method )))
+
+
    +
  1. When runnning a problem, specify the selection method in :parent-selection. For example:
    2. +
+
lein run -m propeller.problems.simple-regression :parent-selection :new-selection-method"
+
+
\ No newline at end of file diff --git a/doc/doc/codox/Experimentation.html b/doc/doc/codox/Experimentation.html new file mode 100644 index 0000000..46a726a --- /dev/null +++ b/doc/doc/codox/Experimentation.html @@ -0,0 +1,6 @@ + +A Guide to Experimentation

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A Guide to Experimentation

+

You can use Propeller to run experiments either on

+

+
\ No newline at end of file diff --git a/doc/doc/codox/Genetic_Programming_Loop.html b/doc/doc/codox/Genetic_Programming_Loop.html new file mode 100644 index 0000000..4d3e7c0 --- /dev/null +++ b/doc/doc/codox/Genetic_Programming_Loop.html @@ -0,0 +1,4 @@ + +Genetic Programming Loop

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Genetic Programming Loop

+
\ No newline at end of file diff --git a/doc/doc/codox/Genome.html b/doc/doc/codox/Genome.html new file mode 100644 index 0000000..196d903 --- /dev/null +++ b/doc/doc/codox/Genome.html @@ -0,0 +1,14 @@ + +Genome

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Genome

+

A plushy is a list of Push instructions that represent a Push program. They hold the genetic material for an individual. In the initial population, we create random plushys.

+ + + + + + + + +
Function Parameters Description
make-random-plushy instructions max-initial-plushy-size Creates and returns a new plushy made of random instructions and of a maximum size of max-initial-plushy-size
plushy->push plushy argmap Returns the Push program expressed by the given plushy representation.
+
\ No newline at end of file diff --git a/doc/doc/codox/Library_Reference.html b/doc/doc/codox/Library_Reference.html new file mode 100644 index 0000000..5c421bb --- /dev/null +++ b/doc/doc/codox/Library_Reference.html @@ -0,0 +1,32 @@ + +Library Reference

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Library Reference

+

An overly-detailed description of (almost) all the functions contained within propeller.

+ + + +

Genetic Operators

+

https://en.wikipedia.org/wiki/Genetic_operator

+

Variation

+

Selection

+

Genetic Programming Loop

+

gp.cljc

+

Genome

+

Utility Functions

+

Found in propeller.utils.cljc, these are functions just to make life easier when writing other functions.

+

Push

+

simplification

+

Problems

+
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Project

Topics

Namespaces

propeller-documentation

+

propeller is an implementation of the Push programming language and the PushGP genetic programming system in Clojure.

+

For more information on Push and PushGP see http://pushlanguage.org.

+

Overview

+

propeller is a Push-based genetic programming system in Clojure.

+

What can you do with propeller?

+

You can evolve a Push program to solve a problem.

+

Installation

+

If you have installed leiningen, 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.

+

How do I run a problem in propeller?

+

To run a problem in propeller, you want to call the -main function in the problem file using leiningen. The -main function will create a map of arguments from the input and run the main genetic programming loop.

+

Below is the general format to run a problem through the command-line:

+
lein run -m [path of the problem file you want to test]
+
+

Additional command-line arguments may be provided to override the default key/value pairs specified in the problem file,

+
lein run -m [path of the problem file you want to test] [key and value] [key and value]...
+
+

The possible keys come from the table below:

+ + + + + + + + + + + + + + + + + + + +
Key Description
:instructions List of possible Push instructions used to create a plushy
:error-function The error function used to evaluate individuals, specified in the given problem’s namespace
:training-data Map of inputs and desired outputs used to evaluate individuals of the form: {:input1 first-input :input2 second-input … :output1 first-output …}
:testing-data Map of inputs and desired outputs not in the training-data to test generalizability of a program that fits the training-data. The map is of the form: {:input1 first-input :input2 second-input … :output1 first-output …}
:max-generations Maximum number of generations
:population-size Size of population in a generation
:max-initial-plushy-size Maximum number of Push instructions in the initial plushy
:step-limit The maximum number of steps that a Push program will be executed by interpret-program
:parent-selection Function from propeller.selection that determines method of parent selection method. Propeller includes :tournament-selection, :lexicase-selection, and :epsilon-lexicase-selection.
:tournament-size If using a tournament selection method, the number of individuals in each tournaments used to determine parents
:umad-rate Rate (decimal between 0 and 1) of uniform mutation by addition and deletion (UMAD) genetic operator
:variation Map with genetic operators as keys and probabilities as values. For example, {:umad 0.3 :crossover 0.7}. This would mean that when the system needs to generate a child, it will use UMAD 30% of the time and crossover 70% of the time. The probabilities should sum to 1.
:elitism When true, will cause the individual with the lowest error in the population to survive, without variation, into the next generation.
+

When you run a problem, you will get a report each generation with the following information:

+
:generation            
+ :best-plushy 
+ :best-program          
+ :best-total-error      
+ :best-errors        
+ :best-behaviors        
+ :genotypic-diversity   
+ :behavioral-diversity  
+ :average-genome-length 
+ :average-total-error 
+
+
+

An Example

+

For example, you can run the simple-regression genetic programming problem with:

+
lein run -m propeller.problems.simple-regression
+
+

This will run simple-regression with the default set of arguments in the simple-regression problem file.

+
{: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}
+
+

You can override the default key/value pairs with additional arguments. 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}"
+
+

Can you use a REPL?

+

Yes!

+

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).

+

Tutorials

+
    +
  • Adding genetic operators
    • +
  • Adding selection methods
    • +
  • Adding a new problem
    • +
  • How to use simplification
    • +
+

Contributing

+

https://deap.readthedocs.io/en/master/contributing.html

+

License

+

Eclipse Public License 2.0 This commercially-friendly copyleft license provides the ability to commercially license binaries; a modern royalty-free patent license grant; and the ability for linked works to use other licenses, including commercial ones.

+

Citation

+

Cite the link to the repository.

+

About Propeller

+

https://deap.readthedocs.io/en/master/about.html

+

Contact

+
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Project

Topics

Namespaces

Selection

+

Propeller includes many kinds of genetic operators to select parents within the population.

+ + + + + + + + + +
Selection Method Description
:tournament-selection Selects an individual from the population using tournaments of tournament-size by taking the individual in the tournament with the lowest :total-error.
: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.
: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.
+
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Project

Topics

Namespaces

Simplification

+

Propeller allows you to automatically simplify plushys by removing instructions that have no impact on the error values when evaluating the individual on test cases. To use Propeller’s auto-simplification system, simply include the following four command line arguments when running a problem:

+
:simplification? true
+
+

Toggle auto-simplification

+
:simplification-k 4
+
+

This is the upper bound for elements deleted from the plushy every step. Every step, a number in 1, k of elements is deleted from the plushy representation of the solution.

+
:simplification-steps 1000 
+
+

Number of simplification steps to perform

+
:simplification-verbose? true 
+
+

Whether or not to output simplification info into the output of the evolutionary run. The output with verbose adds the following lines to the output:

+
{:start-plushy-length 42, :k 4}
+{:final-plushy-length 13, :final-plushy (:in1 :in1 :integer_quot :in1 :in1 :exec_dup :in1 :integer_mult close :exec_dup :integer_add 1 :integer_add)}
+
+
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Project

Topics

Namespaces

Variation

+

Propeller includes many kinds of genetic operators to create variation within the population. You can specify the rate of the variation genetic operators with the :variation map.

+

Crossover

+

individual and plushy are synonymous Crossover genetic operators take two plushy representations of Push programs and exchange genetic material to create a new plushy.

+ + + + + + + + + + +
Function Parameters Description
crossover plushy-a plushy-b Crosses over two individuals using uniform crossover, one Push instruction at a time. Pads shorter one from the end of the list of instructions.
tail-aligned-crossover plushy-a plushy-b Crosses over two individuals using uniform crossover, one Push instruction at a time. Pads shorter one from the beginning of the list of instructions.
diploid-crossover plushy-a plushy-b Crosses over two individuals using uniform crossover with pairs of Push instructions. Pads shorter one from the end of the list of instructions.
tail-aligned-diploid-crossover plushy-a plushy-b Crosses over two individuals using uniform crossover with pairs of Push instructions. Pads shorter one from the beginning of the list of instructions.
+

Addition, Deletion, Replacement, Flip

+

Addition, deletion, replacement, and flip genetic operators take a plushy and a rate of occurrence to create a new plushy.

+ + + + + + + + + + + + +
Function Parameters Description
uniform-addition plushy instructions umad-rate Returns a plushy with new instructions possibly added before or after each existing instruction.
uniform-replacement plushy instructions replacement-rate Returns a plushy with new instructions possibly replacing existing instructions.
diploid-uniform-silent-replacement plushy instructions replacement-rate Returns a plushy with new instructions possibly replacing existing instructions, but only among the silent member of each pair.
diploid-uniform-addition plushy instructions umad-rate Returns a plushy with new instructions possibly added before or after each existing pair of instructions.
uniform-deletion plushy umad-rate Randomly deletes instructions from plushy at some rate.
diploid-uniform-deletion plushy flip-rate Randomly flips pairs in a diploid plushy at some rate.
+

Uniform Mutation by Addition and Deletion

+

Uniform Mutation by Addition and Deletion (UMAD) 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. It has been found that UMAD, with relatively high rates of addition and deletion, results in significant increases in problem-solving performance on a range of program synthesis benchmark problems. When you run a problem in Propeller, you can specify the umad-rate to determine the frequency of addition and deletion.

+

:umad in the :variation map when running a problem will call uniform-addition and uniform-deletion with the umad-rate. Since uniform-addition and uniform-deletion are somewhat stochastic, you can use :rumad to ensure that the actual rates of addition and deletion are equal when mutating a genome.

+

New Individual

+

The function new-individual returns a new individual produced by selection and variation of individuals in the population based on the genetic operators provided in the :variation map.

+
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Project

Topics

Namespaces

Propeller 0.3.0

Released under the EPL-2.0 OR GPL-2.0-or-later WITH Classpath-exception-2.0

Yet another Push-based genetic programming system in Clojure.

Installation

To install, add the following dependency to your project or build file:

[net.clojars.lspector/propeller "0.3.0"]

Topics

Namespaces

propeller.core

Public variables and functions:
propeller.genome
Public variables and functions:
propeller.gp
Public variables and functions:
propeller.problems.PSB2.basement
===========  PROBLEM DESCRIPTION  ============================
+BASEMENT from PSB2
+Given a vector of integers, return the first
+index such that the sum of all integers from the start of the
+vector to that index (inclusive) is negative.
Public variables and functions:
propeller.problems.PSB2.bouncing-balls
===========  PROBLEM DESCRIPTION  ===============================
+BOUNCING BALLS from PSB2
+Given a starting height and a height after the first bounce of a
+dropped ball, calculate the bounciness index
+(height of first bounce / starting height). Then, given a number
+of bounces, use the bounciness index to calculate the total
+distance that the ball travels across those bounces.
Public variables and functions:
propeller.problems.PSB2.bowling
===========  PROBLEM DESCRIPTION  ======================
+BOWLING from PSB2
+Given a string representing the individual
+bowls in a 10-frame round of 10 pin bowling, return the
+score of that round.
Public variables and functions:
propeller.problems.PSB2.camel-case
===========  PROBLEM DESCRIPTION  =====================================
+CAMEL CASE from PSB2
+Take a string in kebab-case and convert all of the words to camelCase.
+Each group of words to convert is delimited by "-", and each grouping
+is separated by a space. For example: "camel-case example-test-string"
+→ "camelCase exampleTestString"
Public variables and functions:
propeller.problems.PSB2.dice-game
===========  PROBLEM DESCRIPTION  ===============================
+DICE GAME from PSB2
+Peter has an n sided die and Colin has an m
+sided die. If they both roll their dice at the same time, return
+the probability that Peter rolls strictly higher than Colin.
Public variables and functions:
propeller.problems.PSB2.fizz-buzz
===========  PROBLEM DESCRIPTION  =========================
+FIZZ BUZZ from PSB2
+Given an integer x, return "Fizz" if x is
+divisible by 3, "Buzz" if x is divisible by 5, "FizzBuzz" if x
+is divisible by 3 and 5, and a string version of x if none of
+the above hold.
Public variables and functions:
propeller.problems.PSB2.fuel-cost
===========  PROBLEM DESCRIPTION  =========================
+FUEL COST from PSB2
+Given a vector of positive integers, divide
+each by 3, round the result down to the nearest integer, and
+subtract 2. Return the sum of all of the new integers in the
+vector
Public variables and functions:
propeller.problems.PSB2.gcd
===========  PROBLEM DESCRIPTION  ===============================
+GCD [GREATEST COMMON DIVISOR] from PSB2
+Given two integers, return the largest integer that divides each
+of the integers evenly
Public variables and functions:
propeller.problems.PSB2.luhn
===========  PROBLEM DESCRIPTION  ============================
+LUHN from PSB2
+Given a vector of 16 digits, implement Luhn’s
+algorithm to verify a credit card number, such that it follows
+the following rules: double every other digit starting with
+the second digit. If any of the results are over 9, subtract 9
+from them. Return the sum of all of the new digits.
Public variables and functions:
propeller.problems.PSB2.middle-character
===========  PROBLEM DESCRIPTION  =============================
+MIDDLE CHARACTER from PSB2
+Given a string, return the middle
+character as a string if it is odd length; return the two middle
+characters as a string if it is even length.
Public variables and functions:
propeller.problems.PSB2.paired-digits
===========  PROBLEM DESCRIPTION  =============================
+PAIRED DIGITS from PSB2
+Given a string of digits, return the sum
+of the digits whose following digit is the same.
Public variables and functions:
propeller.problems.PSB2.shopping-list
===========  PROBLEM DESCRIPTION  ===============================
+DICE GAME from PSB2
+Peter has an n sided die and Colin has an m
+sided die. If they both roll their dice at the same time, return
+the probability that Peter rolls strictly higher than Colin.
Public variables and functions:
propeller.problems.PSB2.snow-day
===========  PROBLEM DESCRIPTION  ===============================
+SNOW DAY from PSB2
+Given an integer representing a number
+of hours and 3 floats representing how much snow is on the
+ground, the rate of snow fall, and the proportion of snow
+melting per hour, return the amount of snow on the ground
+after the amount of hours given. Each hour is considered a
+discrete event of adding snow and then melting, not a continuous
+process.
Public variables and functions:
propeller.problems.PSB2.solve-boolean
===========  PROBLEM DESCRIPTION  ================================
+SOLVE BOOLEAN from PSB2
+Given a string representing a Boolean
+expression consisting of T, F, |, and &, evaluate it and return
+the resulting Boolean.
Public variables and functions:
propeller.problems.PSB2.spin-words
===========  PROBLEM DESCRIPTION  ==============================
+SPIN WORDS from PSB2
+Given a string of one or more words
+(separated by spaces), reverse all of the words that are five
+or more letters long and return the resulting string.
Public variables and functions:
propeller.problems.PSB2.square-digits
===========  PROBLEM DESCRIPTION  =========================
+SQUARE DIGITS from PSB2
+Given a positive integer, square each
+digit and concatenate the squares into a returned string.
Public variables and functions:
propeller.problems.PSB2.substitution-cipher
===========  PROBLEM DESCRIPTION  =========================
+SUBSTITUTION CIPHER from PSB2
+This problem gives 3 strings.
+The first two represent a cipher, mapping each character in
+one string to the one at the same index in the other string.
+The program must apply this cipher to the third string and
+return the deciphered message.
Public variables and functions:
propeller.problems.PSB2.twitter
===========  PROBLEM DESCRIPTION  =============================
+TWITTER from PSB2
+Given a string representing a tweet, validate whether the tweet
+meets Twitter’s original character requirements. If the tweet
+has more than 140 characters, return the string "Too many characters".
+If the tweet is empty, return the string "You didn’t type anything".
+Otherwise, return "Your tweet has X characters", where
+the X is the number of characters in the tweet.
Public variables and functions:
propeller.problems.simple-regression
===========  PROBLEM DESCRIPTION  =============================
+Simple Regression:
+Given inputs and outputs, find the target function.
+===============================================================
Public variables and functions:
propeller.problems.software.fizz-buzz
Public variables and functions:
propeller.problems.software.number-io
Public variables and functions:
propeller.problems.software.smallest
Public variables and functions:
propeller.problems.string-classification
===========  PROBLEM DESCRIPTION  =============================
+String Classification:
+Given a string, return true if it contains A, C, G, and T. Else return false.
+===============================================================
Public variables and functions:
propeller.problems.valiant
Public variables and functions:
propeller.push.instructions
Public variables and functions:
propeller.push.instructions.bool
Public variables and functions:
    propeller.push.instructions.character
    Public variables and functions:
      propeller.push.instructions.code
      Public variables and functions:
        propeller.push.instructions.input-output
        Public variables and functions:
        propeller.push.instructions.numeric
        Public variables and functions:
        propeller.push.instructions.polymorphic
        Public variables and functions:
        propeller.push.instructions.string
        Public variables and functions:
          propeller.push.instructions.vector
          Public variables and functions:
          propeller.push.interpreter
          Public variables and functions:
          propeller.push.limits
          Public variables and functions:
          propeller.push.state
          Public variables and functions:
          propeller.selection
          Public variables and functions:
          propeller.session
          Public variables and functions:
            propeller.simplification
            Public variables and functions:
            propeller.tools.calculus
            Public variables and functions:
            propeller.tools.character
            Public variables and functions:
            propeller.tools.distributions
            Public variables and functions:
            propeller.tools.math
            Public variables and functions:
            propeller.tools.metrics
            Public variables and functions:
            propeller.utils
            Public variables and functions:
            propeller.variation
            Public variables and functions:
            
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new file mode 100644
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--- /dev/null
+++ b/doc/doc/codox/intro.html
@@ -0,0 +1,134 @@
+
+Introduction to Propeller
            Project
            Topics
            Namespaces
            Introduction to Propeller
            
+
            Propeller  is an implementation of the Push programming language and the PushGP genetic programming system in Clojure.
            
+
            For more information on Push and PushGP see http://pushlanguage.org.
            
+
            Overview
            
+
            Propeller is a Push-based genetic programming system in Clojure.
            
+
+
+
+
            What can you do with Propeller?
            
+
            You can evolve a program made of Push instructions to solve a problem.
            
+
            Installation
            
+
            You can use either leiningen or deps.edn to run Propeller.
            
+
            If you have installed leiningen, 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.
            
+
            If you have installed Clojure, you can run Propeller on a genetic programming problem with the command clj -m <namespace>, replacing <namespace> with the actual namespace that you will find at the top of the problem file. The examples below use leiningen, but you can replace lein run with clj to run the same problem.
            
+
            How do I run a problem in propeller?
            
+
            To run a problem in propeller, you want to call the -main function in the problem file using leiningen. The -main function will create a map of arguments from the input and run the main genetic programming loop.
            
+
            Below is the general format to run a problem through the command-line:
            
+
            lein run -m <namespace of the problem file you want to test>
+
            
+
            Additional command-line arguments may be provided to override the default key/value pairs specified in the problem file,
            
+
            lein run -m <namespace of the problem file you want to test> <key and value> <key and value>...
+
            
+
            The possible keys come from the table below:
            
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
             Key                         Description                                                                                                                                                                                                                                                                 
             :instructions             List of possible Push instructions used to create a plushy                                                                                                                                                                                                                  
             :error-function           The error function used to evaluate individuals, specified in the given problem’s namespace                                                                                                                                                                                 
             :training-data            Map of inputs and desired outputs used to evaluate individuals of the form: {:input1 first-input :input2 second-input … :output1 first-output …}                                                                                                                        
             :testing-data             Map of inputs and desired outputs not in the training-data to test generalizability of a program that fits the training-data. The map is of the form: {:input1 first-input :input2 second-input … :output1 first-output …}                                            
             :max-generations          Maximum number of generations                                                                                                                                                                                                                                               
             :population-size          Size of population in a generation                                                                                                                                                                                                                                          
             :max-initial-plushy-size  Maximum number of Push instructions in the initial plushy                                                                                                                                                                                                                   
             :step-limit               The maximum number of steps that a Push program will be executed by interpret-program                                                                                                                                                                                     
             :parent-selection         Function from propeller.selection that determines method of parent selection method. Propeller includes :tournament-selection, :lexicase-selection, and :epsilon-lexicase-selection.                                                                                
             :tournament-size          If using a tournament selection method, the number of individuals in each tournaments used to determine parents                                                                                                                                                             
             :umad-rate                Rate (decimal between 0 and 1) of uniform mutation by addition and deletion (UMAD) genetic operator                                                                                                                                                                         
             :variation                Map with genetic operators as keys and probabilities as values. For example, {:umad 0.3 :crossover 0.7}. This would mean that when the system needs to generate a child, it will use UMAD 30% of the time and crossover 70% of the time. The probabilities should sum to 1. 
             :elitism                  When true, will cause the individual with the lowest error in the population to survive, without variation, into the next generation.                                                                                                                                       
            
+
            When you run a problem, you will get a report each generation with the following information:
            
+
            :generation            
+ :best-plushy 
+ :best-program          
+ :best-total-error      
+ :best-errors        
+ :best-behaviors        
+ :genotypic-diversity   
+ :behavioral-diversity  
+ :average-genome-length 
+ :average-total-error 
+
            
+
            An Example
            
+
            For example, you can run the simple-regression genetic programming problem with:
            
+
            lein run -m propeller.problems.simple-regression
+
            
+
            This will run simple-regression with the default set of arguments in the simple-regression problem file.
            
+
            {: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}
+
            
+
            You can override the default key/value pairs with additional arguments. 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}"
+
            
+
            Can you use a REPL?
            
+
            Yes!
            
+
            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).
            
+
            Tutorials
            
+
              
+
            • Adding genetic operators
              • 
+
            • Adding selection methods
              • 
+
            • Adding a new problem
              • 
+
            • How to use simplification
              • 
+
            • Experimentation Guide
              • 
+
            
+
            Contributing
            
+
            You can report a bug on the GitHub issues page.
            
+
            The best way to contribute to propeller is to fork the main GitHub repository and submit a pull request.
            
+
            License
            
+
            Eclipse Public License 2.0 This commercially-friendly copyleft license provides the ability to commercially license binaries; a modern royalty-free patent license grant; and the ability for linked works to use other licenses, including commercial ones.
            
+
            Citation
            
+
            We are in the process of creating a DOI, but in the meantime, we ask that you cite the link to the repository if you use Propeller.
            
+
            About Propeller
            
+
            https://deap.readthedocs.io/en/master/about.html
            
+
            Contact
            
+
            Library Reference
            
+
            
\ No newline at end of file
diff --git a/doc/doc/codox/js/highlight.min.js b/doc/doc/codox/js/highlight.min.js
new file mode 100644
index 0000000..6486ffd
--- /dev/null
+++ b/doc/doc/codox/js/highlight.min.js
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