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added function calls fro yc run_all_ML

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Tanushree Tunstall 2022-05-29 07:31:06 +01:00
parent 7efade3736
commit 429665795c
3 changed files with 68 additions and 4 deletions
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8
UQ_ML_data.py
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@ -251,10 +251,10 @@ def setvars(gene,drug):
, 'ddg_foldx'
, 'deepddg'
, 'ddg_dynamut2'
, 'mmcsm_lig']
foldX_cols = ['contacts'
, 'electro_rr', 'electro_mm', 'electro_sm', 'electro_ss'
, 'mmcsm_lig'
, 'contacts']
foldX_cols = [ 'electro_rr', 'electro_mm', 'electro_sm', 'electro_ss'
, 'disulfide_rr', 'disulfide_mm', 'disulfide_sm', 'disulfide_ss'
, 'hbonds_rr', 'hbonds_mm', 'hbonds_sm', 'hbonds_ss'
, 'partcov_rr', 'partcov_mm', 'partcov_sm', 'partcov_ss'

3
pnca_config.py
View file

@ -57,3 +57,6 @@ print('Categorical features (n):'
, categorical_FN
, '\n================================================================\n')
print('\n#####################################################################\n')
################################################################################

61
uq_ml_models_FS/scriptfsycm.py
View file

@ -295,4 +295,65 @@ CVResultsDF_smnc = YC_resD_smnc['CrossValResultsDF']
CVResultsDF_smnc.sort_values(by=['matthew'], ascending=False, inplace=True)
BTSResultsDF_smnc = YC_resD_smnc['BlindTestResultsDF']
BTSResultsDF_smnc.sort_values(by=['matthew'], ascending=False, inplace=True)
##############################################################################
yC_gf = run_all_ML(input_pd=X[X_genomicFN], target_label=y, blind_test_input_df=X_bts[X_genomicFN], blind_test_target=y_bts, preprocess = True, var_type = 'mixed')
yc_gfCT_baseline= yC_gf['CrossValResultsDF']
yc_gfCT_baseline.sort_values(by=['matthew'], ascending=False, inplace=True)
yc_gfBT_baseline = yC_gf['BlindTestResultsDF']
yc_gfBT_baseline.sort_values(by=['matthew'], ascending=False, inplace=True)
# strucF:All
yC_sfall = run_all_ML(input_pd=X[X_strFN], target_label=y, blind_test_input_df=X_bts[X_strFN], blind_test_target=y_bts, preprocess = True, var_type = 'mixed')
yc_sfallCT_baseline= yC_sfall['CrossValResultsDF']
yc_sfallCT_baseline.sort_values(by=['matthew'], ascending=False, inplace=True)
yc_sfallBT_baseline = yC_sfall['BlindTestResultsDF']
yc_sfallBT_baseline.sort_values(by=['matthew'], ascending=False, inplace=True)
# strucF:Common
yC_sfco= run_all_ML(input_pd=X[common_cols_stabiltyN], target_label=y
, blind_test_input_df=X_bts[common_cols_stabiltyN]
, blind_test_target=y_bts, preprocess = True, var_type = 'mixed')
yc_sfcoCT_baseline= yC_sfco['CrossValResultsDF']
yc_sfcoCT_baseline.sort_values(by=['matthew'], ascending=False, inplace=True)
yc_sfcoBT_baseline = yC_sfco['BlindTestResultsDF']
yc_sfcoBT_baseline.sort_values(by=['matthew'], ascending=False, inplace=True)
# strucF:common_stability + foldX_cols i.e interaction
yC_fxss= run_all_ML(input_pd=X[common_cols_stabiltyN+foldX_cols], target_label=y
, blind_test_input_df=X_bts[common_cols_stabiltyN+foldX_cols]
, blind_test_target=y_bts, preprocess = True, var_type = 'mixed')
yc_fxssCT_baseline= yC_fxss['CrossValResultsDF']
yc_fxssCT_baseline.sort_values(by=['matthew'], ascending=False, inplace=True)
yc_fxssBT_baseline = yC_fxss['BlindTestResultsDF']
yc_fxssBT_baseline.sort_values(by=['matthew'], ascending=False, inplace=True)
# strucF:foldX_cols i.e interaction
yC_fx= run_all_ML(input_pd=X[common_cols_stabiltyN+foldX_cols], target_label=y
, blind_test_input_df=X_bts[common_cols_stabiltyN+foldX_cols]
, blind_test_target=y_bts, preprocess = True, var_type = 'mixed')
yc_fxCT_baseline= yC_fx['CrossValResultsDF']
yc_fxCT_baseline.sort_values(by=['matthew'], ascending=False, inplace=True)
yc_fxBT_baseline = yC_fx['BlindTestResultsDF']
yc_fxBT_baseline.sort_values(by=['matthew'], ascending=False, inplace=True)
# categorical
yC_cat= run_all_ML(input_pd=X[categorical_FN], target_label=y
, blind_test_input_df=X_bts[categorical_FN]
, blind_test_target=y_bts, preprocess = True, var_type = 'mixed')
yc_catCT_baseline= yC_cat['CrossValResultsDF']
yc_catCT_baseline.sort_values(by=['matthew'], ascending=False, inplace=True)
yc_catBT_baseline = yC_cat['BlindTestResultsDF']
yc_catBT_baseline.sort_values(by=['matthew'], ascending=False, inplace=True)
# Evolutionary
yC_ev = run_all_ML(input_pd=X[X_evolFN], target_label=y, blind_test_input_df=X_bts[X_evolFN], blind_test_target=y_bts, preprocess = True, var_type = 'mixed')
yc_evCT_baseline= yC_ev['CrossValResultsDF']
yc_evCT_baseline.sort_values(by=['matthew'], ascending=False, inplace=True)
yc_evBT_baseline = yC_ev['BlindTestResultsDF']
yc_evBT_baseline.sort_values(by=['matthew'], ascending=False, inplace=True)