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Tanushree Tunstall 2022-09-02 10:08:58 +01:00
parent 93e958ae6a
commit f9ce90e3f4
2 changed files with 7 additions and 6 deletions
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7
scripts/ml/combined_model/combined_model_iterator.py
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@ -81,7 +81,7 @@ sys.path.append(homedir + '/git/LSHTM_analysis/scripts/ml/ml_functions')
sys.path
###############################################################################
#outdir = homedir + '/git/LSHTM_ML/output/combined/'
outdir = homedir + '/git/LSHTM_ML/output/test/'
outdir = homedir + '/git/LSHTM_ML/output/cg_oversample/'
#====================
# Import ML functions
@ -264,7 +264,7 @@ def CMLogoSkf(cm_input_df
, 'y_smnc_cm': y_smnc})
#%%:Running Multiple models on LOGO with SKF
# cD3_v2 = MultModelsCl_logo_skf(input_df = cm_X # two func were identical excpet for name
# cD3_v2 = MultModelsCl_logo_skf(input_df = cm_X # two func were identical excpet for name
for i in sampling_names.keys():
print("thing:", "X"+i+"_cm", "y"+i+"_cm")
@ -289,14 +289,13 @@ def CMLogoSkf(cm_input_df
, blind_test_target = cm_bts_y
, return_formatted_output = True
, random_state = 42
, n_jobs = os.cpu_count() # the number of jobs should equal the number of CPU cores
, n_jobs = os.cpu_count()
)
outFile = output_dir + str(n_tr_genes+1) + "genes_" + tts_split_type + '_' + file_suffix + i + ".csv"
cD3_v2.to_csv(outFile)
# outDict.update({'X' : cm_X
# , 'y' : cm_y
# , 'X_bts' : cm_bts_X

6
scripts/ml/combined_model/running_ml_scripts.txt
View file

@ -1,6 +1,8 @@
########################################################################
# COMBINED Model
########################################################################
# no resampling
time ./cm_logo_skf.py 2>&1 | tee cm_skf-$(date --iso).log
# with resampling
time ./combined_model_iterator.py 2>&1 | tee cm_iterator-$(date --iso).log