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src
shogun
converter
DiffusionMaps.cpp
Go to the documentation of this file.
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/*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation; either version 3 of the License, or
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* (at your option) any later version.
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*
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* Written (W) 2011 Sergey Lisitsyn
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* Copyright (C) 2011 Berlin Institute of Technology and Max-Planck-Society
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*/
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#include <
shogun/converter/DiffusionMaps.h
>
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#include <
shogun/converter/EmbeddingConverter.h
>
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#include <
shogun/lib/config.h
>
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#ifdef HAVE_EIGEN3
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#include <
shogun/distance/EuclideanDistance.h
>
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#include <shogun/lib/tapkee/tapkee_shogun.hpp>
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using namespace
shogun;
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CDiffusionMaps::CDiffusionMaps
() :
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CEmbeddingConverter
()
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{
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m_t
= 10;
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m_width
= 1.0;
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set_distance
(
new
CEuclideanDistance
());
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init
();
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}
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void
CDiffusionMaps::init
()
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{
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SG_ADD
(&
m_t
,
"t"
,
"number of steps"
,
MS_AVAILABLE
);
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SG_ADD
(&
m_width
,
"width"
,
"gaussian kernel width"
,
MS_AVAILABLE
);
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}
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CDiffusionMaps::~CDiffusionMaps
()
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{
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}
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void
CDiffusionMaps::set_t
(int32_t t)
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{
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m_t
= t;
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}
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int32_t
CDiffusionMaps::get_t
()
const
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{
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return
m_t
;
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}
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void
CDiffusionMaps::set_width
(
float64_t
width)
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{
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m_width
= width;
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}
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float64_t
CDiffusionMaps::get_width
()
const
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{
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return
m_width
;
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}
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const
char
*
CDiffusionMaps::get_name
()
const
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{
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return
"DiffusionMaps"
;
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};
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CFeatures
*
CDiffusionMaps::apply
(
CFeatures
* features)
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{
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ASSERT
(features)
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// shorthand for simplefeatures
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SG_REF
(features);
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// compute distance matrix
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ASSERT
(
m_distance
)
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m_distance
->
init
(features,features);
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CDenseFeatures<float64_t>
* embedding =
embed_distance
(
m_distance
);
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m_distance
->
cleanup
();
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SG_UNREF
(features);
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return
(
CFeatures
*)embedding;
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}
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CDenseFeatures<float64_t>
*
CDiffusionMaps::embed_distance
(
CDistance
*
distance
)
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{
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TAPKEE_PARAMETERS_FOR_SHOGUN parameters;
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parameters.n_timesteps =
m_t
;
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parameters.gaussian_kernel_width =
m_width
;
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parameters.method = SHOGUN_DIFFUSION_MAPS;
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parameters.target_dimension =
m_target_dim
;
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parameters.distance =
distance
;
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return
tapkee_embed(parameters);
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}
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#endif
/* HAVE_EIGEN3 */
SHOGUN
Machine Learning Toolbox - Documentation