diff --git a/UQ_ML_data.py b/UQ_ML_data.py index 80c327b..40303f8 100644 --- a/UQ_ML_data.py +++ b/UQ_ML_data.py @@ -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' diff --git a/pnca_config.py b/pnca_config.py index 2a75372..db080a4 100755 --- a/pnca_config.py +++ b/pnca_config.py @@ -57,3 +57,6 @@ print('Categorical features (n):' , categorical_FN , '\n================================================================\n') print('\n#####################################################################\n') + +################################################################################ + diff --git a/uq_ml_models_FS/scriptfsycm.py b/uq_ml_models_FS/scriptfsycm.py index 1e2e578..396a4bc 100644 --- a/uq_ml_models_FS/scriptfsycm.py +++ b/uq_ml_models_FS/scriptfsycm.py @@ -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)