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 EIGEN_MAKE_ALIGNED_OPERATOR_NEW 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 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)
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
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 (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	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 ()

Protected Attributes
Attributes
Eigen::MatrixXd	training_result_
Eigen::RowVectorXd	offsets_
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_

Friends
class	RegressionValidation
class	Rescoring

Accessors
RegressionValidation *	validation
const Eigen::MatrixXd *	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 20 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 Eigen::MatrixXd* BALL::QSAR::RegressionModel::getTrainingResult

(

)

const

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

virtual EIGEN_MAKE_ALIGNED_OPERATOR_NEW 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 84 of file regressionModel.h.

friend class Rescoring

friend

Definition at line 85 of file regressionModel.h.

Member Data Documentation

Eigen::RowVectorXd BALL::QSAR::RegressionModel::offsets_

protected

Definition at line 70 of file regressionModel.h.

Eigen::MatrixXd BALL::QSAR::RegressionModel::training_result_

protected

Eigen::MatrixXd containing the coefficients obtained by Model.train().
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 67 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 42 of file regressionModel.h.