BALL::QSAR::KPCRModel Class Reference

#include <BALL/QSAR/kpcrModel.h>

Inheritance diagram for BALL::QSAR::KPCRModel:

Public Member Functions
Constructors and Destructors
	KPCRModel (const QSARData &q, int k_type, double p1, double p2=-1)
	KPCRModel (const QSARData &q, Eigen::VectorXd &w)
	KPCRModel (const QSARData &q, String s1, String s2)
	KPCRModel (const QSARData &q, const LinearModel &lm, int column)
	~KPCRModel ()
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)
	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 ()
virtual bool	optimizeParameters (int, int)
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 ()

Accessors
void	setFracVar (double frac_var)
void	train ()
void	setParameters (vector< double > &v)
vector< double >	getParameters () const

Additional Inherited Members
Kernel *	kernel
RegressionValidation *	validation
const QSARData *	data
Validation *	model_val
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)
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 ()
Eigen::MatrixXd	K_
Protected Attributes inherited from BALL::QSAR::RegressionModel
Eigen::MatrixXd	training_result_
Eigen::RowVectorXd	offsets_
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_

Detailed Description

class for kernel principal component regression

Definition at line 26 of file kpcrModel.h.

Constructor & Destructor Documentation

KPCRModel() [1/4]

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

KPCRModel() [2/4]

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

KPCRModel() [3/4]

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

KPCRModel() [4/4]

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

~KPCRModel()

BALL::QSAR::KPCRModel::~KPCRModel

(

)

Member Function Documentation

getParameters()

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

virtual

Reimplemented from BALL::QSAR::Model.

setFracVar()

void BALL::QSAR::KPCRModel::setFracVar

(

double

frac_var

)

set the fraction of the variance that should be explained by the latente variables.

setParameters()

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

virtual

sets the model parameters according to the given values.

Reimplemented from BALL::QSAR::Model.

train()

void BALL::QSAR::KPCRModel::train ( )

virtual

Starts training the model.

Implements BALL::QSAR::Model.