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minor changes to run combined_model

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Tanushree Tunstall 2022-07-10 13:23:13 +01:00
parent 057c98c2f1
commit 350be30f19
3 changed files with 13 additions and 22 deletions
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15
scripts/ml/combined_model/cm_logo_skf.py
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@ -172,26 +172,25 @@ def CMLogoSkf(cm_input_df
cm_bts_y = cm_test_df.loc[:, target_var] cm_bts_y = cm_test_df.loc[:, target_var]
print('\nTEST data dim:' , cm_bts_X.shape print('\nTEST data dim:' , cm_bts_X.shape
, '\nTEST Target dim:', cm_bts_y.shape) , '\nTEST Target dim:' , cm_bts_y.shape)
print("Running Multiple models on LOGO with SKF") print("Running Multiple models on LOGO with SKF")
#%%:Running Multiple models on LOGO with SKF #%%:Running Multiple models on LOGO with SKF
cD3_v2 = MultModelsCl_logo_skf(input_df = cm_X cD3_v2 = MultModelsCl_logo_skf(input_df = cm_X
, target = cm_y , target = cm_y
#, group = 'none'
, sel_cv = skf_cv , sel_cv = skf_cv
, blind_test_df = cm_bts_X
, blind_test_target = cm_bts_y
, tts_split_type = tts_split_type , tts_split_type = tts_split_type
, resampling_type = 'none' # default , resampling_type = 'none' # default
#, group = 'none'
, add_cm = True , add_cm = True
, add_yn = True , add_yn = True
, var_type = 'mixed' , var_type = 'mixed'
, scale_numeric = ['min_max']
, run_blind_test = True , run_blind_test = True
, blind_test_df = cm_bts_X
, blind_test_target = cm_bts_y
, return_formatted_output = True , return_formatted_output = True
, random_state = 42 , random_state = 42
, n_jobs = os.cpu_count() # the number of jobs should equal the number of CPU cores , n_jobs = os.cpu_count() # the number of jobs should equal the number of CPU cores

5
scripts/ml/combined_model/running_ml_scripts.txt
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@ -1,7 +1,6 @@
######################################################################## ########################################################################
# COMBINED Model
######################################################################## ########################################################################
time ./cm_logo_skf.py 2>&1 | tee log_cm_skf.txt time ./cm_logo_skf.py 2>&1 | tee cm_skf-$(date --iso).log

11
scripts/ml/ml_functions/MultClfs_logo_skf.py
View file

@ -91,9 +91,10 @@ scoring_fn = ({ 'mcc' : make_scorer(matthews_corrcoef)
, 'jcc' : make_scorer(jaccard_score) , 'jcc' : make_scorer(jaccard_score)
}) })
# for sel_cv
#skf_cv = StratifiedKFold(n_splits = 10 #skf_cv = StratifiedKFold(n_splits = 10
# #, shuffle = False, random_state= None) # #, shuffle = False, random_state= None)
# , shuffle = True,**rs) # , shuffle = True, **rs)
#rskf_cv = RepeatedStratifiedKFold(n_splits = 10 #rskf_cv = RepeatedStratifiedKFold(n_splits = 10
# , n_repeats = 3 # , n_repeats = 3
@ -189,14 +190,6 @@ def MultModelsCl_logo_skf(input_df
rs = {'random_state': random_state} rs = {'random_state': random_state}
njobs = {'n_jobs': n_jobs} njobs = {'n_jobs': n_jobs}
skf_cv = StratifiedKFold(n_splits = 10
#, shuffle = False, random_state= None)
, shuffle = True,**rs)
rskf_cv = RepeatedStratifiedKFold(n_splits = 10
, n_repeats = 3
, **rs)
logo = LeaveOneGroupOut()
# select CV type: # select CV type:
# if group == None: # if group == None: