Implements Example 42: Branch and Bound with Partial Prediction (BBPP) optimal feature selection., see also Example 42 source code
/* ========================================================================= Feature Selection Toolbox 3 source code --------------------------------------- */ /* ========================================================================= Copyright: * FST3 software (with exception of any externally linked libraries) is copyrighted by Institute of Information Theory and Automation (UTIA), Academy of Sciences of the Czech Republic. * FST3 source codes as presented here do not contain code of third parties. FST3 may need linkage to external libraries to exploit its functionality in full. For details on obtaining and possible usage restrictions of external libraries follow their original sources (referenced from FST3 documentation wherever applicable). * FST3 software is available free of charge for non-commercial use. Please address all inquires concerning possible commercial use of FST3, or if in doubt, to FST3 maintainer (see http://fst.utia.cz). * Derivative works based on FST3 are permitted as long as they remain non-commercial only. * Re-distribution of FST3 software is not allowed without explicit consent of the copyright holder. Disclaimer of Warranty: * FST3 software is presented "as is", without warranty of any kind, either expressed or implied, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. The entire risk as to the quality and performance of the program is with you. Should the program prove defective, you assume the cost of all necessary servicing, repair or correction. Limitation of Liability: * The copyright holder will in no event be liable to you for damages, including any general, special, incidental or consequential damages arising out of the use or inability to use the code (including but not limited to loss of data or data being rendered inaccurate or losses sustained by you or third parties or a failure of the program to operate with any other programs). ========================================================================== */ #include <boost/smart_ptr.hpp> #include <exception> #include <iostream> #include <cstdlib> #include <string> #include <vector> #include "error.hpp" #include "global.hpp" #include "subset.hpp" #include "data_intervaller.hpp" #include "data_splitter.hpp" #include "data_splitter_5050.hpp" #include "data_splitter_cv.hpp" //#include "data_splitter_holdout.hpp" //#include "data_splitter_leave1out.hpp" //#include "data_splitter_resub.hpp" #include "data_splitter_randrand.hpp" //#include "data_splitter_randfix.hpp" #include "data_scaler.hpp" #include "data_scaler_void.hpp" //#include "data_scaler_to01.hpp" //#include "data_scaler_white.hpp" #include "data_accessor_splitting_memTRN.hpp" #include "data_accessor_splitting_memARFF.hpp" #include "criterion_normal_bhattacharyya.hpp" //#include "criterion_normal_gmahalanobis.hpp" //#include "criterion_normal_divergence.hpp" //#include "criterion_multinom_bhattacharyya.hpp" #include "criterion_wrapper.hpp" //#include "criterion_wrapper_bias_estimate.hpp" //#include "criterion_subsetsize.hpp" //#include "criterion_sumofweights.hpp" //#include "criterion_negative.hpp" //#include "distance_euclid.hpp" //#include "distance_L1.hpp" #include "distance_Lp.hpp" #include "classifier_knn.hpp" //#include "classifier_normal_bayes.hpp" //#include "classifier_multinom_naivebayes.hpp" //#include "classifier_svm.hpp" //#include "search_bif.hpp" //#include "search_bif_threaded.hpp" //#include "search_monte_carlo.hpp" //#include "search_monte_carlo_threaded.hpp" //#include "search_exhaustive.hpp" //#include "search_exhaustive_threaded.hpp" #include "branch_and_bound_predictor_averaging.hpp" //#include "search_branch_and_bound_basic.hpp" //#include "search_branch_and_bound_improved.hpp" #include "search_branch_and_bound_partial_prediction.hpp" //#include "search_branch_and_bound_fast.hpp" //#include "seq_step_straight.hpp" //#include "seq_step_straight_threaded.hpp" //#include "seq_step_hybrid.hpp" //#include "seq_step_ensemble.hpp" //#include "search_seq_sfs.hpp" //#include "search_seq_sffs.hpp" //#include "search_seq_sfrs.hpp" //#include "search_seq_os.hpp" //#include "search_seq_dos.hpp" #include "result_tracker_dupless.hpp" //#include "result_tracker_regularizer.hpp" //#include "result_tracker_feature_stats.hpp" //#include "result_tracker_stabileval.hpp" int main() { try{ typedef double RETURNTYPE; typedef double DATATYPE; typedef double REALTYPE; typedef unsigned int IDXTYPE; typedef unsigned int DIMTYPE; typedef short BINTYPE; typedef FST::Subset<BINTYPE, DIMTYPE> SUBSET; typedef FST::Data_Intervaller<std::vector<FST::Data_Interval<IDXTYPE> >,IDXTYPE> INTERVALLER; typedef boost::shared_ptr<FST::Data_Splitter<INTERVALLER,IDXTYPE> > PSPLITTER; typedef FST::Data_Splitter_5050<INTERVALLER,IDXTYPE> SPLITTER5050; typedef FST::Data_Accessor_Splitting_MemTRN<DATATYPE,IDXTYPE,INTERVALLER> DATAACCESSOR; // uncomment for TRN data format //typedef FST::Data_Accessor_Splitting_MemARFF<DATATYPE,IDXTYPE,INTERVALLER> DATAACCESSOR; // uncomment for ARFF data format typedef FST::Distance_Lp<DATATYPE,REALTYPE,DIMTYPE,SUBSET,3,2> DISTANCE; typedef FST::Classifier_kNN<RETURNTYPE,DATATYPE,IDXTYPE,DIMTYPE,SUBSET,DATAACCESSOR,DISTANCE> CLASSIFIERKNN; typedef FST::Criterion_Wrapper<RETURNTYPE,SUBSET,CLASSIFIERKNN,DATAACCESSOR> WRAPPERKNN; typedef FST::Criterion_Normal_Bhattacharyya<RETURNTYPE,DATATYPE,REALTYPE,IDXTYPE,DIMTYPE,SUBSET,DATAACCESSOR> BHATTCRIT; typedef FST::Result_Tracker_Dupless<RETURNTYPE,IDXTYPE,DIMTYPE,SUBSET> TRACKER; typedef FST::Branch_And_Bound_Predictor_Averaging<RETURNTYPE,DIMTYPE> PREDICTOR; std::cout << "Starting Example 42: Branch and Bound with Partial Prediction (BBPP) optimal feature selection..." << std::endl; // keep second half of data for independent testing of final classification performance PSPLITTER dsp_outer(new SPLITTER5050); // do not scale data boost::shared_ptr<FST::Data_Scaler<DATATYPE> > dsc(new FST::Data_Scaler_void<DATATYPE>()); // set-up data access boost::shared_ptr<std::vector<PSPLITTER> > splitters(new std::vector<PSPLITTER>); splitters->push_back(dsp_outer); boost::shared_ptr<DATAACCESSOR> da(new DATAACCESSOR("data/wdbc_30.trn",splitters,dsc)); da->initialize(); // initiate access to split data parts da->setSplittingDepth(0); if(!da->getFirstSplit()) throw FST::fst_error("50/50 data split failed."); // initiate the storage for subset to-be-selected boost::shared_ptr<SUBSET> sub(new SUBSET(da->getNoOfFeatures())); sub->deselect_all(); // set-up normal Bhattacharyya criterion boost::shared_ptr<BHATTCRIT> cb(new BHATTCRIT); cb->initialize(da); // initialization = normal model parameter estimation on training data on the current split // set-up 3-Nearest Neighbor classifier based on Euclidean distances boost::shared_ptr<CLASSIFIERKNN> cknn(new CLASSIFIERKNN); cknn->set_k(3); // wrap the 3-NN classifier to enable its usage as FS criterion (criterion value will be estimated by 3-fold cross-val.) boost::shared_ptr<WRAPPERKNN> wknn(new WRAPPERKNN); wknn->initialize(cknn,da); // set-up Branch and Bound procedure FST::Search_Branch_And_Bound_Partial_Prediction<RETURNTYPE,DIMTYPE,SUBSET,BHATTCRIT,PREDICTOR> srch; // set-up result tracker to enable logging of candidate solutions, ordered descending by value // (optionally limit the number of kept records to 50000 highest valued to prevent memory exhaustion due to possibly excessive number of candidates) boost::shared_ptr<TRACKER> tracker(new TRACKER(50000)); // let the tracker register only solution no worse than "the best known criterion value minus 0.05" tracker->set_inclusion_margin(0.05); // register the result tracker with the used search object srch.enable_result_tracking(tracker); // run the search std::cout << "Feature selection setup:" << std::endl << *da << std::endl << srch << std::endl << *wknn << std::endl << std::endl; RETURNTYPE critval_train, critval_test; srch.set_output_detail(FST::NORMAL); // set FST::SILENT to disable all text output in the course of search (FST::NORMAL is default) const DIMTYPE target_d=10; // target subset size to be specified by the user if(!srch.search(target_d,critval_train,sub,cb,std::cout)) throw FST::fst_error("Search not finished."); // (optionally) validate result by estimating kNN accuracy on selected feature sub-space on independent test data cknn->train(da,sub); cknn->test(critval_test,da); std::cout << "Validated "<<cknn->get_k()<<"-NN accuracy=" << critval_test << std::endl << std::endl; // report tracker contents std::cout << "Result tracker records " << tracker->size(0.0) << " solutions with criterion value equal to " << critval_train << "." << std::endl << std::endl; for(unsigned int i=1;i<5;i++) std::cout << "Result tracker records " << tracker->size((double)i*0.01) << " solutions with criterion value greater or equal to " << critval_train-(double)i*0.005 << "." << std::endl << std::endl; TRACKER::PResultRec result; if(tracker->get_first(result) && tracker->size(0.0)>1) { RETURNTYPE firstvalue=result->value; std::cout << "All recorded feature subsets yielding the same best known criterion value " << firstvalue << ":" << std::endl; while(tracker->get_next(result) && result->value==firstvalue) std::cout << *(result->sub) << std::endl; } // print out BBPP predictor statistics std::cout<<srch<<std::endl; } catch(FST::fst_error &e) {std::cerr<<"FST ERROR: "<< e.what() << ", code=" << e.code() << std::endl;} catch(std::exception &e) {std::cerr<<"non-FST ERROR: "<< e.what() << std::endl;} return 0; }