#include <BALL/QSAR/gpModel.h>

Inheritance diagram for BALL::QSAR::GPModel:

Public Member Functions
Constructors and Destructors
	GPModel (const QSARData &q, int k_type, double p1, double p2=-1)

	GPModel (const QSARData &q, Vector< double > &w)

	GPModel (const QSARData &q, String s1, String s2)

	GPModel (const QSARData &q, const LinearModel &lm, int column)

	~GPModel ()

Accessors
void	train ()

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

double	calculateStdErr ()

void	setParameters (vector< double > &v)

vector< double >	getParameters () const

Public Member Functions inherited from BALL::QSAR::KernelModel
	KernelModel (const QSARData &q, int k_type, double p1, double p2)

	KernelModel (const QSARData &q, String f, String g)

	KernelModel (const QSARData &q, Vector< double > &w)

	KernelModel (const QSARData &q, const LinearModel &lm, int column)

	~KernelModel ()

virtual void	saveToFile (string filename)

virtual void	readFromFile (string filename)

void	operator= (const Model &m)

Public Member Functions inherited from BALL::QSAR::NonLinearModel
	NonLinearModel (const QSARData &q)

	~NonLinearModel ()

Private Attributes
Attributes
Matrix< double >	L_

Vector< double >	input_

Vector< double >	K_t_

double	lambda_

Additional Inherited Members
Public Attributes inherited from BALL::QSAR::KernelModel
Kernel *	kernel

Public Attributes inherited from BALL::QSAR::RegressionModel
RegressionValidation *	validation

Public Attributes inherited from BALL::QSAR::Model
const QSARData *	data

Validation *	model_val

Protected Member Functions inherited from BALL::QSAR::KernelModel
void	calculateOffsets ()

void	readKernelParametersFromFile (std::ifstream &in)

void	saveKernelParametersToFile (std::ofstream &out)

void	saveTrainingResult (std::ofstream &out)

void	readTrainingResult (std::ifstream &input, int no_substances, int no_y)

Protected Member Functions inherited from BALL::QSAR::NonLinearModel
Protected Member Functions inherited from BALL::QSAR::RegressionModel
void	readDescriptorInformationFromFile (std::ifstream &in, int no_descriptors, bool transformation, int no_coefficients)

void	saveDescriptorInformationToFile (std::ofstream &out)

Protected Attributes inherited from BALL::QSAR::KernelModel
Matrix< double >	K_

Protected Attributes inherited from BALL::QSAR::RegressionModel
BALL::Matrix< double >	training_result_

Vector< double >	offsets_

Friends inherited from BALL::QSAR::KernelModel

Detailed Description

class for gaussian process regression

Definition at line 41 of file gpModel.h.

Constructor & Destructor Documentation

BALL::QSAR::GPModel::GPModel	(	const QSARData &	q,
		int	k_type,
		double	p1,
		double	p2 = `-1`
	)

BALL::QSAR::GPModel::GPModel	(	const QSARData &	q,
		Vector< double > &	w
	)

BALL::QSAR::GPModel::GPModel	(	const QSARData &	q,
		String	s1,
		String	s2
	)

constructor that sets KernelModel.f to s1 and KernelModel.g to s2

BALL::QSAR::GPModel::GPModel	(	const QSARData &	q,
		const LinearModel &	lm,
		int	column
	)

BALL::QSAR::GPModel::~GPModel ( )

Member Function Documentation

double BALL::QSAR::GPModel::calculateStdErr ( )

virtual

calculates standart error for the last prediction as $\sqrt{k(x_*,x_*)-\sum_{i=1}^n \sum_{j=1}^n k(x_*,x_i)*k(x_*,x_j)-L_{ij} }$

Reimplemented from BALL::QSAR::Model.

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

virtual

Reimplemented from BALL::QSAR::Model.

Vector<double> BALL::QSAR::GPModel::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

Reimplemented from BALL::QSAR::KernelModel.

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

virtual

sets the model parameters according to the given values.

Reimplemented from BALL::QSAR::Model.

void BALL::QSAR::GPModel::train ( )

virtual

Starts training the model.

Implements BALL::QSAR::Model.

Member Data Documentation

Vector<double> BALL::QSAR::GPModel::input_

private

the last predicted substance

Definition at line 81 of file gpModel.h.

Vector<double> BALL::QSAR::GPModel::K_t_

private

Definition at line 83 of file gpModel.h.

Matrix<double> BALL::QSAR::GPModel::L_

private

Definition at line 78 of file gpModel.h.

double BALL::QSAR::GPModel::lambda_

private

Definition at line 85 of file gpModel.h.

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation