diff --git a/cami_src/cami_suite.py b/cami_src/cami_suite.py index d41005f8bb9f5cb51ba870e624704c6832592c8d..d5abfb6aae9842ee1b45b437de4365cf0c534f7e 100644 --- a/cami_src/cami_suite.py +++ b/cami_src/cami_suite.py @@ -212,6 +212,8 @@ class cami(): print(f'{tool.name} predicted {len(preds)} active vertices (seeds not excluded):') print(preds) return preds + + def make_evaluation(self): seed_gene_lst = [self.ppi_vertex2gene[seed] for seed in self.seed_lst] @@ -364,13 +366,47 @@ class cami(): 'intersection':cami_v1.make_intersection, '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} + } + + params_tr5 = {'hub_penalty': [0.5], + 'damping_factor': [0.75], + 'confidence_level': [0.2, 0.5], 'ranking': ['trustrank'], - 'function': {'cami_v2': cami_v2.run_cami, - 'cami_v3':cami_v3.run_cami}} + '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]: