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Introduced NeighborhoodPreservingEmbedding (NPE)
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examples/undocumented/libshogun/converter_neighborhoodpreservingembedding.cpp
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| /* | ||
| * This program is free software; you can redistribute it and/or modify | ||
| * it under the terms of the GNU General Public License as published by | ||
| * the Free Software Foundation; either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * Written (W) 2011 Sergey Lisitsyn | ||
| * Copyright (C) 2011 Berlin Institute of Technology and Max-Planck-Society | ||
| */ | ||
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| #include <shogun/base/init.h> | ||
| #include <shogun/features/SimpleFeatures.h> | ||
| #include <shogun/converter/NeighborhoodPreservingEmbedding.h> | ||
| #include <shogun/mathematics/Math.h> | ||
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| using namespace shogun; | ||
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| int main(int argc, char** argv) | ||
| { | ||
| init_shogun(); | ||
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| int N = 100; | ||
| int dim = 3; | ||
| float64_t* matrix = new double[N*dim]; | ||
| for (int i=0; i<N*dim; i++) | ||
| matrix[i] = CMath::random(1,100); | ||
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| CSimpleFeatures<double>* features = new CSimpleFeatures<double>(SGMatrix<double>(matrix,dim,N)); | ||
| SG_REF(features); | ||
| CNeighborhoodPreservingEmbedding* npe = new CNeighborhoodPreservingEmbedding(); | ||
| npe->set_target_dim(2); | ||
| npe->set_k(15); | ||
| npe->parallel->set_num_threads(4); | ||
| CSimpleFeatures<double>* embedding = npe->embed(features); | ||
| SG_UNREF(embedding); | ||
| SG_UNREF(npe); | ||
| SG_UNREF(features); | ||
| exit_shogun(); | ||
| return 0; | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| /* | ||
| * This program is free software; you can redistribute it and/or modify | ||
| * it under the terms of the GNU General Public License as published by | ||
| * the Free Software Foundation; either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * Written (W) 2011 Sergey Lisitsyn | ||
| * Copyright (C) 2011 Sergey Lisitsyn | ||
| */ | ||
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| #include <shogun/converter/NeighborhoodPreservingEmbedding.h> | ||
| #include <shogun/lib/config.h> | ||
| #ifdef HAVE_LAPACK | ||
| #include <shogun/converter/EmbeddingConverter.h> | ||
| #include <shogun/mathematics/arpack.h> | ||
| #include <shogun/mathematics/lapack.h> | ||
| #include <shogun/lib/FibonacciHeap.h> | ||
| #include <shogun/base/DynArray.h> | ||
| #include <shogun/mathematics/Math.h> | ||
| #include <shogun/io/SGIO.h> | ||
| #include <shogun/lib/Time.h> | ||
| #include <shogun/distance/Distance.h> | ||
| #include <shogun/lib/Signal.h> | ||
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| using namespace shogun; | ||
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| CNeighborhoodPreservingEmbedding::CNeighborhoodPreservingEmbedding() : | ||
| CLocallyLinearEmbedding() | ||
| { | ||
| } | ||
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| CNeighborhoodPreservingEmbedding::~CNeighborhoodPreservingEmbedding() | ||
| { | ||
| } | ||
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| const char* CNeighborhoodPreservingEmbedding::get_name() const | ||
| { | ||
| return "NeighborhoodPreservingEmbedding"; | ||
| } | ||
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| SGMatrix<float64_t> CNeighborhoodPreservingEmbedding::construct_embedding(CFeatures* features, SGMatrix<float64_t> matrix, int dimension) | ||
| { | ||
| CSimpleFeatures<float64_t>* simple_features = (CSimpleFeatures<float64_t>*)features; | ||
| ASSERT(simple_features); | ||
| int i,j; | ||
| int N = simple_features->get_num_vectors(); | ||
| int dim = simple_features->get_num_features(); | ||
| ASSERT(dimension<=dim); | ||
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| SGMatrix<float64_t> feature_matrix = simple_features->get_feature_matrix(); | ||
| float64_t* XTM = SG_MALLOC(float64_t, dim*N); | ||
| float64_t* lhs_M = SG_MALLOC(float64_t, dim*dim); | ||
| float64_t* rhs_M = SG_MALLOC(float64_t, dim*dim); | ||
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| cblas_dgemm(CblasColMajor,CblasNoTrans,CblasNoTrans,dim,N,N,1.0,feature_matrix.matrix,dim,matrix.matrix,N,0.0,XTM,dim); | ||
| cblas_dgemm(CblasColMajor,CblasNoTrans,CblasTrans,dim,dim,N,1.0,XTM,dim,feature_matrix.matrix,dim,0.0,lhs_M,dim); | ||
| cblas_dgemm(CblasColMajor,CblasNoTrans,CblasTrans,dim,dim,N,1.0,feature_matrix.matrix,dim,feature_matrix.matrix,dim,0.0,rhs_M,dim); | ||
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| float64_t* evals = SG_MALLOC(float64_t, dim); | ||
| float64_t* evectors = SG_MALLOC(float64_t, dimension*dim); | ||
| int32_t info = 0; | ||
| wrap_dsygvx(1,'V','U',dim,lhs_M,dim,rhs_M,dim,dim-dimension+1,dim,evals,evectors,&info); | ||
| ASSERT(info==0); | ||
| SG_FREE(lhs_M); | ||
| SG_FREE(rhs_M); | ||
| SG_FREE(evals); | ||
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| for (i=0; i<dimension/2; i++) | ||
| { | ||
| cblas_dswap(dim,evectors+i*dim,1,evectors+(dimension-i-1)*dim,1); | ||
| } | ||
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| cblas_dgemm(CblasColMajor,CblasTrans,CblasNoTrans,N,dimension,dim,1.0,feature_matrix.matrix,dim,evectors,dim,0.0,XTM,N); | ||
| SG_FREE(evectors); | ||
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| float64_t* new_features = SG_MALLOC(float64_t, dimension*N); | ||
| for (i=0; i<dimension; i++) | ||
| { | ||
| for (j=0; j<N; j++) | ||
| new_features[j*dimension+i] = XTM[i*N+j]; | ||
| } | ||
| SG_FREE(XTM); | ||
| return SGMatrix<float64_t>(new_features,dimension,N); | ||
| } | ||
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| #endif /* HAVE_LAPACK */ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| /* | ||
| * This program is free software; you can redistribute it and/or modify | ||
| * it under the terms of the GNU General Public License as published by | ||
| * the Free Software Foundation; either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * Written (W) 2011 Sergey Lisitsyn | ||
| * Copyright (C) 2011 Sergey Lisitsyn | ||
| */ | ||
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| #ifndef NEIGHBORHOODPRESERVINGEMBEDDING_H_ | ||
| #define NEIGHBORHOODPRESERVINGEMBEDDING_H_ | ||
| #include <shogun/lib/config.h> | ||
| #ifdef HAVE_LAPACK | ||
| #include <shogun/converter/LocallyLinearEmbedding.h> | ||
| #include <shogun/features/Features.h> | ||
| #include <shogun/features/SimpleFeatures.h> | ||
| #include <shogun/distance/Distance.h> | ||
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| namespace shogun | ||
| { | ||
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| class CFeatures; | ||
| class CDistance; | ||
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| /** @brief NeighborhoodPreservingEmbedding | ||
| */ | ||
| class CNeighborhoodPreservingEmbedding: public CLocallyLinearEmbedding | ||
| { | ||
| public: | ||
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| /** constructor */ | ||
| CNeighborhoodPreservingEmbedding(); | ||
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| /** destructor */ | ||
| virtual ~CNeighborhoodPreservingEmbedding(); | ||
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| /** get name */ | ||
| virtual const char* get_name() const; | ||
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| protected: | ||
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| /** constructs embedding | ||
| * @param simple features to be used | ||
| * @param matrix weight matrix | ||
| * @param dimension dimension of embedding | ||
| * @return null-space approximation feature matrix | ||
| */ | ||
| virtual SGMatrix<float64_t> construct_embedding(CFeatures* features, SGMatrix<float64_t> matrix, int dimension); | ||
| }; | ||
| } | ||
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| #endif /* HAVE_LAPACK */ | ||
| #endif /* NEIGHBORHOODPRESERVINGEMBEDDING_H_ */ |