BALL 1.5.0
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BALL::QSAR::RegressionModel Class Referenceabstract

#include <BALL/QSAR/regressionModel.h>

Inheritance diagram for BALL::QSAR::RegressionModel:
BALL::QSAR::Model BALL::QSAR::LinearModel BALL::QSAR::NonLinearModel BALL::QSAR::MLRModel BALL::QSAR::PCRModel BALL::QSAR::PLSModel BALL::QSAR::ALLModel BALL::QSAR::KernelModel BALL::QSAR::RRModel BALL::QSAR::OPLSModel BALL::QSAR::KNNModel BALL::QSAR::GPModel BALL::QSAR::KPCRModel BALL::QSAR::KPLSModel BALL::QSAR::SVRModel BALL::QSAR::LibsvmModel

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< doublegetParameters () 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 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_
 

Accessors

RegressionValidationvalidation
 
const Eigen::MatrixXd * getTrainingResult () const
 
virtual void saveToFile (string filename)
 
virtual void readFromFile (string filename)
 
void show ()
 

Input and Output. The following methods can be used to implement the functions saveToFile() and readFromFile() in final classes derived from this base-class

class RegressionValidation
 
class Rescoring
 
virtual void calculateOffsets ()=0
 
void readDescriptorInformationFromFile (std::ifstream &in, int no_descriptors, bool transformation, int no_coefficients)
 
void saveDescriptorInformationToFile (std::ofstream &out)
 

Additional Inherited Members

- Public Attributes inherited from BALL::QSAR::Model
const QSARDatadata
 
Validationmodel_val
 
- 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 ()
 

Detailed Description

Definition at line 20 of file regressionModel.h.

Constructor & Destructor Documentation

◆ RegressionModel()

BALL::QSAR::RegressionModel::RegressionModel ( const QSARData & q)

constructur,

Parameters
qQSAR-wrapper object, from which the data for this model should be taken

◆ ~RegressionModel()

BALL::QSAR::RegressionModel::~RegressionModel ( )

Member Function Documentation

◆ calculateOffsets()

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

◆ getTrainingResult()

const Eigen::MatrixXd * BALL::QSAR::RegressionModel::getTrainingResult ( ) const

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

◆ operator=()

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

◆ readDescriptorInformationFromFile()

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

◆ readFromFile()

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.

◆ saveDescriptorInformationToFile()

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.

◆ saveToFile()

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.

◆ show()

void BALL::QSAR::RegressionModel::show ( )

Friends And Related Symbol Documentation

◆ RegressionValidation

friend class RegressionValidation
friend

Definition at line 84 of file regressionModel.h.

◆ Rescoring

friend class Rescoring
friend

Definition at line 85 of file regressionModel.h.

Member Data Documentation

◆ offsets_

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

Definition at line 70 of file regressionModel.h.

◆ training_result_

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.

◆ validation

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.