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124 changes: 124 additions & 0 deletions
124
src/shogun/converter/SupervisedKernelLocalTangentSpaceAlignment.cpp
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,124 @@ | ||
| /* | ||
| * 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) 2012 Sergey Lisitsyn | ||
| * Copyright (C) 2012 Sergey Lisitsyn | ||
| */ | ||
|
|
||
| #include <shogun/converter/SupervisedKernelLocalTangentSpaceAlignment.h> | ||
| #ifdef HAVE_LAPACK | ||
| #include <shogun/converter/KernelLocallyLinearEmbedding.h> | ||
| #include <shogun/lib/Time.h> | ||
| #include <shogun/lib/common.h> | ||
| #include <shogun/mathematics/Math.h> | ||
| #include <shogun/io/SGIO.h> | ||
| #include <shogun/distance/Distance.h> | ||
| #include <shogun/lib/Signal.h> | ||
| #include <shogun/base/Parallel.h> | ||
|
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| using namespace shogun; | ||
|
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| class SKLTSA_COVERTREE_POINT | ||
| { | ||
| public: | ||
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| SKLTSA_COVERTREE_POINT(int32_t index, const SGMatrix<float64_t>& dmatrix) | ||
| { | ||
| this->point_index = index; | ||
| this->kernel_matrix = dmatrix; | ||
| this->kii = dmatrix[index*dmatrix.num_rows+index]; | ||
| } | ||
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| inline double distance(const SKLTSA_COVERTREE_POINT& p) const | ||
| { | ||
| int32_t N = kernel_matrix.num_rows; | ||
| return kii+kernel_matrix[p.point_index*N+p.point_index]-2.0*kernel_matrix[point_index*N+p.point_index]; | ||
| } | ||
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| inline bool operator==(const SKLTSA_COVERTREE_POINT& p) const | ||
| { | ||
| return (p.point_index==this->point_index); | ||
| } | ||
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| int32_t point_index; | ||
| float64_t kii; | ||
| SGMatrix<float64_t> kernel_matrix; | ||
| }; | ||
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| CSupervisedKernelLocalTangentSpaceAlignment::CSupervisedKernelLocalTangentSpaceAlignment() : | ||
| CKernelLocalTangentSpaceAlignment(), m_labels(NULL) | ||
| { | ||
| } | ||
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| CSupervisedKernelLocalTangentSpaceAlignment::CSupervisedKernelLocalTangentSpaceAlignment(CKernel* kernel, CLabels* labels) : | ||
| CKernelLocalTangentSpaceAlignment(kernel), m_labels(NULL) | ||
| { | ||
| set_labels(labels); | ||
| } | ||
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| CSupervisedKernelLocalTangentSpaceAlignment::~CSupervisedKernelLocalTangentSpaceAlignment() | ||
| { | ||
| SG_UNREF(m_labels); | ||
| } | ||
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| const char* CSupervisedKernelLocalTangentSpaceAlignment::get_name() const | ||
| { | ||
| return "SupervisedKernelLocalTangentSpaceAlignment"; | ||
| }; | ||
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| SGMatrix<int32_t> CSupervisedKernelLocalTangentSpaceAlignment::get_neighborhood_matrix(SGMatrix<float64_t> kernel_matrix, int32_t k) | ||
| { | ||
| int32_t i; | ||
| int32_t N = kernel_matrix.num_cols; | ||
| ASSERT(m_labels); | ||
| ASSERT(m_labels->get_num_labels()==N); | ||
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| int32_t* neighborhood_matrix = SG_MALLOC(int32_t, N*k); | ||
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| float64_t max_dist=0.0; | ||
| for (i=0; i<N; i++) | ||
| max_dist = CMath::max(max_dist,kernel_matrix[i*N+i]); | ||
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| std::vector<SKLTSA_COVERTREE_POINT> vectors; | ||
| vectors.reserve(N); | ||
| for (i=0; i<N; i++) | ||
| vectors.push_back(SKLTSA_COVERTREE_POINT(i,kernel_matrix)); | ||
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| CoverTree<SKLTSA_COVERTREE_POINT>* coverTree = new CoverTree<SKLTSA_COVERTREE_POINT>(2.0*max_dist,vectors); | ||
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| for (i=0; i<N; i++) | ||
| { | ||
| std::vector<SKLTSA_COVERTREE_POINT> neighbors = | ||
| coverTree->kNearestNeighbors(vectors[i],k+1); | ||
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| ASSERT(neighbors.size()>=unsigned(k+1)); | ||
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| int32_t c = 0; | ||
| for (std::size_t m=1; m<unsigned(k+1); m++) | ||
| { | ||
| if (m_labels->get_int_label(i)==m_labels->get_int_label(neighbors[m].point_index)) | ||
| { | ||
| neighborhood_matrix[i*k+c] = neighbors[m].point_index; | ||
| c++; | ||
| } | ||
| } | ||
| SG_PRINT("c=%d",c); | ||
| for (std::size_t m=1; c<k && m<unsigned(k+1); m++) | ||
| { | ||
| if (m_labels->get_int_label(i)!=m_labels->get_int_label(neighbors[m].point_index)) | ||
| { | ||
| neighborhood_matrix[i*k+c] = neighbors[m].point_index; | ||
| c++; | ||
| } | ||
| } | ||
| } | ||
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| delete coverTree; | ||
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| return SGMatrix<int32_t>(neighborhood_matrix,k,N); | ||
| } | ||
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| #endif /* HAVE_LAPACK */ |
82 changes: 82 additions & 0 deletions
82
src/shogun/converter/SupervisedKernelLocalTangentSpaceAlignment.h
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,82 @@ | ||
| /* | ||
| * 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) 2012 Sergey Lisitsyn | ||
| * Copyright (C) 2012 Sergey Lisitsyn Berlin Institute of Technology and Max-Planck-Society | ||
| */ | ||
|
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| #ifndef SUPERVISEDKERNELLOCALTANGENTSPACEALIGNMENT_H_ | ||
| #define SUPERVISEDKERNELLOCALTANGENTSPACEALIGNMENT_H_ | ||
| #include <shogun/lib/config.h> | ||
| #ifdef HAVE_LAPACK | ||
| #include <shogun/converter/KernelLocalTangentSpaceAlignment.h> | ||
| #include <shogun/features/Features.h> | ||
| #include <shogun/features/Labels.h> | ||
| #include <shogun/kernel/Kernel.h> | ||
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| namespace shogun | ||
| { | ||
|
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| class CFeatures; | ||
| class CKernel; | ||
|
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| /** @brief class LocalTangentSpaceAlignment (part of the | ||
| * Efficient Dimensionality Reduction Toolkit) used to embed | ||
| * data using supervised kernel extension of the Local Tangent Space | ||
| * Alignment (LTSA) algorithm. | ||
| */ | ||
| class CSupervisedKernelLocalTangentSpaceAlignment: public CKernelLocalTangentSpaceAlignment | ||
| { | ||
| public: | ||
|
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| /** constructor */ | ||
| CSupervisedKernelLocalTangentSpaceAlignment(); | ||
|
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| /** constructor with kernel parameter | ||
| * @param kernel kernel to be used | ||
| */ | ||
| CSupervisedKernelLocalTangentSpaceAlignment(CKernel* kernel, CLabels* labels); | ||
|
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| /** set labels */ | ||
| void set_labels(CLabels* labels) | ||
| { | ||
| SG_REF(labels); | ||
| SG_UNREF(m_labels); | ||
| m_labels = labels; | ||
| } | ||
| /** get labels */ | ||
| CLabels* get_labels() const | ||
| { | ||
| SG_REF(m_labels); | ||
| return m_labels; | ||
| } | ||
|
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| /** destructor */ | ||
| virtual ~CSupervisedKernelLocalTangentSpaceAlignment(); | ||
|
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| /** get name */ | ||
| virtual const char* get_name() const; | ||
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| protected: | ||
|
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| /** constructs neighborhood matrix by kernel matrix | ||
| * @param kernel_matrix kernel matrix to be used | ||
| * @param k k | ||
| * @return matrix containing indexes of neighbors of i-th object | ||
| * in i-th column | ||
| */ | ||
| virtual SGMatrix<int32_t> get_neighborhood_matrix(SGMatrix<float64_t> kernel_matrix, int32_t k); | ||
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| protected: | ||
|
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| /** labels */ | ||
| CLabels* m_labels; | ||
|
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| }; | ||
| } | ||
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| #endif /* HAVE_LAPACK */ | ||
| #endif /* SUPERVISEDKERNELLOCALTANGENTSPACEALINGMENT_H_ */ |