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Commit 98654da9 authored by Le, Mia's avatar Le, Mia
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removed hub_penalty as parameter

parent b6b60fab
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......@@ -245,7 +245,7 @@ class cami():
val_res_dct = set_validation_results['input_values']['values'][rel_score_name]
for val in val_res_dct:
f.write(f'{val}\t{val_res_dct[val]}\n')
# sub_validation_results = biodigest.single_validation.single_validation(
# tar=set(self.result_module_sets[result_set]),
# tar_id='entrez',
......@@ -365,23 +365,23 @@ class cami():
'first_neighbours': cami_v1.make_first_neighbor_result_set}
}
params_tr = {'hub_penalty': [0, 0.25, 0.5, 0.75, 1.0],
'damping_factor': [0.1, 0.25, 0.5, 0.75],
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],
'ranking': ['betweenness', 'harmonic'],
'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],
# 'ranking': ['betweenness', 'harmonic'],
# 'function': {'cami_v2': cami_v2.run_cami,
# 'cami_v3':cami_v3.run_cami}}
cami_setting_list = generate_param_combinations(params_0)+\
generate_param_combinations(params_1)+\
generate_param_combinations(params_tr)+\
generate_param_combinations(params_b_m)
generate_param_combinations(params_tr)#+\
#generate_param_combinations(params_b_m)
camis = {}
......
......@@ -55,7 +55,7 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Fal
with open(os.path.join(cami.tmp_dir, f'{used_tools[0]}_{cami.uid}_relevance_scores.tsv'), 'r') as f:
for line in f:
val_name = line.split('\t')[0]
redisc_table.write(f'\t{val_name}')
res_table.write(f'\t{val_name}')
res_table.write('\n')
#result dictionaries of the form {tool:list(value for each iteration)}
......@@ -87,11 +87,7 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Fal
# reinitialize tools
cami.initialize_all_tools()
# repeat consensus
if ident%20==0:
predict_and_make_consensus(cami)
else:
predict_and_make_consensus(cami)
predict_and_make_consensus(cami)
used_seeds = [cami.ppi_vertex2gene[seed] for seed in cami.seed_lst]
......
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