#include <BALL/QSAR/kplsModel.h>

Inheritance diagram for BALL::QSAR::KPLSModel:

Public Member Functions
Constructors and Destructors
	KPLSModel (const QSARData &q, int k_type, double p1, double p2=-1)

	KPLSModel (const QSARData &q, Eigen::VectorXd &w)

	KPLSModel (const QSARData &q, String s1, String s2)

	KPLSModel (const QSARData &q, const LinearModel &lm, int column)

	~KPLSModel ()

Accessors
void	train ()

bool	optimizeParameters (int k, int no_steps)

int	getNoComponents ()

void	setNoComponents (int d)

const Eigen::MatrixXd *	getU ()

void	setParameters (vector< double > &v)

vector< double >	getParameters () const

Public Member Functions inherited from BALL::QSAR::KernelModel
	KernelModel (const QSARData &q, int k_type, double p1, double p2)

	KernelModel (const QSARData &q, String f, String g)

	KernelModel (const QSARData &q, Eigen::VectorXd &w)

	KernelModel (const QSARData &q, const LinearModel &lm, int column)

	~KernelModel ()

virtual void	saveToFile (string filename)

virtual void	readFromFile (string filename)

virtual Eigen::VectorXd	predict (const vector< double > &substance, bool transform)

void	operator= (const Model &m)

Public Member Functions inherited from BALL::QSAR::NonLinearModel
	NonLinearModel (const QSARData &q)

	~NonLinearModel ()

Public Member Functions inherited from BALL::QSAR::RegressionModel
	RegressionModel (const QSARData &q)

	~RegressionModel ()

virtual EIGEN_MAKE_ALIGNED_OPERATOR_NEW void	operator= (const RegressionModel &m)

const Eigen::MatrixXd *	getTrainingResult () const

void	show ()

Public Member Functions inherited from BALL::QSAR::Model
	Model (const QSARData &q)

virtual	~Model ()

void	copyData (const Model &m)

void	copyDescriptorIDs (const Model &m)

void	readTrainingData ()

void	deleteDescriptorIDs ()

bool	optimizeParameters (int k)

virtual double	calculateStdErr ()

std::multiset< unsigned int > *	getDescriptorIDs ()

void	setDataSource (const QSARData *q)

const Eigen::MatrixXd *	getDescriptorMatrix ()

const vector< string > *	getSubstanceNames ()

const vector< string > *	getDescriptorNames ()

const Eigen::MatrixXd	getDescriptorTransformations ()

const Eigen::MatrixXd	getYTransformations ()

const Eigen::MatrixXd *	getY ()

void	setDescriptorIDs (const std::multiset< unsigned int > &sl)

const string *	getType ()

void	getUnnormalizedFeatureValue (int compound, int feature, double &return_value)

void	getUnnormalizedResponseValue (int compound, int response, double &return_value)

Public Member Functions inherited from BALL::QSAR::LatentVariableModel
	LatentVariableModel ()

const Eigen::MatrixXd *	getLatentVariables ()

const Eigen::MatrixXd *	getWeights ()

const Eigen::MatrixXd *	getLoadings ()

Protected Attributes
Attributes
Eigen::MatrixXd	U_

int	no_components_

Protected Attributes inherited from BALL::QSAR::KernelModel
Eigen::MatrixXd	K_

Protected Attributes inherited from BALL::QSAR::RegressionModel
Eigen::MatrixXd	training_result_

Eigen::RowVectorXd	offsets_

Protected Attributes inherited from BALL::QSAR::Model
int	default_no_opt_steps_

Eigen::MatrixXd	descriptor_matrix_

vector< string >	substance_names_

vector< string >	descriptor_names_

Eigen::MatrixXd	descriptor_transformations_

Eigen::MatrixXd	y_transformations_

Eigen::MatrixXd	Y_

String	type_

std::multiset< unsigned int >	descriptor_IDs_

Protected Attributes inherited from BALL::QSAR::LatentVariableModel
Eigen::MatrixXd	latent_variables_

Eigen::MatrixXd	loadings_

Eigen::MatrixXd	weights_

Additional Inherited Members
Public Attributes inherited from BALL::QSAR::KernelModel
Kernel *	kernel

Public Attributes inherited from BALL::QSAR::RegressionModel
RegressionValidation *	validation

Public Attributes inherited from BALL::QSAR::Model
const QSARData *	data

Validation *	model_val

Protected Member Functions inherited from BALL::QSAR::KernelModel
void	calculateOffsets ()

void	readKernelParametersFromFile (std::ifstream &in)

void	saveKernelParametersToFile (std::ofstream &out)

void	saveTrainingResult (std::ofstream &out)

void	readTrainingResult (std::ifstream &input, int no_substances, int no_y)

Protected Member Functions inherited from BALL::QSAR::NonLinearModel
Protected Member Functions inherited from BALL::QSAR::RegressionModel
void	readDescriptorInformationFromFile (std::ifstream &in, int no_descriptors, bool transformation, int no_coefficients)

void	saveDescriptorInformationToFile (std::ofstream &out)

Protected Member Functions inherited from BALL::QSAR::Model
void	readMatrix (Eigen::MatrixXd &mat, std::ifstream &in, unsigned int lines, unsigned int col)

void	readVector (Eigen::RowVectorXd &vec, std::ifstream &in, unsigned int no_cells, bool column_vector)

void	readModelParametersFromFile (std::ifstream &in)

void	saveModelParametersToFile (std::ofstream &out)

virtual void	readDescriptorInformationFromFile (std::ifstream &in, int no_descriptors, bool transformation)

void	readResponseTransformationFromFile (std::ifstream &in, int no_y)

void	saveResponseTransformationToFile (std::ofstream &out)

Eigen::VectorXd	getSubstanceVector (const vector< double > &substance, bool transform)

Eigen::VectorXd	getSubstanceVector (const Eigen::VectorXd &substance, bool transform)

void	backTransformPrediction (Eigen::VectorXd &pred)

void	addLambda (Eigen::MatrixXd &matrix, double &lambda)

void	readDescriptorInformation ()

Detailed Description

kernel partial-least-squares class

Definition at line 26 of file kplsModel.h.

Constructor & Destructor Documentation

BALL::QSAR::KPLSModel::KPLSModel	(	const QSARData &	q,
		int	k_type,
		double	p1,
		double	p2 = `-1`
	)

BALL::QSAR::KPLSModel::KPLSModel	(	const QSARData &	q,
		Eigen::VectorXd &	w
	)

BALL::QSAR::KPLSModel::KPLSModel	(	const QSARData &	q,
		String	s1,
		String	s2
	)

BALL::QSAR::KPLSModel::KPLSModel	(	const QSARData &	q,
		const LinearModel &	lm,
		int	column
	)

BALL::QSAR::KPLSModel::~KPLSModel ( )

Member Function Documentation

int BALL::QSAR::KPLSModel::getNoComponents ( )

returns the number of latente variables (=PLS components)

vector<double> BALL::QSAR::KPLSModel::getParameters ( ) const

virtual

Reimplemented from BALL::QSAR::Model.

const Eigen::MatrixXd* BALL::QSAR::KPLSModel::getU ( )

returns a pointer to the PLS Y-scores matrix U

bool BALL::QSAR::KPLSModel::optimizeParameters	(	int	k,
		int	no_steps
	)

virtual

tries to find the optimal number of latente variables (=PLS components)

Reimplemented from BALL::QSAR::Model.

void BALL::QSAR::KPLSModel::setNoComponents ( int d )

void BALL::QSAR::KPLSModel::setParameters ( vector< double > & )

virtual

sets the model parameters according to the given values.

Reimplemented from BALL::QSAR::Model.

void BALL::QSAR::KPLSModel::train ( )

virtual

Starts training the model.

Implements BALL::QSAR::Model.

Member Data Documentation

int BALL::QSAR::KPLSModel::no_components_

protected

Definition at line 74 of file kplsModel.h.

Eigen::MatrixXd BALL::QSAR::KPLSModel::U_

protected

Definition at line 72 of file kplsModel.h.

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation