saving work
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5 changed files with 1289 additions and 1102 deletions
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@ -41,6 +41,9 @@ from sklearn.compose import make_column_transformer
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from sklearn.metrics import make_scorer, confusion_matrix, accuracy_score, balanced_accuracy_score, precision_score, average_precision_score, recall_score
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from sklearn.metrics import roc_auc_score, roc_curve, f1_score, matthews_corrcoef, jaccard_score, classification_report
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# added
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from sklearn.model_selection import train_test_split, cross_validate, cross_val_score, LeaveOneOut, KFold, RepeatedKFold, cross_val_predict
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from sklearn.model_selection import train_test_split, cross_validate, cross_val_score
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from sklearn.model_selection import StratifiedKFold,RepeatedStratifiedKFold, RepeatedKFold
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@ -69,6 +72,8 @@ from sklearn.model_selection import GridSearchCV
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from sklearn.base import BaseEstimator
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from sklearn.impute import KNNImputer as KNN
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import json
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import argparse
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import re
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#%% GLOBALS
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rs = {'random_state': 42}
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@ -98,6 +103,8 @@ jacc_score_fn = {'jcc': make_scorer(jaccard_score)}
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def MultModelsCl(input_df, target, skf_cv
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, blind_test_input_df
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, blind_test_target
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, add_cm = True # adds confusion matrix based on cross_val_predict
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, add_yn = True # adds target var class numbers
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, var_type = ['numerical', 'categorical','mixed']):
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'''
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@ -117,13 +124,17 @@ def MultModelsCl(input_df, target, skf_cv
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Dict containing multiple classification scores for each model and mean of each Stratified Kfold including training
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'''
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#======================================================
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# Determine categorical and numerical features
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#======================================================
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numerical_ix = input_df.select_dtypes(include=['int64', 'float64']).columns
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numerical_ix
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categorical_ix = input_df.select_dtypes(include=['object', 'bool']).columns
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categorical_ix
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#======================================================
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# Determine preprocessing steps ~ var_type
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#======================================================
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if var_type == 'numerical':
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t = [('num', MinMaxScaler(), numerical_ix)]
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@ -138,38 +149,38 @@ def MultModelsCl(input_df, target, skf_cv
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, remainder='passthrough')
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#======================================================
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# Specify multiple Classification models
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# Specify multiple Classification Models
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#======================================================
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models = [('Logistic Regression' , LogisticRegression(**rs) )
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, ('Logistic RegressionCV' , LogisticRegressionCV(**rs) )
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, ('Gaussian NB' , GaussianNB() )
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, ('Naive Bayes' , BernoulliNB() )
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, ('K-Nearest Neighbors' , KNeighborsClassifier() )
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, ('SVC' , SVC(**rs) )
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, ('MLP' , MLPClassifier(max_iter = 500, **rs) )
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, ('Decision Tree' , DecisionTreeClassifier(**rs) )
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, ('Extra Trees' , ExtraTreesClassifier(**rs) )
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, ('Extra Tree' , ExtraTreeClassifier(**rs) )
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, ('Random Forest' , RandomForestClassifier(**rs, n_estimators = 1000 ) )
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, ('Random Forest2' , RandomForestClassifier(min_samples_leaf = 5
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, n_estimators = 1000
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, bootstrap = True
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, oob_score = True
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, **njobs
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, **rs
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, max_features = 'auto') )
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, ('XGBoost' , XGBClassifier(**rs, verbosity = 0, use_label_encoder =False) )
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, ('LDA' , LinearDiscriminantAnalysis() )
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, ('Multinomial' , MultinomialNB() )
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, ('Passive Aggresive' , PassiveAggressiveClassifier(**rs, **njobs) )
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, ('Stochastic GDescent' , SGDClassifier(**rs, **njobs) )
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, ('AdaBoost Classifier' , AdaBoostClassifier(**rs) )
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, ('Bagging Classifier' , BaggingClassifier(**rs, **njobs, bootstrap = True, oob_score = True) )
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, ('Gaussian Process' , GaussianProcessClassifier(**rs) )
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, ('Gradient Boosting' , GradientBoostingClassifier(**rs) )
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, ('QDA' , QuadraticDiscriminantAnalysis() )
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, ('Ridge Classifier' , RidgeClassifier(**rs) )
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, ('Ridge ClassifierCV' , RidgeClassifierCV(cv = 10) )
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# , ('K-Nearest Neighbors' , KNeighborsClassifier() )
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# , ('SVC' , SVC(**rs) )
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# , ('MLP' , MLPClassifier(max_iter = 500, **rs) )
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# , ('Decision Tree' , DecisionTreeClassifier(**rs) )
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# , ('Extra Trees' , ExtraTreesClassifier(**rs) )
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# , ('Extra Tree' , ExtraTreeClassifier(**rs) )
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# , ('Random Forest' , RandomForestClassifier(**rs, n_estimators = 1000 ) )
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# , ('Random Forest2' , RandomForestClassifier(min_samples_leaf = 5
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# , n_estimators = 1000
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# , bootstrap = True
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# , oob_score = True
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# , **njobs
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# , **rs
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# , max_features = 'auto') )
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# , ('XGBoost' , XGBClassifier(**rs, verbosity = 0, use_label_encoder =False) )
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# , ('LDA' , LinearDiscriminantAnalysis() )
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# , ('Multinomial' , MultinomialNB() )
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# , ('Passive Aggresive' , PassiveAggressiveClassifier(**rs, **njobs) )
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# , ('Stochastic GDescent' , SGDClassifier(**rs, **njobs) )
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# , ('AdaBoost Classifier' , AdaBoostClassifier(**rs) )
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# , ('Bagging Classifier' , BaggingClassifier(**rs, **njobs, bootstrap = True, oob_score = True) )
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# , ('Gaussian Process' , GaussianProcessClassifier(**rs) )
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# , ('Gradient Boosting' , GradientBoostingClassifier(**rs) )
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# , ('QDA' , QuadraticDiscriminantAnalysis() )
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# , ('Ridge Classifier' , RidgeClassifier(**rs) )
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# , ('Ridge ClassifierCV' , RidgeClassifierCV(cv = 10) )
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]
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mm_skf_scoresD = {}
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@ -200,6 +211,72 @@ def MultModelsCl(input_df, target, skf_cv
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, scoring = scoring_fn
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, return_train_score = True)
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#######################################################################
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#======================================================
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# Option: Add confusion matrix from cross_val_predict
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# Understand and USE with caution
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# cross_val_score, cross_val_predict, "Passing these predictions into an evaluation metric may not be a valid way to measure generalization performance. Results can differ from cross_validate and cross_val_score unless all tests sets have equal size and the metric decomposes over samples."
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# https://stackoverflow.com/questions/65645125/producing-a-confusion-matrix-with-cross-validate
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#======================================================
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if add_cm:
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#-----------------------------------------------------------
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# Initialise dict of Confusion Matrix (cm)
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#-----------------------------------------------------------
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cmD = {}
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# Calculate cm
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y_pred = cross_val_predict(model_pipeline, input_df, target, cv = skf_cv, **njobs)
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#_tn, _fp, _fn, _tp = confusion_matrix(y_pred, y).ravel() # internally
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tn, fp, fn, tp = confusion_matrix(y_pred, target).ravel()
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# Build dict
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cmD = {'TN' : tn
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, 'FP': fp
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, 'FN': fn
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, 'TP': tp}
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#---------------------------------
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# Update cv dict with cmD and tbtD
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#----------------------------------
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skf_cv_modD.update(cmD)
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else:
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skf_cv_modD = skf_cv_modD
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#######################################################################
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#=============================================
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# Option: Add targety numbers for data
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#=============================================
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if add_yn:
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#-----------------------------------------------------------
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# Initialise dict of target numbers: training and blind (tbt)
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#-----------------------------------------------------------
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tbtD = {}
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# training y
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tyn = Counter(target)
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tyn_neg = tyn[0]
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tyn_pos = tyn[1]
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# blind test y
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btyn = Counter(blind_test_target)
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btyn_neg = btyn[0]
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btyn_pos = btyn[1]
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# Build dict
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tbtD = {'trainingY_neg' : tyn_neg
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, 'trainingY_pos' : tyn_pos
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, 'blindY_neg' : btyn_neg
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, 'blindY_pos' : btyn_pos}
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#---------------------------------
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# Update cv dict with cmD and tbtD
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#----------------------------------
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skf_cv_modD.update(tbtD)
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else:
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skf_cv_modD = skf_cv_modD
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#######################################################################
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#==============================
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# Extract mean values for CV
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#==============================
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@ -207,15 +284,15 @@ def MultModelsCl(input_df, target, skf_cv
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for key, value in skf_cv_modD.items():
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print('\nkey:', key, '\nvalue:', value)
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print('\nmean value:', mean(value))
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mm_skf_scoresD[model_name][key] = round(mean(value),2)
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print('\nmean value:', np.mean(value))
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mm_skf_scoresD[model_name][key] = round(np.mean(value),2)
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#return(mm_skf_scoresD)
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#%%
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#=========================
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# Blind test: BTS results
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#=========================
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# Build the final results with all scores for a feature selected model
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# Build the final results with all scores for the model
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#bts_predict = gscv_fs.predict(blind_test_input_df)
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model_pipeline.fit(input_df, target)
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bts_predict = model_pipeline.predict(blind_test_input_df)
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@ -228,25 +305,13 @@ def MultModelsCl(input_df, target, skf_cv
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# train_test_diff_MCC = cvtrain_mcc - bts_mcc_score
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# print('\nDiff b/w train and blind test score (MCC):', train_test_diff)
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# # create a dict with all scores
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# lr_btsD = { 'model_name': model_name
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# , 'bts_mcc':None
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# , 'bts_fscore':None
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# , 'bts_precision':None
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# , 'bts_recall':None
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# , 'bts_accuracy':None
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# , 'bts_roc_auc':None
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# , 'bts_jaccard':None}
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mm_skf_scoresD[model_name]['bts_mcc'] = bts_mcc_score
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mm_skf_scoresD[model_name]['bts_fscore'] = round(f1_score(blind_test_target, bts_predict),2)
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mm_skf_scoresD[model_name]['bts_precision'] = round(precision_score(blind_test_target, bts_predict),2)
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mm_skf_scoresD[model_name]['bts_recall'] = round(recall_score(blind_test_target, bts_predict),2)
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mm_skf_scoresD[model_name]['bts_accuracy'] = round(accuracy_score(blind_test_target, bts_predict),2)
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mm_skf_scoresD[model_name]['bts_roc_auc'] = round(roc_auc_score(blind_test_target, bts_predict),2)
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mm_skf_scoresD[model_name]['bts_jaccard'] = round(jaccard_score(blind_test_target, bts_predict),2)
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mm_skf_scoresD[model_name]['bts_jcc'] = round(jaccard_score(blind_test_target, bts_predict),2)
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#mm_skf_scoresD[model_name]['diff_mcc'] = train_test_diff_MCC
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return(mm_skf_scoresD)
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@ -72,6 +72,8 @@ from sklearn.model_selection import GridSearchCV
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from sklearn.base import BaseEstimator
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from sklearn.impute import KNNImputer as KNN
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import json
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import argparse
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import re
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#%% GLOBALS
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rs = {'random_state': 42}
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@ -98,7 +100,7 @@ mcc_score_fn = {'mcc': make_scorer(matthews_corrcoef)}
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jacc_score_fn = {'jcc': make_scorer(jaccard_score)}
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#%%
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# Multiple Classification - Model Pipeline
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def MultModelsCl_dissected(input_df, target, skf_cv
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def MultModelsCl(input_df, target, skf_cv
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, blind_test_input_df
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, blind_test_target
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, add_cm = True # adds confusion matrix based on cross_val_predict
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@ -299,6 +301,10 @@ def MultModelsCl_dissected(input_df, target, skf_cv
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print('\nMCC on Blind test:' , bts_mcc_score)
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print('\nAccuracy on Blind test:', round(accuracy_score(blind_test_target, bts_predict),2))
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# Diff b/w train and bts test scores
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# train_test_diff_MCC = cvtrain_mcc - bts_mcc_score
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# print('\nDiff b/w train and blind test score (MCC):', train_test_diff)
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mm_skf_scoresD[model_name]['bts_mcc'] = bts_mcc_score
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mm_skf_scoresD[model_name]['bts_fscore'] = round(f1_score(blind_test_target, bts_predict),2)
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mm_skf_scoresD[model_name]['bts_precision'] = round(precision_score(blind_test_target, bts_predict),2)
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@ -29,46 +29,74 @@ score_type_ordermapD = { 'mcc' : 1
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, 'fit_time' : 16
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, 'score_time' : 17
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}
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###############################################################################
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#==================
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# Specify outdir
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#==================
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outdir_ml = outdir + 'ml/uq_v1/fgs/'
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print('\nOutput directory:', outdir_ml)
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outFile = outdir_ml + gene.lower() + '_baseline_FG.csv'
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#==================
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# Baseline models
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# other vars
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#==================
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# cm_di2 = MultModelsCl_dissected(input_df = X
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# , target = y
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# , var_type = 'mixed'
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# , skf_cv = skf_cv
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# , blind_test_input_df = X_bts
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# , blind_test_target = y_bts
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# , add_cm = True
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# , add_yn = True)
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# baseline_all2 = pd.DataFrame(cm_di2)
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# baseline_all2T = baseline_all2.T
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# baseline_CTBT2 = baseline_all2T.filter(regex = 'test_.*|bts_.*|TN|FP|FN|TP|.*_neg|.*_pos' , axis = 1)
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tts_split_name = 'original'
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sampling_type_name = 'none'
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###############################################################################
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#================
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# Stability cols
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# Evolutionary
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# X_evolFN
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#================
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feature_gp_nameEV = 'evolutionary'
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n_featuresEV = len(X_evolFN)
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scores_mmEV = MultModelsCl_dissected(input_df = X[X_evolFN]
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, target = y
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, var_type = 'mixed'
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, skf_cv = skf_cv
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, blind_test_input_df = X_bts[X_evolFN]
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, blind_test_target = y_bts
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, add_cm = True
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, add_yn = True)
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#================
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# Affinity cols
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#================
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baseline_allEV = pd.DataFrame(scores_mmEV)
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baseline_EV = baseline_allEV.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
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baseline_EV = baseline_EV.reset_index()
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baseline_EV.rename(columns = {'index': 'original_names'}, inplace = True)
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#================
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# Residue level
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#================
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# Indicate whether BT or CT
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bt_pattern = re.compile(r'bts_.*')
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baseline_EV['data_source'] = baseline_EV.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
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baseline_EV['score_type'] = baseline_EV['original_names'].str.replace('bts_|test_', '', regex = True)
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score_type_uniqueN = set(baseline_EV['score_type'])
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cL1 = list(score_type_ordermapD.keys())
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cL2 = list(score_type_uniqueN)
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if set(cL1).issubset(cL2):
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print('\nPASS: sorting df by score that is mapped onto the order I want')
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baseline_EV['score_order'] = baseline_EV['score_type'].map(score_type_ordermapD)
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baseline_EV.sort_values(by = ['data_source', 'score_order'], ascending = [True, True], inplace = True)
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else:
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sys.exit('\nFAIL: could not sort df as score mapping for ordering failed')
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baseline_EV['feature_group'] = feature_gp_nameEV
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baseline_EV['sampling_type'] = sampling_type_name
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baseline_EV['tts_split'] = tts_split_name
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baseline_EV['n_features'] = n_featuresEV
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###############################################################################
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#================
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# Genomics
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# X_genomicFN
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#================
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feature_gp_name = 'genomics'
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feature_gp_nameGN = 'genomics'
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n_featuresGN = len(X_genomicFN)
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scores_mm_gn = MultModelsCl_dissected(input_df = X[X_genomicFN]
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scores_mmGN = MultModelsCl_dissected(input_df = X[X_genomicFN]
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, target = y
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, var_type = 'mixed'
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, skf_cv = skf_cv
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@ -77,9 +105,9 @@ scores_mm_gn = MultModelsCl_dissected(input_df = X[X_genomicFN]
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, add_cm = True
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, add_yn = True)
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baseline_all_gn = pd.DataFrame(scores_mm_gn)
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baseline_allGN = pd.DataFrame(scores_mmGN)
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baseline_GN = baseline_all_gn.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
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baseline_GN = baseline_allGN.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
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baseline_GN = baseline_GN.reset_index()
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baseline_GN.rename(columns = {'index': 'original_names'}, inplace = True)
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@ -100,47 +128,340 @@ if set(cL1).issubset(cL2):
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else:
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sys.exit('\nFAIL: could not sort df as score mapping for ordering failed')
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baseline_GN['feature_group'] = feature_gp_name
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baseline_GN['feature_group'] = feature_gp_nameGN
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baseline_GN['sampling_type'] = sampling_type_name
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baseline_GN['tts_split'] = tts_split_name
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baseline_GN['n_features'] = n_featuresGN
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###############################################################################
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#all_featuresN = X_evolFN + X_structural_FN + X_genomicFN
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# X_structural_FN = X_stability_FN + X_affinityFN + X_resprop_FN
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# X_resprop_FN = X_aaindex_Fnum + X_str_Fnum + X_aap_Fcat
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#================
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# Structural cols
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# X_structural_FN
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#================
|
||||
feature_gp_nameSTR = 'structural'
|
||||
n_featuresSTR = len(X_structural_FN)
|
||||
|
||||
#-------------
|
||||
# Blind test
|
||||
#-------------
|
||||
baseline_BT = baseline_all_gn.filter(regex = 'bts_', axis = 0)
|
||||
baseline_BT = baseline_BT.reset_index()
|
||||
baseline_BT.rename(columns = {'index': 'original_names'}, inplace = True)
|
||||
baseline_BT['score_type'] = baseline_BT['original_names']
|
||||
baseline_BT['score_type'] = baseline_BT['score_type'].str.replace('bts_*', '', regex = True)
|
||||
baseline_BT['data_source'] = 'BT_score'
|
||||
scores_mmSTR = MultModelsCl_dissected(input_df = X[X_structural_FN]
|
||||
, target = y
|
||||
, var_type = 'mixed'
|
||||
, skf_cv = skf_cv
|
||||
, blind_test_input_df = X_bts[X_structural_FN]
|
||||
, blind_test_target = y_bts
|
||||
, add_cm = True
|
||||
, add_yn = True)
|
||||
|
||||
#--------
|
||||
# CV
|
||||
#--------
|
||||
baseline_CT = baseline_all_gn.filter(regex = '.*_time|test_.*|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
|
||||
baseline_CT = baseline_CT.reset_index()
|
||||
baseline_CT.rename(columns = {'index': 'original_names'}, inplace = True)
|
||||
baseline_CT['score_type'] = baseline_CT['original_names']
|
||||
baseline_CT['score_type'] = baseline_CT['score_type'].str.replace('test_*', '', regex = True)
|
||||
baseline_CT['data_source'] = 'CT_score'
|
||||
baseline_allSTR = pd.DataFrame(scores_mmSTR)
|
||||
|
||||
#----------------------
|
||||
# rpow bind: CT and BT
|
||||
#----------------------
|
||||
if all(baseline_BT.columns == baseline_CT.columns):
|
||||
print('\nPASS: Colnames match, proceeding to row bind for data:', feature_gp_name
|
||||
, '\nDim of df1 (BT):', baseline_BT.shape
|
||||
, '\nDim of df2 (CT):', baseline_CT.shape)
|
||||
comb_df_gn = pd.concat([baseline_BT, baseline_CT], axis = 0, ignore_index = True)
|
||||
comb_df_gn['feature_group'] = feature_gp_name
|
||||
print('\nDim of combined df:', comb_df_gn.shape)
|
||||
baseline_STR = baseline_allSTR.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
|
||||
baseline_STR = baseline_STR.reset_index()
|
||||
baseline_STR.rename(columns = {'index': 'original_names'}, inplace = True)
|
||||
|
||||
# Indicate whether BT or CT
|
||||
bt_pattern = re.compile(r'bts_.*')
|
||||
baseline_STR['data_source'] = baseline_STR.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
|
||||
|
||||
baseline_STR['score_type'] = baseline_STR['original_names'].str.replace('bts_|test_', '', regex = True)
|
||||
|
||||
score_type_uniqueN = set(baseline_STR['score_type'])
|
||||
cL1 = list(score_type_ordermapD.keys())
|
||||
cL2 = list(score_type_uniqueN)
|
||||
|
||||
if set(cL1).issubset(cL2):
|
||||
print('\nPASS: sorting df by score that is mapped onto the order I want')
|
||||
baseline_STR['score_order'] = baseline_STR['score_type'].map(score_type_ordermapD)
|
||||
baseline_STR.sort_values(by = ['data_source', 'score_order'], ascending = [True, True], inplace = True)
|
||||
else:
|
||||
print('\nFAIL: colnames mismatch, cannot combine')
|
||||
sys.exit('\nFAIL: could not sort df as score mapping for ordering failed')
|
||||
|
||||
# good way but I don't like to have to rearrange the columns later
|
||||
#frames_tocombine = [baseline_BT, baseline_CT]
|
||||
#common_cols = list(set.intersection(*(set(df.columns) for df in frames_tocombine)))
|
||||
#a = pd.concat([df[common_cols] for df in frames_tocombine], ignore_index=True)
|
||||
baseline_STR['feature_group'] = feature_gp_nameSTR
|
||||
baseline_STR['sampling_type'] = sampling_type_name
|
||||
baseline_STR['tts_split'] = tts_split_name
|
||||
baseline_STR['n_features'] = n_featuresSTR
|
||||
##############################################################################
|
||||
#================
|
||||
# Stability cols
|
||||
# X_stability_FN
|
||||
#================
|
||||
feature_gp_nameSTB = 'stability'
|
||||
n_featuresSTB = len(X_stability_FN)
|
||||
|
||||
scores_mmSTB = MultModelsCl_dissected(input_df = X[X_stability_FN]
|
||||
, target = y
|
||||
, var_type = 'mixed'
|
||||
, skf_cv = skf_cv
|
||||
, blind_test_input_df = X_bts[X_stability_FN]
|
||||
, blind_test_target = y_bts
|
||||
, add_cm = True
|
||||
, add_yn = True)
|
||||
|
||||
baseline_allSTB = pd.DataFrame(scores_mmSTB)
|
||||
|
||||
baseline_STB = baseline_allSTB.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
|
||||
baseline_STB = baseline_STB.reset_index()
|
||||
baseline_STB.rename(columns = {'index': 'original_names'}, inplace = True)
|
||||
|
||||
# Indicate whether BT or CT
|
||||
bt_pattern = re.compile(r'bts_.*')
|
||||
baseline_STB['data_source'] = baseline_STB.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
|
||||
|
||||
baseline_STB['score_type'] = baseline_STB['original_names'].str.replace('bts_|test_', '', regex = True)
|
||||
|
||||
score_type_uniqueN = set(baseline_STB['score_type'])
|
||||
cL1 = list(score_type_ordermapD.keys())
|
||||
cL2 = list(score_type_uniqueN)
|
||||
|
||||
if set(cL1).issubset(cL2):
|
||||
print('\nPASS: sorting df by score that is mapped onto the order I want')
|
||||
baseline_STB['score_order'] = baseline_STB['score_type'].map(score_type_ordermapD)
|
||||
baseline_STB.sort_values(by = ['data_source', 'score_order'], ascending = [True, True], inplace = True)
|
||||
else:
|
||||
sys.exit('\nFAIL: could not sort df as score mapping for ordering failed')
|
||||
|
||||
baseline_STB['feature_group'] = feature_gp_nameSTB
|
||||
baseline_STB['sampling_type'] = sampling_type_name
|
||||
baseline_STB['tts_split'] = tts_split_name
|
||||
baseline_STB['n_features'] = n_featuresSTB
|
||||
###############################################################################
|
||||
#================
|
||||
# Evolution
|
||||
# Affinity cols
|
||||
# X_affinityFN
|
||||
#================
|
||||
feature_gp_nameAFF = 'affinity'
|
||||
n_featuresAFF = len(X_affinityFN)
|
||||
|
||||
scores_mmAFF = MultModelsCl_dissected(input_df = X[X_affinityFN]
|
||||
, target = y
|
||||
, var_type = 'mixed'
|
||||
, skf_cv = skf_cv
|
||||
, blind_test_input_df = X_bts[X_affinityFN]
|
||||
, blind_test_target = y_bts
|
||||
, add_cm = True
|
||||
, add_yn = True)
|
||||
|
||||
baseline_allAFF = pd.DataFrame(scores_mmAFF)
|
||||
|
||||
baseline_AFF = baseline_allAFF.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
|
||||
baseline_AFF = baseline_AFF.reset_index()
|
||||
baseline_AFF.rename(columns = {'index': 'original_names'}, inplace = True)
|
||||
|
||||
# Indicate whether BT or CT
|
||||
bt_pattern = re.compile(r'bts_.*')
|
||||
baseline_AFF['data_source'] = baseline_AFF.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
|
||||
|
||||
baseline_AFF['score_type'] = baseline_AFF['original_names'].str.replace('bts_|test_', '', regex = True)
|
||||
|
||||
score_type_uniqueN = set(baseline_AFF['score_type'])
|
||||
cL1 = list(score_type_ordermapD.keys())
|
||||
cL2 = list(score_type_uniqueN)
|
||||
|
||||
if set(cL1).issubset(cL2):
|
||||
print('\nPASS: sorting df by score that is mapped onto the order I want')
|
||||
baseline_AFF['score_order'] = baseline_AFF['score_type'].map(score_type_ordermapD)
|
||||
baseline_AFF.sort_values(by = ['data_source', 'score_order'], ascending = [True, True], inplace = True)
|
||||
else:
|
||||
sys.exit('\nFAIL: could not sort df as score mapping for ordering failed')
|
||||
|
||||
baseline_AFF['feature_group'] = feature_gp_nameAFF
|
||||
baseline_AFF['sampling_type'] = sampling_type_name
|
||||
baseline_AFF['tts_split'] = tts_split_name
|
||||
baseline_AFF['n_features'] = n_featuresAFF
|
||||
###############################################################################
|
||||
#================
|
||||
# Residue level
|
||||
# X_resprop_FN
|
||||
#================
|
||||
feature_gp_nameRES = 'residue_prop'
|
||||
n_featuresRES = len(X_resprop_FN)
|
||||
|
||||
scores_mmRES = MultModelsCl_dissected(input_df = X[X_resprop_FN]
|
||||
, target = y
|
||||
, var_type = 'mixed'
|
||||
, skf_cv = skf_cv
|
||||
, blind_test_input_df = X_bts[X_resprop_FN]
|
||||
, blind_test_target = y_bts
|
||||
, add_cm = True
|
||||
, add_yn = True)
|
||||
|
||||
baseline_allRES = pd.DataFrame(scores_mmRES)
|
||||
|
||||
baseline_RES = baseline_allRES.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
|
||||
baseline_RES = baseline_RES.reset_index()
|
||||
baseline_RES.rename(columns = {'index': 'original_names'}, inplace = True)
|
||||
|
||||
# Indicate whether BT or CT
|
||||
bt_pattern = re.compile(r'bts_.*')
|
||||
baseline_RES['data_source'] = baseline_RES.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
|
||||
|
||||
baseline_RES['score_type'] = baseline_RES['original_names'].str.replace('bts_|test_', '', regex = True)
|
||||
|
||||
score_type_uniqueN = set(baseline_RES['score_type'])
|
||||
cL1 = list(score_type_ordermapD.keys())
|
||||
cL2 = list(score_type_uniqueN)
|
||||
|
||||
if set(cL1).issubset(cL2):
|
||||
print('\nPASS: sorting df by score that is mapped onto the order I want')
|
||||
baseline_RES['score_order'] = baseline_RES['score_type'].map(score_type_ordermapD)
|
||||
baseline_RES.sort_values(by = ['data_source', 'score_order'], ascending = [True, True], inplace = True)
|
||||
else:
|
||||
sys.exit('\nFAIL: could not sort df as score mapping for ordering failed')
|
||||
|
||||
baseline_RES['feature_group'] = feature_gp_nameRES
|
||||
baseline_RES['sampling_type'] = sampling_type_name
|
||||
baseline_RES['tts_split'] = tts_split_name
|
||||
baseline_RES['n_features'] = n_featuresRES
|
||||
###############################################################################
|
||||
#================
|
||||
# Residue level-AAindex
|
||||
#X_resprop_FN - X_aaindex_Fnum
|
||||
#================
|
||||
X_respropNOaaFN = list(set(X_resprop_FN) - set(X_aaindex_Fnum))
|
||||
|
||||
feature_gp_nameRNAA = 'ResPropNoAA'
|
||||
n_featuresRNAA = len(X_respropNOaaFN)
|
||||
|
||||
scores_mmRNAA = MultModelsCl_dissected(input_df = X[X_respropNOaaFN]
|
||||
, target = y
|
||||
, var_type = 'mixed'
|
||||
, skf_cv = skf_cv
|
||||
, blind_test_input_df = X_bts[X_respropNOaaFN]
|
||||
, blind_test_target = y_bts
|
||||
, add_cm = True
|
||||
, add_yn = True)
|
||||
|
||||
baseline_allRNAA = pd.DataFrame(scores_mmRNAA)
|
||||
|
||||
baseline_RNAA = baseline_allRNAA.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
|
||||
baseline_RNAA = baseline_RNAA.reset_index()
|
||||
baseline_RNAA.rename(columns = {'index': 'original_names'}, inplace = True)
|
||||
|
||||
# Indicate whether BT or CT
|
||||
bt_pattern = re.compile(r'bts_.*')
|
||||
baseline_RNAA['data_source'] = baseline_RNAA.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
|
||||
|
||||
baseline_RNAA['score_type'] = baseline_RNAA['original_names'].str.replace('bts_|test_', '', regex = True)
|
||||
|
||||
score_type_uniqueN = set(baseline_RNAA['score_type'])
|
||||
cL1 = list(score_type_ordermapD.keys())
|
||||
cL2 = list(score_type_uniqueN)
|
||||
|
||||
if set(cL1).issubset(cL2):
|
||||
print('\nPASS: sorting df by score that is mapped onto the order I want')
|
||||
baseline_RNAA['score_order'] = baseline_RNAA['score_type'].map(score_type_ordermapD)
|
||||
baseline_RNAA.sort_values(by = ['data_source', 'score_order'], ascending = [True, True], inplace = True)
|
||||
else:
|
||||
sys.exit('\nFAIL: could not sort df as score mapping for ordering failed')
|
||||
|
||||
baseline_RNAA['feature_group'] = feature_gp_nameRNAA
|
||||
baseline_RNAA['sampling_type'] = sampling_type_name
|
||||
baseline_RNAA['tts_split'] = tts_split_name
|
||||
baseline_RNAA['n_features'] = n_featuresRNAA
|
||||
###############################################################################
|
||||
#================
|
||||
# Structural cols-AAindex
|
||||
#X_structural_FN - X_aaindex_Fnum
|
||||
#================
|
||||
X_strNOaaFN = list(set(X_structural_FN) - set(X_aaindex_Fnum))
|
||||
|
||||
feature_gp_nameSNAA = 'StrNoAA'
|
||||
n_featuresSNAA = len(X_strNOaaFN)
|
||||
|
||||
scores_mmSNAA = MultModelsCl_dissected(input_df = X[X_strNOaaFN]
|
||||
, target = y
|
||||
, var_type = 'mixed'
|
||||
, skf_cv = skf_cv
|
||||
, blind_test_input_df = X_bts[X_strNOaaFN]
|
||||
, blind_test_target = y_bts
|
||||
, add_cm = True
|
||||
, add_yn = True)
|
||||
|
||||
baseline_allSNAA = pd.DataFrame(scores_mmSNAA)
|
||||
|
||||
baseline_SNAA = baseline_allSNAA.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
|
||||
baseline_SNAA = baseline_SNAA.reset_index()
|
||||
baseline_SNAA.rename(columns = {'index': 'original_names'}, inplace = True)
|
||||
|
||||
# Indicate whether BT or CT
|
||||
bt_pattern = re.compile(r'bts_.*')
|
||||
baseline_SNAA['data_source'] = baseline_SNAA.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
|
||||
|
||||
baseline_SNAA['score_type'] = baseline_SNAA['original_names'].str.replace('bts_|test_', '', regex = True)
|
||||
|
||||
score_type_uniqueN = set(baseline_SNAA['score_type'])
|
||||
cL1 = list(score_type_ordermapD.keys())
|
||||
cL2 = list(score_type_uniqueN)
|
||||
|
||||
if set(cL1).issubset(cL2):
|
||||
print('\nPASS: sorting df by score that is mapped onto the order I want')
|
||||
baseline_SNAA['score_order'] = baseline_SNAA['score_type'].map(score_type_ordermapD)
|
||||
baseline_SNAA.sort_values(by = ['data_source', 'score_order'], ascending = [True, True], inplace = True)
|
||||
else:
|
||||
sys.exit('\nFAIL: could not sort df as score mapping for ordering failed')
|
||||
|
||||
baseline_SNAA['feature_group'] = feature_gp_nameSNAA
|
||||
baseline_SNAA['sampling_type'] = sampling_type_name
|
||||
baseline_SNAA['tts_split'] = tts_split_name
|
||||
baseline_SNAA['n_features'] = n_featuresSNAA
|
||||
###############################################################################
|
||||
#%% COMBINING all FG dfs
|
||||
#================
|
||||
# Combine all
|
||||
# https://stackoverflow.com/questions/39862654/pandas-concat-of-multiple-data-frames-using-only-common-columns
|
||||
#================
|
||||
dfs_combine = [baseline_EV, baseline_GN, baseline_STR, baseline_STB, baseline_AFF, baseline_RES , baseline_RNAA , baseline_SNAA]
|
||||
|
||||
dfs_nrows = []
|
||||
for df in dfs_combine:
|
||||
dfs_nrows = dfs_nrows + [len(df)]
|
||||
dfs_nrows = max(dfs_nrows)
|
||||
|
||||
dfs_ncols = []
|
||||
for df in dfs_combine:
|
||||
dfs_ncols = dfs_ncols + [len(df.columns)]
|
||||
dfs_ncols = max(dfs_ncols)
|
||||
|
||||
# dfs_ncols = []
|
||||
# dfs_ncols2 = mode(dfs_ncols.append(len(df.columns) for df in dfs_combine)
|
||||
# dfs_ncols2
|
||||
|
||||
expected_nrows = len(dfs_combine) * dfs_nrows
|
||||
expected_ncols = dfs_ncols
|
||||
|
||||
common_cols = list(set.intersection(*(set(df.columns) for df in dfs_combine)))
|
||||
|
||||
if len(common_cols) == dfs_ncols :
|
||||
combined_FG_baseline = pd.concat([df[common_cols] for df in dfs_combine], ignore_index=True)
|
||||
fgs = combined_FG_baseline[['feature_group', 'n_features']]
|
||||
fgs = fgs.drop_duplicates()
|
||||
print('\nConcatenating dfs with feature groups after ML analysis (sampling type):'
|
||||
, '\nNo. of dfs combining:', len(dfs_combine)
|
||||
, '\nSampling type:', sampling_type
|
||||
, '\nThe feature groups are:'
|
||||
, '\n', fgs)
|
||||
if len(combined_FG_baseline) == expected_nrows and len(combined_FG_baseline.columns) == expected_ncols:
|
||||
print('\nPASS:', len(dfs_combine), 'dfs successfully combined'
|
||||
, '\nnrows in combined_df:', len(combined_FG_baseline)
|
||||
, '\nncols in combined_df:', len(combined_FG_baseline.columns))
|
||||
else:
|
||||
print('\nFAIL: concatenating failed'
|
||||
, '\nExpected nrows:', expected_nrows
|
||||
, '\nGot:', len(combined_FG_baseline)
|
||||
, '\nExpected ncols:', expected_ncols
|
||||
, '\nGot:', len(combined_FG_baseline.columns))
|
||||
sys.exit()
|
||||
else:
|
||||
sys.exit('\nConcatenting dfs not possible,check numbers ')
|
||||
|
||||
# # rpow bind
|
||||
# if all(ll((baseline_EV.columns == baseline_GN.columns == baseline_STR.columns)):
|
||||
# print('\nPASS:colnames match, proceeding to rowbind')
|
||||
# comb_df = pd.concat()], axis = 0, ignore_index = True )
|
||||
###############################################################################
|
||||
#====================
|
||||
# Write output file
|
||||
#====================
|
||||
|
||||
combined_FG_baseline.to_csv(outFile)
|
||||
print('\nFile successfully written:', outFile)
|
||||
###############################################################################
|
||||
|
|
@ -5,7 +5,7 @@ Created on Sun Mar 6 13:41:54 2022
|
|||
|
||||
@author: tanu
|
||||
"""
|
||||
#def setvars(gene,drug):
|
||||
def setvars(gene,drug):
|
||||
#https://stackoverflow.com/questions/51695322/compare-multiple-algorithms-with-sklearn-pipeline
|
||||
import os, sys
|
||||
import pandas as pd
|
||||
|
|
@ -34,6 +34,8 @@ from sklearn.model_selection import train_test_split, cross_validate, cross_val_
|
|||
from sklearn.model_selection import StratifiedKFold,RepeatedStratifiedKFold, RepeatedKFold
|
||||
|
||||
from sklearn.pipeline import Pipeline, make_pipeline
|
||||
import argparse
|
||||
import re
|
||||
#%% GLOBALS
|
||||
rs = {'random_state': 42}
|
||||
njobs = {'n_jobs': 10}
|
||||
|
|
|
|||
|
|
@ -1,207 +0,0 @@
|
|||
#!/usr/bin/env python3
|
||||
# -*- coding: utf-8 -*-
|
||||
"""
|
||||
Created on Sat May 28 05:25:30 2022
|
||||
|
||||
@author: tanu
|
||||
"""
|
||||
|
||||
import os
|
||||
|
||||
gene = 'pncA'
|
||||
drug = 'pyrazinamide'
|
||||
#total_mtblineage_uc = 8
|
||||
|
||||
homedir = os.path.expanduser("~")
|
||||
os.chdir( homedir + '/git/LSHTM_analysis/scripts/ml/')
|
||||
|
||||
#---------------------------
|
||||
# Version 1: no AAindex
|
||||
#from UQ_ML_data import *
|
||||
#setvars(gene,drug)
|
||||
#from UQ_ML_data import *
|
||||
#---------------------------
|
||||
|
||||
from ml_data_dissected import *
|
||||
setvars(gene,drug)
|
||||
from ml_data_dissected import *
|
||||
|
||||
# from YC run_all_ML: run locally
|
||||
#from UQ_yc_RunAllClfs import run_all_ML
|
||||
|
||||
# TT run all ML clfs: baseline mode
|
||||
from MultModelsCl_dissected import MultModelsCl_dissected
|
||||
|
||||
############################################################################
|
||||
print('\n#####################################################################\n'
|
||||
, '\nRunning ML analysis: UQ [without AA index but with active site annotations]'
|
||||
, '\nGene name:', gene
|
||||
, '\nDrug name:', drug)
|
||||
|
||||
#==================
|
||||
# Specify outdir
|
||||
#==================
|
||||
|
||||
outdir_ml = outdir + 'ml/uq_v1/dissected'
|
||||
|
||||
print('\nOutput directory:', outdir_ml)
|
||||
|
||||
#%%###########################################################################
|
||||
print('\n================================================================\n')
|
||||
|
||||
|
||||
X_structural_FN = X_stability_FN + X_affinityFN + X_resprop_FN
|
||||
X_aaindex_Fnum + X_str_Fnum + X_aap_Fcat
|
||||
all_featuresN = X_evolFN + X_structural_FN + X_genomicFN
|
||||
|
||||
print('\n================================================================'
|
||||
|
||||
, '\nTotal Evolutionary features (n):' , len(X_evolFN)
|
||||
, '\n--------------Evol. feature colnames:', X_evolFN
|
||||
|
||||
, '\n================================================================'
|
||||
|
||||
, '\n\nTotal structural features (n):', len(X_structural_FN)
|
||||
|
||||
, '\n--------Stability ncols:' , len(X_stability_FN)
|
||||
, '\n--------------Common stability colnames:' , X_common_stability_Fnum
|
||||
, '\n--------------Foldx colnames:' , X_foldX_Fnum
|
||||
|
||||
, '\n--------Affinity ncols:' , len(X_affinityFN)
|
||||
, '\n--------------Common affinity colnames:' , common_affinity_Fnum
|
||||
, '\n--------------Gene specific affinity colnames:', gene_affinity_colnames
|
||||
|
||||
, '\n--------Residue prop ncols:' , len(X_resprop_FN)
|
||||
, '\n--------------Residue Prop cols:' , X_str_Fnum
|
||||
, '\n--------------AA change Prop cols:' , X_aap_Fcat
|
||||
, '\n--------------AA index cols:' , X_aaindex_Fnum
|
||||
|
||||
, '\n================================================================'
|
||||
|
||||
, '\n\nTotal Genomic features (n):' , len(X_genomicFN)
|
||||
, '\n--------MAF+OR cols:' , len(X_gn_mafor_Fnum)
|
||||
, '\n--------------MAF+OR colnames:' , X_gn_mafor_Fnum
|
||||
|
||||
, '\n--------Lineage cols:' , len(X_gn_linegae_Fnum)
|
||||
, '\n--------------Lineage cols:' , X_gn_linegae_Fnum
|
||||
|
||||
, '\n--------Other cols:' , len(X_gn_Fcat)
|
||||
, '\n--------------Other cols:' , X_gn_Fcat
|
||||
|
||||
, '\n================================================================')
|
||||
|
||||
# Sanity check
|
||||
if ( len(X.columns) == len(X_evolFN) + len(X_structural_FN) + len(X_genomicFN)):
|
||||
print('\nPass: No. of features match')
|
||||
else:
|
||||
print('\nFail: Count of feature mismatch'
|
||||
, '\nExpected:', len(X_evolFN) + len(X_structural_FN) + len(X_genomicFN)
|
||||
, '\nGot:', len(X.columns))
|
||||
sys.exit()
|
||||
|
||||
print('\n#####################################################################\n')
|
||||
|
||||
# ###############################################################################
|
||||
# #==================
|
||||
# # Baseline models
|
||||
# #==================
|
||||
# mm_skf_scoresD = MultModelsCl_dissected(input_df = X
|
||||
# , target = y
|
||||
# , var_type = 'mixed'
|
||||
# , skf_cv = skf_cv
|
||||
# , blind_test_input_df = X_bts
|
||||
# , blind_test_target = y_bts)
|
||||
|
||||
# baseline_all = pd.DataFrame(mm_skf_scoresD)
|
||||
# baseline_all = baseline_all.T
|
||||
# #baseline_train = baseline_all.filter(like='train_', axis=1)
|
||||
# baseline_CT = baseline_all.filter(like='test_', axis=1)
|
||||
# baseline_CT.sort_values(by=['test_mcc'], ascending=False, inplace=True)
|
||||
|
||||
# baseline_BT = baseline_all.filter(like='bts_', axis=1)
|
||||
# baseline_BT.sort_values(by = ['bts_mcc'], ascending = False, inplace = True)
|
||||
|
||||
# # Write csv
|
||||
# baseline_CT.to_csv(outdir_ml + gene.lower() + '_baseline_CT_allF.csv')
|
||||
# baseline_BT.to_csv(outdir_ml + gene.lower() + '_baseline_BT_allF.csv')
|
||||
|
||||
|
||||
# #%% SMOTE NC: Oversampling [Numerical + categorical]
|
||||
# mm_skf_scoresD7 = MultModelsCl(input_df = X_smnc
|
||||
# , target = y_smnc
|
||||
# , var_type = 'mixed'
|
||||
# , skf_cv = skf_cv
|
||||
# , blind_test_input_df = X_bts
|
||||
# , blind_test_target = y_bts)
|
||||
# smnc_all = pd.DataFrame(mm_skf_scoresD7)
|
||||
# smnc_all = smnc_all.T
|
||||
|
||||
# smnc_CT = smnc_all.filter(like='test_', axis=1)
|
||||
# smnc_CT.sort_values(by = ['test_mcc'], ascending = False, inplace = True)
|
||||
|
||||
# smnc_BT = smnc_all.filter(like='bts_', axis=1)
|
||||
# smnc_BT.sort_values(by = ['bts_mcc'], ascending = False, inplace = True)
|
||||
|
||||
# # Write csv
|
||||
# smnc_CT.to_csv(outdir_ml + gene.lower() + '_smnc_CT_allF.csv')
|
||||
# smnc_BT.to_csv(outdir_ml + gene.lower() + '_smnc_BT_allF.csv')
|
||||
|
||||
# #%% ROS: Numerical + categorical
|
||||
# mm_skf_scoresD3 = MultModelsCl(input_df = X_ros
|
||||
# , target = y_ros
|
||||
# , var_type = 'mixed'
|
||||
# , skf_cv = skf_cv
|
||||
# , blind_test_input_df = X_bts
|
||||
# , blind_test_target = y_bts)
|
||||
# ros_all = pd.DataFrame(mm_skf_scoresD3)
|
||||
# ros_all = ros_all.T
|
||||
|
||||
# ros_CT = ros_all.filter(like='test_', axis=1)
|
||||
# ros_CT.sort_values(by = ['test_mcc'], ascending = False, inplace = True)
|
||||
|
||||
# ros_BT = ros_all.filter(like='bts_', axis=1)
|
||||
# ros_BT.sort_values(by = ['bts_mcc'], ascending = False, inplace = True)
|
||||
|
||||
# # Write csv
|
||||
# ros_CT.to_csv(outdir_ml + gene.lower() + '_ros_CT_allF.csv')
|
||||
# ros_BT.to_csv(outdir_ml + gene.lower() + '_ros_BT_allF.csv')
|
||||
|
||||
# #%% RUS: Numerical + categorical
|
||||
# mm_skf_scoresD4 = MultModelsCl(input_df = X_rus
|
||||
# , target = y_rus
|
||||
# , var_type = 'mixed'
|
||||
# , skf_cv = skf_cv
|
||||
# , blind_test_input_df = X_bts
|
||||
# , blind_test_target = y_bts)
|
||||
# rus_all = pd.DataFrame(mm_skf_scoresD4)
|
||||
# rus_all = rus_all.T
|
||||
|
||||
# rus_CT = rus_all.filter(like='test_', axis=1)
|
||||
# rus_CT.sort_values(by = ['test_mcc'], ascending = False, inplace = True)
|
||||
|
||||
# rus_BT = rus_all.filter(like='bts_' , axis=1)
|
||||
# rus_BT.sort_values(by = ['bts_mcc'], ascending = False, inplace = True)
|
||||
|
||||
# # Write csv
|
||||
# rus_CT.to_csv(outdir_ml + gene.lower() + '_rus_CT_allF.csv')
|
||||
# rus_BT.to_csv(outdir_ml + gene.lower() + '_rus_BT_allF.csv')
|
||||
|
||||
# #%% ROS + RUS Combined: Numerical + categorical
|
||||
# mm_skf_scoresD8 = MultModelsCl(input_df = X_rouC
|
||||
# , target = y_rouC
|
||||
# , var_type = 'mixed'
|
||||
# , skf_cv = skf_cv
|
||||
# , blind_test_input_df = X_bts
|
||||
# , blind_test_target = y_bts)
|
||||
# rouC_all = pd.DataFrame(mm_skf_scoresD8)
|
||||
# rouC_all = rouC_all.T
|
||||
|
||||
# rouC_CT = rouC_all.filter(like='test_', axis=1)
|
||||
# rouC_CT.sort_values(by = ['test_mcc'], ascending = False, inplace = True)
|
||||
|
||||
# rouC_BT = rouC_all.filter(like='bts_', axis=1)
|
||||
# rouC_BT.sort_values(by = ['bts_mcc'], ascending = False, inplace = True)
|
||||
|
||||
# # Write csv
|
||||
# rouC_CT.to_csv(outdir_ml + gene.lower() + '_rouC_CT_allF.csv')
|
||||
# rouC_BT.to_csv(outdir_ml + gene.lower() + '_rouC_BT_allF.csv')
|
||||
Loading…
Add table
Add a link
Reference in a new issue