#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_

Protected Attributes inherited from BALL::QSAR::ClassificationModel
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)

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_

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 (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

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

Member Function Documentation

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.

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.

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

pure virtual

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

Member Data Documentation

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.

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.

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation