run a test experiment

Makefile

@@ -104,4 +104,4 @@ clean:
 	-rm -Rf build
 	-rm -Rf bin
 	-rm -Rf $(COVCLEANFILES)
-	-rm -Rf test.hdt test.hdt.index.v1-1 test.log
+	-rm -Rf test.hdt test.hdt.index.v1-1 test.log entity.log

README.md

@@ -9,7 +9,5 @@ Run experiments using tada-hdt-entity library
 * T2Dv2
 
 # T2Dv2
-`classes_GS.csv` and updated version of the original one
-**the original one has some mislabeled entries**
-`subject_column_gold.csv`
-**these too files are taked from tada-gam experiment**
+`classes_with_col_GS.csv`: this file contains the file names, the column id of the subject columns, and their classes
+This is update version from the `classes_GS.csv` provided by the T2Dv2. We changed the concept column with the subject column id and we fixed some mislabels.

scripts/setup.sh

@@ -19,10 +19,10 @@ rm v1.1.zip
 cd tabular-parser-1.1;make install;cd ..;rm -Rf tabular-parser-1.1
 
 echo "Installing tada-hdt-entity... "
-wget https://github.com/oeg-upm/tada-hdt-entity/archive/v1.1.zip
-unzip v1.1.zip
-rm v1.1.zip
-cd tada-hdt-entity-1.1;make install;cd ..;rm -Rf tada-hdt-entity-1.1
+wget https://github.com/oeg-upm/tada-hdt-entity/archive/v1.2.zip
+unzip v1.2.zip
+rm v1.2.zip
+cd tada-hdt-entity-1.2;make install;cd ..;rm -Rf tada-hdt-entity-1.2
 
 echo "update linker caches..."
 ldconfig

src/t2dv2.cpp

@@ -2,92 +2,139 @@
 #include<tada_hdt_entity/entity.h>
 #include<tabular_parser/parser.h>
 
-T2Dv2::T2Dv2(string hdt_dir, string log_file_dir ,string classes_file_dir, string files_dir){
+T2Dv2::T2Dv2(string hdt_dir, string log_file_dir, string classes_file_dir, string files_dir) {
     m_classes_file_dir = classes_file_dir;
     m_files_dir = files_dir;
     m_correct = m_incorrect = m_notfound = 0;
     m_hdt = HDTManager::mapIndexedHDT(hdt_dir.c_str());
     m_logger = new EasyLogger(log_file_dir);
-    m_k = new unordered_map<string,long>;
+    m_k = new unordered_map<string, long>;
 }
 
-void T2Dv2::set_file_sep(string sep){
+void T2Dv2::set_file_sep(string sep) {
     m_file_sep = sep;
 }
 
-string T2Dv2::get_file_sep(){
+string T2Dv2::get_file_sep() {
     return m_file_sep;
 }
 
-std::list<string>* T2Dv2::annotate_column(string fname, unsigned int col_idx, bool context, double alpha){
-    EntityAnn *ea = new EntityAnn(m_hdt, "entity.log", alpha);
+EntityAnn* T2Dv2::get_ea_model(string fname, unsigned int col_idx, bool context) {
+    EntityAnn* ea = new EntityAnn(m_hdt, "entity.log", 0.0);
     string file_dir;
-    std::list<string> *candidates;
+    std::list<string>* candidates;
     file_dir = m_files_dir;
-    if(file_dir.substr(m_files_dir.length()-m_file_sep.length()) != m_file_sep){
+    if(file_dir.substr(m_files_dir.length()-m_file_sep.length()) != m_file_sep) {
         file_dir += m_file_sep;
     }
     file_dir += fname;
     Parser p(file_dir);
-    if(context){
-        candidates = ea->annotate_column(p.parse_vertical(),col_idx, context, context);
+    if(context) {
+        candidates = ea->annotate_column(p.parse_vertical(), col_idx, context, context);
     }
-    else{
-        candidates = ea->annotate_column(p.parse(),col_idx);
+    else {
+        candidates = ea->annotate_column(p.parse(), col_idx);
+    }
+    //    ea->get_graph()->print_nodes();
+    //    delete ea;
+    delete candidates;
+    return ea;
+}
+
+std::list<string>* T2Dv2::annotate_column(string fname, unsigned int col_idx, bool context, double alpha) {
+    EntityAnn* ea = new EntityAnn(m_hdt, "entity.log", alpha);
+    string file_dir;
+    std::list<string>* candidates;
+    file_dir = m_files_dir;
+    if(file_dir.substr(m_files_dir.length()-m_file_sep.length()) != m_file_sep) {
+        file_dir += m_file_sep;
     }
-    ea->get_graph()->print_nodes();
+    file_dir += fname;
+    Parser p(file_dir);
+    if(context) {
+        candidates = ea->annotate_column(p.parse_vertical(), col_idx, context, context);
+    }
+    else {
+        candidates = ea->annotate_column(p.parse(), col_idx);
+    }
+    //    ea->get_graph()->print_nodes();
     delete ea;
     return candidates;
 }
 
-bool T2Dv2::evaluate_column(string fname,string class_uri, unsigned int col_idx, bool context, double alpha){
-    std::list<string> *candidates;
+bool T2Dv2::evaluate_column(string fname, string class_uri, unsigned int col_idx, bool context, double alpha) {
+    std::list<string>* candidates;
     candidates = this->annotate_column(fname, col_idx, context, alpha);
     long k=0;
     m_logger->log("evaluate_column> fname: "+fname);
-    for(auto it = candidates->cbegin();it!=candidates->cend();it++,k++){
+    for(auto it = candidates->cbegin(); it!=candidates->cend(); it++, k++) {
         m_logger->log("evaluate_column> candidate "+to_string(k)+" is: "+((*it)));
-        if((*it)==class_uri){
-            m_k->insert({fname,k});
+        if((*it)==class_uri) {
+            m_k->insert({fname, k});
             delete candidates;
             return true;
         }
-        else{
-            cout << "not the same: "<<(*it)<<endl;
+        else {
+            //            cout << "not the same: "<<(*it)<<endl;
         }
     }
     k=-1;
-    m_k->insert({fname,k});
+    m_k->insert({fname, k});
     delete candidates;
     return false;
 }
 
-long T2Dv2::get_k(string fname){
+
+bool T2Dv2::evaluate_column_at_k(EntityAnn* ea, string class_uri, double alpha, unsigned long k_max) {
+    long k=0, kkmax;
+    std::list<string>* candidates;
+    //    cout<< "ea will get candidates : "<<endl;
+    candidates = ea->recompute_f(alpha);
+    //    cout<< "got candidates\n";
+    //    cout<< "num of candidates: "<<candidates->size()<<endl;
+    kkmax = static_cast<long> (k_max);
+    for(auto it = candidates->cbegin(); it!=candidates->cend() && k<=kkmax; it++, k++) {
+        m_logger->log("evaluate_column_at_k> candidate "+to_string(k)+" is: "+((*it)));
+        if((*it)==class_uri) {
+            delete candidates;
+            return true;
+        }
+        else {
+            //            cout << "not the same: "<<(*it)<<endl;
+        }
+    }
+    k=-1;
+    delete candidates;
+    return false;
+}
+
+
+long T2Dv2::get_k(string fname) {
     return m_k->at(fname);
 }
 
-void T2Dv2::print_k(){
+void T2Dv2::print_k() {
     cout << "\n\nprint k> \n";
-    for(auto it=m_k->cbegin();it!=m_k->cend();it++){
+    for(auto it=m_k->cbegin(); it!=m_k->cend(); it++) {
         cout<< it->first << " --- " << it->second <<endl;
     }
 }
 
-void T2Dv2::computer_scores(long k){
+void T2Dv2::computer_scores(long k) {
     m_correct=m_incorrect=m_notfound = 0;
     m_prec=m_rec=m_f1 = 0.0;
-    for(auto it=m_k->cbegin();it!=m_k->cend();it++){
-        if(it->second == -1){
+    for(auto it=m_k->cbegin(); it!=m_k->cend(); it++) {
+        if(it->second == -1) {
             m_notfound++;
         }
-        else if(it->second > k){
+        else if(it->second > k) {
             m_incorrect++;
         }
-        else if(it->second <= k){
+        else if(it->second <= k) {
             m_correct++;
         }
     }
-    float corr,incorr, notf;
+    float corr, incorr, notf;
     corr = static_cast<float>(m_correct);
     incorr = static_cast<float>(m_incorrect);
     notf = static_cast<float>(m_notfound);
@@ -96,23 +143,121 @@ void T2Dv2::computer_scores(long k){
     m_f1 = 2 * corr * incorr / (corr+incorr);
 }
 
-float T2Dv2::get_prec(){
+float T2Dv2::get_prec() {
     return m_prec;
 }
 
-float T2Dv2::get_rec(){
+float T2Dv2::get_rec() {
     return m_rec;
 }
 
-float T2Dv2::get_f1(){
+float T2Dv2::get_f1() {
     return m_f1;
 }
 
 
+void T2Dv2::run_test(double from_alpha, double to_alpha, double step, unsigned long k) {
+    std::list<std::list<string>*>*  data;
+    string class_uri, col_id_str, fname;
+    EntityAnn* ea;
+    unsigned int col_id;
+    //    double from_a,to_a;
+    std::list<double>* from_a_list = new std::list<double>;
+    std::list<double>* to_a_list = new std::list<double>;
+    double from_a, to_a;
+    std::list<string>::iterator col_iter;
+    Parser p(m_classes_file_dir);
+    data = p.parse_vertical();
+    for(auto it=data->cbegin(); it!=data->cend(); it++) {
+        //        for(auto it2=(*it)->cbegin(); it2!=(*it)->cend();it2++){
+        //            cout << (*it2) << "| ";
+        //        }
+        cout << "---------------\n";
+        col_iter = (*it)->begin();
+        fname = clean_str(*col_iter);
+        col_iter++;
+        col_id_str = clean_str(*col_iter);
+        col_id = static_cast<unsigned int>(stoul(col_id_str));
+        col_iter++;
+        class_uri = clean_str(*col_iter);
+        cout << "class_uri: " << class_uri<<endl;
+        cout<< "col_idx: " << col_id_str <<endl;
+        cout<<"fname: "<<fname<<endl;
+        ea = get_ea_model(fname, col_id, true);
+        //        ea->get_graph()->print_nodes();
+        from_a = to_a = -1;
+        for(double a=from_alpha; a<=to_alpha; a+=step) {
+            if(evaluate_column_at_k(ea, class_uri, a, k)) {
+                from_a = a;
+                from_a_list->push_back(a);
+                cout<< "from a: "<<a;
+                //from_a = a;
+                break;
+            }
+        }
+        if(from_a >= 0.0) {
+            for(double a=to_alpha; a>=from_alpha; a-=step) {
+                if(evaluate_column_at_k(ea, class_uri, a, k)) {
+                    to_a = a;
+                    to_a_list->push_back(a);
+                    //                to_a = a;
+                    cout << "  to a: "<<a<<endl;
+                    break;
+                }
+            }
+        }
+        delete ea;
+    }
+    cout << "Alpha from median: "<<get_median(from_a_list)<<endl;
+    cout << "Alpha to median: "<<get_median(to_a_list)<<endl;
+}
 
 
+string T2Dv2::clean_str(string s) {
+    string c;
+    unsigned long start_idx=0, len;
+    if(s[0]=='"') {
+        start_idx=1;
+    }
+    if(s[s.length()-1]=='"') {
+        len = s.length()-1-start_idx;
+    }
+    else {
+        len = s.length();
+    }
+    c = s.substr(start_idx, len);
+    //    cout << "<"<<s<<"> to <"<<c<<">\n";
+    return c;
+}
 
-
+double T2Dv2::get_median(std::list<double>* a){
+    unsigned long len;
+    std::list<double>::iterator b;
+    double res;
+    a->sort();
+    b = a->begin();
+//    for(auto it=a->cbegin();it!=a->cend();it++){
+//        cout<< *it << " - ";
+//    }
+//    cout<<endl;
+    len = a->size();
+    if(len%2==1){//odd
+        std::advance(b,len/2);
+        res = *b;
+//        cout << "odd: "<<res<<endl;
+    }
+    else{
+        std::advance(b,(len-1)/2);
+//        cout << "front: ["<<*b <<" --- ";
+        res = *b;
+        std::advance(b,1);
+//        cout << ""<<*b <<" ] ";
+        res+= *b;
+        res = res/2;
+//        cout << "even: "<<res<<endl;
+    }
+    return res;
+}
 
 
 

src/t2dv2.h

@@ -6,6 +6,7 @@
 #include<list>
 #include<unordered_map>
 
+#include<tada_hdt_entity/entity.h>
 #include <easy_logger/easy_logger.h>
 #include <HDTManager.hpp>
 
@@ -18,13 +19,18 @@ class T2Dv2 {
         void set_file_sep(string);
         string get_file_sep();
         std::list<string>* annotate_column(string fname, unsigned int col_idx, bool context, double alpha);
+        EntityAnn* get_ea_model(string fname, unsigned int col_idx, bool context);
         bool evaluate_column(string fname,string class_uri, unsigned int col_idx, bool context, double alpha);
+        bool evaluate_column_at_k(EntityAnn* ea,string class_uri, double alpha, unsigned long k_max);
+        void run_test(double from_alpha, double to_alpha, double step, unsigned long k);
         long get_k(string fname);
         void print_k();
         void computer_scores(long k);
         float get_prec();
         float get_rec();
         float get_f1();
+        string clean_str(string);
+        double get_median(std::list<double>* a);
     private:
         string m_classes_file_dir;
         string m_files_dir;