PLearn 0.1
plearn_noblas_inc.h
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00001 // -*- C++ -*-
00002 
00003 // plearn_noblas_inc.h
00004 //
00005 // Copyright (C) 2006 Pascal Vincent
00006 // 
00007 // Redistribution and use in source and binary forms, with or without
00008 // modification, are permitted provided that the following conditions are met:
00009 // 
00010 //  1. Redistributions of source code must retain the above copyright
00011 //     notice, this list of conditions and the following disclaimer.
00012 // 
00013 //  2. Redistributions in binary form must reproduce the above copyright
00014 //     notice, this list of conditions and the following disclaimer in the
00015 //     documentation and/or other materials provided with the distribution.
00016 // 
00017 //  3. The name of the authors may not be used to endorse or promote
00018 //     products derived from this software without specific prior written
00019 //     permission.
00020 // 
00021 // THIS SOFTWARE IS PROVIDED BY THE AUTHORS ``AS IS'' AND ANY EXPRESS OR
00022 // IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
00023 // OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN
00024 // NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
00025 // SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
00026 // TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
00027 // PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
00028 // LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
00029 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
00030 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
00031 // 
00032 // This file is part of the PLearn library. For more information on the PLearn
00033 // library, go to the PLearn Web site at www.plearn.org
00034 
00035 /* *******************************************************      
00036  * $Id: plearn_noblas_inc.h 6346 2006-10-24 17:02:02Z lamblin $ 
00037  ******************************************************* */
00038 
00039 // Authors: Olivier Delalleau
00040 
00047 #ifndef plearn_noblas_inc_INC
00048 #define plearn_noblas_inc_INC
00049 
00050 /*****************
00051  * Miscellaneous *
00052  *****************/
00053 #include <plearn/db/UCISpecification.h>
00054 #include <plearn/io/openUrl.h>
00055 #include <plearn/io/RPPath.h>
00056 #include <plearn/math/ManualBinner.h>
00057 #include <plearn/math/SoftHistogramBinner.h>
00058 #include <plearn/misc/ShellScript.h>
00059 #include <plearn/misc/Redirect.h>
00060 #include <plearn/misc/RunObject.h>
00061 #include <plearn_learners/misc/Grapher.h>
00062 #include <plearn_learners/misc/VariableSelectionWithDirectedGradientDescent.h>
00063 #include <plearn_learners/testers/PTester.h>
00064 #include <plearn/misc/HTMLHelpGenerator.h>
00065 
00066 
00067 /***********
00068  * Command *
00069  ***********/
00070 #include <commands/PLearnCommands/VMatCommand.h>
00071 #include <commands/PLearnCommands/AutoRunCommand.h>
00072 #include <commands/PLearnCommands/DiffCommand.h>
00073 #include <commands/PLearnCommands/FieldConvertCommand.h>
00074 #include <commands/PLearnCommands/HelpCommand.h>
00075 #include <commands/PLearnCommands/JulianDateCommand.h>
00076 #include <commands/PLearnCommands/KolmogorovSmirnovCommand.h>
00077 #include <commands/PLearnCommands/LearnerCommand.h>
00078 #include <commands/PLearnCommands/PairwiseDiffsCommand.h>
00079 #include <commands/PLearnCommands/ReadAndWriteCommand.h>
00080 #include <commands/PLearnCommands/RunCommand.h>
00081 #include <commands/PLearnCommands/ServerCommand.h>
00082 #include <commands/PLearnCommands/TestDependenciesCommand.h>
00083 #include <commands/PLearnCommands/TestDependencyCommand.h>
00084 #include <commands/PLearnCommands/StatsCommand.h>
00085 
00086 // * extra stuff from Boost to generate help *
00087 //#include <commands/PLearnCommands/HTMLHelpCommand.h>//<! DEPRECATED (will disappear soon)
00088 
00089 //#include <commands/PLearnCommands/TxtmatCommand.h>
00090 
00091 
00092 /**************
00093  * Dictionary *
00094  **************/
00095 #include <plearn/dict/Dictionary.h>
00096 #include <plearn/dict/FileDictionary.h>
00097 #include <plearn/dict/VecDictionary.h>
00098 #include <plearn/dict/ConditionalDictionary.h>
00099 
00100 /****************
00101  * HyperCommand *
00102  ****************/
00103 #include <plearn_learners/hyper/HyperOptimize.h>
00104 #include <plearn_learners/hyper/HyperRetrain.h>
00105 #include <plearn_learners/hyper/HyperSetOption.h>
00106 
00107 /**********
00108  * Kernel *
00109  **********/
00110 #include <plearn/ker/AdditiveNormalizationKernel.h>
00113 //#include <plearn/ker/BetaKernel.h>
00114 #include <plearn/ker/CosKernel.h>
00115 #include <plearn/ker/DistanceKernel.h>
00116 #include <plearn/ker/DotProductKernel.h>
00117 #include <plearn/ker/EpanechnikovKernel.h>
00118 #include <plearn/ker/GaussianKernel.h>
00119 #include <plearn/ker/GaussianDensityKernel.h>
00120 #include <plearn/ker/GeodesicDistanceKernel.h>
00121 #include <plearn/ker/IIDNoiseKernel.h>
00122 #include <plearn/ker/LinearARDKernel.h>
00123 #include <plearn/ker/NegOutputCostFunction.h>
00124 #include <plearn/ker/NeuralNetworkARDKernel.h>
00125 #include <plearn/ker/PolynomialKernel.h>
00126 #include <plearn/ker/RationalQuadraticARDKernel.h>
00127 #include <plearn/ker/SquaredExponentialARDKernel.h>
00128 #include <plearn/ker/SummationKernel.h>
00129 #include <plearn/ker/ThresholdedKernel.h>
00130 #include <plearn/ker/VMatKernel.h>
00131 #include <plearn/ker/DTWKernel.h>
00132 
00133 /*************
00134  * Optimizer *
00135  *************/
00136 #include <plearn/opt/AdaptGradientOptimizer.h>
00137 #include <plearn/opt/ConjGradientOptimizer.h>
00138 #include <plearn/opt/GradientOptimizer.h>
00139 
00140 /****************
00141  * OptionOracle *
00142  ****************/
00143 #include <plearn_learners/hyper/CartesianProductOracle.h>
00144 #include <plearn_learners/hyper/EarlyStoppingOracle.h>
00145 #include <plearn_learners/hyper/ExplicitListOracle.h>
00146 #include <plearn_learners/hyper/OptimizeOptionOracle.h>
00147 
00148 /************
00149  * PLearner *
00150  ************/
00151 
00152 // Classifiers
00153 #include <plearn_learners/classifiers/BinaryStump.h>
00154 #include <plearn_learners/classifiers/ClassifierFromConditionalPDistribution.h>
00155 #include <plearn_learners/classifiers/ClassifierFromDensity.h>
00156 #include <plearn_learners/classifiers/KNNClassifier.h>
00157 //#include <plearn_learners/classifiers/SVMClassificationTorch.h>
00158 #include <plearn_learners/classifiers/MultiInstanceNNet.h>
00159 //#include <plearn_learners/classifiers/OverlappingAdaBoost.h> // Does not currently compile.
00160 #include <plearn_learners/classifiers/ToBagClassifier.h>
00161 
00162 // Generic
00163 #include <plearn_learners/generic/AddCostToLearner.h>
00164 #include <plearn_learners/generic/AddLayersNNet.h>
00165 #include <plearn_learners/generic/BestAveragingPLearner.h>
00166 //#include <plearn_learners/generic/DistRepNNet.h>
00167 #include <plearn_learners/generic/NNet.h>
00168 #include <plearn_learners/generic/SelectInputSubsetLearner.h>
00169 #include <plearn_learners/generic/ChainedLearners.h>
00170 #include <plearn_learners/generic/StackedLearner.h>
00171 #include <plearn_learners/generic/TestingLearner.h>
00172 #include <plearn_learners/generic/TransformOutputLearner.h>
00173 #include <plearn_learners/generic/VPLPreprocessedLearner.h>
00174 #include <plearn_learners/generic/VPLPreprocessedLearner2.h>
00175 #include <plearn_learners/generic/VPLCombinedLearner.h>
00176 
00177 // Hyper
00178 #include <plearn_learners/hyper/HyperLearner.h>
00179 
00180 // Meta
00181 #include <plearn_learners/meta/AdaBoost.h>
00182 #include <plearn_learners/meta/MultiClassAdaBoost.h>
00183 #include <plearn_learners/meta/BaggingLearner.h>
00184 
00185 // Regressors
00186 #include <plearn_learners/regressors/ConstantRegressor.h>
00187 #include <plearn_learners/regressors/CubicSpline.h>
00188 #include <plearn_learners/regressors/GaussianProcessRegressor.h>
00189 #include <plearn_learners/regressors/KernelRidgeRegressor.h>
00190 #include <plearn_learners/regressors/KNNRegressor.h>
00191 #include <plearn_learners/regressors/RankLearner.h>
00192 #include <plearn_learners/regressors/RegressorFromDistribution.h>
00193 #include <plearn_learners/regressors/RegressionTree.h>
00194 #include <plearn_learners/regressors/RegressionTreeMulticlassLeave.h>
00195 #include <plearn_learners/regressors/RegressionTreeMulticlassLeaveFast.h>
00196 #include <plearn_learners/regressors/RegressionTreeMulticlassLeaveProb.h>
00197 
00198 // Unsupervised
00199 #include <plearn_learners/unsupervised/UniformizeLearner.h>
00200 
00201 // PDistribution
00202 #include <plearn_learners/distributions/MixtureDistribution.h>
00203 #include <plearn_learners/distributions/SpiralDistribution.h>
00204 #include <plearn_learners/distributions/UniformDistribution.h>
00205 #include <plearn_learners/distributions/KernelDensityEstimator.h>
00206 
00207 // Nearest-Neighbors
00208 #include <plearn_learners/nearest_neighbors/BallTreeNearestNeighbors.h>
00209 #include <plearn_learners/nearest_neighbors/ExhaustiveNearestNeighbors.h>
00210 #include <plearn_learners/nearest_neighbors/GenericNearestNeighbors.h>
00211 
00212 // Experimental
00213 #include <plearn_learners_experimental/DeepFeatureExtractorNNet.h>
00214 
00215 // Online
00216 #include <plearn_learners/online/ArgmaxModule.h>
00217 #include <plearn_learners/online/BackConvolution2DModule.h>
00218 #include <plearn_learners/online/ClassErrorCostModule.h>
00219 #include <plearn_learners/online/CombiningCostsModule.h>
00220 #include <plearn_learners/online/Convolution2DModule.h>
00221 #include <plearn_learners/online/CostModule.h>
00222 #include <plearn_learners/online/CrossEntropyCostModule.h>
00223 #include <plearn_learners/online/DeepBeliefNet.h>
00224 #include <plearn_learners/online/ForwardModule.h>
00225 #include <plearn_learners/online/GradNNetLayerModule.h>
00226 #include <plearn_learners/online/IdentityModule.h>
00227 #include <plearn_learners/online/InferenceRBM.h>
00228 #include <plearn_learners/online/LayerCostModule.h>
00229 #include <plearn_learners/online/LinearCombinationModule.h>
00230 #include <plearn_learners/online/LinearFilterModule.h>
00231 #include <plearn_learners/online/LogaddOnBagsModule.h>
00232 #include <plearn_learners/online/MatrixModule.h>
00233 #include <plearn_learners/online/MaxSubsampling2DModule.h>
00234 #include <plearn_learners/online/ModuleLearner.h>
00235 #include <plearn_learners/online/ModulesLearner.h>
00236 #include <plearn_learners/online/ModuleStackModule.h>
00237 #include <plearn_learners/online/ModuleTester.h>
00238 #include <plearn_learners/online/NetworkModule.h>
00239 #include <plearn_learners/online/NLLCostModule.h>
00240 #include <plearn_learners/online/OnlineLearningModule.h>
00241 #include <plearn_learners/online/ProcessInputCostModule.h>
00242 #include <plearn_learners/online/RBMBinomialLayer.h>
00243 #include <plearn_learners/online/RBMClassificationModule.h>
00244 #include <plearn_learners/online/RBMConnection.h>
00245 #include <plearn_learners/online/RBMConv2DConnection.h>
00246 #include <plearn_learners/online/RBMGaussianLayer.h>
00247 #include <plearn_learners/online/RBMLayer.h>
00248 #include <plearn_learners/online/RBMLocalMultinomialLayer.h>
00249 #include <plearn_learners/online/RBMMatrixConnection.h>
00250 #include <plearn_learners/online/RBMMatrixTransposeConnection.h>
00251 #include <plearn_learners/online/RBMMixedConnection.h>
00252 #include <plearn_learners/online/RBMMixedLayer.h>
00253 #include <plearn_learners/online/RBMModule.h>
00254 #include <plearn_learners/online/RBMMultinomialLayer.h>
00255 #include <plearn_learners/online/RBMSparse1DMatrixConnection.h>
00256 #include <plearn_learners/online/RBMTrainer.h>
00257 #include <plearn_learners/online/RBMTruncExpLayer.h>
00258 #include <plearn_learners/online/ScaleGradientModule.h>
00259 #include <plearn_learners/online/ShuntingNNetLayerModule.h>
00260 #include <plearn_learners/online/SoftmaxModule.h>
00261 #include <plearn_learners/online/SoftmaxNLLCostModule.h>
00262 #include <plearn_learners/online/SplitModule.h>
00263 #include <plearn_learners/online/SquaredErrorCostModule.h>
00264 #include <plearn_learners/online/BinarizeModule.h>
00265 #include <plearn_learners/online/StackedAutoassociatorsNet.h>
00266 #include <plearn_learners/online/Subsampling2DModule.h>
00267 #include <plearn_learners/online/Supersampling2DModule.h>
00268 #include <plearn_learners/online/TanhModule.h>
00269 
00270 /************
00271  * Splitter *
00272  ************/
00273 #include <plearn/vmat/BinSplitter.h>
00274 #include <plearn/vmat/BootstrapSplitter.h>
00275 #include <plearn/vmat/ClassSeparationSplitter.h>
00276 #include <plearn/vmat/ConcatSetsSplitter.h>
00277 #include <plearn/vmat/DBSplitter.h>
00278 #include <plearn/vmat/ExplicitSplitter.h>
00279 #include <plearn/vmat/FilterSplitter.h>
00280 #include <plearn/vmat/FractionSplitter.h>
00281 #include <plearn/vmat/KFoldSplitter.h>
00282 #include <plearn/vmat/NoSplitSplitter.h>
00283 #include <plearn/vmat/MultiTaskSeparationSplitter.h>
00284 #include <plearn/vmat/RepeatSplitter.h>
00285 #include <plearn/vmat/SelectSetsSplitter.h>
00286 #include <plearn/vmat/SourceVMatrixSplitter.h>
00287 #include <plearn/vmat/StackedSplitter.h>
00288 #include <plearn/vmat/TestInTrainSplitter.h>
00289 #include <plearn/vmat/ToBagSplitter.h>
00290 #include <plearn/vmat/TrainTestSplitter.h>
00291 #include <plearn/vmat/TrainValidTestSplitter.h>
00292 
00293 /************
00294  * Variable *
00295  ************/
00296 #include <plearn/var/MatrixElementsVariable.h>
00297 
00298 /*********************
00299  * VecStatsCollector *
00300  *********************/
00301 #include <plearn/math/LiftStatsCollector.h>
00302 
00303 /***********
00304  * VMatrix *
00305  ***********/
00306 #include <plearn/vmat/AddMissingVMatrix.h>
00307 #include <plearn/vmat/AddBagInformationVMatrix.h>
00308 #include <plearn/vmat/AppendNeighborsVMatrix.h>
00309 #include <plearn/vmat/AsciiVMatrix.h>
00310 #include <plearn/vmat/AutoVMatrix.h>
00311 #include <plearn/vmat/AutoVMatrixSaveSource.h>
00312 #include <plearn/vmat/BootstrapVMatrix.h>
00313 #include <plearn/vmat/CenteredVMatrix.h>
00314 #include <plearn/vmat/ClassSubsetVMatrix.h>
00315 #include <plearn/vmat/CompactVMatrix.h>
00316 #include <plearn/vmat/CompactFileVMatrix.h>
00317 #include <plearn/vmat/CompressedVMatrix.h>
00318 #include <plearn/vmat/CumVMatrix.h>
00319 #include <plearn/vmat/ConcatColumnsVMatrix.h>
00320 #include <plearn/vmat/ConstantVMatrix.h>
00321 #include <plearn/vmat/DatedJoinVMatrix.h>
00322 // #include <plearn/vmat/DictionaryVMatrix.h>
00323 #include <plearn/vmat/DisregardRowsVMatrix.h>
00324 #include <plearn/vmat/DichotomizeVMatrix.h>
00325 #include <plearn/vmat/BinaryNumbersVMatrix.h>
00326 #include <plearn/vmat/ExtractNNetParamsVMatrix.h>
00327 #include <plearn/vmat/FilteredVMatrix.h>
00328 #include <plearn/vmat/FinancePreprocVMatrix.h>
00329 #include <plearn/vmat/GaussianizeVMatrix.h>
00330 #include <plearn/vmat/GeneralizedOneHotVMatrix.h>
00331 #include <plearn/vmat/GetInputVMatrix.h>
00332 #include <plearn/vmat/GramVMatrix.h>
00333 #include <plearn/vmat/IndexedVMatrix.h>
00334 #include <plearn/vmat/JulianizeVMatrix.h>
00335 #include <plearn/vmat/KNNVMatrix.h>
00336 #include <plearn/vmat/KNNImputationVMatrix.h>
00337 // Commented out because triggers WordNet, which does not work really fine yet.
00338 //#include <plearn/vmat/LemmatizeVMatrix.h>
00339 #include <plearn/vmat/LIBSVMSparseVMatrix.h>
00340 #include <plearn/vmat/LocalNeighborsDifferencesVMatrix.h>
00341 #include <plearn/vmat/LocallyPrecomputedVMatrix.h>
00342 #include <plearn/vmat/MeanImputationVMatrix.h>
00343 #include <plearn/vmat/MemoryVMatrixNoSave.h>
00344 #include <plearn/vmat/MissingInstructionVMatrix.h>
00345 #include <plearn/vmat/MixtureVMatrix.h>
00346 //#include <plearn/vmat/MixUnlabeledNeighbourVMatrix.h>
00347 #include <plearn/vmat/MultiInstanceVMatrix.h>
00348 #include <plearn/vmat/MultiTargetOneHotVMatrix.h>
00349 #include <plearn/vmat/MultiToUniInstanceSelectRandomVMatrix.h>
00350 #include <plearn/vmat/OneHotVMatrix.h>
00351 #include <plearn/vmat/PLearnerOutputVMatrix.h>
00352 #include <plearn/vmat/PairsVMatrix.h>
00353 #include <plearn/vmat/PrecomputedVMatrix.h>
00354 #include <plearn/vmat/ProcessDatasetVMatrix.h>
00355 #include <plearn/vmat/ProcessingVMatrix.h>
00356 #include <plearn/vmat/ProcessSymbolicSequenceVMatrix.h>
00357 #include <plearn/vmat/PutSubVMatrix.h>
00358 #include <plearn/vmat/RandomSamplesVMatrix.h>
00359 #include <plearn/vmat/RandomSamplesFromVMatrix.h>
00360 #include <plearn/vmat/RankedVMatrix.h>
00361 #include <plearn/vmat/RepeatVMatrix.h>
00362 #include <plearn/vmat/RegularGridVMatrix.h>
00363 #include <plearn/vmat/RemoveDuplicateVMatrix.h>
00364 #include <plearn/vmat/ReorderByMissingVMatrix.h>
00365 #include <plearn/vmat/ReplicateSamplesVMatrix.h>
00366 //#include <plearn/vmat/SelectAttributsSequenceVMatrix.h>
00367 #include <plearn/vmat/SelectRowsMultiInstanceVMatrix.h>
00368 #include <plearn/vmat/ShuffleColumnsVMatrix.h>
00369 #include <plearn/vmat/SortRowsVMatrix.h>
00370 #include <plearn/vmat/SparseVMatrix.h>
00371 #include <plearn/vmat/SplitWiseValidationVMatrix.h>
00372 #include <plearn/vmat/StochasticBinarizeVMatrix.h>
00373 #include <plearn/vmat/SubInputVMatrix.h>
00374 #include <plearn/vmat/TemporaryDiskVMatrix.h>
00375 #include <plearn/vmat/TemporaryFileVMatrix.h>
00376 #include <plearn/vmat/TextFilesVMatrix.h>
00377 #include <plearn/vmat/ThresholdVMatrix.h>
00378 #include <plearn/vmat/TransposeVMatrix.h>
00379 #include <plearn/vmat/UCIDataVMatrix.h>
00380 #include <plearn/vmat/UniformizeVMatrix.h>
00381 #include <plearn/vmat/VariableDeletionVMatrix.h>
00382 #include <plearn/vmat/ViewSplitterVMatrix.h>
00383 #include <plearn/vmat/VMatrixFromDistribution.h>
00384 
00385 
00386 
00387 // **** Require LAPACK and BLAS
00388 
00389 // Unsupervised/KernelProjection
00390 //#include <plearn_learners/unsupervised/Isomap.h>
00391 //#include <plearn_learners/unsupervised/KernelPCA.h>
00392 //#include <plearn_learners/unsupervised/LLE.h>
00393 //#include <plearn_learners/unsupervised/PCA.h>
00394 //#include <plearn_learners/unsupervised/SpectralClustering.h>
00395 
00396 // Kernels
00397 //#include <plearn/ker/LLEKernel.h>
00398 //#include <plearn/ker/ReconstructionWeightsKernel.h>
00399 
00400 // Regressors
00401 //#include <plearn_learners/regressors/LinearRegressor.h>
00402 //#include <plearn_learners/regressors/PLS.h>
00403 
00404 // PDistribution
00405 //#include <plearn_learners/distributions/GaussianDistribution.h>
00406 //#include <plearn_learners/distributions/GaussMix.h>
00407 //#include <plearn_learners/distributions/RandomGaussMix.h>
00408 //#include <plearn_learners/distributions/ParzenWindow.h>
00409 //#include <plearn_learners/distributions/ManifoldParzen2.h>
00410 
00411 // Experimental
00412 //#include <plearn_learners_experimental/LinearInductiveTransferClassifier.h>
00413 
00414 // SurfaceTemplate
00415 // #include <plearn_learners_experimental/SurfaceTemplate/SurfaceTemplateLearner.h>
00416 
00417 
00418 #endif
00419 
00420 
00421 /*
00422   Local Variables:
00423   mode:c++
00424   c-basic-offset:4
00425   c-file-style:"stroustrup"
00426   c-file-offsets:((innamespace . 0)(inline-open . 0))
00427   indent-tabs-mode:nil
00428   fill-column:79
00429   End:
00430 */
00431 // vim: filetype=cpp:expandtab:shiftwidth=4:tabstop=8:softtabstop=4:encoding=utf-8:textwidth=79 :
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