BALL::QSAR::NBModel Class Reference

#include <BALL/QSAR/nBModel.h>

Inheritance diagram for BALL::QSAR::NBModel:

Public Member Functions
Constructors and Destructors
	NBModel (const QSARData &q)
	~NBModel ()
Accessors
void	train ()
Vector< double >	predict (const vector< double > &substance, bool transform=1)
void	saveToFile (string filename)
void	readFromFile (string filename)
vector< double >	getParameters () const
void	setParameters (vector< double > &v)
bool	isTrained ()
vector< double >	calculateProbabilities (int activitiy_index, int feature_index, double feature_value)
int	getNoResponseVariables ()
Public Member Functions inherited from BALL::QSAR::BayesModel
	BayesModel (const QSARData &q)
Public Member Functions inherited from BALL::QSAR::ClassificationModel
	ClassificationModel (const QSARData &q)
	~ClassificationModel ()
virtual void	operator= (ClassificationModel &m)
std::vector< int >	getClassLabels ()
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 ()
void	deleteDescriptorIDs ()
virtual bool	optimizeParameters (int, int)
bool	optimizeParameters (int k)
virtual double	calculateStdErr ()
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)

Private Attributes
Attributes
uint	discretization_steps_
Matrix< double >	min_max_
vector< vector< Matrix< double > > >	probabilities_

Additional Inherited Members
Public Attributes inherited from BALL::QSAR::ClassificationModel
ClassificationValidation *	validation
Public Attributes inherited from BALL::QSAR::Model
const QSARData *	data
Validation *	model_val
Protected Member Functions inherited from BALL::QSAR::ClassificationModel
void	readClassInformationFromFile (std::ifstream &input, int no_classes)
void	saveClassInformationToFile (std::ofstream &out)
void	readLabels ()
void	equalSpaceDiscretization (uint bins, BALL::Matrix< double > &discretization_information)
void	equalSpaceDiscretizationTestData (Vector< double > &compound, uint bins, const BALL::Matrix< double > &discretization_information)
Protected Attributes inherited from BALL::QSAR::BayesModel
double	min_prob_diff_
double	undef_act_class_id_

Detailed Description

class for Naive Bayes

Definition at line 43 of file nBModel.h.

Constructor & Destructor Documentation

BALL::QSAR::NBModel::NBModel

(

const QSARData &

q

)

BALL::QSAR::NBModel::~NBModel

(

)

Member Function Documentation

vector<double> BALL::QSAR::NBModel::calculateProbabilities ( int  activitiy_index, int  feature_index, double  feature_value  )

virtual

calculate the probability for the specified feature to assume the given value for each class

Returns

a probability for each class

Implements BALL::QSAR::BayesModel.

int BALL::QSAR::NBModel::getNoResponseVariables ( )

virtual

returns the number of response variables for which this model has been trained

Implements BALL::QSAR::BayesModel.

vector<double> BALL::QSAR::NBModel::getParameters ( ) const

virtual

Reimplemented from BALL::QSAR::Model.

bool BALL::QSAR::NBModel::isTrained ( )

virtual

Implements BALL::QSAR::BayesModel.

Vector<double> BALL::QSAR::NBModel::predict ( const vector< double > &  substance, bool  transform = 1  )

virtual

Predicts the activities of a given substance

Parameters

substance

the substance which activity is to be predicted in form of a vecor containing the values for all descriptors (if neccessary, relevant descriptors will be selected automatically)

transform

determines whether the values for each descriptor of the given substance should be transformed before prediction of activity. If (transform==1): each descriptor value is transformed according to the centering of the respective column of QSARData.descriptor_matrix used to train this model. If the substance to be predicted is part of the same input data (e.g. same SD-file) as the training data (as is the case during cross validation), transform should therefore be set to 0.

Returns

a RowVector containing one value for each predicted activity

Implements BALL::QSAR::Model.

void BALL::QSAR::NBModel::readFromFile ( string  filename )

virtual

reconstruct a saved Model from a file

Implements BALL::QSAR::Model.

void BALL::QSAR::NBModel::saveToFile ( string  filename )

virtual

save Model to a file

Implements BALL::QSAR::Model.

void BALL::QSAR::NBModel::setParameters ( vector< double > &  )

virtual

sets the model parameters according to the given values.

Reimplemented from BALL::QSAR::Model.

void BALL::QSAR::NBModel::train ( )

virtual

Starts training the model.

Implements BALL::QSAR::Model.

Member Data Documentation

uint BALL::QSAR::NBModel::discretization_steps_

private

Definition at line 83 of file nBModel.h.

Matrix<double> BALL::QSAR::NBModel::min_max_

private

the minmum (row1) and maximum (row2) of each feature.

Definition at line 87 of file nBModel.h.

vector<vector<Matrix<double> > > BALL::QSAR::NBModel::probabilities_

private

One probability Matrix for each modelled activity and each class. \n

Each Matrix stores in each cell the probability for a feature lying within a specific range to be in a specific class

Definition at line 91 of file nBModel.h.