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NOCCO.h
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NOCCO.h
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/*
* Copyright (c) The Shogun Machine Learning Toolbox
* Written (w) 2014 Soumyajit De
* Written (w) 2012-2013 Heiko Strathmann
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
* The views and conclusions contained in the software and documentation are those
* of the authors and should not be interpreted as representing official policies,
* either expressed or implied, of the Shogun Development Team.
*/
#ifndef NOCCO_H_
#define NOCCO_H_
#include <shogun/lib/config.h>
#include <shogun/statistics/KernelIndependenceTest.h>
namespace shogun
{
template<class T> class SGMatrix;
/** @brief This class implements the NOrmalized Cross Covariance Operator
* (NOCCO) based independence test as described in [1].
*
* The test of independence is performed as follows: Given samples \f$Z=\{(x_i,
* y_i)\}_{i=1}^n\f$ from the joint distribution \f$\textbf{P}_{XY}\f$,
* does the joint distribution factorize as \f$\textbf{P}_{XY}=\textbf{P}_X
* \textbf{P}_Y\f$? The null hypothesis says yes and the alternative hypothesis
* says no.
*
* The dependence of the random variables \f$\mathbf X=\{x_i\}\f$ and \f$
* \mathbf Y=\{y_i\}\f$ can be measured via the cross-covariance operator
* \f$\boldsymbol\Sigma_{YX}\f$ which becomes \f$\mathbf{0}\f$ if and only if
* \f$\mathbf X\f$ and \f$\mathbf Y\f$ are independent. This term factorizes as
* \f$\boldsymbol\Sigma_{YX}=\boldsymbol\Sigma_{YY}^{\frac{1}{2}}\mathbf{V}_
* {YX}\boldsymbol\Sigma_{XX}^{\frac{1}{2}}\f$, where \f$\boldsymbol\Sigma_
* {XX}\f$ and \f$\boldsymbol\Sigma_{YY}\f$ are known as covariance operator and
* \f$\mathbf{V}_{YX}\f$ is known as normalized cross-covariance operator. The
* paper uses the Hilbert-Schmidt norm of \f$\mathbf V_{YX}\f$ as a dependence
* measure of the independence test (see paper for theroretical details).
*
* This class overrides the compute_statistic() method of the superclass which
* computes an unbiased estimate of the normalized cross covariance operator
* norm. Given the kernels \f$K\f$ (for \f$\mathbf X\f$) and \f$L\f$ (for
* \f$\mathbf Y\f$), if we denote the doubly centered Gram matrices as
* \f$\mathbf{G}_X=\mathbf{HKH}\f$ and \f$\mathbf{G}_Y=\mathbf{HLH}\f$
* (where \f$\mathbf H=\mathbf I-\frac{1}{n}\mathbf{1}\f$), then the operator
* norm is estimated as
* \f[
* \hat{I}^{\text{NOCCO}}=\text{Trace}\left[\mathbf{R_X R_Y}\right]
* \f]
* where \f$\mathbf{R}_X=\mathbf{G}_X(\mathbf{G}_X+n\varepsilon_n\mathbf{I})
* ^{-1}\f$ and \f$\mathbf{R}_Y=\mathbf{G}_Y(\mathbf{G}_Y+n\varepsilon_n
* \mathbf{I})^{-1}\f$ and \f$\varepsilon_n\gt 0\f$ is a regularization
* constant.
*
* In order to avoid computing direct inverse in the above terms for avoiding
* numerical issues, this class uses Cholesky decomposition of matrices
* \f$\mathbf{GG}_*=\mathbf{LL}^\top\f$ (where \f$\mathbf{GG}_*=(\mathbf{G}_*+
* n\varepsilon_n\mathbf{I})^{-1}\f$) and solve systems \f$\mathbf{GG}_*
* \mathbf x_i=\mathbf{LL}^\top\mathbf x_i=\mathbf e_i\f$ (\f$\mathbf e_i\f$
* being the \f$i^{\text{th}}\f$ column of \f$\mathbf I_n\f$) one by one. On
* the fly it then uses the solution vectors \f$\mathbf x_i\f$ to compute the
* matrix-matrix product \f$\mathbf C_*=\mathbf G_*\mathbf{GG}_*^{-1}\f$
* using \f$\mathbf C_{*,(j,i)}=\mathbf G_{*,j}\cdot \mathbf x_i\f$, where
* \f$\mathbf G_{*,j}\f$ is the \f$j^{\text{th}}\f$ row of \f$\mathbf G_*\f$ (or
* column, since it is symmetric) and then discarding the vector.
*
* The final trace computation is also simplified using the symmetry of the
* matrices \f$\mathbf R_X\f$ and \f$\mathbf R_Y\f$. Computation of the off-
* diagonal elements are avoided using
* \f[
* \text{Trace}\left[\mathbf R_X \mathbf R_Y\right ]=\sum_{i=1}^n
* \mathbf R_X^i\cdot \mathbf R_Y^i
* \f]
*
* For performing the independence test, PERMUTATION test is used by first
* randomly shuffling the samples from one of the distributions while keeping
* the samples from the other distribution in the original order. This way we
* sample the null distribution and compute p-value and threshold for a given
* test power.
*
* [1]: Kenji Fukumizu, Arthur Gretton, Xiaohai Sun, Bernhard Scholkopf:
* Kernel Measures of Conditional Dependence. NIPS 2007
*/
class CNOCCO : public CKernelIndependenceTest
{
public:
/** Constructor */
CNOCCO();
/** Constructor.
*
* Initializes the kernels and features from the two distributions and
* SG_REFs them
*
* @param kernel_p kernel to use on samples from p
* @param kernel_q kernel to use on samples from q
* @param p samples from distribution p
* @param q samples from distribution q
*/
CNOCCO(CKernel* kernel_p, CKernel* kernel_q, CFeatures* p, CFeatures* q);
/** Destructor */
virtual ~CNOCCO();
/** Computes the NOCCO statistic (see class description) for underlying
* kernels and data.
*
* Note that since kernel matrices have to be stored, it has quadratic
* space costs.
*
* @return unbiased estimate of NOCCO
*/
virtual float64_t compute_statistic();
/** Computes a p-value based on current method for approximating the
* null-distribution. The p-value is the 1-p quantile of the null-
* distribution where the given statistic lies in.
*
* @param statistic statistic value to compute the p-value for
* @return p-value parameter statistic is the (1-p) percentile of the
* null distribution
*/
virtual float64_t compute_p_value(float64_t statistic);
/** Computes a threshold based on current method for approximating the
* null-distribution. The threshold is the value that a statistic has
* to have in ordner to reject the null-hypothesis.
*
* @param alpha test level to reject null-hypothesis
* @return threshold for statistics to reject null-hypothesis
*/
virtual float64_t compute_threshold(float64_t alpha);
/** @return the class name */
virtual const char* get_name() const
{
return "NOCCO";
}
/** @return the statistic type of this test statistic */
virtual EStatisticType get_statistic_type() const
{
return S_NOCCO;
}
/** Setter for features from distribution p, SG_REFs it
*
* @param p features from p
*/
virtual void set_p(CFeatures* p);
/** Setter for features from distribution q, SG_REFs it
*
* @param q features from q
*/
virtual void set_q(CFeatures* q);
/**
* Setter for regularization parameter epsilon
* @param epsilon the regularization parameter
*/
void set_epsilon(float64_t epsilon);
/** @return epsilon the regularization parameter */
float64_t get_epsilon() const;
/** Merges both sets of samples and computes the test statistic
* m_num_null_sample times. This version precomputes the kenrel matrix
* once by hand, then samples using this one. The matrix has
* to be stored anyway when statistic is computed.
*
* @return vector of all statistics
*/
virtual SGVector<float64_t> sample_null();
protected:
/**
* Helper method which computes the matrix times matrix inverse using LLT
* solve (Cholesky) withoout storing the inverse (see class documentation).
*
* @param m the centered Gram matrix
* @return the result matrix of the multiplication
*/
SGMatrix<float64_t> compute_helper(SGMatrix<float64_t> m);
private:
/** Register parameters and initialize with defaults */
void init();
/** Number of features from the distributions (should be equal for both) */
index_t m_num_features;
/** The regularization constant */
float64_t m_epsilon;
};
}
#endif // NOCCO_H_