diff --git a/exploration/ml_pipeline_classification.py b/exploration/ml_pipeline_classification.py index 0b5dc15..53607ad 100644 --- a/exploration/ml_pipeline_classification.py +++ b/exploration/ml_pipeline_classification.py @@ -13,7 +13,7 @@ # name: straw2analysis # --- -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} # %matplotlib inline import os import sys @@ -35,26 +35,29 @@ InteractiveShell.ast_node_interactivity = "all" nb_dir = os.path.split(os.getcwd())[0] if nb_dir not in sys.path: sys.path.append(nb_dir) - + # %% [markdown] # # RAPIDS models # %% [markdown] # ## Set script's parameters +# + +# %% jupyter={"source_hidden": false, "outputs_hidden": false} nteract={"transient": {"deleting": false}} cv_method_str = '5kfold' # logo, half_logo, 5kfold # Cross-validation method (could be regarded as a hyperparameter) n_sl = 3 # Number of largest/smallest accuracies (of particular CV) outputs undersampling = True # (bool) If True this will train and test data on balanced dataset (using undersampling method) -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} model_input = pd.read_csv("../data/stressfulness_event_with_target_0_ver2/input_appraisal_stressfulness_event_mean.csv") # model_input = model_input[model_input.columns.drop(list(model_input.filter(regex='empatica_temperature')))] -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} index_columns = ["local_segment", "local_segment_label", "local_segment_start_datetime", "local_segment_end_datetime"] model_input.set_index(index_columns, inplace=True) model_input['target'].value_counts() -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} # bins = [-10, 0, 10] # bins for z-scored targets bins = [-1, 0, 4] # bins for stressfulness (0-4) target model_input['target'], edges = pd.cut(model_input.target, bins=bins, labels=['low', 'high'], retbins=True, right=True) #['low', 'medium', 'high'] @@ -64,20 +67,20 @@ model_input['target'] = model_input['target'].astype(str).apply(lambda x: 0 if x model_input['target'].value_counts() -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} # UnderSampling if undersampling: model_input.groupby("pid").count() no_stress = model_input[model_input['target'] == 0] stress = model_input[model_input['target'] == 1] - + no_stress = no_stress.sample(n=len(stress)) model_input = pd.concat([stress,no_stress], axis=0) - + model_input["target"].value_counts() -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} if cv_method_str == 'half_logo': model_input['pid_index'] = model_input.groupby('pid').cumcount() model_input['pid_count'] = model_input.groupby('pid')['pid'].transform('count') @@ -90,7 +93,7 @@ else: data_x, data_y, data_groups = model_input.drop(["target", "pid"], axis=1), model_input["target"], model_input["pid"] -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} categorical_feature_colnames = ["gender", "startlanguage"] additional_categorical_features = [col for col in data_x.columns if "mostcommonactivity" in col or "homelabel" in col] categorical_feature_colnames += additional_categorical_features @@ -110,7 +113,7 @@ numerical_features = data_x.drop(categorical_feature_colnames, axis=1) train_x = pd.concat([numerical_features, categorical_features], axis=1) train_x.dtypes -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} cv_method = StratifiedKFold(n_splits=5, shuffle=True) # Defaults to 5 k-folds in cross_validate method if cv_method_str == 'logo' or cv_method_str == 'half_logo': cv_method = LeaveOneGroupOut() @@ -120,14 +123,16 @@ if cv_method_str == 'logo' or cv_method_str == 'half_logo': groups=data_groups, ) -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} imputer = SimpleImputer(missing_values=np.nan, strategy='median') # %% [markdown] # ### Baseline: Dummy Classifier (most frequent) + +# %% jupyter={"source_hidden": false, "outputs_hidden": false} nteract={"transient": {"deleting": false}} dummy_class = DummyClassifier(strategy="most_frequent") -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} dummy_classifier = cross_validate( dummy_class, X=imputer.fit_transform(train_x), @@ -138,7 +143,7 @@ dummy_classifier = cross_validate( error_score='raise', scoring=('accuracy', 'precision', 'recall', 'f1') ) -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} print("Acc (median)", np.nanmedian(dummy_classifier['test_accuracy'])) print("Acc (mean)", np.mean(dummy_classifier['test_accuracy'])) print("Precision", np.mean(dummy_classifier['test_precision'])) @@ -150,10 +155,10 @@ print(f"Smallest {n_sl} ACC:", np.sort(np.partition(dummy_classifier['test_accur # %% [markdown] # ### Logistic Regression -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} logistic_regression = linear_model.LogisticRegression() -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} log_reg_scores = cross_validate( logistic_regression, X=imputer.fit_transform(train_x), @@ -163,7 +168,7 @@ log_reg_scores = cross_validate( n_jobs=-1, scoring=('accuracy', 'precision', 'recall', 'f1') ) -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} print("Acc (median)", np.nanmedian(log_reg_scores['test_accuracy'])) print("Acc (mean)", np.mean(log_reg_scores['test_accuracy'])) print("Precision", np.mean(log_reg_scores['test_precision'])) @@ -175,10 +180,10 @@ print(f"Smallest {n_sl} ACC:", np.sort(np.partition(log_reg_scores['test_accurac # %% [markdown] # ### Support Vector Machine -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} svc = svm.SVC() -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} svc_scores = cross_validate( svc, X=imputer.fit_transform(train_x), @@ -188,7 +193,7 @@ svc_scores = cross_validate( n_jobs=-1, scoring=('accuracy', 'precision', 'recall', 'f1') ) -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} print("Acc (median)", np.nanmedian(svc_scores['test_accuracy'])) print("Acc (mean)", np.mean(svc_scores['test_accuracy'])) print("Precision", np.mean(svc_scores['test_precision'])) @@ -200,10 +205,10 @@ print(f"Smallest {n_sl} ACC:", np.sort(np.partition(svc_scores['test_accuracy'], # %% [markdown] # ### Gaussian Naive Bayes -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} gaussian_nb = naive_bayes.GaussianNB() -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} gaussian_nb_scores = cross_validate( gaussian_nb, X=imputer.fit_transform(train_x), @@ -214,7 +219,7 @@ gaussian_nb_scores = cross_validate( error_score='raise', scoring=('accuracy', 'precision', 'recall', 'f1') ) -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} print("Acc (median)", np.nanmedian(gaussian_nb_scores['test_accuracy'])) print("Acc (mean)", np.mean(gaussian_nb_scores['test_accuracy'])) print("Precision", np.mean(gaussian_nb_scores['test_precision'])) @@ -226,10 +231,10 @@ print(f"Smallest {n_sl} ACC:", np.sort(np.partition(gaussian_nb_scores['test_acc # %% [markdown] # ### Stochastic Gradient Descent Classifier -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} sgdc = linear_model.SGDClassifier() -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} sgdc_scores = cross_validate( sgdc, X=imputer.fit_transform(train_x), @@ -240,7 +245,7 @@ sgdc_scores = cross_validate( error_score='raise', scoring=('accuracy', 'precision', 'recall', 'f1') ) -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} print("Acc (median)", np.nanmedian(sgdc_scores['test_accuracy'])) print("Acc (mean)", np.mean(sgdc_scores['test_accuracy'])) print("Precision", np.mean(sgdc_scores['test_precision'])) @@ -252,10 +257,10 @@ print(f"Smallest {n_sl} ACC:", np.sort(np.partition(sgdc_scores['test_accuracy'] # %% [markdown] # ### K-nearest neighbors -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} knn = neighbors.KNeighborsClassifier() -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} knn_scores = cross_validate( knn, X=imputer.fit_transform(train_x), @@ -266,7 +271,7 @@ knn_scores = cross_validate( error_score='raise', scoring=('accuracy', 'precision', 'recall', 'f1') ) -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} print("Acc (median)", np.nanmedian(knn_scores['test_accuracy'])) print("Acc (mean)", np.mean(knn_scores['test_accuracy'])) print("Precision", np.mean(knn_scores['test_precision'])) @@ -278,10 +283,10 @@ print(f"Smallest {n_sl} ACC:", np.sort(np.partition(knn_scores['test_accuracy'], # %% [markdown] # ### Decision Tree -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} dtree = tree.DecisionTreeClassifier() -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} dtree_scores = cross_validate( dtree, X=imputer.fit_transform(train_x), @@ -292,7 +297,7 @@ dtree_scores = cross_validate( error_score='raise', scoring=('accuracy', 'precision', 'recall', 'f1') ) -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} print("Acc (median)", np.nanmedian(dtree_scores['test_accuracy'])) print("Acc (mean)", np.mean(dtree_scores['test_accuracy'])) print("Precision", np.mean(dtree_scores['test_precision'])) @@ -304,10 +309,10 @@ print(f"Smallest {n_sl} ACC:", np.sort(np.partition(dtree_scores['test_accuracy' # %% [markdown] # ### Random Forest Classifier -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} rfc = ensemble.RandomForestClassifier() -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} rfc_scores = cross_validate( rfc, X=imputer.fit_transform(train_x), @@ -319,7 +324,7 @@ rfc_scores = cross_validate( scoring=('accuracy', 'precision', 'recall', 'f1'), return_estimator=True ) -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} print("Acc (median)", np.nanmedian(rfc_scores['test_accuracy'])) print("Acc (mean)", np.mean(rfc_scores['test_accuracy'])) print("Precision", np.mean(rfc_scores['test_precision'])) @@ -331,7 +336,7 @@ print(f"Smallest {n_sl} ACC:", np.sort(np.partition(rfc_scores['test_accuracy'], # %% [markdown] # ### Feature importance (RFC) -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} rfc_es_fimp = pd.DataFrame(columns=list(train_x.columns)) for idx, estimator in enumerate(rfc_scores['estimator']): feature_importances = pd.DataFrame(estimator.feature_importances_, @@ -353,10 +358,10 @@ train_x['empatica_temperature_cr_stdDev_X_SO_mean'].value_counts() # %% [markdown] # ### Gradient Boosting Classifier -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} gbc = ensemble.GradientBoostingClassifier() -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} gbc_scores = cross_validate( gbc, X=imputer.fit_transform(train_x), @@ -367,7 +372,7 @@ gbc_scores = cross_validate( error_score='raise', scoring=('accuracy', 'precision', 'recall', 'f1') ) -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} print("Acc (median)", np.nanmedian(gbc_scores['test_accuracy'])) print("Acc (mean)", np.mean(gbc_scores['test_accuracy'])) print("Precision", np.mean(gbc_scores['test_precision'])) @@ -379,10 +384,10 @@ print(f"Smallest {n_sl} ACC:", np.sort(np.partition(gbc_scores['test_accuracy'], # %% [markdown] # ### LGBM Classifier -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} lgbm = LGBMClassifier() -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} lgbm_scores = cross_validate( lgbm, X=imputer.fit_transform(train_x), @@ -393,7 +398,7 @@ lgbm_scores = cross_validate( error_score='raise', scoring=('accuracy', 'precision', 'recall', 'f1') ) -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} print("Acc (median)", np.nanmedian(lgbm_scores['test_accuracy'])) print("Acc (mean)", np.mean(lgbm_scores['test_accuracy'])) print("Precision", np.mean(lgbm_scores['test_precision'])) @@ -405,10 +410,10 @@ print(f"Smallest {n_sl} ACC:", np.sort(np.partition(lgbm_scores['test_accuracy'] # %% [markdown] # ### XGBoost Classifier -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} xgb_classifier = xg.sklearn.XGBClassifier() -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} xgb_classifier_scores = cross_validate( xgb_classifier, X=imputer.fit_transform(train_x), @@ -419,7 +424,7 @@ xgb_classifier_scores = cross_validate( error_score='raise', scoring=('accuracy', 'precision', 'recall', 'f1') ) -# %% jupyter={"source_hidden": true} +# %% jupyter={"source_hidden": false, "outputs_hidden": false} print("Acc (median)", np.nanmedian(xgb_classifier_scores['test_accuracy'])) print("Acc (mean)", np.mean(xgb_classifier_scores['test_accuracy'])) print("Precision", np.mean(xgb_classifier_scores['test_precision'])) @@ -428,4 +433,4 @@ print("F1", np.mean(xgb_classifier_scores['test_f1'])) print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-xgb_classifier_scores['test_accuracy'], n_sl)[:n_sl])[::-1]) print(f"Smallest {n_sl} ACC:", np.sort(np.partition(xgb_classifier_scores['test_accuracy'], n_sl)[:n_sl])) -# %% +# %% jupyter={"outputs_hidden": false, "source_hidden": false}