#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, Eigen::VectorXd &w)

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

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

	~GPModel ()

Accessors
void	train ()

Eigen::VectorXd	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, Eigen::VectorXd &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 ()

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

	~RegressionModel ()

virtual EIGEN_MAKE_ALIGNED_OPERATOR_NEW void	operator= (const RegressionModel &m)

const Eigen::MatrixXd *	getTrainingResult () const

void	show ()

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

virtual	~Model ()

void	copyData (const Model &m)

void	copyDescriptorIDs (const Model &m)

void	readTrainingData ()

void	deleteDescriptorIDs ()

virtual bool	optimizeParameters (int, int)

bool	optimizeParameters (int k)

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)

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 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 ()

Protected Attributes inherited from BALL::QSAR::KernelModel
Eigen::MatrixXd	K_

Protected Attributes inherited from BALL::QSAR::RegressionModel
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_

Detailed Description

class for gaussian process regression

Definition at line 21 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,
		Eigen::VectorXd &	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.

Eigen::VectorXd 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.

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation