#include <BALL/QSAR/classificationValidation.h>

Inheritance diagram for BALL::QSAR::ClassificationValidation:

Public Member Functions
Constructors and Destructors
	ClassificationValidation (ClassificationModel *m)

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

virtual	~Validation ()

const Matrix< double > &	getYRandResults () const

int	getStat () const

Private Attributes
Attributes
BALL::Matrix< double >	confusion_matrix_

Vector< double >	class_results_

double	quality_

double	quality_input_test_

double	quality_cv_

ClassificationModel *	clas_model

void(ClassificationValidation::*	qualCalculation )()

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

double	getCVRes ()

double	getFitRes ()

void	setCVRes (double d)

void	testInputData (bool transform=0)

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

const BALL::Vector< double > *	getClassResults ()

void	bootstrap (int k, bool restore=1)

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

double	getAccuracyCV ()

double	getAccuracyInputTest ()

void	selectStat (int s)

void	saveToFile (string filename) const

void	saveToFile (string filename, const double &quality_input_test, const double &predictive_quality) const

void	readFromFile (string filename)

void	testAllSubstances (bool transform)

void	calculateAverageSensitivity ()

void	calculateWeightedSensitivity ()

void	calculateOverallAccuracy ()

void	calculateAverageMCC ()

void	calculateOverallMCC ()

void	calculateTDR ()

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 48 of file classificationValidation.h.

Constructor & Destructor Documentation

BALL::QSAR::ClassificationValidation::ClassificationValidation ( ClassificationModel * m )

constructor

Parameters

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

Member Function Documentation

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

virtual

starts bootstrapping with k samples \n

Parameters

k	no of bootstrap samples

Implements BALL::QSAR::Validation.

void BALL::QSAR::ClassificationValidation::calculateAverageMCC ( )

private

calculate one MCC for each class and use the average

void BALL::QSAR::ClassificationValidation::calculateAverageSensitivity ( )

private

calculate average accuracy with the current values of TP, FP, FN, TN in matrix ClassificationValidation.predictions.

void BALL::QSAR::ClassificationValidation::calculateOverallAccuracy ( )

private

calculate accuracy for all classes at once

void BALL::QSAR::ClassificationValidation::calculateOverallMCC ( )

private

calculate MCC for all classes at once

void BALL::QSAR::ClassificationValidation::calculateTDR ( )

private

calculate the True Discovery Rate (only applicable to binary classification validation results).

void BALL::QSAR::ClassificationValidation::calculateWeightedSensitivity ( )

private

calculate weighted average accuracy of all classes. Weighted by the number of training compounds within each class

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

virtual

Starts cross-validation with k steps. \n

Data is taken from QSARData.descriptor_matrix and is in each step divided into training- and test-data.
(Data having already been copied into Model.descriptor_matrix will be deleted)

Implements BALL::QSAR::Validation.

double BALL::QSAR::ClassificationValidation::getAccuracyCV ( )

get average accuracy value as determined after cross validation

double BALL::QSAR::ClassificationValidation::getAccuracyInputTest ( )

get average accuracy value as determined after testing of input data();

const BALL::Vector<double>* BALL::QSAR::ClassificationValidation::getClassResults ( )

returns a RowVector holding the one value contituting the validation result for each class if "average accuracy" or "average MCC" is chosen (see selectStat()).

const BALL::Matrix<double>* BALL::QSAR::ClassificationValidation::getConfusionMatrix ( )

return pointer to the matrix containing the number of TP, FP, TN, FN in one column for each class

double BALL::QSAR::ClassificationValidation::getCVRes ( )

virtual

fetches the result of cross-validation

Implements BALL::QSAR::Validation.

double BALL::QSAR::ClassificationValidation::getFitRes ( )

virtual

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

Implements BALL::QSAR::Validation.

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

virtual

restore validation-results from a file

Implements BALL::QSAR::Validation.

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

virtual

save the result of the applied validation methods to a file

Implements BALL::QSAR::Validation.

void BALL::QSAR::ClassificationValidation::saveToFile	(	string	filename,
		const double &	quality_input_test,
		const double &	predictive_quality
	)		const

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

virtual

set the result of cross-validation to the given value

Implements BALL::QSAR::Validation.

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

private

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

void BALL::QSAR::ClassificationValidation::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::ClassificationValidation::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 accuracy_input_test and accuracy_cv value to a vector, where BALL::Matrix<double>(i,0)=accuracy_input_test, BALL::Matrix<double>(i,1)=accuracy_cv

Parameters

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

Implements BALL::QSAR::Validation.

Member Data Documentation

ClassificationModel* BALL::QSAR::ClassificationValidation::clas_model

private

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

Definition at line 148 of file classificationValidation.h.

Vector<double> BALL::QSAR::ClassificationValidation::class_results_

private

RowVector holding the one value contituting the validation result for each class if "average sensitivity" or "average MCC" is chosen (see selectStat()).

Definition at line 139 of file classificationValidation.h.

BALL::Matrix<double> BALL::QSAR::ClassificationValidation::confusion_matrix_

private

matrix containing the number of TP, FP, FN, TN in one column for each class

Definition at line 136 of file classificationValidation.h.

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

private

Definition at line 150 of file classificationValidation.h.

double BALL::QSAR::ClassificationValidation::quality_

private

Definition at line 141 of file classificationValidation.h.

double BALL::QSAR::ClassificationValidation::quality_cv_