BALL::QSAR::ClassificationModel Class Reference

#include <BALL/QSAR/classificationModel.h>

Inheritance diagram for BALL::QSAR::ClassificationModel:

Public Member Functions
Constructors and Destructors
	ClassificationModel (const QSARData &q)
	~ClassificationModel ()
virtual void	operator= (ClassificationModel &m)
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 ()
virtual Vector< double >	predict (const vector< double > &substance, bool transform)=0
void	deleteDescriptorIDs ()
virtual void	train ()=0
virtual bool	optimizeParameters (int, int)
bool	optimizeParameters (int k)
virtual double	calculateStdErr ()
virtual void	setParameters (vector< double > &)
virtual vector< double >	getParameters () const
std::multiset< unsigned int > *	getDescriptorIDs ()
void	setDataSource (const QSARData *q)
virtual void	saveToFile (string filename)=0
virtual void	readFromFile (string filename)=0
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)

Protected Member Functions
Input and Output. The following methods can be used to implement the functions saveToFile() and readFromFile() in final classes derived from this base-class
void	readClassInformationFromFile (std::ifstream &input, int no_classes)
void	saveClassInformationToFile (std::ofstream &out)
Protected Member Functions inherited from BALL::QSAR::Model
void	readMatrix (Matrix< double > &mat, std::ifstream &in, uint lines, uint col)
void	readVector (Vector< double > &vec, std::ifstream &in, uint no_cells, bool column_vector)
void	readModelParametersFromFile (std::ifstream &in)
void	saveModelParametersToFile (std::ofstream &out)
virtual void	saveDescriptorInformationToFile (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)
Vector< double >	getSubstanceVector (const vector< double > &substance, bool transform)
Vector< double >	getSubstanceVector (const Vector< double > &substance, bool transform)
void	backTransformPrediction (Vector< double > &pred)
void	addLambda (Matrix< double > &matrix, double &lambda)
void	readDescriptorInformation ()

Friends
class	ClassificationValidation

Attributes
ClassificationValidation *	validation
std::vector< int >	labels_
std::vector< int >	getClassLabels ()

Accessors
std::vector< int >	no_substances_
void	readLabels ()

Feature discretization function
void(ClassificationModel::*	discretizeFeatures )(uint bins, BALL::Matrix< double > &discretization_information)
void(ClassificationModel::*	discretizeTestDataFeatures )(Vector< double > &compound, uint bins, const BALL::Matrix< double > &discretization_information)
void	equalSpaceDiscretization (uint bins, BALL::Matrix< double > &discretization_information)
void	equalSpaceDiscretizationTestData (Vector< double > &compound, uint bins, const BALL::Matrix< double > &discretization_information)

Additional Inherited Members
Public Attributes inherited from BALL::QSAR::Model
const QSARData *	data
Validation *	model_val
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

Definition at line 46 of file classificationModel.h.

Constructor & Destructor Documentation

BALL::QSAR::ClassificationModel::ClassificationModel

(

const QSARData &

q

)

constructur,

Parameters

q	QSAR-wrapper object, from which the data for this model should be taken

BALL::QSAR::ClassificationModel::~ClassificationModel

(

)

Member Function Documentation

void BALL::QSAR::ClassificationModel::equalSpaceDiscretization ( uint  bins, BALL::Matrix< double > &  discretization_information  )

protected

discretizes each feature in such a way that each created bin has an equal range of values

void BALL::QSAR::ClassificationModel::equalSpaceDiscretizationTestData ( Vector< double > &  compound, uint  bins, const BALL::Matrix< double > &  discretization_information  )

protected

std::vector<int> BALL::QSAR::ClassificationModel::getClassLabels

(

)

virtual void BALL::QSAR::ClassificationModel::operator= ( ClassificationModel &  m )

virtual

void BALL::QSAR::ClassificationModel::readClassInformationFromFile ( std::ifstream &  input, int  no_classes  )

protected

void BALL::QSAR::ClassificationModel::readLabels ( )

protected

read all different class labels from matrix Y into ClassificationModel.labels

void BALL::QSAR::ClassificationModel::saveClassInformationToFile ( std::ofstream &  out )

protected

Friends And Related Function Documentation

friend class ClassificationValidation

friend

Definition at line 126 of file classificationModel.h.

Member Data Documentation

void(ClassificationModel::* BALL::QSAR::ClassificationModel::discretizeFeatures)(uint bins, BALL::Matrix< double > &discretization_information)

protected

Interface function-definition for discretization of features.\n

Thus, various functions that do the actual discretization can be created as members of ClassificationModel, allowing switching of the discretization technique by only (re-)setting this function-pointer.

Parameters

bins	the number of discrete values to be created for each features
discretization_information	a BALL::Matrix<double> into which the information about the applied discretization should be saved (into one column per feature). This BALL::Matrix<double> can later be used to discretize test data according to the discretization of the training data.

Definition at line 101 of file classificationModel.h.

void(ClassificationModel::* BALL::QSAR::ClassificationModel::discretizeTestDataFeatures)(Vector< double > &compound, uint bins, const BALL::Matrix< double > &discretization_information)

protected

Discretizes test data according to the given discretization of the training data.

Parameters

discretization_information

the discretization according to which the current descriptor_matrix should be discretized.

Definition at line 105 of file classificationModel.h.

std::vector<int> BALL::QSAR::ClassificationModel::labels_

protected

labels for the different classes

Definition at line 123 of file classificationModel.h.

std::vector<int> BALL::QSAR::ClassificationModel::no_substances_

protected

the number of substances in each class of the training data

Definition at line 81 of file classificationModel.h.

ClassificationValidation* BALL::QSAR::ClassificationModel::validation

a ClassificationValidation object, that is used to validate this model and that will contain the results of the validations

Definition at line 66 of file classificationModel.h.