added standard KFold as well
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2 changed files with 128 additions and 61 deletions
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Tanushree Tunstall,tanu,panino.tunstall.in,03.03.2022 11:47,file:///home/tanu/.config/libreoffice/4;
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184
my_datap4.py
184
my_datap4.py
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@ -84,7 +84,13 @@ Y = my_df['resistance']
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#%%
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# GET X
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cols = my_df.columns
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X = my_df[['ligand_distance', 'ligand_affinity_change', 'duet_stability_change', 'ddg_foldx', 'deepddg', 'ddg_dynamut2', 'consurf_score']]
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X = my_df[['ligand_distance'
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, 'ligand_affinity_change'
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, 'duet_stability_change', 'ddg_foldx', 'deepddg', 'ddg_dynamut2', 'consurf_score'
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, 'snap2_score'
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#, 'snap2_accuracy_pc'
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, 'asa'
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, 'rsa']]
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#%%
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####################################
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@ -215,79 +221,141 @@ print(f" There are {len(rf_classifier.feature_importances_)} features in total")
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#%%
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####################################
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# Model 2: case of stratified K-fold
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# Random forest
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# Logistic regression
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# MinMaxScaler
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# https://towardsdatascience.com/stratified-k-fold-what-it-is-how-to-use-it-cf3d107d3ea2
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# https://towardsdatascience.com/stratified-k-fold-what-it-is-how-to-use-it-cf3d107d3ea2 [ Didn't work!]
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# https://www.geeksforgeeks.org/stratified-k-fold-cross-validation/
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####################################
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print('Class Ratio:',
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sum(Y)/len(Y))
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print('Class Ratio:',
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sum(my_df['resistance'])/len(my_df['resistance'])
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)
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sum(my_df['resistance'])/len(my_df['resistance']))
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seed_skf = 50
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skf = StratifiedKFold(n_splits = 10
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, shuffle = True
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, random_state = seed_skf)
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target = my_df.loc[:,'resistance']
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lst_accu_stratified = []
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scaler = preprocessing.MinMaxScaler()
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X_scaled = scaler.fit_transform(X)
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#X_scaled = X_scaled[:,[1,2,3]]
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df = my_df[['ligand_distance'
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, 'ligand_affinity_change'
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, 'duet_stability_change'
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, 'ddg_foldx'
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, 'deepddg'
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, 'ddg_dynamut2'
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, 'consurf_score'
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, 'resistance']]
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# To start with we’ll just split our data and print the class ratio for
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# each fold to check that they are all close to the full data set.
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# Test set contains a single fold so we use the test split to determine the
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# class ratio for each fold. You can see that each fold’s class ratio is close
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# to the full data set which is obviously what we want
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#lr = linear_model.LogisticRegression(class_weight = 'unbalanced')
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lr = linear_model.LogisticRegression()
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fold_no = 1 # to label the folds for printing output
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for train_index, test_index in skf.split(df, target):
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train = df.loc[train_index,:]
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test = df.loc[test_index,:]
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print('Fold',str(fold_no)
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, 'Class Ratio:'
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, sum(test['resistance'])/len(test['resistance']))
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fold_no += 1
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for train_index, test_index in skf.split(X, Y):
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#print(train_index)
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#print(test_index)
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x_train_fold, x_test_fold = X_scaled[train_index], X_scaled[test_index]
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y_train_fold, y_test_fold = Y[train_index], Y[test_index]
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lr.fit(x_train_fold, y_train_fold)
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lst_accu_stratified.append(lr.score(x_test_fold, y_test_fold))
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# print output
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print('List of possible accuracy', lst_accu_stratified)
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print('Max accuracy:', max(lst_accu_stratified)*100, "%")
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print('Min accuracy:', min(lst_accu_stratified)*100, "%")
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print('Mean accuracy:', mean(lst_accu_stratified)*100,"%")
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print('St Dev:', stdev(lst_accu_stratified)*100,"%")
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#%%
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#--------------------------------------
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# Model2.1: same one but with pipeline
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# slightly different results when using
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# transformed or untransformed values!
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#--------------------------------------
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model_logisP = Pipeline(steps = [('preprocess', preprocessing.MinMaxScaler())
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, ('logis', LogisticRegression(class_weight = 'balanced'))
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])
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model = LogisticRegression()
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# Next we’ll build a custom function that we can pass our data splits to for
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# training and testing.
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def train_model(train, test, fold_no):
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X = my_df[['ligand_distance'
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, 'ligand_affinity_change'
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, 'duet_stability_change'
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, 'ddg_foldx'
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, 'deepddg'
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, 'ddg_dynamut2'
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, 'consurf_score']]
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y = my_df.loc[:,'resistance']
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X_train = train[X]
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y_train = train[y]
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X_test = test[X]
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y_test = test[y]
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model.fit(X_train,y_train)
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predictions = model.predict(X_test)
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print('Fold',str(fold_no),
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'Accuracy:',
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accuracy_score(y_test,predictions))
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, ('logis', LogisticRegression(class_weight = 'unbalanced')) ]) # changes stdev
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seed_skf = 50
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skf = StratifiedKFold(n_splits = 10
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, shuffle = True
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, random_state = seed_skf)
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# Finally, let’s modify the for loop we created above to call the build_model
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# function on each of our splits.
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X_array = np.array(X)
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lst_accu_stratified = []
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for train_index, test_index in skf.split(X_array, Y):
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x_train_fold, x_test_fold = X_array[train_index], X_array[test_index]
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y_train_fold, y_test_fold = Y[train_index], Y[test_index]
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model_logisP.fit(x_train_fold, y_train_fold)
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lst_accu_stratified.append(model_logisP.score(x_test_fold, y_test_fold))
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fold_no = 1
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for train_index, test_index in skf.split(df, target):
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train = df.loc[train_index,:]
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test = df.loc[test_index,:]
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train_model(train,test,fold_no)
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fold_no += 1
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# print output
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print('List of possible accuracy', lst_accu_stratified)
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print('Max accuracy:', max(lst_accu_stratified)*100, "%")
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print('Min accuracy:', min(lst_accu_stratified)*100, "%")
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print('Mean accuracy:', mean(lst_accu_stratified)*100,"%")
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print('St Dev:', stdev(lst_accu_stratified)*100,"%")
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####################################
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# Model 3: stratified K-fold
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# Random forest
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# MinMaxScaler
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# X: needs to be an array for str Kfold
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####################################
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model_rf = Pipeline(steps = [('preprocess', preprocessing.MinMaxScaler())
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, ('rf' , RandomForestClassifier(n_estimators=100, random_state=42))])
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seed_skf = 50
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skf = StratifiedKFold(n_splits = 10
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, shuffle = True
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, random_state = seed_skf)
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X_array = np.array(X)
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lst_accu_stratified_rf = []
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for train_index, test_index in skf.split(X_array, Y):
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x_train_fold, x_test_fold = X_array[train_index], X_array[test_index]
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y_train_fold, y_test_fold = Y[train_index], Y[test_index]
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model_rf.fit(x_train_fold, y_train_fold)
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lst_accu_stratified_rf.append(model_rf.score(x_test_fold, y_test_fold))
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# print output
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print('List of possible accuracy', lst_accu_stratified_rf)
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print('Max accuracy:', max(lst_accu_stratified_rf)*100, "%")
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print('Min accuracy:', min(lst_accu_stratified_rf)*100, "%")
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print('Mean accuracy:', mean(lst_accu_stratified_rf)*100,"%")
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print('St Dev:', stdev(lst_accu_stratified_rf)*100,"%")
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####################################
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# Model 4: Cross validate K-fold
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# Random forest
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# MinMaxScaler
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# X: needs to be an array for Kfold
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# FIXME: DOESNT WORK BECAUSE MSE is for LR, not Logistic or random?
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####################################
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from sklearn.metrics import mean_squared_error, make_scorer
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from sklearn.model_selection import cross_validate
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score_fn = make_scorer(mean_squared_error)
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scores = cross_validate(model_rf, X_train, y_train
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, scoring = score_fn
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, cv = 10)
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from itertools import combinations
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def train(X):
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return cross_validate(model_rf, X, y_train
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, scoring = score_fn
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, cv = 10
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, return_estimator = True)['test_score']
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scores = [train(X_train.loc[:,vars]) for vars in combinations(X_train.columns,11)]
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means = [score.mean() for score in scores]
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#%%
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# https://stackoverflow.com/questions/52316237/finding-logistic-regression-weights-from-k-fold-cv
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from sklearn.linear_model import LogisticRegressionCV
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from sklearn.model_selection import KFold
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kf = KFold(n_splits=10, shuffle=True, random_state=42)
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logistic = LogisticRegressionCV(Cs=2, fit_intercept=True, cv=kf, verbose =1, random_state=42)
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logistic.fit(X_train, y_train)
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print("Train Coefficient:" , logistic.coef_) #weights of each feature
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print("Train Intercept:" , logistic.intercept_) #value of intercept
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#%%
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# https://machinelearningmastery.com/repeated-k-fold-cross-validation-with-python/
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from sklearn.model_selection import cross_val_score
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from numpy import std
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cv = KFold(n_splits=10, random_state=1, shuffle=True)
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scores = cross_val_score(model_rf, X,Y, scoring='accuracy', cv=cv, n_jobs=-1)
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scores2 = cross_val_score(model_logisP, X, Y, scoring='accuracy', cv=cv, n_jobs=-1)
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# report performance
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print('Accuracy: %.3f (%.3f)' % (mean(scores), std(scores)))
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print('Accuracy: %.3f (%.3f)' % (mean(scores2), stdev(scores2)))
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