def detailed_analysis(self):
print_to_consol(
'Making a confusion matrix for test set classification outcomes')
matrix_stats = confusion_matrix_and_stats(self.y_test, self.y_pred,
self.directory)
logging.info(f'Detailed analysis of confusion matrix for test set. \n'
f'True positives: {matrix_stats["TP"]} \n'
f'True negatives: {matrix_stats["TN"]} \n'
f'False positives: {matrix_stats["FP"]} \n'
f'False negatives: {matrix_stats["FN"]} \n'
f'Classification accuracy: {matrix_stats["acc"]} \n'
f'Classification error: {matrix_stats["err"]} \n'
f'Sensitivity: {matrix_stats["sensitivity"]} \n'
f'Specificity: {matrix_stats["specificity"]} \n'
f'False positive rate: {matrix_stats["FP-rate"]} \n'
f'False negative rate: {matrix_stats["FN-rate"]} \n'
f'Precision: {matrix_stats["precision"]} \n'
f'F1-score: {matrix_stats["F1-score"]} \n')
print_to_consol(
'Plotting precision recall curve for test set class 1 probabilities'
)
logging.info(
f'Plotting precision recall curve for class 1 in test set probabilities. \n'
)
plot_precision_recall_vs_threshold(self.y_test, self.y_pred_proba_ones,
self.directory)
print_to_consol(
'Plotting ROC curve ad calculating AUC for test set class 1 probabilities'
)
logging.info(
f'Plotting ROC curve for class 1 in test set probabilities. \n')
self.fpr, self.tpr, self.thresholds = plot_roc_curve(
self.y_test, self.y_pred_proba_ones, self.directory)
AUC = round(
roc_auc_score(self.y_test, self.y_pred_proba_ones) * 100, 2)
logging.info(
f'Calculating AUC for ROC curve for class 1 in test set probabilities: {AUC} \n'
)
print_to_consol('Make a radar plot for performance metrics')
radar_dict = {
'Classification accuracy': matrix_stats["acc"],
'Classification error': matrix_stats["err"],
'Sensitivity': matrix_stats["sensitivity"],
'Specificity': matrix_stats["specificity"],
'False positive rate': matrix_stats["FP-rate"],
'False negative rate': matrix_stats["FN-rate"],
'Precision': matrix_stats["precision"],
'F1-score': matrix_stats["F1-score"],
'ROC AUC': AUC
}
plot_radar_chart(radar_dict, self.directory)
print_to_consol(
'Exploring probability thresholds, sensitivity, specificity for class 1'
)
threshold_dict = evaluate_threshold(self.tpr, self.fpr,
self.thresholds)
logging.info(
f'Exploring different probability thresholds and sensitivity-specificity trade-offs. \n'
f'Threshold 0.2: {threshold_dict["0.2"]} \n'
f'Threshold 0.3: {threshold_dict["0.3"]} \n'
f'Threshold 0.4: {threshold_dict["0.4"]} \n'
f'Threshold 0.5: {threshold_dict["0.5"]} \n'
f'Threshold 0.6: {threshold_dict["0.6"]} \n'
f'Threshold 0.7: {threshold_dict["0.7"]} \n'
f'Threshold 0.8: {threshold_dict["0.8"]} \n'
f'Threshold 0.9: {threshold_dict["0.9"]} \n')
end = datetime.now()
duration = end - self.start
logging.info(
f'Prediction and analysis lasted for {duration} minutes \n')
logging.info(f'Prediction and analysis completed \n')
print_to_consol('Prediction and analysis completed')
def detailed_analysis(self):
print_to_consol(
'Making a confusion matrix for test set classification outcomes')
matrix_stats, report = confusion_matrix_and_stats_multiclass(
self.y_test, self.y_pred, 'before_cal', self.directory)
logging.info(f'Detailed analysis of confusion matrix for test set. \n'
f'True positives: {matrix_stats["TP"]} \n'
f'True negatives: {matrix_stats["TN"]} \n'
f'False positives: {matrix_stats["FP"]} \n'
f'False negatives: {matrix_stats["FN"]} \n'
f'Classification accuracy: {matrix_stats["acc"]} \n'
f'Classification error: {matrix_stats["err"]} \n'
f'Sensitivity: {matrix_stats["sensitivity"]} \n'
f'Specificity: {matrix_stats["specificity"]} \n'
f'False positive rate: {matrix_stats["FP-rate"]} \n'
f'False negative rate: {matrix_stats["FN-rate"]} \n'
f'Precision: {matrix_stats["precision"]} \n'
f'F1-score: {matrix_stats["F1-score"]} \n')
logging.info(
f'Classification report on test set before calibration. \n'
f'{report} \n')
print_to_consol('Make a radar plot for performance metrics')
radar_dict = {
'Classification accuracy': matrix_stats["acc"],
'Classification error': matrix_stats["err"],
'Sensitivity': matrix_stats["sensitivity"],
'Specificity': matrix_stats["specificity"],
'False positive rate': matrix_stats["FP-rate"],
'False negative rate': matrix_stats["FN-rate"],
'Precision': matrix_stats["precision"],
'F1-score': matrix_stats["F1-score"],
'ROC AUC': None
}
plot_radar_chart(radar_dict, self.directory)
print_to_consol(
'Calibrating classifier and writing to disk; getting new accuracy')
self.calibrated_clf, clf_acc = calibrate_classifier(
self.model, self.X_cal_scaled, self.y_cal)
date = datetime.strftime(datetime.now(), '%Y%m%d_%H%M')
joblib.dump(
self.calibrated_clf,
os.path.join(self.directory,
'best_calibrated_predictor_' + date + '.pkl'))
logging.info(
f'Calibrated the best classifier with X_cal and y_cal and new accuracy {clf_acc}\n'
f'Writing file to disk disk in {self.directory} \n')
print_to_consol(
'Getting 95% confidence interval for calibrated classifier')
alpha, upper, lower = get_confidence_interval(
self.X_train_scaled, self.y_train, self.X_test_scaled, self.y_test,
self.calibrated_clf, self.directory, self.bootiter, 'calibrated')
logging.info(f'{alpha}% confidence interval {upper}% and {lower}% \n'
f'for calibrated classifier. \n')
print_to_consol('Running prediction for calibrated classifier')
print_to_consol(
'Getting class predictions and probabilities for test set with calibrated classifier'
)
test_stats_cal, self.y_pred_cal, self.y_pred_proba_cal = testing_predict_stats_multiclass(
self.calibrated_clf, self.X_test_scaled, self.y_test)
y_pred_cal_out = os.path.join(self.directory,
"y_pred_after_calibration.csv")
np.savetxt(y_pred_cal_out, self.y_pred_cal, delimiter=",")
y_pred_proba_cal_out = os.path.join(
self.directory, "y_pred_proba_after_calibration.csv")
np.savetxt(y_pred_proba_cal_out, self.y_pred_proba_cal, delimiter=",")
logging.info(
f'Writing y_pred and y_pred_proba after calibration to disk. \n'
f'Predicting on the test set with calibrated classifier. \n'
f'Storing classes for calibrated classifier in y_pred and probabilities in y_pred_proba. \n'
)
print_to_consol(
'Calculate prediction stats for y_pred and y_pred_proba of test set with calibrated classifier'
)
logging.info(
f'Basic stats on the test set woth calibrated classifier. \n'
f'Prediction accuracy on the test set: {test_stats_cal["predict_acc"]} \n'
f'Class distributio in the test set: {test_stats_cal["class_distribution"]} \n'
f'Matthews Correlation Coefficient: {test_stats_cal["mcc"]} \n')
print_to_consol(
'Making a confusion matrix for test set classification outcomes with calibrated classifier'
)
matrix_stats_cal, report_cal = confusion_matrix_and_stats_multiclass(
self.y_test, self.y_pred_cal, 'after_cal', self.directory)
logging.info(
f'Detailed analysis of confusion matrix for test set with calibrated classifier. \n'
f'True positives: {matrix_stats_cal["TP"]} \n'
f'True negatives: {matrix_stats_cal["TN"]} \n'
f'False positives: {matrix_stats_cal["FP"]} \n'
f'False negatives: {matrix_stats_cal["FN"]} \n'
f'Classification accuracy: {matrix_stats_cal["acc"]} \n'
f'Classification error: {matrix_stats_cal["err"]} \n'
f'Sensitivity: {matrix_stats_cal["sensitivity"]} \n'
f'Specificity: {matrix_stats_cal["specificity"]} \n'
f'False positive rate: {matrix_stats_cal["FP-rate"]} \n'
f'False negative rate: {matrix_stats_cal["FN-rate"]} \n'
f'Precision: {matrix_stats_cal["precision"]} \n'
f'F1-score: {matrix_stats_cal["F1-score"]} \n')
logging.info(
f'Classification report on test set afetr callibration. \n'
f'{report_cal} \n')
print_to_consol(
'Make a radar plot for performance metrics with calibrated classifier'
)
radar_dict_cal = {
'Classification accuracy': matrix_stats_cal["acc"],
'Classification error': matrix_stats_cal["err"],
'Sensitivity': matrix_stats_cal["sensitivity"],
'Specificity': matrix_stats_cal["specificity"],
'False positive rate': matrix_stats_cal["FP-rate"],
'False negative rate': matrix_stats_cal["FN-rate"],
'Precision': matrix_stats_cal["precision"],
'F1-score': matrix_stats_cal["F1-score"],
'ROC AUC': None
}
plot_radar_chart(radar_dict_cal, self.directory)
end = datetime.now()
duration = end - self.start
logging.info(f'Training lasted for {duration} minutes \n')
logging.info(f'Training completed \n')
print_to_consol('Training completed')
def detailed_analysis(self):
print_to_consol(
'Making a confusion matrix for test set classification outcomes')
matrix_stats = confusion_matrix_and_stats(self.y_test, self.y_pred,
'before_cal', self.directory)
logging.info(f'Detailed analysis of confusion matrix for test set. \n'
f'True positives: {matrix_stats["TP"]} \n'
f'True negatives: {matrix_stats["TN"]} \n'
f'False positives: {matrix_stats["FP"]} \n'
f'False negatives: {matrix_stats["FN"]} \n'
f'Classification accuracy: {matrix_stats["acc"]} \n'
f'Classification error: {matrix_stats["err"]} \n'
f'Sensitivity: {matrix_stats["sensitivity"]} \n'
f'Specificity: {matrix_stats["specificity"]} \n'
f'False positive rate: {matrix_stats["FP-rate"]} \n'
f'False negative rate: {matrix_stats["FN-rate"]} \n'
f'Precision: {matrix_stats["precision"]} \n'
f'F1-score: {matrix_stats["F1-score"]} \n')
print_to_consol(
'Plotting precision recall curve for test set class 1 probabilities'
)
logging.info(
f'Plotting precision recall curve for class 1 in test set probabilities. \n'
)
plot_precision_recall_vs_threshold(self.y_test, self.y_pred_proba_ones,
self.directory)
print_to_consol(
'Plotting ROC curve ad calculating AUC for test set class 1 probabilities'
)
logging.info(
f'Plotting ROC curve for class 1 in test set probabilities. \n')
self.fpr, self.tpr, self.thresholds = plot_roc_curve(
self.y_test, self.y_pred_proba_ones, self.directory)
AUC = round(
roc_auc_score(self.y_test, self.y_pred_proba_ones) * 100, 2)
logging.info(
f'Calculating AUC for ROC curve for class 1 in test set probabilities: {AUC} \n'
)
print_to_consol('Make a radar plot for performance metrics')
radar_dict = {
'Classification accuracy': matrix_stats["acc"],
'Classification error': matrix_stats["err"],
'Sensitivity': matrix_stats["sensitivity"],
'Specificity': matrix_stats["specificity"],
'False positive rate': matrix_stats["FP-rate"],
'False negative rate': matrix_stats["FN-rate"],
'Precision': matrix_stats["precision"],
'F1-score': matrix_stats["F1-score"],
'ROC AUC': AUC
}
plot_radar_chart(radar_dict, self.directory)
print('*' * 80)
print(
'* Exploring probability thresholds, sensitivity, specificity for class 1 '
)
print('*' * 80)
threshold_dict = evaluate_threshold(self.tpr, self.fpr,
self.thresholds)
logging.info(
f'Exploring different probability thresholds and sensitivity-specificity trade-offs. \n'
f'Threshold 0.2: {threshold_dict["0.2"]} \n'
f'Threshold 0.3: {threshold_dict["0.3"]} \n'
f'Threshold 0.4: {threshold_dict["0.4"]} \n'
f'Threshold 0.5: {threshold_dict["0.5"]} \n'
f'Threshold 0.6: {threshold_dict["0.6"]} \n'
f'Threshold 0.7: {threshold_dict["0.7"]} \n'
f'Threshold 0.8: {threshold_dict["0.8"]} \n'
f'Threshold 0.9: {threshold_dict["0.9"]} \n')
print_to_consol(
'Calibrating classifier and writing to disk; getting new accuracy')
self.calibrated_clf, clf_acc = calibrate_classifier(
self.model, self.X_cal_scaled, self.y_cal)
date = datetime.strftime(datetime.now(), '%Y%m%d_%H%M')
joblib.dump(
self.calibrated_clf,
os.path.join(self.directory,
'best_calibrated_predictor_' + date + '.pkl'))
logging.info(
f'Calibrated the best classifier with X_cal and y_cal and new accuracy {clf_acc}\n'
f'Writing file to disk disk in {self.directory} \n')
print_to_consol(
'Getting 95% confidence interval for calibrated classifier')
alpha, upper, lower = get_confidence_interval(
self.X_train_scaled, self.y_train, self.X_test_scaled, self.y_test,
self.calibrated_clf, self.directory, self.bootiter, 'calibrated')
logging.info(f'{alpha}% confidence interval {upper}% and {lower}% \n'
f'for calibrated classifier. \n')
print_to_consol('Running prediction for calibrated classifier')
print_to_consol(
'Getting class predictions and probabilities for test set with calibrated classifier'
)
test_stats_cal, self.y_pred_cal, self.y_pred_proba_cal = testing_predict_stats(
self.calibrated_clf, self.X_test_scaled, self.y_test)
logging.info(
f'Predicting on the test set with calibrated classifier. \n'
f'Storing classes for calibrated classifier in y_pred and probabilities in y_pred_proba. \n'
)
print_to_consol(
'Calculate prediction stats for y_pred and y_pred_proba of test set with calibrated classifier'
)
logging.info(
f'Basic stats on the test set woth calibrated classifier. \n'
f'Prediction accuracy on the test set: {test_stats_cal["predict_acc"]} \n'
f'Class distributio in the test set: {test_stats_cal["class_distribution"]} \n'
f'Matthews Correlation Coefficient: {test_stats_cal["mcc"]} \n'
f'Average number of class 1 samples: {test_stats_cal["class_one"]} \n'
f'Average number of class 0 samples: {test_stats_cal["class_zero"]} \n'
f'Null accuracy: {test_stats_cal["null_acc"]} \n')
print_to_consol(
'Plotting histogram for class 1 prediction probabilities for test set'
)
#store the predicted probabilities for class 1 of test set
self.y_pred_proba_cal_ones = self.y_pred_proba_cal[:, 1]
plot_hist_pred_proba(self.y_pred_proba_cal_ones, self.directory)
logging.info(
f'Plotting prediction probabilities for class 1 in test set in histogram for calibrated classifier. \n'
)
print_to_consol(
'Making a confusion matrix for test set classification outcomes with calibrated classifier'
)
matrix_stats_cal = confusion_matrix_and_stats(self.y_test,
self.y_pred_cal,
'after_cal',
self.directory)
logging.info(
f'Detailed analysis of confusion matrix for test set with calibrated classifier. \n'
f'True positives: {matrix_stats_cal["TP"]} \n'
f'True negatives: {matrix_stats_cal["TN"]} \n'
f'False positives: {matrix_stats_cal["FP"]} \n'
f'False negatives: {matrix_stats_cal["FN"]} \n'
f'Classification accuracy: {matrix_stats_cal["acc"]} \n'
f'Classification error: {matrix_stats_cal["err"]} \n'
f'Sensitivity: {matrix_stats_cal["sensitivity"]} \n'
f'Specificity: {matrix_stats_cal["specificity"]} \n'
f'False positive rate: {matrix_stats_cal["FP-rate"]} \n'
f'False negative rate: {matrix_stats_cal["FN-rate"]} \n'
f'Precision: {matrix_stats_cal["precision"]} \n'
f'F1-score: {matrix_stats_cal["F1-score"]} \n')
print_to_consol(
'Plotting precision recall curve for test set class 1 probabilities with calibrated classifier'
)
logging.info(
f'Plotting precision recall curve for class 1 in test set probabilities with calibrated classifier. \n'
)
plot_precision_recall_vs_threshold(self.y_test,
self.y_pred_proba_cal_ones,
self.directory)
print_to_consol(
'Plotting ROC curve ad calculating AUC for test set class 1 probabilities with calibrated classifier'
)
logging.info(
f'Plotting ROC curve for class 1 in test set probabilities with calibrated classifier. \n'
)
self.fpr_cal, self.tpr_cal, self.thresholds_cal = plot_roc_curve(
self.y_test, self.y_pred_proba_cal_ones, self.directory)
AUC_cal = round(
roc_auc_score(self.y_test, self.y_pred_proba_cal_ones) * 100, 2)
logging.info(
f'Calculating AUC for ROC curve for class 1 in test set probabilities with calibrated classifier: {AUC_cal} \n'
)
print_to_consol(
'Make a radar plot for performance metrics with calibrated classifier'
)
radar_dict_cal = {
'Classification accuracy': matrix_stats_cal["acc"],
'Classification error': matrix_stats_cal["err"],
'Sensitivity': matrix_stats_cal["sensitivity"],
'Specificity': matrix_stats_cal["specificity"],
'False positive rate': matrix_stats_cal["FP-rate"],
'False negative rate': matrix_stats_cal["FN-rate"],
'Precision': matrix_stats_cal["precision"],
'F1-score': matrix_stats_cal["F1-score"],
'ROC AUC': AUC_cal
}
plot_radar_chart(radar_dict_cal, self.directory)
print_to_consol(
'Exploring probability thresholds, sensitivity, specificity for class 1 with calibrated classifier'
)
threshold_dict_cal = evaluate_threshold(self.tpr_cal, self.fpr_cal,
self.thresholds_cal)
logging.info(
f'Exploring different probability thresholds and sensitivity-specificity trade-offs \n'
f'for calibrated classifier. \n'
f'Threshold 0.2: {threshold_dict_cal["0.2"]} \n'
f'Threshold 0.3: {threshold_dict_cal["0.3"]} \n'
f'Threshold 0.4: {threshold_dict_cal["0.4"]} \n'
f'Threshold 0.5: {threshold_dict_cal["0.5"]} \n'
f'Threshold 0.6: {threshold_dict_cal["0.6"]} \n'
f'Threshold 0.7: {threshold_dict_cal["0.7"]} \n'
f'Threshold 0.8: {threshold_dict_cal["0.8"]} \n'
f'Threshold 0.9: {threshold_dict_cal["0.9"]} \n')
end = datetime.now()
duration = end - self.start
logging.info(f'Training lasted for {duration} minutes \n')
logging.info(f'Training completed \n')
print_to_consol('Training completed')
def detailed_analysis(self):
print('*' * 80)
print(
'* Making a confusion matrix for test set classification outcomes'
)
print('*' * 80)
matrix_stats = confusion_matrix_and_stats(self.y_test, self.y_pred,
self.directory)
logging.info(f'Detailed analysis of confusion matrix for test set. \n'
f'True positives: {matrix_stats["TP"]} \n'
f'True negatives: {matrix_stats["TN"]} \n'
f'False positives: {matrix_stats["FP"]} \n'
f'False negatives: {matrix_stats["FN"]} \n'
f'Classification accuracy: {matrix_stats["acc"]} \n'
f'Classification error: {matrix_stats["err"]} \n'
f'Sensitivity: {matrix_stats["sensitivity"]} \n'
f'Specificity: {matrix_stats["specificity"]} \n'
f'False positive rate: {matrix_stats["FP-rate"]} \n'
f'False negative rate: {matrix_stats["FN-rate"]} \n'
f'Precision: {matrix_stats["precision"]} \n'
f'F1-score: {matrix_stats["F1-score"]} \n')
print('*' * 80)
print(
'* Plotting precision recall curve for test set class 1 probabilities'
)
print('*' * 80)
logging.info(
f'Plotting precision recall curve for class 1 in test set probabilities. \n'
)
plot_precision_recall_vs_threshold(self.y_test, self.y_pred_proba_ones,
self.directory)
print('*' * 80)
print(
'* Plotting ROC curve ad calculating AUC for test set class 1 probabilities'
)
print('*' * 80)
logging.info(
f'Plotting ROC curve for class 1 in test set probabilities. \n')
self.fpr, self.tpr, self.thresholds = plot_roc_curve(
self.y_test, self.y_pred_proba_ones, self.directory)
AUC = round(
roc_auc_score(self.y_test, self.y_pred_proba_ones) * 100, 2)
logging.info(
f'Calculating AUC for ROC curve for class 1 in test set probabilities: {AUC} \n'
)
print('*' * 80)
print('* Make a radar plot for performance metrics')
print('*' * 80)
radar_dict = {
'Classification accuracy': matrix_stats["acc"],
'Classification error': matrix_stats["err"],
'Sensitivity': matrix_stats["sensitivity"],
'Specificity': matrix_stats["specificity"],
'False positive rate': matrix_stats["FP-rate"],
'False negative rate': matrix_stats["FN-rate"],
'Precision': matrix_stats["precision"],
'F1-score': matrix_stats["F1-score"],
'ROC AUC': AUC
}
plot_radar_chart(radar_dict, self.directory)
print('*' * 80)
print(
'* Exploring probability thresholds, sensitivity, specificity for class 1 '
)
print('*' * 80)
threshold_dict = evaluate_threshold(self.tpr, self.fpr,
self.thresholds)
logging.info(
f'Exploring different probability thresholds and sensitivity-specificity trade-offs. \n'
f'Threshold 0.2: {threshold_dict["0.2"]} \n'
f'Threshold 0.3: {threshold_dict["0.3"]} \n'
f'Threshold 0.4: {threshold_dict["0.4"]} \n'
f'Threshold 0.5: {threshold_dict["0.5"]} \n'
f'Threshold 0.6: {threshold_dict["0.6"]} \n'
f'Threshold 0.7: {threshold_dict["0.7"]} \n'
f'Threshold 0.8: {threshold_dict["0.8"]} \n'
f'Threshold 0.9: {threshold_dict["0.9"]} \n')
print('*' * 80)
print(
'* Calibrating classifier and writing to disk; getting new accuracy'
)
print('*' * 80)
self.calibrated_clf, clf_acc = calibrate_classifier(
self.model, self.X_cal, self.y_cal)
date = datetime.strftime(datetime.now(), '%Y%m%d_%H%M')
joblib.dump(
self.calibrated_clf,
os.path.join(self.directory,
'best_calibrated_predictor_' + date + '.pkl'))
logging.info(
f'Calibrated the best classifier with X_cal and y_cal and new accuracy {clf_acc}\n'
f'Writing file to disk disk in {self.directory} \n')
end = datetime.now()
duration = end - self.start
logging.info(f'Training lasted for {duration} minutes \n')
logging.info(f'Training completed \n')
print('*' * 80)
print('* Training completed')
print('*' * 80)
