#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 Eigen::VectorXd	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 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)

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 (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	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)

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 ()

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 )(unsigned int bins, Eigen::MatrixXd &discretization_information)

void(ClassificationModel::*	discretizeTestDataFeatures )(Eigen::VectorXd &compound, unsigned int bins, const Eigen::MatrixXd &discretization_information)

void	equalSpaceDiscretization (unsigned int bins, Eigen::MatrixXd &discretization_information)

void	equalSpaceDiscretizationTestData (Eigen::VectorXd &compound, unsigned int bins, const Eigen::MatrixXd &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_

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_

Detailed Description

Definition at line 26 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	(	unsigned int	bins,
		Eigen::MatrixXd &	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	(	Eigen::VectorXd &	compound,
		unsigned int	bins,
		const Eigen::MatrixXd &	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 105 of file classificationModel.h.

Member Data Documentation

void(ClassificationModel::* BALL::QSAR::ClassificationModel::discretizeFeatures)(unsigned int bins, Eigen::MatrixXd &discretization_information)

protected

Interface function-definition for discretization of features.
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 Eigen::MatrixXd into which the information about the applied discretization should be saved (into one column per feature). This Eigen::MatrixXd can later be used to discretize test data according to the discretization of the training data.

Definition at line 82 of file classificationModel.h.

void(ClassificationModel::* BALL::QSAR::ClassificationModel::discretizeTestDataFeatures)(Eigen::VectorXd &compound, unsigned int bins, const Eigen::MatrixXd &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 86 of file classificationModel.h.

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

protected

labels for the different classes

Definition at line 102 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 62 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 47 of file classificationModel.h.

Public Member Functions

Protected Member Functions

Friends

Attributes

Accessors

Feature discretization function

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation