def predict(X_train, X_test, y_train, y_test, k, method_name):
print('Start knn predicting...')
knn = neighbors.KNeighborsClassifier(n_neighbors=k,
weights='distance',
algorithm='auto',
leaf_size=30,
p=2,
metric='minkowski',
metric_params=None,
n_jobs=-1)
knn_ovo = OneVsOneClassifier(knn)
knn_ovo.fit(X_train, y_train.values.ravel())
print('Accuracy score of knn_ovo: ' +
'%.3f' % knn_ovo.score(X_test, y_test))
knn_ovr = OneVsRestClassifier(knn)
knn_ovr.fit(X_train, y_train.values.ravel())
print('Accuracy score of knn_ovr: ' +
'%.3f' % knn_ovr.score(X_test, y_test))
plot.plot_conf_matrix(X_test, y_test, knn_ovr, method_name + '_ovr')
plot.plot_conf_matrix(X_test, y_test, knn_ovo, method_name + '_ovo')
plot.plot_roc(X_train, X_test, y_train, y_test, knn_ovr,
method_name + '_ovr')
def display_scores(self, plot_flag=False):
Scorer.display_scores(self)
# if fprs/tprs is an array, don't print it
if isinstance(self.rows[2][2], np.ndarray):
rows_print = [row[:2] for row in self.rows]
else:
rows_print = self.rows
print(tabulate(rows_print, headers=self.headers, floatfmt=".3f"))
if plot_flag is True:
try:
plot.plot_roc(classes=self.rows_by_classes.keys(),
class_data=self.rows_by_classes,
metric=self.metric)
except:
print("Cannot plot.")
def predict(X_train, X_test, y_train, y_test, method_name):
print('Start SVM predicting...')
svm_ovo = OneVsOneClassifier(SVC(kernel='rbf', probability=True))
svm_ovo.fit(X_train, y_train.values.ravel())
print('Accuracy score of svm_ovo: ' +
'%.3f' % svm_ovo.score(X_test, y_test))
svm_ovr = OneVsRestClassifier(SVC(kernel='rbf', probability=True))
svm_ovr.fit(X_train, y_train.values.ravel())
print('Accuracy score of svm_ovr: ' +
'%.3f' % svm_ovr.score(X_test, y_test))
plot.plot_conf_matrix(X_test, y_test, svm_ovo, method_name + '_ovo')
plot.plot_conf_matrix(X_test, y_test, svm_ovr, method_name + '_ovr')
plot.plot_roc(X_train, X_test, y_train, y_test, svm_ovr,
method_name + '_ovr')
def training(train_ds, val_ds, test_ds, model, EPOCHS):
@tf.function
def train_step(images, labels):
with tf.GradientTape() as tape:
# training=True is only needed if there are layers with different
# behavior during training versus inference (e.g. Dropout).
predictions, feature_map = model(images, training=True)
loss = loss_object(labels, predictions)
gradients = tape.gradient(loss, model.trainable_variables)
optimizer.apply_gradients(zip(gradients, model.trainable_variables))
train_loss(loss)
train_accuracy(labels, predictions)
pred_label = tf.math.argmax(predictions, axis=1)
_ = train_AUC.update_state(labels, pred_label)
# pred_axis0, pred_axis1 = tf.unstack(predictions, axis=1)
# _ = train_ROC.update_state(labels, pred_axis0, pred_axis1)
@tf.function
def val_step(images, labels):
# training=False is only needed if there are layers with different
# behavior during training versus inference (e.g. Dropout).
predictions = model(images, training=False)
v_loss = loss_object(labels, predictions)
val_loss(v_loss)
val_accuracy(labels, predictions)
@tf.function
def test_step(images, labels):
# training=False is only needed if there are layers with different
# behavior during training versus inference (e.g. Dropout).
predictions = model(images, training=False)
t_loss = loss_object(labels, predictions)
test_loss(t_loss)
test_accuracy(labels, predictions)
pred_label = tf.math.argmax(predictions, axis=1)
_ = test_AUC.update_state(labels, pred_label)
# _ = test_ROC.update_state(labels, predictions)
loss_object = tf.keras.losses.SparseCategoricalCrossentropy(from_logits=False)
optimizer = tf.keras.optimizers.Adam()
ckpt = tf.train.Checkpoint(step=tf.Variable(1), optimizer=optimizer, model=model)
manager = tf.train.CheckpointManager(ckpt, './tf_ckpts', max_to_keep=3)
train_loss = tf.keras.metrics.Mean(name='train_loss')
train_accuracy = tf.keras.metrics.SparseCategoricalAccuracy(name='train_accuracy')
train_AUC = tf.keras.metrics.AUC(
num_thresholds=200, curve='ROC', summation_method='interpolation')
train_ROC = ROC()
num_class = 2
# train_CM = C_M(num_class)
val_loss = tf.keras.metrics.Mean(name='val_loss')
val_accuracy = tf.keras.metrics.SparseCategoricalAccuracy(name='val_accuracy')
test_loss = tf.keras.metrics.Mean(name='test_loss')
test_accuracy = tf.keras.metrics.SparseCategoricalAccuracy(name='test_accuracy')
test_AUC = tf.keras.metrics.AUC(
num_thresholds=200, curve='ROC', summation_method='interpolation')
test_ROC = ROC()
# test_CM = C_M(num_class)
# EPOCHS = 10
current_time = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
train_log_dir = 'logs/gradient_tape/' + current_time + '/train'
test_log_dir = 'logs/gradient_tape/' + current_time + '/test'
val_log_dir = 'logs/gradient_tape/' + current_time + '/val'
ROC_log_dir = 'logs/gradient_tape/' + current_time + '/ROC'
train_summary_writer = tf.summary.create_file_writer(train_log_dir)
test_summary_writer = tf.summary.create_file_writer(test_log_dir)
validation_summary_writer = tf.summary.create_file_writer(val_log_dir)
ROC_summary_writer = tf.summary.create_file_writer(ROC_log_dir)
ckpt.restore(manager.latest_checkpoint)
if manager.latest_checkpoint:
print("Restored from {}".format(manager.latest_checkpoint))
else:
print("Initializing from scratch.")
for epoch in range(EPOCHS):
train_loss.reset_states()
train_accuracy.reset_states()
train_AUC.reset_states()
# train_CM.reset_states()
train_ROC.reset_states()
test_loss.reset_states()
test_accuracy.reset_states()
test_AUC.reset_states()
test_ROC.reset_states()
# test_CM.reset_states()
val_loss.reset_states()
val_accuracy.reset_states()
for sample in train_ds:
size_shape = tf.random.uniform([], minval=200, maxval=256)
train_img = sample[0]
train_label = sample[2]
train_img, train_label = augment(train_img, train_label, size_shape)
train_step(train_img, train_label)
predictions = model(train_img, training=True)
label_pred = tf.math.argmax(predictions, axis=1)
_ = train_ROC.update_state(train_label, predictions)
# _ = train_CM.update_state(train_label,label_pred)
ckpt.step.assign_add(1)
if int(ckpt.step) % 2 == 0:
save_path = manager.save()
print("Saved checkpoint for step {}: {}".format(int(ckpt.step), save_path))
print(manager.checkpoints)
# 画ROC的图并保存
fp, tp = train_ROC.result()
plot_roc('ROC_train', fp, tp) # create figure & 1 axis
plt.savefig('ROC_train_img.png') # save the figure to file
plt.show()
fig = mpimg.imread('ROC_train_img.png')
fig = tf.expand_dims(fig, 0)
with train_summary_writer.as_default():
tf.summary.scalar('train_loss', train_loss.result(), step=epoch)
tf.summary.scalar('train_accuracy', train_accuracy.result(), step=epoch)
tf.summary.scalar('AUC_train', train_AUC.result(), step=epoch)
tf.summary.image("ROC_train", fig, step=epoch)
# tf.summary.image('Confusion Matrix train', fig_CM, step=epoch)
for sample in val_ds:
val_img = sample[0]
val_label = sample[2]
val_step(val_img, val_label)
with validation_summary_writer.as_default():
tf.summary.scalar('val_loss', val_loss.result(), step=epoch)
tf.summary.scalar('val_accuracy', val_accuracy.result(), step=epoch)
template = 'Epoch {}, Loss: {}, Accuracy: {}, Val Loss: {}, Val Accuracy: {}'
print(template.format(epoch + 1,
train_loss.result(),
train_accuracy.result() * 100,
val_loss.result(),
val_accuracy.result() * 100))
train_loss.result(),
train_accuracy.result() * 100,
val_loss.result(),
val_accuracy.result() * 100))
for sample in test_ds:
test_img = sample[0]
test_label = sample[2]
test_step(test_img, test_label)
predictions = model(test_img, training=True)
label_pred = tf.math.argmax(predictions, axis=1)
_ = test_ROC.update_state(test_label, predictions)
# _ = test_CM.update_state(test_label,label_pred)
# 画ROC的图并保存
fp, tp = test_ROC.result()
plot_roc('ROC_test', fp, tp) # create figure & 1 axis
plt.savefig('ROC_test_img.png') # save the figure to file
plt.show()
fig = mpimg.imread('ROC_test_img.png')
fig = tf.expand_dims(fig, 0)
with test_summary_writer.as_default():
tf.summary.scalar('test_loss', test_loss.result(), step=0)
tf.summary.scalar('test_accuracy', test_accuracy.result(), step=0)
tf.summary.scalar('AUC_test', train_AUC.result(), step=0)
tf.summary.image("ROC_train", fig, step=0)
# tf.summary.image('Confusion Matrix test', fig_CM, step=0)
template = 'Test Loss: {}, Test Accuracy: {}'
print(template.format(test_loss.result(),
test_accuracy.result() * 100))
print("max_specificity:", max_specificity)
#FINAL TESTING
k_best_features = 4
datasetX = do_feature_selection(X, y, k_best_features)
X_train, X_test, y_train, y_test = train_test_split(datasetX,
y,
test_size=0.2,
random_state=1,
shuffle=False)
X_train, X_val, y_train, y_val = train_test_split(X_train,
y_train,
test_size=0.25,
random_state=1,
shuffle=False)
X_train_final = np.concatenate((X_train, X_test), axis=0)
y_train_final = np.concatenate((y_train, y_test), axis=0)
dtree = train_DecisionTree(X_train_final, y_train_final)
y_pred = predict_testdata(dtree, X_val)
evaluation_metric = EvaluationMetric()
# confusion_matrix = confusion_matrix(y_test.values, y_pred)
result = evaluation_metric.get_evaluation_metrics(y_val.values, y_pred)
print(result)
probs = dtree.predict_proba(X_val)
probs = probs[:, 1]
plot_roc(y_val.values, probs)
plot_precision_recall(y_val.values, y_pred, probs)
# please provide the path to your training and testing datasets
training = pd.read_csv("...")
test = pd.read_csv("....")
complications = ['SBI', 'AKI', 'ARDS']
framework_train = apply_stratified_framework(training, complications)
framework_test = apply_stratified_framework(test, complications)
train_columns = [
'Diastolic Blood Pressure_mean', 'Diastolic Blood Pressure_min',
'Oxygen Saturation_max', 'Oxygen Saturation_mean', 'Oxygen Saturation_min',
'Peripheral Pulse Rate_max', 'Peripheral Pulse Rate_mean',
'Peripheral Pulse Rate_min', 'Respiratory Rate_max',
'Respiratory Rate_mean', 'Respiratory Rate_min',
'Systolic Blood Pressure_max', 'Systolic Blood Pressure_mean',
'Systolic Blood Pressure_min', 'Temperature Axillary_max',
'Temperature Axillary_mean', 'Temperature Axillary_min', 'GCS_mean',
'GCS_min', 'GCS_max', 'GENDER', 'AGE', 'COUGH', 'FEVER', 'SOB',
'SORE_THROAT', 'RASH', 'BMI', 'DIABETES', 'HYPERTENSION', 'CKD', 'CANCER'
]
models_all, trainsets, classifers = get_models(complications, framework_train,
train_columns)
true_ouctomes, predicted_ouctomes = get_results(framework_test, complications,
models_all, train_columns)
plot_roc(complications, true_ouctomes, predicted_ouctomes, "testset")
plot_PRC(complications, true_ouctomes, predicted_ouctomes, "testset")
# plt.scatter(x_train[:,0].tolist(), y_train.tolist())
# plt.show()
# plt.scatter(x_train[:, 1].tolist(), y_train.tolist())
# plt.show()
# plt.scatter(x_train[:, 2].tolist(), y_train.tolist())
# plt.show()
# plt.scatter(x_train[:, 3].tolist(), y_train.tolist())
# plt.show()
# plt.scatter(x_train[:, 4].tolist(), y_train.tolist())
# plt.show()
# plt.scatter(x_train[:, 5].tolist(), y_train.tolist())
# plt.show()
precision, recall, F1, _ = precision_recall_fscore_support(
y_test, y_test_predict)
print(precision, recall, F1)
plot.plot_roc(x_train, x_test, y_train, y_test)
#绘制混淆矩阵
obj1 = confusion_matrix(y_test, y_test_predict)
print('confusion_matrix\n', obj1)
classes = list(set(y_test_predict))
classes.sort()
plt.figure(figsize=(12, 8), dpi=100)
plt.imshow(obj1, cmap=plt.cm.Blues)
indices = range(len(obj1))
plt.xticks(indices, classes)
plt.yticks(indices, classes)
plt.colorbar()
plt.xlabel('label of test set sample')
plt.ylabel('label of predict')
plt.title('Confusion Matrix', fontsize='10', fontproperties='arial')
test_size=0.3,
random_state=56)
df_train = df_notnull.loc[train_idx]
features_train = features.loc[train_idx]
target_train = target.loc[train_idx]
df_test = df_notnull.loc[test_idx]
features_test = features.loc[test_idx]
target_test = target.loc[test_idx]
#%% train logistic classifier
classifier = LogisticRegression()
classifier.fit(features_train, target_train)
#%% score on train
scores_train = classifier.predict_proba(features_train)[:, 1]
(tp_train, fp_train, tsh) = plot_roc(target_train, scores_train)
#%% score on test
scores_test = classifier.predict_proba(features_test)[:, 1]
(tp_test, fp_test, tsh) = plot_roc(target_test, scores_test)
#%% plot treshold values
pd.DataFrame(nested_to_list(zip(tsh, tp_test, fp_test, fp_test - tp_test)),
columns=[
'Threshold', 'True Positive Rate', 'False Positive Rate',
'Difference'
]).plot(x='Threshold')
plt.xlim(0, 0.4)
plt.ylim([0, 1])
plt.grid()
plt.show()
try:
os.mkdir('plots')
except OSError as error:
print(error)
# please provide the path to your training and testing datasets
training = pd.read_csv("...")
test = pd.read_csv("....")
complications = [
'Elevated_troponin', 'Elevated_d-dimer', 'Elevated_Amino', 'Elevated_IL6',
'SBI', 'AKI', 'ARDS'
]
framework_train = apply_stratified_framework(training, complications)
framework_test = apply_stratified_framework(test, complications)
targets = get_targets(complications)
train_columns = [x for x in training.columns if x not in targets]
models_all, trainsets, classifers = get_models(complications, framework_train,
train_columns)
true_ouctomes, predicted_ouctomes = get_results(framework_test, complications,
models_all, train_columns)
plot_roc(complications, true_ouctomes, predicted_ouctomes)
plot_PRC(complications, true_ouctomes, predicted_ouctomes)
