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  1. Jul 14, 2015
    • Jan Žegklitz's avatar
      Introduced variable subtree mutation. · 7a66eed0
      Jan Žegklitz authored
      * Minor documentation tweaks and corrections.
      * Grammar in evo.ge.Ge is always transformed into the evolutils.gramar.Grammar as it is needed by the subtree mutation.
      * Mutations are set up similarly like crossover using the setup_mutation() method.
      * Changed annotations from subtree crossover are stored in the offsprings.
      * Introduced subrree mutation, variable mutation.
      * evo.utils.grammar.Grammar.to_tree() now can take extra argument allowing to override the start symbol.
      * Annotations returned from evo.utils.grammar.Grammar.to_tree() are now lists instead of tuples.
      7a66eed0
  2. Jul 02, 2015
  3. Jun 25, 2015
    • Jan Žegklitz's avatar
      Minor improvements and documentation changes. · 92205c8a
      Jan Žegklitz authored
      * BSF solution and its data is pretty-printed after a run of evo.ge.Ge finishes.
      * End of evo.ge.support.RampedHalfInitializer intialization run is logged.
      * Adjusted .gitignore to ignore logging.yaml wich serves only for manual testing purposes.
      92205c8a
  4. Jun 18, 2015
  5. Jun 09, 2015
  6. Apr 03, 2015
  7. Mar 30, 2015
  8. Mar 27, 2015
    • Jan Žegklitz's avatar
      Grammar utility methods. · fd2e4616
      Jan Žegklitz authored
      * New method get_minimum_expansion_depth() in evo.utils.grammar.Grammar that returns the minimum depth of a derivation tree that forms a fully expanded grammar.
       * Unit test created too.
      fd2e4616
  9. Mar 26, 2015
  10. Mar 23, 2015
    • Jan Žegklitz's avatar
      Symbolic Regression: Multi-Gene GE · 0fd2eccc
      Jan Žegklitz authored
      * Different error handling in evo.sr.MultiGeneGeSrFitness
      ** A fitness value when an error occurs (error fitness) is specified separately from the unfinished-transcription fitness
      ** Errors handled by the error fitness can be specified manually (ZeroDivisionError and FloatingPointError are handled by default).
      ** numpy.linalg.linalg.LinAlgError is handled by the error fitness too (when SVD does not converge)
      * New class evo.sr.MultiGeneGe
      ** Derives from evo.ge.Ge.
      ** Implements special multi-gene operators.
      * Fixed bug in evo.ge.support.RampedHalfHalfInitializer.
      * Adjustments of evo.ge.Ge
      ** Setting up the crossover algorithm removed from the constructor to a separate method which can be overriden.
      ** All crossovers unset the annotations.
      0fd2eccc
  11. Mar 17, 2015
    • Jan Žegklitz's avatar
      GE: minor imporovements. · f0b76e37
      Jan Žegklitz authored
      * Methods to_tree and to_text of evo.utils.grammar.Grammar return the annotations as tuples (in order to be hashable).
      * evo.ge.support.RandomWalkInitializer and RampedHalfHalfInitializer can add extra "useless" codons after the main codon sequence.
      f0b76e37
  12. Mar 16, 2015
  13. Mar 09, 2015
  14. Mar 08, 2015
  15. Mar 05, 2015
    • Jan Žegklitz's avatar
      Variable crossover, fast mutation, minor tweaks. · 9cae1de9
      Jan Žegklitz authored
      * The data field in evo.Individual (and its subclasses) made private (by renaming to _data).
      ** It is not to be manipulated directly but through new methods get_data() and set_data().
      * Variable crossover in evo.ge.Ge. Works with any supported ground crossover methods.
      * Fastu mutation by sampling the index of the codon to be mutadet from a geometric distribution, lowering the number of random number generator calls.
      9cae1de9
  16. Mar 04, 2015
    • Jan Žegklitz's avatar
      Subtree crossover tweaking and bugfixes. · 7062b03f
      Jan Žegklitz authored
      * If the genotype of either parent is too short that it did not expand any rule the subtree crossover is not performed (there are no offsprings of such parents).
      * Annotations are properly cloned in evo.ge.support.CodonGenotypeIndividual.clone().
      * All acquired annotations are returned, even if the expansion was not fully finished.
      7062b03f
  17. Mar 03, 2015
  18. Mar 02, 2015
  19. Feb 26, 2015
    • Jan Žegklitz's avatar
      MGGE · dd9328d7
      Jan Žegklitz authored
      * Created class evo.sr.MultiGeneGeSrFitness
      ** Converts the low-level grammar to the multi-gene grammar - no need to manually design the multi-gene grammar.
      ** Performs the evaluation of multi-gene individuals.
      ** Takes care of comparing fitness values (not sorting).
      * New methods for trees (and unit tests).
      * Added numpy dependency.
      * Added numpy intersphinx link.
      dd9328d7
  20. Feb 23, 2015
  21. Feb 16, 2015
    • Jan Žegklitz's avatar
      Symbolic Regression. · 5690f05c
      Jan Žegklitz authored
      * Created a SR module (sr.py) skeleton which will contain symbolic-regression-specific implementations of GP.
      5690f05c
  22. Feb 12, 2015
    • Jan Žegklitz's avatar
      GE fitness classes refactoring. · 69c5b281
      Jan Žegklitz authored
      * Common base class GeFitness for fitnesses to work with GE.
      * Two abstract subclasses of GeFitness
      ** GeTreeFitness that decodes the genome to a derivation tree (which is then further processed)
      ** GeTextFitness that decodes the genome to a text string (which is then further processed).
      69c5b281
    • Jan Žegklitz's avatar
      Subtree crossover in GE. · fbfe563b
      Jan Žegklitz authored
      * Completed unit test.
      * Finished implementation.
      
      Fixes #1
      fbfe563b
  23. Feb 11, 2015
  24. Feb 10, 2015
  25. Feb 09, 2015
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