void startValidation(ValidationConfiguration& conf, QSARData* q, String* data_filename)
{
bool created_data_object=0;
if(q==NULL || data_filename==NULL)
{
q = new QSARData;
created_data_object=1;
}
Registry reg;
Model* m;
String model_type;
ifstream model_input(conf.model.c_str()); // read model-abbreviation
if(!model_input)
{
Log.error()<<"Error: Model-file '"<<conf.model<<"' does not exist!!"<<endl;
return;
}
getline(model_input,model_type);
getline(model_input,model_type);
model_type = model_type.getField(0,"\t");
model_input.close();
RegistryEntry* entry = reg.getEntry(model_type);
if(!entry->kernel)
{
m = (*entry->create)(*q);
}
else
{
// parameters irrelevant; will be overwritten by those read from file
m = (*entry->createKernel1)(*q,1,1, -1);
}
m->readFromFile(conf.model.c_str());
m->model_val->selectStat(conf.statistic);
if(conf.data!="")
{
if(!data_filename || conf.data!=*data_filename)
{
q->readFromFile(conf.data);
if(data_filename) *data_filename = conf.data;
}
if(conf.val_type==1) m->model_val->testInputData(1);
else if(conf.val_type==2) m->model_val->crossValidation(conf.k_folds,1);
else if(conf.val_type==3) m->model_val->bootstrap(conf.bootstrap_samples);
else if(conf.val_type==4) m->model_val->yRandomizationTest(conf.no_of_permutation_tests,conf.k_folds);
else if(conf.val_type==6)
{
if(entry->regression)
{
((RegressionModel*)m)->validation->calculateCoefficientStdErrors(conf.bootstrap_samples);
}
}
else if(conf.val_type==7)
{
if(!data_filename || conf.validation_data!=*data_filename)
{
q->readFromFile(conf.validation_data.c_str());
*data_filename = conf.validation_data;
}
m->model_val->testInputData(1);
}
}
// save the result of the validation to the specified file
m->model_val->saveToFile(conf.output);
if(created_data_object) delete q;
delete m;
}
Model* AutomaticModelCreator::generateModel()
{
Registry registry;
bool use_regression = !data_->checkforDiscreteY();
bool use_random_testsets = 0;
Size no_folds = 3;
if (use_random_testsets) no_folds = 10;
Size best_model_id = 0;
Size best_kernel_id = 0;
double best_nested_quality = 0;
/// Do 4-fold nested cross validation, including feature selection steps, for each model type and, if applicable, each kernel function
Log.level(10)<<"model-name kernel #features nested Q^2 stddev"<<std::endl;
Log.level(10)<<"---------------------------------------------------"<<std::endl;
Log.level(10)<<std::setiosflags(std::ios::fixed)<<std::left;
for (Size model_id = 1; model_id < 14; model_id++)
{
RegistryEntry* reg_entry;
try
{
reg_entry = registry.getEntry(model_id);
}
catch(BALL::Exception::GeneralException e)
{
// a model with the current id does not exist
continue;
}
if (use_regression != reg_entry->regression) continue;
Size no_kernel_types = 1;
if (reg_entry->kernel) no_kernel_types = 3;
for (Size kernel_id = 1; kernel_id <= no_kernel_types; kernel_id++)
{
double nested_q2 = 0;
int no_features = 0;
vector<double> q2_values;
for (Size fold_id = 0; fold_id < no_folds; fold_id++)
{
vector<QSARData*> sets;
if (use_random_testsets)
{
// randomly select 25% of compounds for external validation set
sets = data_->generateExternalSet(0.25);
}
else
{
sets = data_->evenSplit(no_folds, fold_id);
}
if (data_->isDataCentered())
{
bool center_y = data_->isResponseCentered();
sets[0]->centerData(center_y); // train-partition
sets[1]->centerData(center_y); // test-partition
}
Model* model;
if (!reg_entry->kernel) model = (*reg_entry->create)(*sets[0]);
else model = (*reg_entry->createKernel1)(*sets[0], kernel_id, 1, -1);
model->setParameters(reg_entry->parameterDefaults);
optimizeParameters(model);
// select relevant features using training partition
selectFeatures(model);
no_features += model->getDescriptorIDs()->size();
// train model using only the training partition
model->readTrainingData();
model->train();
// test fit to external validation data
model->data = sets[1];
model->model_val->testInputData(true);
nested_q2 += model->model_val->getFitRes();
q2_values.push_back(model->model_val->getFitRes());
delete sets[0];
delete sets[1];
delete model;
}
nested_q2 /= no_folds;
no_features /= no_folds;
double stddev = Statistics::getStddev(q2_values);
Log.level(10)<<std::setw(10)<<reg_entry->name_abreviation<<" ";
if (reg_entry->kernel)
{
if (kernel_id == 1) Log.level(10)<<setw(6)<<"polyn.";
else if (kernel_id == 2) Log.level(10)<<setw(6)<<"rbf";
else if (kernel_id == 3) Log.level(10)<<setw(6)<<"sigm.";
}
else Log.level(10)<<setw(6)<<"none";
Log.level(10)<<" ";
Log.level(10)<<setw(9)<<no_features<<" "<<setw(10)<<nested_q2<<" "<<setw(6)<<stddev<<endl<<flush;
double quality = nested_q2-stddev; // make sure to prefer models w/ low stddev
if (quality > best_nested_quality)
{
best_nested_quality = quality;
best_model_id = model_id;
best_kernel_id = kernel_id;
}
}
}
if (best_nested_quality < min_quality_)
{
Log.level(10)<<"Sorry, no model with satisfactory prediction quality found!"<<endl;
return 0;
}
/// Create best model using ENTIRE data set and return it
RegistryEntry* reg_entry = registry.getEntry(best_model_id);
Model* model;
if (!reg_entry->kernel) model = (*reg_entry->create)(*data_);
else model = (*reg_entry->createKernel1)(*data_, best_kernel_id, 1, -1);
model->setParameters(reg_entry->parameterDefaults);
optimizeParameters(model);
selectFeatures(model);
model->readTrainingData();
model->train();
return model;
}
void startModelCreation(ModelConfiguration& conf, QSARData* q, String* data_filename)
{
bool created_data_object=0;
if(q==NULL || data_filename==NULL || conf.data_file!=*data_filename)
{
if(q==NULL)
{
q = new QSARData;
created_data_object=1;
}
q->readFromFile(conf.data_file);
if(data_filename) *data_filename = conf.data_file;
}
else
{
Log.level(2)<<"[ModelCreator debug-info:] QSARData object for file "<<conf.data_file<<" already in memory; not reading it again."<<endl;
}
Registry reg;
Model* model;
bool kernel=0;
RegistryEntry* entry = reg.getEntry(conf.model_no);
if(entry->create!=NULL)
{
model = (*entry->create)(*q);
}
else
{
if(conf.kernel_type==0 || conf.kernel_par1==0)
{
Log.error()<<"For kernel based model, kernel-type and kernel-parameter(s) must be specified!"<<endl;
return;
}
model = (*entry->createKernel1)(*q,conf.kernel_type,conf.kernel_par1, conf.kernel_par2);
kernel=1;
}
if(conf.model_parameters.size()>0)
{
model->setParameters(conf.model_parameters);
}
if(!conf.no_training && conf.optimize_model_parameters)
{
if(conf.k_fold==0)
{
Log.error()<<"'k_fold' must be set if model parameters are to be optimized!"<<endl;
return;
}
model->optimizeParameters(conf.k_fold);
}
if(!conf.no_training && kernel && conf.grid_search_steps>0)
{
if(conf.k_fold==0)
{
Log.error()<<"'k_fold' must be set if grid search is to be done!"<<endl;
return;
}
if(conf.grid_search_stepwidth==0 && conf.kernel_type!=2)
{
Log.error()<<"'grid_search_stepwidth' must be set if grid search is to be done!"<<endl;
return;
}
((KernelModel*)model)->kernel->gridSearch(conf.grid_search_stepwidth, conf.grid_search_steps, conf.grid_search_recursions, conf.k_fold);
}
model->readTrainingData();
if(!conf.no_training)
{
try
{
model->train();
}
catch(BALL::Exception::GeneralException e)
{
Log.error()<<e.getMessage();
}
}
model->saveToFile(conf.output);
if(created_data_object) delete q;
delete model;
}
void startFeatureSelection(FeatureSelectionConfiguration& conf, QSARData* q, String* data_filename)
{
bool created_data_object=0;
if(q==NULL || data_filename==NULL || conf.data_file!=*data_filename)
{
if(q==NULL)
{
q = new QSARData;
created_data_object=1;
}
q->readFromFile(conf.data_file);
if(data_filename) *data_filename = conf.data_file;
}
else
{
Log.level(2)<<"[FeatureSelector debug-info:] QSARData object for file "<<conf.data_file<<" already in memory; not reading it again."<<endl;
}
Registry reg;
Model* m;
String model_type;
ifstream model_input(conf.model.c_str()); // read model-abbreviation
if(!model_input)
{
Log.error()<<"Error: Model-file '"<<conf.model<<"' does not exist!!"<<endl;
return;
}
getline(model_input,model_type);
getline(model_input,model_type);
model_type = model_type.getField(0,"\t");
model_input.close();
RegistryEntry* entry = reg.getEntry(model_type);
if(!entry->kernel)
{
m = (*entry->create)(*q);
}
else
{
// parameters irrelevant; will be overwritten by those read from file
m = (*entry->createKernel1)(*q,1,1, -1);
}
if(conf.statistic>0)
{
Log.level(3)<<" using "<<conf.statistic_name<<" to assess qualitiy of the model ... "<<endl;
m->model_val->selectStat(conf.statistic);
}
m->readFromFile(conf.model.c_str());
FeatureSelection fs(*m);
if(conf.quality_increase_cutoff!=-1)
{
fs.setQualityIncreaseCutoff(conf.quality_increase_cutoff);
}
if(conf.remove_correlated || conf.feat_type==0)
{
fs.removeHighlyCorrelatedFeatures(conf.cor_threshold);
}
if(conf.feat_type==1)
{
fs.forwardSelection(conf.k_fold,conf.opt);
}
else if(conf.feat_type==2)
{
fs.backwardSelection(conf.k_fold,conf.opt);
}
else if(conf.feat_type==3)
{
fs.stepwiseSelection(conf.k_fold,conf.opt);
}
else if(conf.feat_type==4)
{
fs.removeLowResponseCorrelation(conf.cor_threshold);
}
else if(conf.feat_type==6)
{
fs.twinScan(conf.k_fold,conf.opt);
}
if(conf.opt_model_after_fs)
{
m->optimizeParameters(conf.opt_k_fold);
}
KernelModel* km = dynamic_cast<KernelModel*>(m);
if(km && conf.opt_kernel_after_fs)
{
/// search locally around current kernel parameters
try
{
// specifing start-values for grid search now obsolete; grid search will automatically search locally around current kernel parameter(s)
km->kernel->gridSearch(conf.grid_search_stepwidth, conf.grid_search_steps,conf.grid_search_recursions,conf.opt_k_fold,conf.opt/*,start_par1,start_par2*/);
}
catch(BALL::Exception::GeneralException e)
{
Log.error()<<e.getName()<<" : "<<e.getMessage()<<endl;
return;
}
}
m->readTrainingData();
m->train();
m->saveToFile(conf.output);
if(created_data_object) delete q;
delete m;
}
int main(int argc, char* argv[])
{
CommandlineParser par("ModelCreator","create a QSAR model ","1.1",String(__DATE__), "QuEasy (QSAR)");
par.registerMandatoryInputFile("i", "input dat-file");
par.registerMandatoryOutputFile("o", "output model file");
par.registerMandatoryStringParameter("type", "model type");
par.registerOptionalStringParameter("kernel", "kernel type (in case of kernel-model)");
Registry reg;
list<String> restr;
for(RegistryEntryIterator it=reg.beginEntry(); it!=reg.endEntry(); it++)
{
restr.push_back(it->second.name_abreviation);
}
par.setParameterRestrictions("type", restr);
restr.clear();
restr.push_back("none");
restr.push_back("polynomial");
restr.push_back("rbf");
restr.push_back("sigmoidal");
par.setParameterRestrictions("kernel", restr);
String man = "ModelCreator creates a QSAR model using an input data set as generated by InputReader.\n\nThe type of QSAR model to be used can be specified by '-type', the type of kernel-function (if any) can be chosen by '-kernel'. Optimization of model- and kernel-parmeters will be done automatically using cross-validation.\n\nOutput of this tool is a model-file that can be used by other QuEasy tools (e.g. FeatureSelector).";
par.setToolManual(man);
par.setSupportedFormats("i","dat");
par.setSupportedFormats("o","mod");
par.parse(argc,argv);
ModelConfiguration conf;
conf.data_file = par.get("i");
conf.output = par.get("o");
conf.optimize_model_parameters = true;
conf.kernel_par1 = reg.default_kernel_par1;
conf.kernel_par1 = reg.default_kernel_par2;
conf.k_fold = reg.default_k;
conf.grid_search_recursions = reg.default_gridsearch_recursion;
conf.grid_search_stepwidth = reg.default_gridsearch_stepwidth;
conf.grid_search_steps = reg.default_gridsearch_steps;
try
{
conf.model_no = reg.getModelNo(par.get("type"));
}
catch(BALL::Exception::GeneralException e)
{
cerr << "A model-type '"<<par.get("type")<<"' does not exist; possible choices are:"<<endl;
for(RegistryEntryIterator it=reg.beginEntry(); it!=reg.endEntry(); it++)
{
cerr<<" "<<it->second.name_abreviation<<" : "<<it->second.name<<" ";
if(it->second.regression) cerr<<"(regression)"<<endl;
else cerr<<"(classification)"<<endl;
}
cerr<<endl;
exit(1);
}
String kernel = par.get("kernel");
if(kernel!=CommandlineParser::NOT_FOUND && kernel != "none")
{
if(!reg.getEntry(par.get("type"))->kernel)
{
cerr << "[Error:] The chosen model-type has no kernel but you specified a kernel-type!"<<endl;
exit(1);
}
if(kernel=="polynomial")
{
conf.kernel_type = 1;
}
else if(kernel=="rbf")
{
conf.kernel_type = 2;
}
else if(kernel=="sigmoidal")
{
conf.kernel_type = 3;
}
else
{
cerr << "Specified kernel-type '"<<kernel<<"' unknown; possible choices are: polynomial, rbf, sigmoidal"<<endl;
exit(1);
}
}
startModelCreation(conf,0,0);
}
