charlie 0.6.0 → 0.7.0

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Files changed (66) hide show
  1. data/History.txt +14 -0
  2. data/Manifest.txt +13 -22
  3. data/README.txt +3 -3
  4. data/Rakefile +1 -1
  5. data/TODO.txt +11 -21
  6. data/data/BENCHMARK +25 -23
  7. data/data/CROSSOVER +5 -1
  8. data/data/GENOTYPE +6 -6
  9. data/data/MUTATION +19 -7
  10. data/data/SELECTION +2 -1
  11. data/data/template.html +2 -1
  12. data/examples/EXAMPLES_README.txt +70 -0
  13. data/examples/bitstring.rb +72 -0
  14. data/examples/{gladiatorial_sunburn.rb → coevolution.rb} +80 -22
  15. data/examples/function_optimization.rb +113 -0
  16. data/examples/output/{royalroad1_report.html → bitstring_royalroad.html} +822 -655
  17. data/examples/output/function_optimization_sombrero.html +2289 -0
  18. data/examples/output/function_optimization_twopeak.csv +210 -0
  19. data/examples/output/function_optimization_twopeak.html +2477 -0
  20. data/examples/output/string_weasel.html +513 -0
  21. data/examples/output/tsp.html +633 -882
  22. data/examples/{money.rb → permutation.rb} +20 -8
  23. data/examples/string.rb +98 -0
  24. data/examples/tree.rb +37 -12
  25. data/examples/tsp.rb +34 -22
  26. data/lib/charlie.rb +5 -1
  27. data/lib/charlie/1.9fixes.rb +46 -0
  28. data/lib/charlie/crossover.rb +31 -14
  29. data/lib/charlie/etc/minireport.rb +5 -4
  30. data/lib/charlie/etc/monkey.rb +11 -8
  31. data/lib/charlie/gabenchmark.rb +230 -0
  32. data/lib/charlie/genotype.rb +4 -0
  33. data/lib/charlie/list/list_crossover.rb +25 -5
  34. data/lib/charlie/mutate.rb +34 -7
  35. data/lib/charlie/permutation/permutation.rb +34 -6
  36. data/lib/charlie/population.rb +12 -122
  37. data/lib/charlie/selection.rb +1 -0
  38. data/lib/charlie/tree/tree.rb +179 -17
  39. data/test/t_common.rb +1 -1
  40. data/test/test_benchmark.rb +19 -5
  41. data/test/test_cross.rb +23 -1
  42. data/test/test_evolve.rb +14 -1
  43. data/test/test_mutator.rb +28 -2
  44. data/test/test_permutation.rb +23 -1
  45. data/test/test_sel.rb +3 -1
  46. data/test/test_tree.rb +63 -1
  47. metadata +17 -25
  48. data/examples/bit.rb +0 -10
  49. data/examples/function_opt_2peak.rb +0 -24
  50. data/examples/function_opt_sombero.rb +0 -38
  51. data/examples/gladiatorial_simple.rb +0 -17
  52. data/examples/gridwalk.rb +0 -29
  53. data/examples/output/flattened_sombero.html +0 -6400
  54. data/examples/output/flattened_sombero2_.html +0 -3576
  55. data/examples/output/fopt1_dblopt.html +0 -2160
  56. data/examples/output/hill10.html +0 -5816
  57. data/examples/output/hill2.csv +0 -24
  58. data/examples/output/hill2.html +0 -384
  59. data/examples/output/royalroad2_report.html +0 -1076
  60. data/examples/output/royalroadquick_report.html +0 -504
  61. data/examples/output/weasel1_report.html +0 -1076
  62. data/examples/output/weasel2_report.html +0 -240
  63. data/examples/royalroad.rb +0 -26
  64. data/examples/royalroad2.rb +0 -18
  65. data/examples/simple_climb_hill2.rb +0 -47
  66. data/examples/weasel.rb +0 -36
data/examples/output/weasel2_report.html DELETED
@@ -1,240 +0,0 @@
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- <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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-
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- <html xmlns="http://www.w3.org/1999/xhtml">
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- <head>
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- <meta http-equiv="content-type" content="text/html;charset=UTF-8" />
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- <title>GA Benchmark Report</title>
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- <style type='text/css'>
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- table{
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- background: #ccc;
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- font-family: Verdana, Helvetica, sans-serif;
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- }
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- th {
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- background: #666;
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- color: white;
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- padding: 3px;
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- font-weight: bold;
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- }
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- td {
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- color: #333;
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- background: #e2e2e2;
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- padding: 2px;
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- text-align: center;
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- }
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- </style>
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-
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- </script>
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- <script type="text/javascript">
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-
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- </script>
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- </head>
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- <body>
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- <h1>Information</h1>
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-
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- <table>
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- <tr><td>Genotype class</td><td>Weasel</td></tr>
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- <tr><td>Population size</td><td>20</td></tr>
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- <tr><td># of generations per run</td><td>50</td></tr>
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- <tr><td>Number of tests </td><td>12</td></tr>
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- <tr><td>Tests repeated </td><td>10 times</td></tr>
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- <tr><td>Number of runs </td><td>120</td></tr>
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- <tr><td>Total number of generations </td><td>6000</td></tr>
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- <tr><td>Total time</td><td>23.51 seconds</td></tr>
43
- </table
44
- <h1>Stats for all</h1><table>
45
- <tr><th>.</th><th>min</th><th>max</th><th>avg</th><th>stddev</th><th>avg-time</th></tr>
46
- <tr>
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- <td>All</td>
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- <td>13.00000</td>
49
- <td>22.00000</td>
50
- <td>17.80833</td>
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- <td>2.25202</td>
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- <td>0.19585</td>
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- </tr>
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- </table><h1>Stats for selection</h1><table>
55
- <tr><th>selection</th><th>min</th><th>max</th><th>avg</th><th>stddev</th><th>avg-time</th></tr>
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- <tr>
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- <td>TruncationSelection(0.2)</td>
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- <td>13.00000</td>
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- <td>22.00000</td>
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- <td>17.86667</td>
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- <td>2.17153</td>
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- <td>0.19556</td>
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- </tr>
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- <tr>
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- <td>TruncationSelection(1)</td>
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- <td>13.00000</td>
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- <td>22.00000</td>
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- <td>17.75000</td>
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- <td>2.32827</td>
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- <td>0.19614</td>
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- </tr>
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- </table><h1>Stats for crossover</h1><table>
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- <tr><th>crossover</th><th>min</th><th>max</th><th>avg</th><th>stddev</th><th>avg-time</th></tr>
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- <tr>
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- <td>UniformCrossover</td>
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- <td>14.00000</td>
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- <td>22.00000</td>
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- <td>19.00000</td>
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- <td>2.00000</td>
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- <td>0.21745</td>
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- </tr>
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- <tr>
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- <td>SinglePointCrossover</td>
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- <td>14.00000</td>
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- <td>22.00000</td>
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- <td>18.20000</td>
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- <td>1.90000</td>
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- <td>0.18830</td>
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- </tr>
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- <tr>
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- <td>NullCrossover</td>
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- <td>13.00000</td>
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- <td>20.00000</td>
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- <td>16.22500</td>
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- <td>1.87733</td>
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- <td>0.18179</td>
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- </tr>
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- </table><h1>Stats for mutation</h1><table>
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- <tr><th>mutation</th><th>min</th><th>max</th><th>avg</th><th>stddev</th><th>avg-time</th></tr>
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- <tr>
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- <td>ListMutator([:n_point, 2],[:replace, "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", " "])</td>
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- <td>13.00000</td>
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- <td>22.00000</td>
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- <td>18.23333</td>
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- <td>2.01136</td>
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- <td>0.20229</td>
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- </tr>
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- <tr>
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- <td>ListMutator(:single_point,[:replace, "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", " "])</td>
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- <td>13.00000</td>
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- <td>22.00000</td>
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- <td>17.38333</td>
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- <td>2.39508</td>
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- <td>0.18940</td>
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- </tr>
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- </table><h1>Raw Stats</h1><table>
117
- <tr><th>selection</th><th>crossover</th><th>mutation</th><th>min</th><th>max</th><th>avg</th><th>stddev</th><th>avg-time</th></tr>
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- <tr>
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- <td>TruncationSelection(1)</td>
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- <td>UniformCrossover</td>
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- <td>ListMutator([:n_point, 2],[:replace, "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", " "])</td>
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- <td>18.00000</td>
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- <td>22.00000</td>
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- <td>19.50000</td>
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- <td>1.02470</td>
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- <td>0.22375</td>
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- </tr>
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- <tr>
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- <td>TruncationSelection(0.2)</td>
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- <td>UniformCrossover</td>
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- <td>ListMutator([:n_point, 2],[:replace, "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", " "])</td>
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- <td>17.00000</td>
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- <td>22.00000</td>
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- <td>19.50000</td>
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- <td>1.50000</td>
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- <td>0.22246</td>
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- </tr>
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- <tr>
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- <td>TruncationSelection(1)</td>
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- <td>SinglePointCrossover</td>
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- <td>ListMutator([:n_point, 2],[:replace, "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", " "])</td>
142
- <td>16.00000</td>
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- <td>22.00000</td>
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- <td>18.80000</td>
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- <td>2.03961</td>
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- <td>0.19627</td>
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- </tr>
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- <tr>
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- <td>TruncationSelection(0.2)</td>
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- <td>UniformCrossover</td>
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- <td>ListMutator(:single_point,[:replace, "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", " "])</td>
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- <td>14.00000</td>
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- <td>22.00000</td>
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- <td>18.50000</td>
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- <td>2.37697</td>
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- <td>0.21168</td>
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- </tr>
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- <tr>
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- <td>TruncationSelection(1)</td>
160
- <td>UniformCrossover</td>
161
- <td>ListMutator(:single_point,[:replace, "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", " "])</td>
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- <td>16.00000</td>
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- <td>22.00000</td>
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- <td>18.50000</td>
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- <td>2.45967</td>
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- <td>0.21192</td>
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- </tr>
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- <tr>
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- <td>TruncationSelection(0.2)</td>
170
- <td>SinglePointCrossover</td>
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- <td>ListMutator([:n_point, 2],[:replace, "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", " "])</td>
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- <td>16.00000</td>
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- <td>21.00000</td>
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- <td>18.20000</td>
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- <td>1.53623</td>
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- <td>0.19442</td>
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- </tr>
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- <tr>
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- <td>TruncationSelection(0.2)</td>
180
- <td>SinglePointCrossover</td>
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- <td>ListMutator(:single_point,[:replace, "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", " "])</td>
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- <td>14.00000</td>
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- <td>21.00000</td>
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- <td>18.10000</td>
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- <td>2.21133</td>
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- <td>0.18162</td>
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- </tr>
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- <tr>
189
- <td>TruncationSelection(1)</td>
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- <td>SinglePointCrossover</td>
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- <td>ListMutator(:single_point,[:replace, "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", " "])</td>
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- <td>15.00000</td>
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- <td>20.00000</td>
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- <td>17.70000</td>
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- <td>1.55242</td>
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- <td>0.18088</td>
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- </tr>
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- <tr>
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- <td>TruncationSelection(1)</td>
200
- <td>NullCrossover</td>
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- <td>ListMutator([:n_point, 2],[:replace, "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", " "])</td>
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- <td>14.00000</td>
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- <td>20.00000</td>
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- <td>16.80000</td>
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- <td>1.83303</td>
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- <td>0.18853</td>
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- </tr>
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- <tr>
209
- <td>TruncationSelection(0.2)</td>
210
- <td>NullCrossover</td>
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- <td>ListMutator([:n_point, 2],[:replace, "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", " "])</td>
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- <td>13.00000</td>
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- <td>20.00000</td>
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- <td>16.60000</td>
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- <td>1.68523</td>
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- <td>0.18833</td>
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- </tr>
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- <tr>
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- <td>TruncationSelection(0.2)</td>
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- <td>NullCrossover</td>
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- <td>ListMutator(:single_point,[:replace, "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", " "])</td>
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- <td>14.00000</td>
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- <td>19.00000</td>
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- <td>16.30000</td>
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- <td>1.73494</td>
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- <td>0.17482</td>
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- </tr>
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- <tr>
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- <td>TruncationSelection(1)</td>
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- <td>NullCrossover</td>
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- <td>ListMutator(:single_point,[:replace, "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", " "])</td>
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- <td>13.00000</td>
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- <td>18.00000</td>
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- <td>15.20000</td>
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- <td>1.83303</td>
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- <td>0.17549</td>
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- </tr>
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- </table>
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- </body>
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- </html>
data/examples/royalroad.rb DELETED
@@ -1,26 +0,0 @@
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- require '../lib/charlie'
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-
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- class RoyalRoad < BitStringGenotype(64) # Royal Road problem
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- def fitness
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- 1e-6 + genes.enum_slice(8).find_all{|e| e.all?{|x|x==1} }.size
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- end
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- #use TruncationSelection()
8
- use RouletteSelection
9
- end
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-
11
- Population.new(RoyalRoad).evolve_on_console(1000)
12
-
13
- Population.benchmark(RoyalRoad,'output/royalroad1_report.html'){
14
- selection TruncationSelection(), Elitism(ScaledRouletteSelection(),1), Elitism(RouletteSelection,1), BestOnlySelection, ScaledRouletteSelection()
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- crossover NullCrossover, SinglePointCrossover, UniformCrossover
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- mutator ListMutator(:single_point,:flip), ListMutator(:n_point[2],:flip),ListMutator(:n_point[3],:flip),
17
- ListMutator(:expected_n[1],:flip), ListMutator(:expected_n[2],:flip), ListMutator(:expected_n[3],:flip)
18
-
19
- }
20
-
21
- Population.benchmark(RoyalRoad,'output/royalroad2_report.html'){
22
- selection TruncationSelection(0.2), TruncationSelection(0.3), TruncationSelection(0.4), Elitism(ScaledRouletteSelection(),1), Elitism(RouletteSelection,1)
23
- crossover NullCrossover, SinglePointCrossover, UniformCrossover
24
- mutator *( (2..4).map{|n| [ListMutator(:n_point[n],:flip), ListMutator(:expected_n[n],:flip)] }.flatten)
25
- }
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-
data/examples/royalroad2.rb DELETED
@@ -1,18 +0,0 @@
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- require '../lib/charlie'
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-
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- class RoyalRoad < BitStringGenotype(64) # Royal Road problem
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- def fitness
5
- genes.enum_slice(8).find_all{|e| e.all?{|x|x==1} }.size
6
- end
7
-
8
- #use TruncationSelection(0.1)
9
- #use PCross(0.75,SingleChild(UniformCrossover))
10
- end
11
-
12
- Population.benchmark(RoyalRoad,'output/royalroadquick_report.html'){
13
- selection TruncationSelection(), Elitism(ScaledRouletteSelection(),1), TournamentSelection(4)
14
-
15
- crossover SinglePointCrossover, UniformCrossover, PCross(0.75,UniformCrossover), SingleChild(UniformCrossover)
16
- mutator ListMutator(:expected_n[1],:flip), ListMutator(:expected_n[2],:flip), ListMutator(:expected_n[3],:flip)
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- self.repeat = 50
18
- }
data/examples/simple_climb_hill2.rb DELETED
@@ -1,47 +0,0 @@
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- require '../lib/charlie'
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-
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- class Hill2 < FloatListGenotype(2,(-1..1)) # simple hill function
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-
5
- def fitness
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- x,y=genes
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- 1 / (1+x*x+y*y)
8
- end
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- #use BestOnlySelection
10
- use TournamentSelection(4)
11
- use NullCrossover
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- end
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-
14
- Population.new(Hill2,10).evolve_on_console(20)
15
-
16
-
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- class Hill10 < FloatListGenotype(10,(-1..1)) # 10-dimensional simple hill function
18
- def fitness
19
- 1 / (1 + genes.inject(0){|s,x|s+x*x})
20
- end
21
- #use BestOnlySelection
22
- #use TournamentSelection(4)
23
- #use NullCrossover
24
- end
25
-
26
- Population.benchmark(Hill2,'output/hill2.html','output/hill2.csv') {
27
- selection BestOnlySelection, TournamentSelection(4)
28
- crossover NullCrossover,SinglePointCrossover
29
-
30
- mt = [:expected_n[1],:expected_n[2]].map{|s|
31
- [:uniform[0.1],:uniform[0.2],:gaussian[0.3]].map{|p| ListMutator(s,p) } }.flatten
32
- mutator *mt
33
- self.generations = 20
34
- self.population_size = 10
35
- }
36
-
37
- Population.benchmark(Hill10,'output/hill10.html') {
38
- selection BestOnlySelection, TournamentSelection(4), TournamentSelection(3), RouletteSelection, Elitism(RouletteSelection,1)
39
- crossover NullCrossover,SinglePointCrossover,UniformCrossover
40
-
41
- mt = [:expected_n[1],:expected_n[2],:expected_n[3],:single_point,:n_point[2],:n_point[3]].map{|s|
42
- [:uniform[0.1],:uniform[0.2],:uniform[0.3],:gaussian[0.1],:gaussian[0.2],:gaussian[0.3]].map{|p| ListMutator(s,p) } }.flatten
43
-
44
- mutator *mt
45
- self.generations = 20
46
- self.population_size = 10
47
- }
data/examples/weasel.rb DELETED
@@ -1,36 +0,0 @@
1
- require '../lib/charlie'
2
-
3
- STR = 'methinks it is like a weasel'
4
- Schars = ('a'..'z').to_a << ' '
5
-
6
- class Weasel < StringGenotype(STR.size,Schars)
7
- def fitness
8
- genes.zip(STR.chars).find_all{|a,b|a==b}.size
9
- end
10
-
11
- def to_s
12
- genes.join.inspect
13
- end
14
- use BestOnlySelection
15
- use UniformCrossover
16
- use ListMutator(:single_point,:replace[*Schars])
17
- end
18
-
19
- Population.new(Weasel).evolve_on_console(200)
20
-
21
- Population.benchmark(Weasel,'output/weasel1_report.html'){
22
- selection TruncationSelection(), Elitism(ScaledRouletteSelection(),1), Elitism(RouletteSelection,1), BestOnlySelection, ScaledRouletteSelection()
23
- crossover NullCrossover, SinglePointCrossover, UniformCrossover
24
- mutator ListMutator(:single_point,:replace[*Schars]), ListMutator(:n_point[2],:replace[*Schars]),ListMutator(:n_point[3],:replace[*Schars]),
25
- ListMutator(:expected_n[1],:replace[*Schars]), ListMutator(:expected_n[2],:replace[*Schars]), ListMutator(:expected_n[3],:replace[*Schars])
26
-
27
- }
28
-
29
-
30
- Population.benchmark(Weasel,'output/weasel2_report.html'){
31
- selection TruncationSelection(0.2), BestOnlySelection
32
- crossover NullCrossover, SinglePointCrossover, UniformCrossover
33
- mutator ListMutator(:single_point,:replace[*Schars]), ListMutator(:n_point[2],:replace[*Schars])
34
- }
35
-
36
-