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Added a wrapper for a manifold sculpting DR method implemented in tap…
…kee; added a modular wrapper for the wrapper:); fixed some bugs in the algorithm itself.
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| Original file line number | Diff line number | Diff line change |
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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) 2013 Vladyslav S. Gorbatiuk | ||
| * Copyright (C) 2011-2013 Vladyslav S. Gorbatiuk | ||
| */ | ||
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| #include <shogun/converter/ManifoldSculpting.h> | ||
| #ifdef HAVE_EIGEN3 | ||
| #include <shogun/lib/tapkee/tapkee_shogun.hpp> | ||
| #include <shogun/features/DenseFeatures.h> | ||
| #include <shogun/distance/EuclideanDistance.h> | ||
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| using namespace shogun; | ||
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| CManifoldSculpting::CManifoldSculpting() : | ||
| CEmbeddingConverter() | ||
| { | ||
| // Default values | ||
| m_k = 10; | ||
| m_squishing_rate = 0.8; | ||
| m_max_iteration = 80; | ||
| init(); | ||
| } | ||
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| void CManifoldSculpting::init() | ||
| { | ||
| SG_ADD(&m_k, "k", "number of neighbors", MS_NOT_AVAILABLE); | ||
| SG_ADD(&m_squishing_rate, "quishing_rate", | ||
| "squishing rate",MS_NOT_AVAILABLE); | ||
| SG_ADD(&m_max_iteration, "max_iteration", | ||
| "maximum number of algorithm's iterations", MS_NOT_AVAILABLE); | ||
| } | ||
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| CManifoldSculpting::~CManifoldSculpting() | ||
| { | ||
| } | ||
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| const char* CManifoldSculpting::get_name() const | ||
| { | ||
| return "ManifoldSculpting"; | ||
| } | ||
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| void CManifoldSculpting::set_k(const int32_t k) | ||
| { | ||
| ASSERT(k>0) | ||
| m_k = k; | ||
| } | ||
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| int32_t CManifoldSculpting::get_k() const | ||
| { | ||
| return m_k; | ||
| } | ||
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| void CManifoldSculpting::set_squishing_rate(const float64_t squishing_rate) | ||
| { | ||
| ASSERT(squishing_rate >= 0 && squishing_rate < 1) | ||
| m_squishing_rate = squishing_rate; | ||
| } | ||
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| float64_t CManifoldSculpting::get_squishing_rate() const | ||
| { | ||
| return m_squishing_rate; | ||
| } | ||
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| void CManifoldSculpting::set_max_iteration(const int32_t max_iteration) | ||
| { | ||
| ASSERT(max_iteration > 0) | ||
| m_max_iteration = max_iteration; | ||
| } | ||
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| int32_t CManifoldSculpting::get_max_iteration() const | ||
| { | ||
| return m_max_iteration; | ||
| } | ||
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| CFeatures* CManifoldSculpting::apply(CFeatures* features) | ||
| { | ||
| CDenseFeatures<float64_t>* feats = (CDenseFeatures<float64_t>*)features; | ||
| SG_REF(feats); | ||
| CDistance* euclidean_distance = | ||
| new CEuclideanDistance(feats, feats); | ||
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| TAPKEE_PARAMETERS_FOR_SHOGUN parameters; | ||
| parameters.n_neighbors = m_k; | ||
| parameters.squishing_rate = m_squishing_rate; | ||
| parameters.max_iteration = m_max_iteration; | ||
| parameters.features = feats; | ||
| parameters.distance = euclidean_distance; | ||
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| parameters.method = SHOGUN_MANIFOLD_SCULPTING; | ||
| parameters.target_dimension = m_target_dim; | ||
| CDenseFeatures<float64_t>* embedding = tapkee_embed(parameters); | ||
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| SG_UNREF(euclidean_distance); | ||
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| return embedding; | ||
| } | ||
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| #endif /* HAVE_EIGEN */ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,105 @@ | ||
| /* | ||
| * 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) 2013 Vladyslav S. Gorbatiuk | ||
| * Copyright (C) 2011-2013 Vladyslav S. Gorbatiuk | ||
| */ | ||
|
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| #ifndef MANIFOLDSCULPTING_H_ | ||
| #define MANIFOLDSCULPTING_H_ | ||
| #include <shogun/lib/config.h> | ||
| #ifdef HAVE_EIGEN3 | ||
| #include <shogun/converter/EmbeddingConverter.h> | ||
| #include <shogun/features/Features.h> | ||
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| namespace shogun | ||
| { | ||
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| /** @class class CManifoldSculpting used to embed | ||
| * data using manifold sculpting embedding algorithm. | ||
| * | ||
| * Uses implementation from the Tapkee library. | ||
| * | ||
| */ | ||
| class CManifoldSculpting : public CEmbeddingConverter | ||
| { | ||
| public: | ||
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| /** constructor */ | ||
| CManifoldSculpting(); | ||
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| /** destructor */ | ||
| virtual ~CManifoldSculpting(); | ||
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| /** get name */ | ||
| virtual const char* get_name() const; | ||
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| /** apply preprocessor to features | ||
| * | ||
| * @param features features to embed | ||
| */ | ||
| virtual CFeatures* apply(CFeatures* features); | ||
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| /** setter for the k | ||
| * | ||
| * @param k the number of neighbors | ||
| */ | ||
| void set_k(const int32_t k); | ||
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| /** getter for the number of neighbors | ||
| * | ||
| * @return the number of neighbors k | ||
| */ | ||
| int32_t get_k() const; | ||
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| /** setter for squishing_rate | ||
| * | ||
| * @param squishing_rate the squishing rate | ||
| */ | ||
| void set_squishing_rate(const float64_t squishing_rate); | ||
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| /** getter for squishing_rate | ||
| * | ||
| * @return squishing_rate | ||
| */ | ||
| float64_t get_squishing_rate() const; | ||
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| /** setter for the maximum number of iterations | ||
| * | ||
| * @param max_iteration the maximum number of iterations | ||
| */ | ||
| void set_max_iteration(const int32_t max_iteration); | ||
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| /** getter for the maximum number of iterations | ||
| * | ||
| * @return the maximum number of iterations | ||
| */ | ||
| int32_t get_max_iteration() const; | ||
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| private: | ||
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| /** default init */ | ||
| void init(); | ||
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| private: | ||
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| /** k - number of neighbors */ | ||
| float64_t m_k; | ||
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| /** squishing_rate */ | ||
| float64_t m_squishing_rate; | ||
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| /** max_iteration - the maximum number of algorithm's | ||
| * iterations | ||
| */ | ||
| float64_t m_max_iteration; | ||
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| }; /* class CManifoldSculpting */ | ||
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| } /* namespace shogun */ | ||
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| #endif /* HAVE_EIGEN3 */ | ||
| #endif /* MANIFOLDSCULPTING_H_ */ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| #include <shogun/converter/ManifoldSculpting.h> | ||
| #include <shogun/features/DenseFeatures.h> | ||
| #include <shogun/features/DataGenerator.h> | ||
| #include <gtest/gtest.h> | ||
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| using namespace shogun; | ||
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| #ifdef HAVE_EIGEN3 | ||
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| /* Basic test for manifold sculpting, that just checks that it works anyhow */ | ||
| TEST(ManifoldSculptingTest,basic) | ||
| { | ||
| const index_t n_samples = 15; | ||
| const index_t n_dimensions = 3; | ||
| const index_t n_target_dimensions = 2; | ||
| CDenseFeatures<float64_t>* high_dimensional_features = | ||
| new CDenseFeatures<float64_t>(CDataGenerator::generate_gaussians(n_samples, 1, n_dimensions)); | ||
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| CManifoldSculpting* embedder = | ||
| new CManifoldSculpting(); | ||
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| embedder->set_target_dim(n_target_dimensions); | ||
| EXPECT_EQ(n_target_dimensions, embedder->get_target_dim()); | ||
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| embedder->set_k(5); | ||
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| CDenseFeatures<float64_t>* low_dimensional_features = | ||
| embedder->embed(high_dimensional_features); | ||
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| EXPECT_EQ(n_target_dimensions,low_dimensional_features->get_dim_feature_space()); | ||
| EXPECT_EQ(high_dimensional_features->get_num_vectors(),low_dimensional_features->get_num_vectors()); | ||
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| SG_UNREF(embedder); | ||
| SG_UNREF(high_dimensional_features); | ||
| } | ||
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| #endif |