#include <BALL/QSAR/regressionValidation.h>

Inheritance diagram for BALL::QSAR::RegressionValidation:

Classes
struct	BackupData

Public Member Functions
Constructors and Destructors
	RegressionValidation (RegressionModel *m)

	~RegressionValidation ()

Public Member Functions inherited from BALL::QSAR::Validation
	Validation (Model *m)

virtual	~Validation ()

const Matrix< double > &	getYRandResults () const

int	getStat () const

Accessors
void	crossValidation (int k, bool restore=1)

void	crossValidation (int k, vector< BALL::Matrix< double > > *results, bool restore=1)

void	bootstrap (int k, bool restore=1)

void	bootstrap (int k, vector< BALL::Matrix< double > > *results, bool restore=1)

void	bootstrap1 (int k, vector< BALL::Matrix< double > > *results, bool restore=1)

const BALL::Matrix< double > &	yRandomizationTest (int runs, int k)

double	getQ2 ()

double	getR2 ()

double	getFregr ()

double	getFcv ()

double	getCVRes ()

double	getFitRes ()

double	getMaxError ()

void	setCVRes (double d)

void	setQ2 (double d)

void	testInputData (bool transform=0)

void	selectStat (int s)

void	calculateCoefficientStdErrors (int k, bool b=1)

const BALL::Matrix< double > *	getCoefficientStdErrors ()

void	setCoefficientStdErrors (const BALL::Matrix< double > *stddev)

void	saveToFile (string filename) const

void	saveToFile (string filename, const double &r2, const double &q2, const Matrix< double > &coefficient_stddev, const Matrix< double > &yRand_results) const

void	readFromFile (string filename)

void	testAllSubstances (bool transform)

void	backupTrainingResults ()

void	restoreTrainingResults ()

Attributes
double	ssR_

double	ssE_

double	ssY_

double	std_err_

double	Q2_

double	F_cv_

double	F_regr_

double	R2_

double	max_error_

double	quality_

double(RegressionValidation::*	predQualFetcher_ )()

double(RegressionValidation::*	fitQualFetcher_ )()

BALL::Matrix< double >	coefficient_stderr_

RegressionModel *	regr_model_

BackupData	backup_data_

void(RegressionValidation::*	qualCalculation )()

void	calculateQOF ()

Additional Inherited Members
Protected Member Functions inherited from BALL::QSAR::Validation
void	setTrainingLine (int train_line, int current_line)

void	setTestLine (int test_line, int current_line, bool back_transform=0)

void	yRand ()

Protected Attributes inherited from BALL::QSAR::Validation
vector< vector< double > >	test_substances_

Matrix< double >	test_Y_

vector< string >	substances_names_

Model *	model_

int	validation_statistic_

Matrix< double >	yRand_results_

Detailed Description

class for validation of QSAR regression models

Definition at line 53 of file regressionValidation.h.

Constructor & Destructor Documentation

BALL::QSAR::RegressionValidation::RegressionValidation ( RegressionModel * m )

constructor

Parameters

m	pointer to the regression model, which the object of this class should test

BALL::QSAR::RegressionValidation::~RegressionValidation ( )

Member Function Documentation

void BALL::QSAR::RegressionValidation::backupTrainingResults ( )

private

void BALL::QSAR::RegressionValidation::bootstrap	(	int	k,
		bool	restore = `1`
	)

virtual

starts bootstrapping with k samples \n

Parameters

k	no of bootstrap samples
restore	if restore==1, Model.descriptor_matrix and RegressionModel.training_result is restored after bootstrapping

Implements BALL::QSAR::Validation.

void BALL::QSAR::RegressionValidation::bootstrap	(	int	k,
		vector< BALL::Matrix< double > > *	results,
		bool	restore = `1`
	)

starts bootstrapping with k samples \n

Parameters

k	no of bootstrap samples
restore	if restore==1, Model.descriptor_matrix and RegressionModel.training_result is restored after bootstrapping
results	pointer to vector that should take all matrices RegressionModel.training_result produced during this bootstrapping

void BALL::QSAR::RegressionValidation::bootstrap1	(	int	k,
		vector< BALL::Matrix< double > > *	results,
		bool	restore = `1`
	)

void BALL::QSAR::RegressionValidation::calculateCoefficientStdErrors	(	int	k,
		bool	b = `1`
	)

calculates standart deviations for all predicted coefficients and saves them to coefficient_stddev_ \n

Parameters

b	if b==1, bootstrapping is used; else: cross-validation
k	number of bootstrap samples resp. cross-validation steps

void BALL::QSAR::RegressionValidation::calculateQOF ( )

private

void BALL::QSAR::RegressionValidation::crossValidation	(	int	k,
		bool	restore = `1`
	)

virtual

starts k-fold cross validation \n

Parameters

k	no of cross validation folds
restore	if restore==1, Model.descriptor_matrix and RegressionModel.training_result is restored after cross validation

Implements BALL::QSAR::Validation.

void BALL::QSAR::RegressionValidation::crossValidation	(	int	k,
		vector< BALL::Matrix< double > > *	results,
		bool	restore = `1`
	)

starts k-fold cross validation \n

Parameters

k	no of cross validation folds
restore	if restore==1, Model.descriptor_matrix and RegressionModel.training_result is restored after cross validation
results	pointer to vector that should take all matrices RegressionModel.training_result produced during this cross validation run

const BALL::Matrix<double>* BALL::QSAR::RegressionValidation::getCoefficientStdErrors ( )

returns a const pointer to the matrix containing the standart deviations of all predicted coefficients

double BALL::QSAR::RegressionValidation::getCVRes ( )

virtual

fetches the result of cross-validation

Implements BALL::QSAR::Validation.

double BALL::QSAR::RegressionValidation::getFcv ( )

get the F-value as calculated by cross validation.\n

If crossValidation() has not been run yet, -1 is returned

double BALL::QSAR::RegressionValidation::getFitRes ( )

virtual

fetches the quality of fit to the input data, as calculated by testInputData()

Implements BALL::QSAR::Validation.

double BALL::QSAR::RegressionValidation::getFregr ( )

get the F-value as calculated by testInputData().\n

If testInputData() has not been run yet, -1 is returned

double BALL::QSAR::RegressionValidation::getMaxError ( )

returns the maximal error of the prediction

double BALL::QSAR::RegressionValidation::getQ2 ( )

get the Q^2 value.\n

If no cross-validation has been done yet, -1 is returned

double BALL::QSAR::RegressionValidation::getR2 ( )

get the R^2 value.\n

If testInputData() has not been run yet, -1 is returned

void BALL::QSAR::RegressionValidation::readFromFile ( string filename )

virtual

restore validation-results from a file

Implements BALL::QSAR::Validation.

void BALL::QSAR::RegressionValidation::restoreTrainingResults ( )

private

void BALL::QSAR::RegressionValidation::saveToFile ( string filename ) const

virtual

save the result of the applied validation methods to a file

Implements BALL::QSAR::Validation.

void BALL::QSAR::RegressionValidation::saveToFile	(	string	filename,
		const double &	r2,
		const double &	q2,
		const Matrix< double > &	coefficient_stddev,
		const Matrix< double > &	yRand_results
	)		const

void BALL::QSAR::RegressionValidation::selectStat ( int s )

virtual

select the desired statistic to be used for validating the models

Parameters

s	if (s==1) R^2 and Q^2 are used if(s==2) F_regr and F_cv are used.

Implements BALL::QSAR::Validation.

void BALL::QSAR::RegressionValidation::setCoefficientStdErrors ( const BALL::Matrix< double > * stddev )

void BALL::QSAR::RegressionValidation::setCVRes ( double d )

virtual

set the result of cross-validation to the given value

Implements BALL::QSAR::Validation.

void BALL::QSAR::RegressionValidation::setQ2 ( double d )

set the Q^2 value

void BALL::QSAR::RegressionValidation::testAllSubstances ( bool transform )

private

Tests the current model with all substances in the (unchanged) test data set

void BALL::QSAR::RegressionValidation::testInputData ( bool transform = 0 )

virtual

Fetches input data from QSARData and tests the current (unchanged) model with all these new substances (without cross-validation!). \n

Parameters

transform if transform==1, the test data is transformed in the same way that the training data was transformed before predicting activities.
If training and test substances are taken from the same input file, set transform to 0

Implements BALL::QSAR::Validation.

const BALL::Matrix<double>& BALL::QSAR::RegressionValidation::yRandomizationTest	(	int	runs,
		int	k
	)

virtual

Y randomization test \n

Randomizes all columns of model.Y, trains the model, runs crossValidation and testInputData and saves the resulting R2 and Q2 value to a matrix with 2 columns; the R2 values makeing up the first colum, the Q2 value the second.

Parameters

runs	this is repeated as often as specified by 'runs'

Implements BALL::QSAR::Validation.

Member Data Documentation

BackupData BALL::QSAR::RegressionValidation::backup_data_

private

Definition at line 221 of file regressionValidation.h.

BALL::Matrix<double> BALL::QSAR::RegressionValidation::coefficient_stderr_

private

contains the standart deviations of all predicted coefficients in one column for each modelled activity

Definition at line 216 of file regressionValidation.h.

double BALL::QSAR::RegressionValidation::F_cv_

private

F-value as calculated after cross-validation

Definition at line 197 of file regressionValidation.h.

double BALL::QSAR::RegressionValidation::F_regr_

private

F-value as calculated after regression for input data

Definition at line 200 of file regressionValidation.h.

double(RegressionValidation::* BALL::QSAR::RegressionValidation::fitQualFetcher_)()

private

Definition at line 211 of file regressionValidation.h.

double BALL::QSAR::RegressionValidation::max_error_

private

Definition at line 204 of file regressionValidation.h.

double(RegressionValidation::* BALL::QSAR::RegressionValidation::predQualFetcher_)()

private

Definition at line 209 of file regressionValidation.h.

double BALL::QSAR::RegressionValidation::Q2_

private

Q^2-value as calculated after cross-validation

Definition at line 194 of file regressionValidation.h.

void(RegressionValidation::* BALL::QSAR::RegressionValidation::qualCalculation)()

private

Definition at line 223 of file regressionValidation.h.

double BALL::QSAR::RegressionValidation::quality_

private

the quality as calcated by the last call of testAllSubstances() according to the chose quality-statistic

Definition at line 207 of file regressionValidation.h.

double BALL::QSAR::RegressionValidation::R2_

private

Definition at line 202 of file regressionValidation.h.

RegressionModel* BALL::QSAR::RegressionValidation::regr_model_

private

pointer to the regression model, which the object of this class should test

Definition at line 219 of file regressionValidation.h.

double BALL::QSAR::RegressionValidation::ssE_

private

Definition at line 185 of file regressionValidation.h.

double BALL::QSAR::RegressionValidation::ssR_

private

Definition at line 183 of file regressionValidation.h.

double BALL::QSAR::RegressionValidation::ssY_

private

the sum of squares of the response

Definition at line 188 of file regressionValidation.h.

double BALL::QSAR::RegressionValidation::std_err_

private

standart error

Definition at line 191 of file regressionValidation.h.

Classes

Public Member Functions

Accessors

Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation