BALL::QSAR::KNNModel Class Reference

#include <BALL/QSAR/knnModel.h>

Inheritance diagram for BALL::QSAR::KNNModel:

Public Member Functions
void	calculateWeights (Eigen::MatrixXd &dist, Eigen::VectorXd &w)
void	setParameters (vector< double > &v)
vector< double >	getParameters () const
bool	optimizeParameters (int k, int no_steps)
Constructors and Destructors
	KNNModel (const QSARData &q, int k=3)
Public Member Functions inherited from BALL::QSAR::ALLModel
	ALLModel (const QSARData &q, double kw=4)
	~ALLModel ()
void	setKw (double kw)
virtual Eigen::VectorXd	predict (const vector< double > &substance, bool transform=1)
void	train ()
double	getKw ()
void	saveToFile (string filename)
void	readFromFile (string filename)
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 ()
virtual void	operator= (const Model &m)
void	copyData (const Model &m)
void	copyDescriptorIDs (const Model &m)
void	readTrainingData ()
void	deleteDescriptorIDs ()
bool	optimizeParameters (int k)
virtual double	calculateStdErr ()
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::RegressionModel
RegressionValidation *	validation
Public Attributes inherited from BALL::QSAR::Model
const QSARData *	data
Validation *	model_val
Protected Member Functions inherited from BALL::QSAR::ALLModel
void	calculateXX (Eigen::VectorXd &w, Eigen::MatrixXd &res)
void	calculateXY (Eigen::VectorXd &w, Eigen::MatrixXd &res)
void	calculateEuclDistanceMatrix (Eigen::MatrixXd &m1, Eigen::MatrixXd &m2, Eigen::MatrixXd &output)
Protected Member Functions inherited from BALL::QSAR::NonLinearModel
virtual void	calculateOffsets ()
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::ALLModel
double	kw_
double	lambda_
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 automated lazy learning (ALL-QSAR)

Definition at line 19 of file knnModel.h.

Constructor & Destructor Documentation

BALL::QSAR::KNNModel::KNNModel	(	const QSARData &	q,
		int	k = 3
	)

Member Function Documentation

void BALL::QSAR::KNNModel::calculateWeights ( Eigen::MatrixXd &  dist, Eigen::VectorXd &  w  )

virtual

Reimplemented from BALL::QSAR::ALLModel.

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

virtual

Reimplemented from BALL::QSAR::ALLModel.

bool BALL::QSAR::KNNModel::optimizeParameters ( int  d, int  no_steps  )

virtual

Tries to find the optimal kernel width for the current data. Therefore some training data must have been read by the connected QSARData object before running this method.

Reimplemented from BALL::QSAR::ALLModel.

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

virtual

sets the model parameters according to the given values.

Reimplemented from BALL::QSAR::ALLModel.