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/*!
@authors Andrei Novikov (pyclustering@yandex.ru)
@date 2014-2020
@copyright BSD-3-Clause
*/
#pragma once
#include <pyclustering/cluster/elbow_data.hpp>
#include <pyclustering/cluster/kmeans.hpp>
#include <pyclustering/cluster/kmeans_plus_plus.hpp>
#include <pyclustering/parallel/parallel.hpp>
#include <pyclustering/utils/metric.hpp>
#include <pyclustering/definitions.hpp>
using namespace pyclustering::parallel;
using namespace pyclustering::utils::metric;
namespace pyclustering {
namespace clst {
/*!
@class elbow elbow.hpp pyclustering/cluster/elbow.hpp
@brief The elbow is a heuristic method to find the appropriate number of clusters in a dataset.
@details The elbow is a heuristic method of interpretation and validation of consistency within cluster analysis designed to help find the appropriate
number of clusters in a dataset. Elbow method performs clustering using K-Means algorithm for each K and estimate clustering results using
sum of square erros. By default K-Means++ algorithm is used to calculate initial centers that are used by K-Means algorithm.
The Elbow is determined by max distance from each point (x, y) to segment from kmin-point (x0, y0) to kmax-point (x1, y1),
where 'x' is K (amount of clusters), and 'y' is within-cluster error. Following expression is used to calculate Elbow
length:
\f[Elbow_{k} = \frac{\left ( y_{0} - y_{1} \right )x_{k} + \left ( x_{1} - x_{0} \right )y_{k} + \left ( x_{0}y_{1} - x_{1}y_{0} \right )}{\sqrt{\left ( x_{1} - x_{0} \right )^{2} + \left ( y_{1} - y_{0} \right )^{2}}}\f]
Usage example of Elbow method for cluster analysis:
@code
#include <pyclustering/cluster/elbow.hpp>
#include <pyclustering/cluster/kmeans.hpp>
#include <pyclustering/cluster/kmeans_plus_plus.hpp>
#include <fstream>
#include <iostream>
using namespace pyclustering;
using namespace pyclustering::clst;
int main() {
// Read two-dimensional input data 'Simple03'.
dataset data = read_data("Simple03.txt"); // See an example of the implementation below.
// Prepare methods's parameters.
const std::size_t kmin = 1; // minimum amount of clusters that should be considered
const std::size_t kmax = 10; // maximum amount of clusters
// Create Elbow method for processing.
elbow<> elbow_instance = elbow<>(kmin, kmax);
// Run Elbow method to get optimal amount of clusters.
elbow_data result;
elbow_instance.process(data, result);
// Obtain results.
const std::size_t amount_clusters = result.get_amount();
const wce_sequence & wce = result.get_wce(); // total within-cluster errors for each K.
// Perform cluster analysis using K-Means algorithm.
// Prepare initial centers before running K-Means algorithm.
dataset initial_centers;
kmeans_plus_plus(amount_clusters, 5).initialize(data, initial_centers);
// Create K-Means algorithm and run it.
kmeans_data clustering_result;
kmeans(initial_centers).process(data, clustering_result);
// Obtain clustering results.
const cluster_sequence & clusters = clustering_result.clusters();
const dataset & centers = clustering_result.centers();
// Print results to console.
for (std::size_t i = 0; i < clusters.size(); i++) {
std::cout << "Cluster #" << i + 1 << " with center at ( ";
const point & center = centers[i];
for (const auto coordinate : center) {
std::cout << coordinate << " ";
}
std::cout << " ): ";
const cluster & group = clusters[i];
for (const auto index : group) {
std::cout << index << " ";
}
std::cout << std::endl;
}
return 0;
}
@endcode
Here is an example how to read input data from simple text file:
@code
dataset read_data(const std::string & filename) {
dataset data;
std::ifstream file(filename);
std::string line;
while (std::getline(file, line)) {
std::stringstream stream(line);
point coordinates;
double value = 0.0;
while (stream >> value) { coordinates.push_back(value); }
data.push_back(coordinates);
}
file.close();
return data;
}
@endcode
By default Elbow uses K-Means++ initializer to calculate initial centers for K-Means algorithm, it can be changed
using argument 'initializer':
@code
// Prepare methods's parameters.
const std::size_t kmin = 1; // minimum amount of clusters that should be considered
const std::size_t kmax = 10; // maximum amount of clusters
// Create and run Elbow method to get optimal amount of clusters using random center initializer.
elbow_data result;
elbow<random_center_initializer>(kmin, kmax).process(data, result);
@endcode
@image html elbow_example_simple_03.png "Elbows analysis with further K-Means clustering."
Implementation based on paper @cite article::cluster::elbow::1.
*/
template <class TypeInitializer = kmeans_plus_plus>
class elbow {
private:
std::size_t m_kmin = 0;
std::size_t m_kmax = 0;
std::size_t m_kstep = 0;
std::size_t m_kamount = 0;
long long m_random_state = RANDOM_STATE_CURRENT_TIME;
std::vector<double> m_elbow = { };
const dataset * m_data = nullptr;
elbow_data * m_result = nullptr; /* temporary pointer to output result */
public:
/*!
@brief Default constructor of Elbow method.
*/
elbow() = default;
/*!
@brief Elbow method constructor with parameters of the method.
@param[in] p_kmin: minimum amount of clusters that should be considered.
@param[in] p_kmax: maximum amount of clusters that should be considered.
*/
elbow(const std::size_t p_kmin, const std::size_t p_kmax) :
elbow(p_kmin, p_kmax, 1, RANDOM_STATE_CURRENT_TIME)
{ }
/*!
@brief Elbow method constructor with parameters of the method.
@param[in] p_kmin: minimum amount of clusters that should be considered.
@param[in] p_kmax: maximum amount of clusters that should be considered.
@param[in] p_kstep: search step in the interval [kmin, kmax].
*/
elbow(const std::size_t p_kmin, const std::size_t p_kmax, const std::size_t p_kstep) :
elbow(p_kmin, p_kmax, p_kstep, RANDOM_STATE_CURRENT_TIME)
{ }
/*!
@brief Elbow method constructor with parameters of the method.
@param[in] p_kmin: minimum amount of clusters that should be considered.
@param[in] p_kmax: maximum amount of clusters that should be considered.
@param[in] p_kstep: search step in the interval [kmin, kmax].
@param[in] p_random_state: seed for random state.
*/
elbow(const std::size_t p_kmin, const std::size_t p_kmax, const std::size_t p_kstep, const long long p_random_state) :
m_kmin(p_kmin),
m_kmax(p_kmax),
m_kstep(p_kstep),
m_kamount((m_kmax - m_kmin) / m_kstep + 1),
m_random_state(p_random_state)
{
verify();
}
/*!
@brief Copy constructor of Elbow method.
*/
elbow(const elbow & p_other) = default;
/*!
@brief Move constructor of Elbow method.
*/
elbow(elbow && p_other) = default;
/*!
@brief Destructor of Elbow method.
*/
~elbow() = default;
public:
/*!
@brief Performs cluster analysis of an input data.
@param[in] p_data: an input data that should be clusted.
@param[out] p_result: elbow input data processing result.
*/
void process(const dataset & p_data, elbow_data & p_result) {
if (p_data.size() < m_kmax) {
throw std::invalid_argument("K max value '" + std::to_string(m_kmax)
+ "' is greater than amount of data points '" + std::to_string(p_data.size()) + "'.");
}
m_data = &p_data;
m_result = &p_result;
m_result->get_wce().resize(m_kamount);
parallel_for(m_kmin, m_kmax + 1, m_kstep, [this](const std::size_t p_index){
calculate_wce(p_index);
});
calculate_elbows();
m_result->set_amount(find_optimal_kvalue());
}
private:
template<class CenterInitializer = TypeInitializer>
typename std::enable_if<std::is_same<CenterInitializer, kmeans_plus_plus>::value, void>::type
static prepare_centers(const std::size_t p_amount, const dataset & p_data, const long long p_random_state, dataset & p_initial_centers) {
kmeans_plus_plus(p_amount, kmeans_plus_plus::FARTHEST_CENTER_CANDIDATE, p_random_state).initialize(p_data, p_initial_centers);
}
template<class CenterInitializer = TypeInitializer>
typename std::enable_if<!std::is_same<CenterInitializer, kmeans_plus_plus>::value, void>::type
static prepare_centers(const std::size_t p_amount, const dataset & p_data, const long long p_random_state, dataset & p_initial_centers) {
TypeInitializer(p_amount, p_random_state).initialize(p_data, p_initial_centers);
}
void calculate_wce(const std::size_t p_kvalue) {
dataset initial_centers;
prepare_centers(p_kvalue, *m_data, m_random_state, initial_centers);
kmeans_data result;
kmeans instance(initial_centers, kmeans::DEFAULT_TOLERANCE);
instance.process(*m_data, result);
m_result->get_wce().at((p_kvalue - m_kmin) / m_kstep) = result.wce();
}
void verify() {
if (m_kmin < 1) {
throw std::invalid_argument("K min value '" + std::to_string(m_kmin) + "' should be greater than 0.");
}
if (m_kmax <= m_kmin) {
throw std::invalid_argument("K max value '" + std::to_string(m_kmax) + "' should be greater than K min value '" + std::to_string(m_kmin) + "'.");
}
if (m_kmax + 1 < 3 + m_kmin) {
throw std::invalid_argument("Amount of K '" + std::to_string(m_kmax - m_kmin) + "' is too small for analysis.");
}
if (m_kamount < 3) {
throw std::invalid_argument("The search step is too high '" + std::to_string(m_kstep) + "' for analysis (amount of K for analysis is '" + std::to_string(m_kamount) + "').");
}
}
void calculate_elbows() {
const wce_sequence & wce = m_result->get_wce();
const double x0 = 0.0;
const double y0 = wce.front();
const double x1 = static_cast<double>(wce.size());
const double y1 = wce.back();
const double norm = euclidean_distance(point({ x0, y0 }), point({ x1, y1 }));
m_elbow.resize(wce.size() - 2, 0.0);
for (std::size_t index_elbow = 1; index_elbow < m_result->get_wce().size() - 1; index_elbow++) {
const double x = static_cast<double>(index_elbow);
const double y = wce.at(index_elbow);
const double segment = std::abs((y0 - y1) * x + (x1 - x0) * y + (x0 * y1 - x1 * y0));
m_elbow[index_elbow - 1] = segment / norm;
}
}
std::size_t find_optimal_kvalue() {
auto optimal_elbow_iter = std::max_element(m_elbow.cbegin(), m_elbow.cend());
return (std::distance(m_elbow.cbegin(), optimal_elbow_iter) + 1) * m_kstep + m_kmin;
}
};
}
}
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