rubyneat 0.3.5.alpha.2

data/neater/xor_neat.rb

@@ -0,0 +1,137 @@
+#!/usr/bin/env neat
+require 'rubyneat/dsl'
+require 'xor'
+
+include NEAT::DSL
+
+#= TEST FOR RubyNEAT
+
+# 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 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 0.25
+
+  # Complete Change of weight
+  mutate_change_gene_weights_prob 0.10
+  mutate_change_gene_weights_sd 1.00
+
+  # Adding new neurons and genes
+  mutate_add_neuron_prob 0.05
+  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
+      #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}]"
+      1.0
+    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/xoranalog_neat.rb

@@ -0,0 +1,138 @@
+#!/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

@@ -0,0 +1,143 @@
+#!/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

@@ -0,0 +1,180 @@
+<?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$/lib/deep_dive" />
+      <RUBY_RUN_CONFIG NAME="SHOULD_USE_SDK" VALUE="false" />
+      <RUBY_RUN_CONFIG NAME="ALTERN_SDK_NAME" VALUE="" />
+      <RUBY_RUN_CONFIG NAME="myPassParentEnvs" VALUE="true" />
+      <envs />
+      <EXTENSION ID="BundlerRunConfigurationExtension" bundleExecEnabled="false" />
+      <EXTENSION ID="JRubyRunConfigurationExtension" NailgunExecEnabled="false" />
+      <EXTENSION ID="RubyCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" track_test_folders="true" runner="rcov">
+        <COVERAGE_PATTERN ENABLED="true">
+          <PATTERN REGEXPS="/.rvm/" INCLUDED="false" />
+        </COVERAGE_PATTERN>
+      </EXTENSION>
+      <EXTENSION ID="org.jetbrains.plugins.ruby.motion.run.MotionSimulatorRunExtension" />
+      <RUBY_RUN_CONFIG NAME="SCRIPT_PATH" VALUE="$MODULE_DIR$/lib/deep_dive/deep_dive.rb" />
+      <RUBY_RUN_CONFIG NAME="SCRIPT_ARGS" VALUE="" />
+      <RunnerSettings RunnerId="RubyDebugRunner" />
+      <ConfigurationWrapper RunnerId="RubyDebugRunner" />
+      <method />
+    </configuration>
+  </component>
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/spec" isTestSource="true" />
+    </content>
+    <orderEntry type="jdk" jdkName="RVM: ruby-2.0.0-p353" jdkType="RUBY_SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
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+</module>
+

data/public/.directory

@@ -0,0 +1,4 @@
+[Dolphin]
+PreviewsShown=true
+Timestamp=2014,2,8,20,33,7
+Version=3