BALL::QSAR::Model Class Reference

#include <BALL/QSAR/Model.h>

Inheritance diagram for BALL::QSAR::Model:
Inheritance graph
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List of all members.

Public Member Functions

Constructors and Destructors

 Model (const QSARData &q)
virtual ~Model ()
virtual void operator= (const Model &m)

Protected Member Functions

Input and Output. The following methods can be used to implement the functions saveToFile() and readFromFile() in final classes derived from this base-class

void readMatrix (Matrix< double > &mat, std::ifstream &in, uint lines, uint col)
void readVector (Vector< double > &vec, std::ifstream &in, uint 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)

Protected Attributes

int default_no_opt_steps_

Friends

class Validation
class RegressionValidation
class ClassificationValidation

Attributes



const QSARData * data
Validation * model_val
Matrix< double > descriptor_matrix_
vector< string > substance_names_
vector< string > descriptor_names_
Matrix< double > descriptor_transformations_
Matrix< double > y_transformations_
Matrix< double > Y_
String type_
std::multiset< unsigned int > descriptor_IDs_

Accessors



void copyData (const Model &m)
void copyDescriptorIDs (const Model &m)
void readTrainingData ()
virtual Vector< double > 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 Matrix< double > * getDescriptorMatrix ()
const vector< string > * getSubstanceNames ()
const vector< string > * getDescriptorNames ()
const Matrix< double > * 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)
Vector< double > getSubstanceVector (const vector< double > &substance, bool transform)
Vector< double > getSubstanceVector (const Vector< double > &substance, bool transform)
void backTransformPrediction (Vector< double > &pred)
void addLambda (Matrix< double > &matrix, double &lambda)
void readDescriptorInformation ()

Detailed Description

Definition at line 52 of file Model.h.

Constructor & Destructor Documentation

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

constructur

Parameters:
q QSARData object, from which the data for this model should be taken
virtual BALL::QSAR::Model::~Model (  )  [virtual]

Member Function Documentation

void BALL::QSAR::Model::addLambda ( Matrix< double > &  matrix,
double &  lambda 
) [protected]

adds offset lambda to the diagonal of the given matrix

void BALL::QSAR::Model::backTransformPrediction ( Vector< double > &  pred  )  [protected]

transforms a prediction (obtained by Model.train()) according to the inverse of the transformation(s) of the activity values of the training data

virtual double BALL::QSAR::Model::calculateStdErr (  )  [inline, virtual]

Reimplemented in BALL::QSAR::GPModel.

Definition at line 109 of file Model.h.

void BALL::QSAR::Model::copyData ( const Model &  m  ) 

copies the data (descriptor matrix, names of substances and descriptors) and the IDs of the selected descriptors from m

void BALL::QSAR::Model::copyDescriptorIDs ( const Model &  m  ) 

copies the IDs of the selected descriptors from m

void BALL::QSAR::Model::deleteDescriptorIDs (  ) 

removes all entries from descriptor_IDs

std::multiset<unsigned int>* BALL::QSAR::Model::getDescriptorIDs (  ) 

returns a const pointer to the descriptor IDs of this model

const Matrix<double>* BALL::QSAR::Model::getDescriptorMatrix (  ) 

returns a const pointer to the descriptor matrix of this model

const vector<string>* BALL::QSAR::Model::getDescriptorNames (  ) 

returns a const pointer to the names of the descriptors of this model

virtual vector<double> BALL::QSAR::Model::getParameters (  )  const [virtual]

Reimplemented in BALL::QSAR::ALLModel, BALL::QSAR::GPModel, BALL::QSAR::KNNModel, BALL::QSAR::KPCRModel, BALL::QSAR::KPLSModel, BALL::QSAR::LDAModel, BALL::QSAR::LibsvmModel, BALL::QSAR::NBModel, BALL::QSAR::OPLSModel, BALL::QSAR::PCRModel, BALL::QSAR::PLSModel, BALL::QSAR::RRModel, and BALL::QSAR::SNBModel.

const vector<string>* BALL::QSAR::Model::getSubstanceNames (  ) 

returns a const pointer to the names of the substances of this model

Vector<double> BALL::QSAR::Model::getSubstanceVector ( const Vector< double > &  substance,
bool  transform 
) [protected]
Vector<double> BALL::QSAR::Model::getSubstanceVector ( const vector< double > &  substance,
bool  transform 
) [protected]

returns a Row-Vector containing only the values for these descriptors, that have been selected for this model

Parameters:
substance a vector of *all* descriptor values for the substance to be predicted
const string* BALL::QSAR::Model::getType (  ) 

returns the type of the current model, e.g. "MLR", "PLS", ...

void BALL::QSAR::Model::getUnnormalizedFeatureValue ( int  compound,
int  feature,
double &  return_value 
)

Fetches the un-normalized value for the specified feature of the desired compound (instance) from the data that this Model currently contains. This method is needed for visualization purposes only.

void BALL::QSAR::Model::getUnnormalizedResponseValue ( int  compound,
int  response,
double &  return_value 
)

Fetches the un-normalized value for the specified response of the desired compound (instance) from the data that this Model currently contains. This method is needed for visualization purposes only.

const Matrix<double>* BALL::QSAR::Model::getY (  ) 

returns a const pointer to the activity values of this model

virtual void BALL::QSAR::Model::operator= ( const Model &  m  )  [virtual]

copy constructur; creates a model with the same specifications as the given one (same model and kernel parameters). If the given model has been trained, the training result is copied as well.
Note, that the input data that has been read by m to m.descriptor_matrix_ and m.Y_ is NOT copied to new model, since the input data is not part of the specification of a model. If nevertheless, copying of the input data is desired, use function copyData() (afterwards).

Reimplemented in BALL::QSAR::KernelModel.

bool BALL::QSAR::Model::optimizeParameters ( int  k  ) 
virtual bool BALL::QSAR::Model::optimizeParameters ( int  ,
int   
) [inline, virtual]

optimizes parameters (!=number of features) of the model, e.g. no of latente variables in case of PLS model or kernel width in case of automated lazy learning model.
The number of selected features (=descriptors) is NOT changed by this method. Use class FeatureSelection in order to do this.

Returns:
1 if parameters were optimized using cross-validation. The best Q2 value is assumed to be saved in ModelValidation.Q2
0 if the model has no parameters to be optimized, so that no cross-validation was done.

Reimplemented in BALL::QSAR::ALLModel, BALL::QSAR::KNNModel, BALL::QSAR::KPLSModel, BALL::QSAR::OPLSModel, and BALL::QSAR::PLSModel.

Definition at line 105 of file Model.h.

virtual Vector<double> BALL::QSAR::Model::predict ( const vector< double > &  substance,
bool  transform 
) [pure 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

Implemented in BALL::QSAR::ALLModel, BALL::QSAR::FitModel, BALL::QSAR::GPModel, BALL::QSAR::KernelModel, BALL::QSAR::LDAModel, BALL::QSAR::LinearModel, BALL::QSAR::LogitModel, BALL::QSAR::NBModel, and BALL::QSAR::SNBModel.

void BALL::QSAR::Model::readDescriptorInformation (  )  [protected]

reads selected descriptors, their names and the information about their transformations (mean and stddev of each descriptor). This function is used after feature selection to read information about the selected features

virtual void BALL::QSAR::Model::readDescriptorInformationFromFile ( std::ifstream &  in,
int  no_descriptors,
bool  transformation 
) [protected, virtual]
virtual void BALL::QSAR::Model::readFromFile ( string  filename  )  [pure virtual]

reconstruct a saved Model from a file

Implemented in BALL::QSAR::ALLModel, BALL::QSAR::KernelModel, BALL::QSAR::LDAModel, BALL::QSAR::LogitModel, BALL::QSAR::NBModel, BALL::QSAR::RegressionModel, and BALL::QSAR::SNBModel.

void BALL::QSAR::Model::readMatrix ( Matrix< double > &  mat,
std::ifstream &  in,
uint  lines,
uint  col 
) [protected]

reconstructs a Matrix<double> from a given input stream after resizing the given Matrix<double> as specified

void BALL::QSAR::Model::readModelParametersFromFile ( std::ifstream &  in  )  [protected]
void BALL::QSAR::Model::readResponseTransformationFromFile ( std::ifstream &  in,
int  no_y 
) [protected]
void BALL::QSAR::Model::readTrainingData (  ) 

copies the data for the relevant descriptors from the bound QSARData object into this model and updates Model.descriptor_transformations and Model.y_transformations .
If no explicit feature selection was done, i.e. if descriptor_IDs is emtpy, all data is fetched.
If feature selection was done, i.e. if descriptor_IDs is not empty, only the columns of the relevant descriptors are fetched.

void BALL::QSAR::Model::readVector ( Vector< double > &  vec,
std::ifstream &  in,
uint  no_cells,
bool  column_vector 
) [protected]
virtual void BALL::QSAR::Model::saveDescriptorInformationToFile ( std::ofstream &  out  )  [protected, virtual]

overloaded by class RegressionModel, whose member function can also save coefficients and coefficient-errors

Reimplemented in BALL::QSAR::RegressionModel.

void BALL::QSAR::Model::saveModelParametersToFile ( std::ofstream &  out  )  [protected]
void BALL::QSAR::Model::saveResponseTransformationToFile ( std::ofstream &  out  )  [protected]
virtual void BALL::QSAR::Model::saveToFile ( string  filename  )  [pure virtual]

save Model to a file

Implemented in BALL::QSAR::ALLModel, BALL::QSAR::KernelModel, BALL::QSAR::LDAModel, BALL::QSAR::LogitModel, BALL::QSAR::NBModel, BALL::QSAR::RegressionModel, and BALL::QSAR::SNBModel.

void BALL::QSAR::Model::setDataSource ( const QSARData *  q  ) 
void BALL::QSAR::Model::setDescriptorIDs ( const std::multiset< unsigned int > &  sl  ) 

manually specify a set of descriptors

virtual void BALL::QSAR::Model::setParameters ( vector< double > &   )  [inline, virtual]

sets the model parameters according to the given values.

Reimplemented in BALL::QSAR::ALLModel, BALL::QSAR::GPModel, BALL::QSAR::KNNModel, BALL::QSAR::KPCRModel, BALL::QSAR::KPLSModel, BALL::QSAR::LDAModel, BALL::QSAR::LibsvmModel, BALL::QSAR::NBModel, BALL::QSAR::OPLSModel, BALL::QSAR::PCRModel, BALL::QSAR::PLSModel, BALL::QSAR::RRModel, and BALL::QSAR::SNBModel.

Definition at line 113 of file Model.h.

virtual void BALL::QSAR::Model::train (  )  [pure virtual]

Starts training the model.

Implemented in BALL::QSAR::ALLModel, BALL::QSAR::FitModel, BALL::QSAR::GPModel, BALL::QSAR::KPCRModel, BALL::QSAR::KPLSModel, BALL::QSAR::LDAModel, BALL::QSAR::LibsvmModel, BALL::QSAR::LogitModel, BALL::QSAR::MLRModel, BALL::QSAR::NBModel, BALL::QSAR::OPLSModel, BALL::QSAR::PCRModel, BALL::QSAR::PLSModel, BALL::QSAR::RRModel, and BALL::QSAR::SNBModel.

Friends And Related Function Documentation

friend class ClassificationValidation [friend]

Reimplemented in BALL::QSAR::ClassificationModel.

Definition at line 248 of file Model.h.

friend class RegressionValidation [friend]

Reimplemented in BALL::QSAR::KernelModel, and BALL::QSAR::RegressionModel.

Definition at line 247 of file Model.h.

friend class Validation [friend]

Definition at line 246 of file Model.h.

Member Data Documentation

const QSARData* BALL::QSAR::Model::data

pointer to the input data class for this model

Definition at line 158 of file Model.h.

int BALL::QSAR::Model::default_no_opt_steps_ [protected]

The default number of steps for model parameter optimization.
It can be adjusted by the different types of models.
Standard default value is 30.

Definition at line 170 of file Model.h.

std::multiset<unsigned int> BALL::QSAR::Model::descriptor_IDs_ [protected]

list containing the IDs of the selected descriptors (=features); with IDs >= 0
If this list is empty, it is assumed that no feature selection was done, i.e. that all descriptors are to be considered for cross-validation and prediction of activity.
If it is not empty, only the descriptors in this list are used for cross-validation and prediction of activity.

Definition at line 243 of file Model.h.

Matrix<double> BALL::QSAR::Model::descriptor_matrix_ [protected]

matrix containing the values of each descriptor for each substance

Definition at line 217 of file Model.h.

vector<string> BALL::QSAR::Model::descriptor_names_ [protected]

names of all descriptors

Definition at line 223 of file Model.h.

Matrix<double> BALL::QSAR::Model::descriptor_transformations_ [protected]

2xm dimensional matrix (m=no of descriptors) containing mean and stddev of each selected descriptor.
The content of this matrix is updated only by Model.readTrainingData()

Definition at line 227 of file Model.h.

Validation* BALL::QSAR::Model::model_val

a ModelValidation object, that is used to validate this model and that will contain the results of the validations

Definition at line 161 of file Model.h.

vector<string> BALL::QSAR::Model::substance_names_ [protected]

names of all substances

Definition at line 220 of file Model.h.

String BALL::QSAR::Model::type_ [protected]

The type of model, e.g. "MLR", "GP", ...

Definition at line 238 of file Model.h.

Matrix<double> BALL::QSAR::Model::Y_ [protected]

Matrix containing the experimentally determined results (active/non-active) for each substance.
Each column contains the values for one activity.

Definition at line 235 of file Model.h.

Matrix<double> BALL::QSAR::Model::y_transformations_ [protected]

2xc dimensional matrix (c=no of activities) containing mean and stddev of each activity.
The content of this matrix is updated only by Model.readTrainingData()

Definition at line 231 of file Model.h.

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