[shark] 53/58: Merge pull request #49 from Shark-ML/InterfaceEvo

[Ghislain Vaillant]

This is an automated email from the git hooks/post-receive script.

ghisvail-guest pushed a commit to branch master
in repository shark.

commit 2b06254d63f0491fc9634b00e41bebfa4159d4d3
Merge: ebf0f74 a60e978
Author: Oswin Krause <oswin.krause at di.ku.dk>
Date:   Tue Mar 1 09:42:10 2016 +0100

    Merge pull request #49 from Shark-ML/InterfaceEvo
    
    Reworked several important aspects of the DirectSearch component of Shark.
    
    features:
    1. New internal interface for the mainline algorithms (CMA-ES, SteadyStateMOCMA, MOCMA, SMSEMOA, NSGAII) which separates the step() into smaller functions which can be queried from derived classes. this allows users deeper analysis of the functions, e.g. getting all generated offspring or changing how points are evaluated.
    
    2. Several fixes to the SMSEMO and NSGAII operators. There were some bugs
    
    3. DirectSearch now relies less on the globalRng and for most algorithms, the user can choose an instance of the Rng in the constructor. This is important when these algorithms are run in parallel, as the Rng is not thread safe.

 Test/Algorithms/DirectSearch/CMA.cpp               |  12 +-
 Test/Algorithms/DirectSearch/MOCMA.cpp             |   8 +-
 .../Operators/Mutation/BitflipMutation.cpp         |   2 +-
 .../DirectSearch/Operators/Selection/Selection.cpp |   4 +-
 Test/Algorithms/DirectSearch/RealCodedNSGAII.cpp   |  13 +-
 .../{RealCodedNSGAII.cpp => SMS-EMOA.cpp}          |  21 +-
 Test/Algorithms/DirectSearch/SteadyStateMOCMA.cpp  |   5 +-
 Test/Algorithms/Hypervolume.cpp                    |  37 +-
 Test/Algorithms/Trainers/FisherLDA.cpp             |   2 +-
 Test/Algorithms/Trainers/LDA.cpp                   |   8 +-
 Test/Algorithms/Trainers/LinearRegression.cpp      |   2 +-
 Test/Algorithms/Trainers/Normalization.cpp         |   6 +-
 Test/Algorithms/Trainers/PCA.cpp                   |   6 +-
 Test/Algorithms/testFunction.h                     |   1 +
 Test/CMakeLists.txt                                |   1 +
 Test/ObjectiveFunctions/Benchmarks.cpp             |   7 -
 Test/ObjectiveFunctions/ErrorFunction.cpp          |   2 +-
 Test/Rng/MultiNomial.cpp                           |   4 +-
 Test/Rng/MultiVariateNormal.cpp                    |   4 +-
 examples/EA/SOO/AckleyES.tpp                       |   4 +-
 examples/EA/SOO/CMASimple.tpp                      |   4 +-
 examples/EA/SOO/TSP.tpp                            |   4 +-
 examples/Unsupervised/PCA.tpp                      |   2 +-
 include/shark/Algorithms/DirectSearch/CMA.h        | 448 +++++++++++----------
 .../Algorithms/DirectSearch/CMA/CMAIndividual.h    |  18 +-
 .../shark/Algorithms/DirectSearch/CMA/Chromosome.h |   7 +-
 include/shark/Algorithms/DirectSearch/CMSA.h       | 240 ++++++-----
 .../Algorithms/DirectSearch/CrossEntropyMethod.h   |   8 +-
 include/shark/Algorithms/DirectSearch/ElitistCMA.h |   4 +-
 .../DirectSearch/Indicators/HypervolumeIndicator.h |   1 +
 include/shark/Algorithms/DirectSearch/LMCMA.h      |   9 +-
 include/shark/Algorithms/DirectSearch/MOCMA.h      | 221 +++++-----
 .../Operators/Mutation/BitflipMutator.h            |   4 +-
 .../Operators/Mutation/PolynomialMutation.h        |  69 ++--
 .../Operators/Recombination/OnePointCrossover.h    |   6 +-
 .../Recombination/SimulatedBinaryCrossover.h       |  86 ++--
 .../Operators/Recombination/UniformCrossover.h     |   8 +-
 .../Operators/Selection/EPTournamentSelection.h    |  10 +-
 .../Operators/Selection/IndicatorBasedSelection.h  |   3 +-
 .../Operators/Selection/LinearRanking.h            |   3 +-
 .../Operators/Selection/RouletteWheelSelection.h   |   4 +-
 .../Operators/Selection/TournamentSelection.h      |   9 +-
 .../Operators/Selection/UniformRanking.h           |   3 +-
 .../Algorithms/DirectSearch/RealCodedNSGAII.h      | 236 +++++++----
 include/shark/Algorithms/DirectSearch/SMS-EMOA.h   | 202 ++++++----
 .../Algorithms/DirectSearch/SteadyStateMOCMA.h     | 220 ++++++----
 include/shark/Algorithms/DirectSearch/VDCMA.h      |   8 +-
 include/shark/Algorithms/QP/QpBoxLinear.h          |  20 +-
 .../Trainers/Distribution/NormalTrainer.h          |   2 +-
 include/shark/Data/DataDistribution.h              |   2 +-
 include/shark/LinAlg/BLAS/kernels/lapack/syev.hpp  |   2 +-
 include/shark/Models/Trees/RFClassifier.h          |   5 +-
 .../shark/ObjectiveFunctions/Benchmarks/DTLZ4.h    |   4 +-
 .../ObjectiveFunctions/Loss/EpsilonHingeLoss.h     |   3 -
 .../Loss/SquaredEpsilonHingeLoss.h                 |   3 +-
 include/shark/Rng/Bernoulli.h                      |  10 +-
 include/shark/Rng/Binomial.h                       |   8 +-
 include/shark/Rng/DiscreteUniform.h                | 128 +++---
 include/shark/Rng/GlobalRng.h                      |   5 -
 include/shark/Rng/Normal.h                         |   9 +-
 include/shark/Rng/Uniform.h                        |   7 +
 .../Distributions/MultiNomialDistribution.h        |  13 +-
 .../Distributions/MultiVariateNormalDistribution.h |  42 +-
 src/Algorithms/DirectSearch/CMA.cpp                | 137 ++++---
 src/Algorithms/DirectSearch/CMSA.cpp               | 109 +++--
 src/Algorithms/DirectSearch/CrossEntropyMethod.cpp |  22 +-
 src/Algorithms/DirectSearch/ElitistCMA.cpp         |   4 +-
 67 files changed, 1417 insertions(+), 1104 deletions(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-science/packages/shark.git