changed consensus approaches to top-performing camis

cami_src/cami_suite.py

@@ -213,6 +213,8 @@ class cami():
             print(preds)
         return preds
     
+      
+
     def make_evaluation(self):
         seed_gene_lst = [self.ppi_vertex2gene[seed] for seed in self.seed_lst]
         ppi_graph_file = os.path.join(self.tmp_dir, f'ppi_graph_{self.uid}.graphml')
@@ -365,12 +367,46 @@ class cami():
                                  'first_neighbours': cami_v1.make_first_neighbor_result_set}
                     }
        
-        params_tr = {'hub_penalty': [0.5], 
-                     'damping_factor': [0.1, 0.25, 0.5, 0.75, 0.85], 
-                     'confidence_level': [0.2, 0.35, 0.5, 0.75],
+        params_tr1 = {'hub_penalty': [0.5],
+                     'damping_factor': [0.85],
+                     'confidence_level': [0.35, 0.5],
+                     'ranking': ['trustrank'],
+                     'function': {'cami_v2': cami_v2.run_cami}}
+       
+        params_tr2 = {'hub_penalty': [0.5],
+                     'damping_factor': [0.1],
+                     'confidence_level': [0.2],
+                     'ranking': ['trustrank'],
+                     'function': {'cami_v3': cami_v3.run_cami}
+       }
+       
+        params_tr3 = {'hub_penalty': [0.5],
+                     'damping_factor': [0.1, 0.25, 0.75],
+                     'confidence_level': [0.2],
+                     'ranking': ['trustrank'],
+                     'function': {'cami_v2': cami_v2.run_cami}
+       }
+       
+        params_tr4 = {'hub_penalty': [0.5],
+                     'damping_factor': [0.85],
+                     'confidence_level': [0.35, 0.5],
                      'ranking': ['trustrank'],
-                     'function': {'cami_v2': cami_v2.run_cami, 
-                                  'cami_v3':cami_v3.run_cami}}
+                     'function': {'cami_v2': cami_v2.run_cami}
+       }
+       
+        params_tr5 = {'hub_penalty': [0.5],
+                     'damping_factor': [0.75],
+                     'confidence_level': [0.2, 0.5],
+                     'ranking': ['trustrank'],
+                     'function': {'cami_v3': cami_v3.run_cami}
+       }              
+        
+        # params_tr = {'hub_penalty': [0.5], 
+        #              'damping_factor': [0.1, 0.25, 0.5, 0.75, 0.85], 
+        #              'confidence_level': [0.2, 0.35, 0.5, 0.75],
+        #              'ranking': ['trustrank'],
+        #              'function': {'cami_v2': cami_v2.run_cami, 
+        #                           'cami_v3':cami_v3.run_cami}}
         
         # params_b_m = {'hub_penalty': [0, 0.25, 0.5, 0.75, 1.0], 
         #              'confidence_level': [0.2, 0.35, 0.5, 0.75],
@@ -380,10 +416,12 @@ class cami():
         
         cami_setting_list = generate_param_combinations(params_0)+\
                             generate_param_combinations(params_1)+\
-                            generate_param_combinations(params_tr)#+\
+                            generate_param_combinations(params_tr1)+\
+                            generate_param_combinations(params_tr2)+\
+                            generate_param_combinations(params_tr3)+\
+                            generate_param_combinations(params_tr4)+\
+                            generate_param_combinations(params_tr5)
                            #generate_param_combinations(params_b_m)
-
-
         camis = {}
         for setting in cami_setting_list:
             if setting[1]: