BALL::QSAR::RegressionModel Class Reference

#include <BALL/QSAR/regressionModel.h>

Inheritance diagram for BALL::QSAR::RegressionModel:

Public Member Functions
Constructors and Destructors
	RegressionModel (const QSARData &q)
	~RegressionModel ()
virtual void	operator= (const RegressionModel &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)
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
virtual void	calculateOffsets ()=0
void	readDescriptorInformationFromFile (std::ifstream &in, int no_descriptors, bool transformation, int no_coefficients)
void	saveDescriptorInformationToFile (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	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 ()

Protected Attributes
Attributes
BALL::Matrix< double >	training_result_
Vector< double >	offsets_
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_

Friends
class	RegressionValidation

Accessors
RegressionValidation *	validation
const BALL::Matrix< double > *	getTrainingResult () const
virtual void	saveToFile (string filename)
virtual void	readFromFile (string filename)
void	show ()

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

Detailed Description

Definition at line 43 of file regressionModel.h.

Constructor & Destructor Documentation

BALL::QSAR::RegressionModel::RegressionModel

(

const QSARData &

q

)

constructur,

Parameters

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

BALL::QSAR::RegressionModel::~RegressionModel

(

)

Member Function Documentation

virtual void BALL::QSAR::RegressionModel::calculateOffsets ( )

protectedpure virtual

Implemented in BALL::QSAR::KernelModel, BALL::QSAR::LinearModel, and BALL::QSAR::NonLinearModel.

const BALL::Matrix<double>* BALL::QSAR::RegressionModel::getTrainingResult

(

)

const

returns a const pointer to the matrix containing the coefficients obtained by Model.train()

virtual void BALL::QSAR::RegressionModel::operator= ( const RegressionModel &  m )

virtual

void BALL::QSAR::RegressionModel::readDescriptorInformationFromFile ( std::ifstream &  in, int  no_descriptors, bool  transformation, int  no_coefficients  )

protected

virtual void BALL::QSAR::RegressionModel::readFromFile ( string  filename )

virtual

reconstruct a saved Model from a file

Implements BALL::QSAR::Model.

Reimplemented in BALL::QSAR::ALLModel, and BALL::QSAR::KernelModel.

void BALL::QSAR::RegressionModel::saveDescriptorInformationToFile ( std::ofstream &  out )

protectedvirtual

overloaded by class RegressionModel, whose member function can also save coefficients and coefficient-errors

Reimplemented from BALL::QSAR::Model.

virtual void BALL::QSAR::RegressionModel::saveToFile ( string  filename )

virtual

save Model to a file

Implements BALL::QSAR::Model.

Reimplemented in BALL::QSAR::ALLModel, and BALL::QSAR::KernelModel.

void BALL::QSAR::RegressionModel::show

(

)

Friends And Related Function Documentation

friend class RegressionValidation

friend

Definition at line 106 of file regressionModel.h.

Member Data Documentation

Vector<double> BALL::QSAR::RegressionModel::offsets_

protected

Definition at line 91 of file regressionModel.h.

BALL::Matrix<double> BALL::QSAR::RegressionModel::training_result_

protected

BALL::Matrix<double> containing the coefficients obtained by Model.train().\n

raining_result will have the following dimensions for the different types of models, with m=no of descriptors and c=no of modelled activities (=no of columns of Model.Y) :
LinearModel : mxc
KernelModel : nxc
ALLModel : mxc
FitModel : mxc
SVMModel : m x (c*no of classes)
SVRModel : m x (c*no of classes)

Definition at line 88 of file regressionModel.h.

RegressionValidation* BALL::QSAR::RegressionModel::validation

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

Definition at line 63 of file regressionModel.h.