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Commit 25f13bbd authored by Le, Mia's avatar Le, Mia
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changed consensus approaches to top-performing camis

parent 98654da9
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......@@ -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]:
......
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