/usr/include/shogun/converter/Isomap.h is in libshogun-dev 1.1.0-4ubuntu2.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 | /*
* 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
*/
#ifndef ISOMAP_H_
#define ISOMAP_H_
#include <shogun/lib/config.h>
#ifdef HAVE_LAPACK
#include <shogun/converter/MultidimensionalScaling.h>
#include <shogun/lib/common.h>
#include <shogun/mathematics/Math.h>
#include <shogun/io/SGIO.h>
#include <shogun/features/SimpleFeatures.h>
#include <shogun/features/Features.h>
#include <shogun/distance/Distance.h>
namespace shogun
{
class CFeatures;
class CDistance;
/** @brief the class Isomap used to preprocess data using K-Isomap algorithm
* as described in
*
* Silva, V. D., & Tenenbaum, J. B. (2003).
* Global versus local methods in nonlinear dimensionality reduction.
* Advances in Neural Information Processing Systems 15, 15(Figure 2), 721-728. MIT Press.
* Retrieved from http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.9.3407&rep=rep1&type=pdf
*
* Shortest paths are being computed with Dijkstra's algorithm with heap
* in parallel. Due to sparsity of the kNN graph Fibonacci Heap with
* amortized O(1) Extract-Min operation time complexity is used.
*
* It is possible to apply preprocessor to specified distance using
* apply_to_distance.
*
*/
class CIsomap: public CMultidimensionalScaling
{
public:
/* constructor */
CIsomap();
/* destructor */
virtual ~CIsomap();
/** get name */
const char* get_name() const;
/** setter for k parameter
* @param k value
*/
void set_k(int32_t k);
/** getter for k parameter
* @return k value
*/
int32_t get_k() const;
/// HELPERS
protected:
/** default init */
virtual void init();
/** process distance matrix (redefined in isomap, for mds does nothing)
* @param distance_matrix distance matrix
* @return processed distance matrix
*/
virtual SGMatrix<float64_t> process_distance_matrix(SGMatrix<float64_t> distance_matrix);
/// FIELDS
protected:
/** k, number of neighbors for K-Isomap */
int32_t m_k;
/// THREADS
protected:
/** run dijkstra thread
* @param p thread params
*/
static void* run_dijkstra_thread(void* p);
/** approximate geodesic distance with shortest path in kNN graph
* @param D_matrix distance matrix (deleted on exit)
* @return approximate geodesic distance matrix
*/
SGMatrix<float64_t> isomap_distance(SGMatrix<float64_t> D_matrix);
};
}
#endif /* HAVE_LAPACK */
#endif /* ISOMAP_H_ */
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