From f58d20ffc227d9277b65ad9d6834787645de2aaa Mon Sep 17 00:00:00 2001 From: junos Date: Wed, 10 May 2023 23:17:44 +0200 Subject: [PATCH] Update classification runner. --- exploration/ml_pipeline_classification.py | 467 +++------------------- 1 file changed, 54 insertions(+), 413 deletions(-) diff --git a/exploration/ml_pipeline_classification.py b/exploration/ml_pipeline_classification.py index 04087f0..709cdc2 100644 --- a/exploration/ml_pipeline_classification.py +++ b/exploration/ml_pipeline_classification.py @@ -6,7 +6,7 @@ # extension: .py # format_name: percent # format_version: '1.3' -# jupytext_version: 1.13.0 +# jupytext_version: 1.14.5 # kernelspec: # display_name: straw2analysis # language: python @@ -18,445 +18,86 @@ import os import sys -import numpy as np -import matplotlib.pyplot as plt import pandas as pd - -from sklearn import linear_model, svm, naive_bayes, neighbors, tree, ensemble -from sklearn.model_selection import LeaveOneGroupOut, cross_validate, StratifiedKFold -from sklearn.dummy import DummyClassifier -from sklearn.impute import SimpleImputer - -from lightgbm import LGBMClassifier -import xgboost as xg from IPython.core.interactiveshell import InteractiveShell + +from machine_learning.helper import ( + impute_encode_categorical_features, + prepare_cross_validator, + prepare_sklearn_data_format, + run_all_classification_models, +) + 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) - -import machine_learning.helper -# %% [markdown] -# # RAPIDS models -# %% [markdown] -# ## Set script's parameters -# - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} nteract={"transient": {"deleting": false}} -cv_method_str = 'logo' # 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 = False # (bool) If True this will train and test data on balanced dataset (using undersampling method) +# %% +CV_METHOD = "logo" # 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 = False +# (bool) If True this will train and test data on balanced dataset +# (using undersampling method) # %% 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')))] +model_input = pd.read_csv( + "E:/STRAWresults/20230415/daily/input_PANAS_negative_affect_mean.csv" +) +# model_input = +# model_input[model_input.columns.drop( +# list(model_input.filter(regex='empatica_temperature')) +# )] # %% 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() +model_input["target"].value_counts() # %% 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'] -model_input['target'].value_counts(), edges +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'] +model_input["target"].value_counts(), edges # model_input = model_input[model_input['target'] != "medium"] -model_input['target'] = model_input['target'].astype(str).apply(lambda x: 0 if x == "low" else 1) +model_input["target"] = ( + model_input["target"].astype(str).apply(lambda x: 0 if x == "low" else 1) +) -model_input['target'].value_counts() +model_input["target"].value_counts() # %% jupyter={"source_hidden": false, "outputs_hidden": false} # UnderSampling -if undersampling: - no_stress = model_input[model_input['target'] == 0] - stress = model_input[model_input['target'] == 1] - +if UNDERSAMPLING: + 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_new = pd.DataFrame(columns=model_input.columns) -# for pid in model_input["pid"].unique(): -# stress = model_input[(model_input["pid"] == pid) & (model_input['target'] == 1)] -# no_stress = model_input[(model_input["pid"] == pid) & (model_input['target'] == 0)] -# if (len(stress) == 0): -# continue -# if (len(no_stress) == 0): -# continue -# model_input_new = pd.concat([model_input_new, stress], axis=0) - -# no_stress = no_stress.sample(n=min(len(stress), len(no_stress))) -# # In case there are more stress samples than no_stress, take all instances of no_stress. -# model_input_new = pd.concat([model_input_new, no_stress], axis=0) -# model_input = model_input_new -# model_input_new = pd.concat([model_input_new, no_stress], axis=0) + model_input = pd.concat([stress, no_stress], axis=0) # %% 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') - - model_input["pid_index"] = (model_input['pid_index'] / model_input['pid_count'] + 1).round() - model_input["pid_half"] = model_input["pid"] + "_" + model_input["pid_index"].astype(int).astype(str) - - data_x, data_y, data_groups = model_input.drop(["target", "pid", "pid_index", "pid_half"], axis=1), model_input["target"], model_input["pid_half"] -else: - data_x, data_y, data_groups = model_input.drop(["target", "pid"], axis=1), model_input["target"], model_input["pid"] - - -# %% 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 - -categorical_features = data_x[categorical_feature_colnames].copy() -mode_categorical_features = categorical_features.mode().iloc[0] - -# fillna with mode -categorical_features = categorical_features.fillna(mode_categorical_features) - -# one-hot encoding -categorical_features = categorical_features.apply(lambda col: col.astype("category")) -if not categorical_features.empty: - categorical_features = pd.get_dummies(categorical_features) - -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": 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() - cv_method.get_n_splits( - train_x, - data_y, - groups=data_groups, - ) - -# %% 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": false, "outputs_hidden": false} -dummy_classifier = cross_validate( - dummy_class, - X=imputer.fit_transform(train_x), - y=data_y, - groups=data_groups, - cv=cv_method, - n_jobs=-1, - error_score='raise', - scoring=('accuracy', 'precision', 'recall', 'f1') -) -# %% 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'])) -print("Recall", np.mean(dummy_classifier['test_recall'])) -print("F1", np.mean(dummy_classifier['test_f1'])) -print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-dummy_classifier['test_accuracy'], n_sl)[:n_sl])[::-1]) -print(f"Smallest {n_sl} ACC:", np.sort(np.partition(dummy_classifier['test_accuracy'], n_sl)[:n_sl])) - -# %% [markdown] nteract={"transient": {"deleting": false}} -# ### All models - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} nteract={"transient": {"deleting": false}} -final_scores = machine_learning.helper.run_all_classification_models(imputer.fit_transform(train_x), data_y, data_groups, cv_method) - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} nteract={"transient": {"deleting": false}} +model_input_encoded = impute_encode_categorical_features(model_input) # %% -final_scores.index.name = "metric" -final_scores = final_scores.set_index(["method", final_scores.index]) -final_scores.to_csv(f"../presentation/event_stressful_detection_{cv_method_str}.csv") - -# %% [markdown] -# ### Logistic Regression - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -logistic_regression = linear_model.LogisticRegression() - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -log_reg_scores = cross_validate( - logistic_regression, - X=imputer.fit_transform(train_x), - y=data_y, - groups=data_groups, - cv=cv_method, - n_jobs=-1, - scoring=('accuracy', 'precision', 'recall', 'f1') +data_x, data_y, data_groups = prepare_sklearn_data_format( + model_input_encoded, CV_METHOD ) -# %% 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'])) -print("Recall", np.mean(log_reg_scores['test_recall'])) -print("F1", np.mean(log_reg_scores['test_f1'])) -print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-log_reg_scores['test_accuracy'], n_sl)[:n_sl])[::-1]) -print(f"Smallest {n_sl} ACC:", np.sort(np.partition(log_reg_scores['test_accuracy'], n_sl)[:n_sl])) +cross_validator = prepare_cross_validator(data_x, data_y, data_groups, CV_METHOD) -# %% [markdown] -# ### Support Vector Machine +# %% +data_y.head() -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -svc = svm.SVC() - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -svc_scores = cross_validate( - svc, - X=imputer.fit_transform(train_x), - y=data_y, - groups=data_groups, - cv=cv_method, - n_jobs=-1, - scoring=('accuracy', 'precision', 'recall', 'f1') +# %% +data_y.tail() +# %% +data_y.shape +# %% +scores = run_all_classification_models(data_x, data_y, data_groups, cross_validator) +# %% +scores.to_csv( + "../presentation/JCQ_supervisor_support_regression_" + CV_METHOD + ".csv", + index=False, ) -# %% 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'])) -print("Recall", np.mean(svc_scores['test_recall'])) -print("F1", np.mean(svc_scores['test_f1'])) -print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-svc_scores['test_accuracy'], n_sl)[:n_sl])[::-1]) -print(f"Smallest {n_sl} ACC:", np.sort(np.partition(svc_scores['test_accuracy'], n_sl)[:n_sl])) - -# %% [markdown] -# ### Gaussian Naive Bayes - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -gaussian_nb = naive_bayes.GaussianNB() - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -gaussian_nb_scores = cross_validate( - gaussian_nb, - X=imputer.fit_transform(train_x), - y=data_y, - groups=data_groups, - cv=cv_method, - n_jobs=-1, - error_score='raise', - scoring=('accuracy', 'precision', 'recall', 'f1') -) -# %% 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'])) -print("Recall", np.mean(gaussian_nb_scores['test_recall'])) -print("F1", np.mean(gaussian_nb_scores['test_f1'])) -print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-gaussian_nb_scores['test_accuracy'], n_sl)[:n_sl])[::-1]) -print(f"Smallest {n_sl} ACC:", np.sort(np.partition(gaussian_nb_scores['test_accuracy'], n_sl)[:n_sl])) - -# %% [markdown] -# ### Stochastic Gradient Descent Classifier - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -sgdc = linear_model.SGDClassifier() - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -sgdc_scores = cross_validate( - sgdc, - X=imputer.fit_transform(train_x), - y=data_y, - groups=data_groups, - cv=cv_method, - n_jobs=-1, - error_score='raise', - scoring=('accuracy', 'precision', 'recall', 'f1') -) -# %% 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'])) -print("Recall", np.mean(sgdc_scores['test_recall'])) -print("F1", np.mean(sgdc_scores['test_f1'])) -print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-sgdc_scores['test_accuracy'], n_sl)[:n_sl])[::-1]) -print(f"Smallest {n_sl} ACC:", np.sort(np.partition(sgdc_scores['test_accuracy'], n_sl)[:n_sl])) - -# %% [markdown] -# ### K-nearest neighbors - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -knn = neighbors.KNeighborsClassifier() - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -knn_scores = cross_validate( - knn, - X=imputer.fit_transform(train_x), - y=data_y, - groups=data_groups, - cv=cv_method, - n_jobs=-1, - error_score='raise', - scoring=('accuracy', 'precision', 'recall', 'f1') -) -# %% 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'])) -print("Recall", np.mean(knn_scores['test_recall'])) -print("F1", np.mean(knn_scores['test_f1'])) -print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-knn_scores['test_accuracy'], n_sl)[:n_sl])[::-1]) -print(f"Smallest {n_sl} ACC:", np.sort(np.partition(knn_scores['test_accuracy'], n_sl)[:n_sl])) - -# %% [markdown] -# ### Decision Tree - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -dtree = tree.DecisionTreeClassifier() - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -dtree_scores = cross_validate( - dtree, - X=imputer.fit_transform(train_x), - y=data_y, - groups=data_groups, - cv=cv_method, - n_jobs=-1, - error_score='raise', - scoring=('accuracy', 'precision', 'recall', 'f1') -) -# %% 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'])) -print("Recall", np.mean(dtree_scores['test_recall'])) -print("F1", np.mean(dtree_scores['test_f1'])) -print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-dtree_scores['test_accuracy'], n_sl)[:n_sl])[::-1]) -print(f"Smallest {n_sl} ACC:", np.sort(np.partition(dtree_scores['test_accuracy'], n_sl)[:n_sl])) - -# %% [markdown] -# ### Random Forest Classifier - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -rfc = ensemble.RandomForestClassifier() - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -rfc_scores = cross_validate( - rfc, - X=imputer.fit_transform(train_x), - y=data_y, - groups=data_groups, - cv=cv_method, - n_jobs=-1, - error_score='raise', - scoring=('accuracy', 'precision', 'recall', 'f1'), - return_estimator=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'])) -print("Recall", np.mean(rfc_scores['test_recall'])) -print("F1", np.mean(rfc_scores['test_f1'])) -print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-rfc_scores['test_accuracy'], n_sl)[:n_sl])[::-1]) -print(f"Smallest {n_sl} ACC:", np.sort(np.partition(rfc_scores['test_accuracy'], n_sl)[:n_sl])) - -# %% [markdown] -# ### Feature importance (RFC) - -# %% 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_, - index = list(train_x.columns), - columns=['importance']) - # print("\nFeatures sorted by their score for estimator {}:".format(idx)) - # print(feature_importances.sort_values('importance', ascending=False).head(10)) - rfc_es_fimp = pd.concat([rfc_es_fimp, feature_importances]).groupby(level=0).mean() - -pd.set_option('display.max_rows', 100) -print(rfc_es_fimp.sort_values('importance', ascending=False).head(30)) - -rfc_es_fimp.sort_values('importance', ascending=False).head(30).plot.bar() - -rfc_es_fimp.sort_values('importance', ascending=False).tail(30).plot.bar() - -train_x['empatica_temperature_cr_stdDev_X_SO_mean'].value_counts() - -# %% [markdown] -# ### Gradient Boosting Classifier - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -gbc = ensemble.GradientBoostingClassifier() - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -gbc_scores = cross_validate( - gbc, - X=imputer.fit_transform(train_x), - y=data_y, - groups=data_groups, - cv=cv_method, - n_jobs=-1, - error_score='raise', - scoring=('accuracy', 'precision', 'recall', 'f1') -) -# %% 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'])) -print("Recall", np.mean(gbc_scores['test_recall'])) -print("F1", np.mean(gbc_scores['test_f1'])) -print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-gbc_scores['test_accuracy'], n_sl)[:n_sl])[::-1]) -print(f"Smallest {n_sl} ACC:", np.sort(np.partition(gbc_scores['test_accuracy'], n_sl)[:n_sl])) - -# %% [markdown] -# ### LGBM Classifier - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -lgbm = LGBMClassifier() - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -lgbm_scores = cross_validate( - lgbm, - X=imputer.fit_transform(train_x), - y=data_y, - groups=data_groups, - cv=cv_method, - n_jobs=-1, - error_score='raise', - scoring=('accuracy', 'precision', 'recall', 'f1') -) -# %% 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'])) -print("Recall", np.mean(lgbm_scores['test_recall'])) -print("F1", np.mean(lgbm_scores['test_f1'])) -print(f"Largest {n_sl} ACC:", np.sort(-np.partition(-lgbm_scores['test_accuracy'], n_sl)[:n_sl])[::-1]) -print(f"Smallest {n_sl} ACC:", np.sort(np.partition(lgbm_scores['test_accuracy'], n_sl)[:n_sl])) - -# %% [markdown] -# ### XGBoost Classifier - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -xgb_classifier = xg.sklearn.XGBClassifier() - -# %% jupyter={"source_hidden": false, "outputs_hidden": false} -xgb_classifier_scores = cross_validate( - xgb_classifier, - X=imputer.fit_transform(train_x), - y=data_y, - groups=data_groups, - cv=cv_method, - n_jobs=-1, - error_score='raise', - scoring=('accuracy', 'precision', 'recall', 'f1') -) -# %% 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'])) -print("Recall", np.mean(xgb_classifier_scores['test_recall'])) -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])) -