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DiffusionMaps.cpp
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DiffusionMaps.cpp
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/*
* This software is distributed under BSD 3-clause license (see LICENSE file).
*
* Authors: Sergey Lisitsyn, Soeren Sonnenburg, Evan Shelhamer,
* Heiko Strathmann, Fernando Iglesias
*/
#include <shogun/converter/DiffusionMaps.h>
#include <shogun/converter/EmbeddingConverter.h>
#include <shogun/lib/config.h>
#include <shogun/distance/EuclideanDistance.h>
#include <shogun/lib/tapkee/tapkee_shogun.hpp>
using namespace shogun;
CDiffusionMaps::CDiffusionMaps() :
CEmbeddingConverter()
{
m_t = 10;
m_width = 1.0;
set_distance(new CEuclideanDistance());
init();
}
void CDiffusionMaps::init()
{
SG_ADD(&m_t, "t", "number of steps", MS_AVAILABLE);
SG_ADD(&m_width, "width", "gaussian kernel width", MS_AVAILABLE);
}
CDiffusionMaps::~CDiffusionMaps()
{
}
void CDiffusionMaps::set_t(int32_t t)
{
m_t = t;
}
int32_t CDiffusionMaps::get_t() const
{
return m_t;
}
void CDiffusionMaps::set_width(float64_t width)
{
m_width = width;
}
float64_t CDiffusionMaps::get_width() const
{
return m_width;
}
const char* CDiffusionMaps::get_name() const
{
return "DiffusionMaps";
};
CFeatures* CDiffusionMaps::apply(CFeatures* features, bool inplace)
{
ASSERT(features)
// shorthand for simplefeatures
SG_REF(features);
// compute distance matrix
ASSERT(m_distance)
m_distance->init(features,features);
CDenseFeatures<float64_t>* embedding = embed_distance(m_distance);
m_distance->cleanup();
SG_UNREF(features);
return (CFeatures*)embedding;
}
CDenseFeatures<float64_t>* CDiffusionMaps::embed_distance(CDistance* distance)
{
TAPKEE_PARAMETERS_FOR_SHOGUN parameters;
parameters.n_timesteps = m_t;
parameters.gaussian_kernel_width = m_width;
parameters.method = SHOGUN_DIFFUSION_MAPS;
parameters.target_dimension = m_target_dim;
parameters.distance = distance;
return tapkee_embed(parameters);
}