BALL::QSAR::LDAModel Class Reference

#include <BALL/QSAR/ldaModel.h>

Inheritance diagram for BALL::QSAR::LDAModel:

Public Member Functions
Constructors and Destructors
	LDAModel (const QSARData &q)
	~LDAModel ()
Accessors
void	train ()
Vector< double >	predict (const vector< double > &substance, bool transform=1)
void	setParameters (vector< double > &v)
vector< double >	getParameters () const
void	saveToFile (string filename)
void	readFromFile (string filename)
Public Member Functions inherited from BALL::QSAR::ClassificationModel
	ClassificationModel (const QSARData &q)
	~ClassificationModel ()
virtual void	operator= (ClassificationModel &m)
std::vector< int >	getClassLabels ()
Public Member Functions inherited from BALL::QSAR::Model
	Model (const QSARData &q)
virtual	~Model ()
virtual void	operator= (const Model &m)
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 Matrix< double > *	getDescriptorMatrix ()
const vector< string > *	getSubstanceNames ()
const vector< string > *	getDescriptorNames ()
const Matrix< double > *	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)

Private Attributes
Attributes
Matrix< double >	sigma_
double	lambda_
vector< Matrix< double > >	mean_vectors_

Additional Inherited Members
Public Attributes inherited from BALL::QSAR::ClassificationModel
ClassificationValidation *	validation
Public Attributes inherited from BALL::QSAR::Model
const QSARData *	data
Validation *	model_val
Protected Member Functions inherited from BALL::QSAR::ClassificationModel
void	readClassInformationFromFile (std::ifstream &input, int no_classes)
void	saveClassInformationToFile (std::ofstream &out)
void	readLabels ()
void	equalSpaceDiscretization (uint bins, BALL::Matrix< double > &discretization_information)
void	equalSpaceDiscretizationTestData (Vector< double > &compound, uint bins, const BALL::Matrix< double > &discretization_information)
Protected Attributes inherited from BALL::QSAR::ClassificationModel
std::vector< int >	labels_
std::vector< int >	no_substances_
void(ClassificationModel::*	discretizeFeatures )(uint bins, BALL::Matrix< double > &discretization_information)
void(ClassificationModel::*	discretizeTestDataFeatures )(Vector< double > &compound, uint bins, const BALL::Matrix< double > &discretization_information)
Protected Attributes inherited from BALL::QSAR::Model
int	default_no_opt_steps_
Matrix< double >	descriptor_matrix_
vector< string >	substance_names_
vector< string >	descriptor_names_
Matrix< double >	descriptor_transformations_
Matrix< double >	y_transformations_
Matrix< double >	Y_
String	type_
std::multiset< unsigned int >	descriptor_IDs_

Detailed Description

class for support vector classification

Definition at line 41 of file ldaModel.h.

Constructor & Destructor Documentation

BALL::QSAR::LDAModel::LDAModel

(

const QSARData &

q

)

BALL::QSAR::LDAModel::~LDAModel

(

)

Member Function Documentation

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

virtual

Reimplemented from BALL::QSAR::Model.

Vector<double> BALL::QSAR::LDAModel::predict ( const vector< double > &  substance, bool  transform = 1  )

virtual

Predicts the activities of a given substance

Parameters

substance

the substance which activity is to be predicted in form of a vecor containing the values for all descriptors (if neccessary, relevant descriptors will be selected automatically)

transform

determines whether the values for each descriptor of the given substance should be transformed before prediction of activity. If (transform==1): each descriptor value is transformed according to the centering of the respective column of QSARData.descriptor_matrix used to train this model. If the substance to be predicted is part of the same input data (e.g. same SD-file) as the training data (as is the case during cross validation), transform should therefore be set to 0.

Returns

a RowVector containing one value for each predicted activity

Implements BALL::QSAR::Model.

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

virtual

reconstruct a saved Model from a file

Implements BALL::QSAR::Model.

void BALL::QSAR::LDAModel::saveToFile ( string  filename )

virtual

save Model to a file

Implements BALL::QSAR::Model.

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

virtual

sets the model parameters according to the given values.

Reimplemented from BALL::QSAR::Model.

void BALL::QSAR::LDAModel::train ( )

virtual

Starts training the model.

Implements BALL::QSAR::Model.

Member Data Documentation

double BALL::QSAR::LDAModel::lambda_

private

Definition at line 78 of file ldaModel.h.

vector<Matrix<double> > BALL::QSAR::LDAModel::mean_vectors_

private

vector containing one matrix for each modelled activity. Each matrix contains a mean vector of a class in each line

Definition at line 81 of file ldaModel.h.

Matrix<double> BALL::QSAR::LDAModel::sigma_

private

covariance matrix of descriptors

Definition at line 75 of file ldaModel.h.