rubyneat 0.3.5.alpha.3 → 0.3.5.alpha.5

data/neater/xoranalog_neat.rb

@@ -1,138 +0,0 @@
-#!/usr/bin/env neat
-require 'rubyneat/dsl'
-require 'xor'
-
-include NEAT::DSL
-
-#= TEST FOR RubyNEAT -- Analog Fitness Vector for XOR
-
-# The number of inputs to the xor function
-XOR_INPUTS = 2
-XOR_STATES = 2 ** XOR_INPUTS
-MAX_FIT    = XOR_STATES
-ALMOST_FIT = XOR_STATES - 0.3
-
-# This defines the controller
-define "XOR Analog Fitness System" do
-  # Define the IO neurons
-  inputs {
-    cinv = Hash[(1..XOR_INPUTS).map{|i| [("i%s" % i).to_sym, InputNeuron]}]
-    cinv[:bias] = BiasNeuron
-    cinv
-  }
-  outputs out: TanhNeuron
-
-  # Hidden neuron specification is optional. 
-  # The name given here is largely meaningless, but may be useful as some sort
-  # of unique flag.
-  hidden tan: TanhNeuron
-
-  ### Settings
-  ## General
-  hash_on_fitness false
-  start_population_size 30
-  population_size 30
-  max_generations 10000
-  max_population_history 10
-
-  ## Evolver probabilities and SDs
-  # Perturbations
-  mutate_perturb_gene_weights_prob 0.10
-  mutate_perturb_gene_weights_sd 0.50
-
-  # Complete Change of weight
-  mutate_change_gene_weights_prob 0.05
-  mutate_change_gene_weights_sd 2.00
-
-
-  # Adding new neurons and genes
-  mutate_add_neuron_prob 0.07
-  mutate_add_gene_prob 0.20
-
-  # Switching genes on and off
-  mutate_gene_disable_prob 0.01
-  mutate_gene_reenable_prob 0.01
-
-  interspecies_mate_rate 0.03
-  mate_only_prob 0.10 #0.7
-
-  # Mating
-  survival_threshold 0.20 # top % allowed to mate in a species.
-  survival_mininum_per_species  4 # for small populations, we need SOMETHING to go on.
-
-  # Fitness costs
-  fitness_cost_per_neuron 0#.00001
-  fitness_cost_per_gene   0#.00001
-
-  # Speciation
-  compatibility_threshold 2.5
-  disjoint_coefficient 0.6
-  excess_coefficient 0.6
-  weight_coefficient 0.2
-  max_species 20
-  dropoff_age 15
-  smallest_species 5
-
-  # Sequencing
-  start_sequence_at 0
-  end_sequence_at 2 ** XOR_INPUTS - 1
-end
-
-evolve do
-  # This query shall return a vector result that will serve
-  # as the inputs to the critter. 
-  query { |seq|
-    # We'll use the seq to create the xor sequences via
-    # the least signficant bits.
-    condition_boolean_vector (0 ... XOR_INPUTS).map{|i| (seq & (1 << i)) != 0}
-  }
-
-  # Compare the fitness of two critters. We may choose a different ordering
-  # here.
-  compare {|f1, f2| f2 <=> f1 }
-
-  # Here we integrate the cost with the fitness.
-  cost { |fitvec, cost|
-    fit = XOR_STATES - fitvec.reduce {|a,r| a+r} - cost
-    $log.debug ">>>>>>> fitvec #{fitvec} => #{fit}, cost #{cost}"
-    fit
-  }
-
-  fitness { |vin, vout, seq|
-    unless vout == :error
-      bin = uncondition_boolean_vector vin
-      bout = uncondition_boolean_vector vout
-      bactual = [xor(*vin)]
-      vactual = condition_boolean_vector bactual
-      #fit = (bout == bactual) ? 0.00 : 1.00
-      fit = simple_fitness_error(vout, vactual) / 2.0
-      bfit = (bout == bactual) ? 'T' : 'F'
-      $log.debug "(%s) Fitness bin=%s, bout=%s, bactual=%s, vout=%s, fit=%6.3f, seq=%s" % [bfit,
-                                                                                           bin,
-                                                                                           bout,
-                                                                                           bactual,
-                                                                                           vout,
-                                                                                           fit,
-                                                                                           seq]
-      fit
-    else
-      $log.debug "Error on #{vin} [#{seq}]"
-      1.0
-    end
-  }
-
-  stop_on_fitness {|fitness, c|
-    puts "*** Generation Run #{c.generation_num}, best is #{fitness[:best]} ***\n\n"
-    fitness[:best] >= ALMOST_FIT
-  }
-end
-
-report do |rept|
-  $log.info "REPORT #{rept.to_yaml}"
-end
-
-# The block here is called upon the completion of each generation
-run_engine do |c|
-  $log.info "******** Run of generation %s completed, history count %d ********" %
-        [c.generation_num, c.population_history.size]
-end

data/neater/xorsin_neat.rb

@@ -1,143 +0,0 @@
-#!/usr/bin/env neat
-require 'rubyneat/dsl'
-require 'xor'
-
-include NEAT::DSL
-
-#= DEBUGGING FOR RubyNEAT using SineNeurons
-
-# The number of inputs to the xor function
-XOR_INPUTS = 2
-XOR_STATES = 2 ** XOR_INPUTS
-MAX_FIT    = XOR_STATES
-ALMOST_FIT = (XOR_STATES - 0.5)
-
-# This defines the controller
-define "XOR Sin CPPN Debug System" do
-  # Define the IO neurons
-  inputs {
-    cinv = Hash[(1..XOR_INPUTS).map{|i| [("i%s" % i).to_sym, InputNeuron]}]
-    cinv[:bias] = BiasNeuron
-    cinv
-  }
-  outputs out: SineNeuron
-
-  # Hidden neuron specification is optional. 
-  # The key names given here is largely meaningless,
-  # but may be useful as some sort
-  # of unique flag.
-  hidden sin: SineNeuron, cos: CosineNeuron, tanh: TanhNeuron
-
-  ### Settings
-  ## General
-  hash_on_fitness = false
-  start_population_size 60
-  population_size 60
-  max_generations 10000
-  max_population_history 10
-
-  ## Evolver probabilities and SDs
-  # Perturbations
-  mutate_perturb_gene_weights_prob 0.200
-  mutate_perturb_gene_weights_sd 0.25
-
-  # Complete Change of weight
-  mutate_change_gene_weights_prob 0.01
-  mutate_change_gene_weights_sd 2.00
-
-  # Adding new neurons and genes
-  mutate_add_neuron_prob 0.20
-  mutate_add_gene_prob 0.20
-
-  # Switching genes on and off
-  mutate_gene_disable_prob 0.01
-  mutate_gene_reenable_prob 0.01
-
-  interspecies_mate_rate 0.03
-  mate_only_prob 0.05
-
-  # Mating
-  survival_threshold 0.20 # top % allowed to mate in a species.
-  survival_mininum_per_species  4 # for small populations, we need SOMETHING to go on.
-
-  # Fitness costs
-  fitness_cost_per_neuron 0.00001
-  fitness_cost_per_gene   0.00001
-
-  # Speciation
-  compatibility_threshold 2.5
-  disjoint_coefficient 0.6
-  excess_coefficient 0.6
-  weight_coefficient 0.2
-  max_species 20
-  dropoff_age 15
-  smallest_species 5
-
-  # Sequencing
-  start_sequence_at 0
-  end_sequence_at 2 ** XOR_INPUTS - 1
-end
-
-evolve do
-  # This query shall return a vector result that will serve
-  # as the inputs to the critter. 
-  query { |seq| @seq = seq
-    # We'll use the seq to create the xor sequences via
-    # the least signficant bits.
-    condition_boolean_vector (0 ... XOR_INPUTS).map{|i| (seq & (1 << i)) != 0}
-  }
-
-  # This block is called directly by the neuron through its yield, if given.
-  # It will be called repeatedly until you return false here.
-  recurrence { |outvec| false }
-
-  # Compare the fitness of two critters. We may choose a different ordering
-  # here.
-  compare {|f1, f2| f2 <=> f1 }
-
-  # Here we integrate the cost with the fitness.
-  cost { |fitvec, cost|
-    fit = (XOR_STATES - fitvec.reduce {|a,r| a+r}) - cost # ((rand(5) == 0) ? cost : 0)
-    $log.debug ">>>>>>> fitvec #{fitvec} => #{fit}, cost #{cost}"
-    fit
-  }
-
-  fitness { |vin, vout, seq|
-    unless vout == :error
-      bin = uncondition_boolean_vector vin
-      bout = uncondition_boolean_vector vout
-      bactual = [xor(*vin)]
-      vactual = condition_boolean_vector bactual
-      fit = (bout == bactual) ? 0.00 : 1.00
-      #simple_fitness_error(vout, vactual.map{|f| f * 0.50 })
-      bfit = (bout == bactual) ? 'T' : 'F'
-      $log.debug "(%s) Fitness bin=%s, bout=%s, bactual=%s, vout=%s, fit=%6.3f, seq=%s" % [bfit,
-                                                                                           bin,
-                                                                                           bout,
-                                                                                           bactual,
-                                                                                           vout,
-                                                                                           fit,
-                                                                                           seq]
-      fit
-    else
-      $log.debug "Error on #{vin} [#{seq}]"
-      1.00
-    end
-  }
-
-  stop_on_fitness {|fitness, c|
-    puts "*** Generation Run #{c.generation_num}, best is #{fitness[:best]} ***\n\n"
-    fitness[:best] >= MAX_FIT - 0.5
-  }
-end
-
-report do |rept|
-  $log.info "REPORT #{rept.to_yaml}"
-end
-
-# The block here is called upon the completion of each generation
-run_engine do |c|
-  $log.info "******** Run of generation %s completed, history count %d ********" %
-        [c.generation_num, c.population_history.size]
-end
-

data/projectFilesBackup/.idea/rubyneat.iml

@@ -1,180 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="RUBY_MODULE" version="4">
-  <component name="ModuleRunConfigurationManager">
-    <configuration default="false" name="Run spec 'oread_spec': rubyneat" type="RSpecRunConfigurationType" factoryName="RSpec" temporary="true">
-      <predefined_log_file id="RUBY_RSPEC" enabled="true" />
-      <module name="rubyneat" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="RUBY_ARGS" VALUE="-e $stdout.sync=true;$stderr.sync=true;load($0=ARGV.shift)" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="WORK DIR" VALUE="$MODULE_DIR$" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="SHOULD_USE_SDK" VALUE="false" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="ALTERN_SDK_NAME" VALUE="" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="myPassParentEnvs" VALUE="true" />
-      <envs>
-        <env name="JRUBY_OPTS" value="-X+O" />
-      </envs>
-      <EXTENSION ID="BundlerRunConfigurationExtension" bundleExecEnabled="false" />
-      <EXTENSION ID="JRubyRunConfigurationExtension" NailgunExecEnabled="false" />
-      <EXTENSION ID="RubyCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" track_test_folders="true" runner="rcov">
-        <COVERAGE_PATTERN ENABLED="true">
-          <PATTERN REGEXPS="/.rvm/" INCLUDED="false" />
-        </COVERAGE_PATTERN>
-      </EXTENSION>
-      <EXTENSION ID="org.jetbrains.plugins.ruby.motion.run.MotionSimulatorRunExtension" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="TESTS_FOLDER_PATH" VALUE="" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="TEST_SCRIPT_PATH" VALUE="$MODULE_DIR$/spec/lib/deep_dive/deep_dive_spec.rb" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="SPEC_RUNNER_PATH" VALUE="" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="TEST_FILE_MASK" VALUE="**/*_spec.rb" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="SPEC_EXAMPLE_NAME" VALUE="" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="TEST_TEST_TYPE" VALUE="TEST_SCRIPT" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="SPEC_ARGS" VALUE="" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="RUNNER_VERSION" VALUE="" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="USE_CUSTOM_SPEC_RUNNER" VALUE="false" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="DRB" VALUE="false" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="ZEUS" VALUE="false" />
-      <RSPEC_RUN_CONFIG_SETTINGS_ID NAME="FULL_BACKTRACE" VALUE="false" />
-      <RunnerSettings RunnerId="RubyDebugRunner" />
-      <ConfigurationWrapper RunnerId="RubyDebugRunner" />
-      <method />
-    </configuration>
-    <configuration default="false" name="neat" type="RubyRunConfigurationType" factoryName="Ruby">
-      <module name="rubyneat" />
-      <RUBY_RUN_CONFIG NAME="RUBY_ARGS" VALUE="-e $stdout.sync=true;$stderr.sync=true;load($0=ARGV.shift)" />
-      <RUBY_RUN_CONFIG NAME="WORK DIR" VALUE="$MODULE_DIR$/bin" />
-      <RUBY_RUN_CONFIG NAME="SHOULD_USE_SDK" VALUE="false" />
-      <RUBY_RUN_CONFIG NAME="ALTERN_SDK_NAME" VALUE="" />
-      <RUBY_RUN_CONFIG NAME="myPassParentEnvs" VALUE="true" />
-      <envs>
-        <env name="RUBYLIB" value="$MODULE_DIR$/lib:$MODULE_DIR$/neater" />
-      </envs>
-      <EXTENSION ID="BundlerRunConfigurationExtension" bundleExecEnabled="false" />
-      <EXTENSION ID="JRubyRunConfigurationExtension" NailgunExecEnabled="false" />
-      <EXTENSION ID="RubyCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" track_test_folders="true" runner="rcov">
-        <COVERAGE_PATTERN ENABLED="true">
-          <PATTERN REGEXPS="/.rvm/" INCLUDED="false" />
-        </COVERAGE_PATTERN>
-      </EXTENSION>
-      <EXTENSION ID="org.jetbrains.plugins.ruby.motion.run.MotionSimulatorRunExtension" />
-      <RUBY_RUN_CONFIG NAME="SCRIPT_PATH" VALUE="$MODULE_DIR$/bin/neat.rb" />
-      <RUBY_RUN_CONFIG NAME="SCRIPT_ARGS" VALUE="run xor" />
-      <RunnerSettings RunnerId="RubyCover" />
-      <RunnerSettings RunnerId="RubyDebugRunner" />
-      <RunnerSettings RunnerId="RubyRunner" />
-      <ConfigurationWrapper RunnerId="RubyCover" />
-      <ConfigurationWrapper RunnerId="RubyDebugRunner" />
-      <ConfigurationWrapper RunnerId="RubyRunner" />
-      <method />
-    </configuration>
-    <configuration default="false" name="xor_neat" type="RubyRunConfigurationType" factoryName="Ruby">
-      <module name="rubyneat" />
-      <RUBY_RUN_CONFIG NAME="RUBY_ARGS" VALUE="-e $stdout.sync=true;$stderr.sync=true;load($0=ARGV.shift)" />
-      <RUBY_RUN_CONFIG NAME="WORK DIR" VALUE="$MODULE_DIR$" />
-      <RUBY_RUN_CONFIG NAME="SHOULD_USE_SDK" VALUE="false" />
-      <RUBY_RUN_CONFIG NAME="ALTERN_SDK_NAME" VALUE="" />
-      <RUBY_RUN_CONFIG NAME="myPassParentEnvs" VALUE="true" />
-      <envs />
-      <EXTENSION ID="BundlerRunConfigurationExtension" bundleExecEnabled="false" />
-      <EXTENSION ID="JRubyRunConfigurationExtension" NailgunExecEnabled="false" />
-      <EXTENSION ID="RubyCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" track_test_folders="true" runner="rcov">
-        <COVERAGE_PATTERN ENABLED="true">
-          <PATTERN REGEXPS="/.rvm/" INCLUDED="false" />
-        </COVERAGE_PATTERN>
-      </EXTENSION>
-      <EXTENSION ID="org.jetbrains.plugins.ruby.motion.run.MotionSimulatorRunExtension" />
-      <RUBY_RUN_CONFIG NAME="SCRIPT_PATH" VALUE="$MODULE_DIR$/xor_neat.rb" />
-      <RUBY_RUN_CONFIG NAME="SCRIPT_ARGS" VALUE="" />
-      <RunnerSettings RunnerId="RubyDebugRunner" />
-      <RunnerSettings RunnerId="RubyRunner" />
-      <ConfigurationWrapper RunnerId="RubyDebugRunner" />
-      <ConfigurationWrapper RunnerId="RubyRunner" />
-      <method />
-    </configuration>
-    <configuration default="false" name="deep_dive" type="RubyRunConfigurationType" factoryName="Ruby" temporary="true">
-      <module name="rubyneat" />
-      <RUBY_RUN_CONFIG NAME="RUBY_ARGS" VALUE="-e $stdout.sync=true;$stderr.sync=true;load($0=ARGV.shift)" />
-      <RUBY_RUN_CONFIG NAME="WORK DIR" VALUE="$MODULE_DIR$/lib/deep_dive" />
-      <RUBY_RUN_CONFIG NAME="SHOULD_USE_SDK" VALUE="false" />
-      <RUBY_RUN_CONFIG NAME="ALTERN_SDK_NAME" VALUE="" />
-      <RUBY_RUN_CONFIG NAME="myPassParentEnvs" VALUE="true" />
-      <envs />
-      <EXTENSION ID="BundlerRunConfigurationExtension" bundleExecEnabled="false" />
-      <EXTENSION ID="JRubyRunConfigurationExtension" NailgunExecEnabled="false" />
-      <EXTENSION ID="RubyCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" track_test_folders="true" runner="rcov">
-        <COVERAGE_PATTERN ENABLED="true">
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-        </COVERAGE_PATTERN>
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-      <EXTENSION ID="org.jetbrains.plugins.ruby.motion.run.MotionSimulatorRunExtension" />
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-    </configuration>
-  </component>
-  <component name="NewModuleRootManager">
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/spec" isTestSource="true" />
-    </content>
-    <orderEntry type="jdk" jdkName="RVM: ruby-2.0.0-p353" jdkType="RUBY_SDK" />
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