BALL::QSAR::BayesModel Class Reference

#include <BALL/QSAR/bayesModel.h>

Inheritance diagram for BALL::QSAR::BayesModel:

Public Member Functions
	BayesModel (const QSARData &q)
virtual bool	isTrained ()=0
virtual vector< double >	calculateProbabilities (int activitiy_index, int feature_index, double feature_value)=0
virtual int	getNoResponseVariables ()=0
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 ()
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 Attributes
double	min_prob_diff_
double	undef_act_class_id_
std::vector< int >	labels_
std::vector< int >	no_substances_
void(ClassificationModel::*	discretizeFeatures )(unsigned int bins, Eigen::MatrixXd &discretization_information)
void(ClassificationModel::*	discretizeTestDataFeatures )(Eigen::VectorXd &compound, unsigned int bins, const Eigen::MatrixXd &discretization_information)
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_

Additional Inherited Members
ClassificationValidation *	validation
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 (unsigned int bins, Eigen::MatrixXd &discretization_information)
void	equalSpaceDiscretizationTestData (Eigen::VectorXd &compound, unsigned int bins, const Eigen::MatrixXd &discretization_information)
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 ()

Detailed Description

interface class for all Bayes classification models

Definition at line 18 of file bayesModel.h.

Constructor & Destructor Documentation

BayesModel()

BALL::QSAR::BayesModel::BayesModel

(

const QSARData &

q

)

Member Function Documentation

calculateProbabilities()

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

pure virtual

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

Returns

a probability for each class

Implemented in BALL::QSAR::NBModel, and BALL::QSAR::SNBModel.

getNoResponseVariables()

virtual int BALL::QSAR::BayesModel::getNoResponseVariables ( )

pure virtual

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

Implemented in BALL::QSAR::NBModel, and BALL::QSAR::SNBModel.

isTrained()

virtual bool BALL::QSAR::BayesModel::isTrained ( )

pure virtual

Implemented in BALL::QSAR::NBModel, and BALL::QSAR::SNBModel.

Member Data Documentation

min_prob_diff_

double BALL::QSAR::BayesModel::min_prob_diff_

protected

the minimal desired difference between the predicted class and the second best class. If the difference is smaller than this value, undef_act_class_id_ should be used instead.

Definition at line 36 of file bayesModel.h.

undef_act_class_id_

double BALL::QSAR::BayesModel::undef_act_class_id_

protected

the class_id that is to be assigned, if no class could be savely predicted, if difference between best and second best potential class is smaller than min_prob_diff_

Definition at line 39 of file bayesModel.h.