def main(_):
config = flags.FLAGS
if config.mode == "train":
train(config)
elif config.mode == "data":
train_test_split(config)
elif config.mode == "sn":
test_spectral_norm()
elif config.mode == "trace":
test_trace_approximation()
def main():
data = datasets.load_digits()
X = normalize(data.data)
y = data.target
# convert the nominal y values to binary
y = to_categorical(y)
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.4)
#mlp
clf = MultilayerPerceptron(n_hidden=16,
n_iterations=1000,
learning_rate=0.01)
clf.fit(X_train, y_train)
y_pred = np.argmax(clf.predict(X_test), axis=1)
y_test = np.argmax(y_test, axis=1)
accuracy = accuracy_score(y_test, y_pred)
print("Accuracy:", accuracy)
# Reduce dimension to two using PCA and plot the results
Plot().plot_in_2d(X_test,
y_pred,
title="Multilayer Perceptron",
accuracy=accuracy,
legend_labels=np.unique(y))
def main():
@run_time
def batch():
print("Tesing the accuracy of LogisticRegression(batch)...")
# Train model
clf = LogisticRegression()
clf.fit(X=X_train, y=y_train, lr=0.008, epochs=5000)
# Model accuracy
get_acc(clf, X_test, y_test)
@run_time
def stochastic():
print("Tesing the accuracy of LogisticRegression(stochastic)...")
# Train model
clf = LogisticRegression()
clf.fit(X=X_train, y=y_train, lr=0.01, epochs=200,
method="stochastic", sample_rate=0.5)
# Model accuracy
get_acc(clf, X_test, y_test)
# Load data
X, y = load_breast_cancer()
X = min_max_scale(X)
# Split data randomly, train set rate 70%
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=10)
batch()
stochastic()
def __init__(self):
'''
Initialize and load dataset
'''
# Get all stop words
self.stop_words = set(stopwords.words('english'))
# Lemmatizer
self.lemmatizer = WordNetLemmatizer()
# stemmer
self.stemmer = PorterStemmer()
# Tokenizer
self.tokenizer = RegexpTokenizer(r'\w+')
# Load data
self.load_data()
X_train, y_train, X_test, y_test = train_test_split(self.X, self.y)
# Train model
self.train(X_train, y_train)
# Evaluate
accuracy, f1measure = self.evaulate(X_test, y_test)
print('Accuracy: {:.3f}, F1-score: {:.3f}'.format(accuracy, f1measure))
def main():
data = datasets.load_digits()
X = normalize(data.data)
y = data.target
# One-hot encoding of nominal y-values
y = to_categorical(y)
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=0.33,
seed=8)
# Perceptron
clf = Perceptron(n_iterations=5000,
learning_rate=0.001,
loss=CrossEntropy,
activation_function=Sigmoid)
clf.fit(X_train, y_train)
y_pred = np.argmax(clf.predict(X_test), axis=1)
y_test = np.argmax(y_test, axis=1)
accuracy = accuracy_score(y_test, y_pred)
print("Accuracy:", accuracy)
# Reduce dimension to two using PCA and plot the results
Plot().plot_in_2d(X_test,
y_pred,
title="Perceptron",
accuracy=accuracy,
legend_labels=np.unique(y))
def fit(self, X, z, split_size):
"""Searches for the optimal hyperparameter combination."""
# model and params are now lists --> sende med navn istedenfor.
# Setup
self.results = {self.name: []}
self.train_scores_mse, self.test_scores_mse = [], []
self.train_scores_r2, self.test_scores_r2 = [], []
# Splitting our original dataset into test and train.
X_train, X_test, z_train, z_test = train_test_split(
X, z, split_size=split_size, random_state=105)
" Returning these dictionaries to plot mse vs model"
self.mse_test = []
self.mse_train = []
self.r2_test = []
self.r2_train = []
self.z_pred = []
self.coef_ = []
# For en model tester vi alle parameterne og returnerer denne.
for param in self.params:
estimator = self.model(lmd=param)
# Train a model for this pair of lambda and random state
estimator.fit(X_train, z_train)
temp = estimator.predict(X_test)
temp2 = estimator.predict(X_train)
self.mse_test.append(mean_squared_error(z_test, temp))
self.mse_train.append(mean_squared_error(z_train, temp2))
self.r2_test.append(r2_score(z_test, temp))
self.r2_train.append(r2_score(z_train, temp2))
self.z_pred.append(temp)
self.coef_.append(estimator.coef_)
return self
def main():
X, y = make_regression(n_samples=100, n_features=1, noise=20)
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.4)
n_samples, n_features = np.shape(X)
model = LinearRegression(n_iterations=100)
model.fit(X_train, y_train)
#training error plot
n = len(model.training_errors)
training,=plt.plot(range(n),model.training_errors, label="training error")
plt.legend(handles=[training])
plt.title("Error Plot")
plt.ylabel("Mean Squared Error")
plt.xlabel("Iterations")
plt.show()
y_pred = model.predict(X_test)
mse = mean_squared_error(y_test, y_pred)
print("Mean squared error: %s"%mse)
y_pred_line = model.predict(X)
#color map
cmap = plt.get_cmap("viridis")
#plot the results
m1 = plt.scatter(366 * X_train, y_train, color=cmap(0.9),s = 10)
m2 = plt.scatter(366 * X_test, y_test, color=cmap(0.5), s=10)
plt.plot(366*X, y_pred_line, color="black", linewidth=2, label="Prediction")
plt.suptitle("Linear Regression")
plt.title("MSE: %.2f"% mse, fontsize=10)
plt.xlabel("Day")
plt.ylabel("Temperature in Celcius")
plt.legend((m1, m2),("Training data", "Test data"), loc="lower right")
plt.show()
def load_data(feature_dict_path, df, test_fold, n_folds):
def _comb_features(base_f, other_f):
return np.concatenate([
base_f,
other_f,
np.square(base_f - other_f),
[spearmanr(base_f, other_f)[0]],
# [np.square(base_f - other_f).sum()],
# [pearsonr(base_f, other_f)[0]],
])
def _get_features(_df, feature_dict):
features = []
y = []
for _, row in _df.iterrows():
datasetId, baseSf, baseAdduct, otherSf, otherAdduct, rank = row
base_ion = '.'.join((baseSf, baseAdduct.replace('+', 'p').replace('-', 'm')))
other_ion = '.'.join((otherSf, otherAdduct.replace('+', 'p').replace('-', 'm')))
base_img = '.'.join((datasetId, base_ion))
other_img = '.'.join((datasetId, other_ion))
base_features = feature_dict[next(key for key in feature_dict.keys() if base_img in key)]
other_features = feature_dict[next(key for key in feature_dict.keys() if other_img in key)]
features.append(_comb_features(base_features, other_features))
y.append(rank / 10.)
return np.array(features), np.array(y)
train_df, test_df = train_test_split(df, test_fold=test_fold, n_folds=n_folds)
with open(feature_dict_path, 'rb') as f:
feature_dict = pickle.load(f)
return _get_features(train_df, feature_dict), _get_features(test_df, feature_dict), test_df.index
def run_random_forest(data, target_column):
st.sidebar.title('Choose parameters for Random Forest')
ts = st.sidebar.slider('Training size', min_value=0.0, max_value=1.0, step=0.01, value=0.7)
n_estimators = st.sidebar.number_input('n_estimators', min_value=1, max_value=1000, step=1)
n_features = st.sidebar.number_input('n_features', min_value=1, max_value=len(data.columns)-1, step=1, value=len(data.columns)-1)
bootstrap_size = st.sidebar.number_input('bootstrap_size', min_value=1, max_value=int(len(data)*ts), step=1, value=int(len(data)*ts))
if st.sidebar.checkbox('Specify Depth'):
max_depth = st.sidebar.number_input('max_depth', min_value=1, max_value=int(len(data)*ts), step=1)
else:
max_depth = None
run_status = st.sidebar.button('Run Algorithm')
if run_status:
with st.spinner('Running...'):
x_train, x_test, y_train, y_test = train_test_split(data.drop([target_column], axis=1),
data[target_column],
test_size=1 - ts)
clf = RandomForest(n_estimators=n_estimators,
n_features=n_features,
max_depth=max_depth,
bootstrap_size=bootstrap_size)
clf.fit(x_train, y_train)
"""
## :dart: Accuracy
"""
st.subheader(accuracy_score(y_test, clf.predict(x_test)))
def main():
print '-- Grandient Boosting Regression --'
data = pd.read_csv('TempLinkoping2016.txt', sep='\t')
time = np.atleast_2d(data['time'].as_matrix()).T
temp = np.atleast_2d(data['temp'].as_matrix()).T
X = time.reshape((-1,1))
X = np.insert(X, 0, values=1, axis=1)
y = temp[:, 0]
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.5)
model = GBDTRegressor()
model.fit(X_train, y_train)
y_pred = model.predict(X_test)
cmap = plt.get_cmap('viridis')
mse = mean_squared_error(y_test, y_pred)
print 'Mean Squared Error:',mse
# Plot the results
m1 = plt.scatter(366 * X_train[:, 1], y_train, color=cmap(0.9), s=10)
m2 = plt.scatter(366 * X_test[:, 1], y_test, color=cmap(0.5), s=10)
m3 = plt.scatter(366 * X_test[:, 1], y_pred, color='black', s=10)
plt.suptitle("Regression Tree")
plt.title("MSE: %.2f" % mse, fontsize=10)
plt.xlabel('Day')
plt.ylabel('Temperature in Celcius')
plt.legend((m1, m2, m3), ("Training data", "Test data", "Prediction"), loc='lower right')
plt.show()
def main():
data = datasets.load_digits()
X = data.data
y = data.target
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=0.4,
seed=2)
print("X_train.shape:", X_train.shape)
print("Y_train.shape:", y_train.shape)
clf = RandomForest(n_estimators=100)
clf.fit(X_train, y_train)
y_pred = clf.predict(X_test)
accuracy = accuracy_score(y_test, y_pred)
print("Accuracy:", accuracy)
Plot().plot_in_2d(X_test,
y_pred,
title="Random Forest",
accuracy=accuracy,
legend_labels=data.target_names)
def main():
@run_time
def batch():
print("Tesing the accuracy of LinearRegression(batch)...")
# Train model
reg = LinearRegression()
reg.fit(X=X_train, y=y_train, lr=0.02, epochs=5000)
# Model accuracy
get_r2(reg, X_test, y_test)
@run_time
def stochastic():
print("Tesing the accuracy of LinearRegression(stochastic)...")
# Train model
reg = LinearRegression()
reg.fit(X=X_train, y=y_train, lr=0.001, epochs=1000,
method="stochastic", sample_rate=0.5)
# Model accuracy
get_r2(reg, X_test, y_test)
# Load data
X, y = load_boston_house_prices()
X = min_max_scale(X)
# Split data randomly, train set rate 70%
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=10)
batch()
stochastic()
def main():
df = pd.read_csv('fishiris.csv')
df['target'] = df.apply(create_target, axis=1)
y = df['target'].to_numpy()
df = df.drop(['Name', 'target'], axis=1)
feature_names = df.columns.tolist()
X = df.to_numpy()
target_names = ['setosa', 'versicolor', 'virginica']
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=0.4,
shuffle=True)
print('X_train\n', X_train)
print('y_train\n', y_train)
print('X_test\n', X_test)
print('y_test\n', y_test)
clf = ClassificationTree()
clf.fit(X_train, y_train)
y_pred = clf.predict(X_test)
print('-' * 40, 'print_tree', '-' * 40)
clf.print_tree(feature_names=feature_names)
print('-' * 40, 'print_tree', '-' * 40)
accuracy = accuracy_score(y_test, y_pred)
print("Accuracy:", accuracy)
Plot().plot_in_2d(X_test,
y_pred,
title="Decision Tree",
accuracy=accuracy,
legend_labels=target_names)
Plot().plot_in_3d(X_test, y_pred)
def model(labels, data, parent_id, go_id):
# Training
batch_size = 64
nb_epoch = 64
train, test = train_test_split(
labels, data, batch_size=batch_size)
train_label, train_data = train
if len(train_data) < 100:
raise Exception("No training data for " + go_id)
test_label, test_data = test
test_label_rep = test_label
model = Sequential()
model.add(Convolution1D(input_dim=20,
input_length=MAXLEN,
nb_filter=320,
filter_length=20,
border_mode='valid',
activation='relu',
subsample_length=1))
model.add(MaxPooling1D(pool_length=10, stride=10))
model.add(Dropout(0.25))
model.add(Convolution1D(nb_filter=32,
filter_length=32,
border_mode='valid',
activation='relu',
subsample_length=1))
model.add(MaxPooling1D(pool_length=8))
model.add(LSTM(128))
model.add(Dense(1024))
model.add(Activation('relu'))
model.add(Dropout(0.5))
model.add(Dense(1))
model.add(Activation('sigmoid'))
model.compile(
loss='binary_crossentropy', optimizer='rmsprop', class_mode='binary')
model_path = DATA_ROOT + parent_id + '/' + go_id + '.hdf5'
checkpointer = ModelCheckpoint(
filepath=model_path, verbose=1, save_best_only=True)
earlystopper = EarlyStopping(monitor='val_loss', patience=7, verbose=1)
model.fit(
X=train_data, y=train_label,
batch_size=batch_size, nb_epoch=nb_epoch,
show_accuracy=True, verbose=1,
validation_split=0.2,
callbacks=[checkpointer, earlystopper])
# Loading saved weights
print 'Loading weights'
model.load_weights(model_path)
pred_data = model.predict_classes(
test_data, batch_size=batch_size)
return classification_report(list(test_label_rep), pred_data)
def validation_curve():
# Test decision tree using cross validation
# Preprocess data
data = pd.read_csv('./arrhythmia.data', header = None, na_values = '?')
data = fill_na(data = data)
features = data.columns.tolist()[:-1]
target = data.columns.tolist()[-1]
feature_types = implicit_feature_type_inferrence(data = data[features], num_unique_values = 3)
train_set, test_set = train_test_split(data = data, train_fraction = 0.8, reindex = False, random_seed = 0)
max_depth_cv = list()
training_error_cv = list()
test_error_cv = list()
# Start cross-validation
for i in range(2,21,2):
tree_max_depth = i
print("Tree Max Depth: %d" %tree_max_depth)
max_depth_cv.append(tree_max_depth)
tree = DecisionTree(tree_max_depth)
training_error, test_error = cross_validation(data = data, features = features, target = target, feature_types = feature_types, model = tree, fold = 3, random_seed = 0)
training_error_cv.append(training_error)
test_error_cv.append(test_error)
print("Training Error: %f" %training_error)
print("Test Error: %f" %test_error)
plot_curve(max_depth = max_depth_cv, training_error = training_error_cv, test_error = test_error_cv)
def main():
# Load dataset
data = datasets.load_iris()
X = normalize(data.data[data.target != 0])
y = data.target[data.target != 0]
y[y == 1] = 0
y[y == 2] = 1
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=0.33,
seed=1)
clf = LogisticRegression()
clf.fit(X_train, y_train)
y_pred = clf.predict(X_test)
y_pred = np.reshape(y_pred, y_test.shape)
accuracy = accuracy_score(y_test, y_pred)
print("Accuracy:", accuracy)
# Reduce dimension to two using PCA and plot the results
Plot().plot_in_2d(X_test,
y_pred,
title="Logistic Regression",
accuracy=accuracy,
legend_labels=data.target_names)
def main():
args = argument_parser()
try:
ratings, movies_data, status = loading_data(args.data_path)
if status == False:
return "Path doesn't exist"
user_rating = ratings.pivot(index="userId",
columns="movieId",
values="rating")
user_rating = user_rating.fillna(0)
user_rating = user_rating.values
train = np.zeros(user_rating.shape)
test = np.zeros(user_rating.shape)
show_rating(ratings)
analyis(ratings, movies_data)
train_test_split(user_rating, train, test)
Itrain = indicator_matrix(train)
Itest = indicator_matrix(test)
print("#" * 100)
print("\n\nNon Negative Matrix Factorization : \n")
worker(user_rating, train, test, Itrain, Itest, movies_data, 10000,
"GD")
print("#" * 100)
print("\n\nNon Negative Matrix Factorization With Regularization : \n")
worker(user_rating, train, test, Itrain, Itest, movies_data, 5000,
"R_GD")
print("#" * 100)
print("\n\n!!!!!!!!!!!!! Different type of Optimizer !!!!!!!!!!!!")
print("\n\nSliding Window protocol for optimizer : ")
optimizer_function(user_rating, train, test, Itrain, Itest,
movies_data)
return "Successfully build"
except Exception as e:
print("Caught an Exception : ", e)
print("Build Failed !!!!!!!!!!!!!!")
def main():
x = y = {"start": -5, "end": 5, "steps": 0.5}
data = generate_gauss_data(x, y)
inputs, targets = data["inputs"], data['targets']
x_train, x_val, y_train, y_val = train_test_split(inputs, targets, 0.20)
#################### NETWORK SIZE ANALYSIS #####################
# losses, batch_losses = [], []
# for layer_size in range(1, 25):
# network = nn.NueralNet(x_train, y_train, hidden_layer_size = layer_size, output_layer_size = 1,
# is_binary = False)
# nnTrainResults = network.train_network(epochs = 400)
#
# results = network.fowardPass(inputs, targets, include_bias = True)
# losses.append(results['loss'])
#
# batch_out = np.reshape(results["Yp"], (data['size'], data['size']))
# # plot_gaussian(data, batch_out, f"Gaussian Out - hidden_layer_size {layer_size}",
# # gif = {"epoch": 1000, "seq": 0})
# batch_losses.append(nnTrainResults['batch_losses'])
#
# for i in [2, 4, 5, 7, 10, 15, 18, 23]:
# # Plot results.
# plt.plot(batch_losses[i], label = f" N. Hidden Layer {i}")
# plt.xlabel("Epochs")
# plt.ylabel("Mean Squared Error loss")
# plt.legend(loc = 'best')
# plt.show()
#################### SPLIT ANALYSIS #########################
split_ratios = [0.8]
hidden_layer_shape = 15
for split in split_ratios:
x_train, x_val, y_train, y_val = train_test_split(inputs, targets, split)
network = nn.NueralNet(x_train, y_train, hidden_layer_size = hidden_layer_shape, output_layer_size = 1,
is_binary = False)
losses = network.train_network(1000, inputs, targets)
plt.plot(losses["val_losses"], label = "Validation loss")
plt.plot(losses["epoch_losses"], label = "Train loss")
plt.xlabel("Epochs")
plt.ylabel("Mean Squared Error loss")
plt.legend()
plt.title(f"Data Split - Training: {round((1 - split) * 100)}%")
plt.show()
def nested_crossvalidation(self):
if self.logging:
print('Nested crossvalidation started.')
print('Number of train_valid-test splits: ' + str(self.args['num_of_test_splits']))
print('Number of train-valid splits:' + str(self.args['num_of_valid_splits']))
test_split_groups = np.array(list(self.df['CLUSTER']))
train_valid_test = train_test_split(test_split_groups, num_splits = self.args['num_of_test_splits'])
outer = torch.zeros(self.args['num_of_test_splits'])
for i, (train_valid_data, test_data) in enumerate(train_valid_test):
# print('Fold ' + str(i+1))
# print('Train dataset: ' + str(len(train_valid_data)))
# print('Test dataset: ' + str(len(test_data)))
# train model
df_train_valid = self.df.iloc[sorted(train_valid_data)]
#print(df_train_valid.index.tolist())
df_train_valid = df_train_valid.set_index(pd.Index(list(range(len(df_train_valid)))))
#print(df_train_valid.index.tolist())
#break
valid_split_groups = np.array(list(df_train_valid['CLUSTER']))
train_valid = train_test_split(valid_split_groups, num_splits = self.args['num_of_valid_splits'])
inner = torch.zeros(len(self.hyperparameters), self.args['num_of_valid_splits'])
for j, (train_data, valid_data) in enumerate(train_valid):
# print(j)
# print(len(train_data))
# print(len(valid_data))
df_train = df_train_valid.iloc[sorted(train_data)]
df_train = df_train.set_index(pd.Index(list(range(len(df_train)))))
train_loader = self.prepare_data_loader(df_train, self.args['train_batch_size'], str(i+1) + '_' + str(j+1)+ '_' +'train')
df_valid = df_train_valid.iloc[sorted(valid_data)]
df_valid = df_valid.set_index(pd.Index(list(range(len(df_valid)))))
valid_loader = self.prepare_data_loader(df_valid, self.args['valid_batch_size'], str(i+1) + '_' + str(j+1)+ '_' +'valid')
for k, hp in enumerate(self.hyperparameters):
inner[k][j] = self.train(train_loader, hp, save_model = False, valid_loader=valid_loader)
hp_best = self.hyperparameters[self.tune_hparam(inner)]
df_test = self.df.iloc[sorted(test_data)]
trainvalid_loader = self.prepare_data_loader(train_valid, self.args['train_batch_size'], str(i+1) + '_' +'trainvalid')
test_loader = self.prepare_data_loader(df_test, self.args['test_batch_size'], str(i+1) + '_' +'test')
outer[i] = self.train(trainvalid_loader, hp_best, save_model=True, valid_loader=test_loader)
return {'mean_objective_loss': torch.mean(outer), 'std_objective_loss': torch.std(outer)}
def test_split():
n = int(len(x)*0.8)
with mock.patch("numpy.random.choice", return_value=np.arange(n)):
X_train, X_test, z_train, z_test = train_test_split(X, z, split_size=0.2, random_state=1)
print(np.shape(X))
print("--------------")
print(np.shape(X_train.tolist()+X_test.tolist()))
assert (np.allclose(X_train.tolist()+X_test.tolist(), X) and np.allclose(z_train.tolist()+ z_test.tolist(), z ))
def main(args):
torch.multiprocessing.set_start_method('spawn')
torch.distributed.init_process_group(backend="nccl")
with open(args.config_path, 'r') as file:
config = AttrDict(json.load(file))
set_seed(config.seed + torch.distributed.get_rank())
train_data_csv, test_data_csv = train_test_split(
config.train_data_csv_path, config.n_test_experiments)
train_image_ids, train_labels = get_data(train_data_csv, is_train=True)
train_transform = TrainTransform(config.crop_size)
train_dataset = CellsDataset(config.train_images_dir, train_image_ids,
train_labels, train_transform)
test_image_ids, test_labels = get_data(test_data_csv, is_train=True)
test_dataset = CellsDataset(config.train_images_dir, test_image_ids,
test_labels)
if torch.distributed.get_rank() == 0:
print(
f'Train size: {len(train_dataset)}, test_size: {len(test_dataset)}'
)
encoder = Encoder(config.n_image_channels, config.n_emedding_channels,
config.n_classes, config.encoder_model,
config.encoder_pretrained, config.encoder_dropout,
config.encoder_scale)
if config.restore_checkpoint_path is not None:
state_dict = torch.load(config.restore_checkpoint_path,
map_location='cpu')
encoder.load_state_dict(state_dict, strict=False)
decoder = Decoder(config.n_emedding_channels, config.n_image_channels,
config.n_classes, config.decoder_n_channels)
trainer = Trainer(encoder=encoder,
decoder=decoder,
optimizer_params={
'lr': config.lr,
'weight_decay': config.weight_decay,
'warmap': config.warmap,
'amsgrad': config.amsgrad
},
amp_params={
'opt_level': config.opt_level,
'loss_scale': config.loss_scale
},
rank=args.local_rank,
n_jobs=config.n_jobs)
trainer.train(train_data=train_dataset,
n_epochs=config.n_epochs,
batch_size=config.batch_size,
test_data=test_dataset,
best_checkpoint_path=config.best_checkpoint_path)
def main(df_path, dates, params_path, suffix):
df = pd.read_csv(df_path)
X_train, X_test, y_train, y_test, _, ids_test = train_test_split(df, dates)
b_params = best_params(params_path)
preds = run_model(X_train, y_train, X_test, y_test, b_params)
save_preds(X_test, y_test, preds, ids_test, suffix)
print('predictions_saved')
def main():
# Load temperature data
data = pd.read_csv(
'https://raw.githubusercontent.com/eriklindernoren/ML-From-Scratch/master/mlfromscratch/data/TempLinkoping2016.txt',
sep="\t")
time = np.atleast_2d(data["time"].values).T
temp = data["temp"].values
X = time # fraction of the year [0, 1]
y = temp
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.4)
poly_degree = 13
model = LassoRegression(degree=15,
reg_factor=0.05,
learning_rate=0.001,
n_iterations=4000)
model.fit(X_train, y_train)
# Training error plot
n = len(model.training_errors)
training, = plt.plot(range(n),
model.training_errors,
label="Training Error")
plt.legend(handles=[training])
plt.title("Error Plot")
plt.ylabel('Mean Squared Error')
plt.xlabel('Iterations')
plt.show()
y_pred = model.predict(X_test)
mse = mean_squared_error(y_test, y_pred)
print("Mean squared error: %s (given by reg. factor: %s)" % (mse, 0.05))
y_pred_line = model.predict(X)
# Color map
cmap = plt.get_cmap('viridis')
# Plot the results
m1 = plt.scatter(366 * X_train, y_train, color=cmap(0.9), s=10)
m2 = plt.scatter(366 * X_test, y_test, color=cmap(0.5), s=10)
plt.plot(366 * X,
y_pred_line,
color='black',
linewidth=2,
label="Prediction")
plt.suptitle("Lasso Regression")
plt.title("MSE: %.2f" % mse, fontsize=10)
plt.xlabel('Day')
plt.ylabel('Temperature in Celcius')
plt.legend((m1, m2), ("Training data", "Test data"), loc='lower right')
plt.show()
def load_data(self, filename):
df = pd.read_csv(filename, header=None)
dfx = df.iloc[:, :-1]
dfx = (dfx - dfx.mean()) / (dfx.max() - dfx.min())
X = dfx.values
y = df.iloc[:, -1].values
self.d = X.shape[1]
self.out = self.d
self.X_train, self.y_train, self.X_test, self.y_test = train_test_split(X, y)
self.y_test = self.y_test.reshape(-1, 1)
def _training(Model):
features, targets = engine.get_features(Model, train=True)
X_train, X_test, y_train, y_test = utils.train_test_split(features,
targets,
test_size=0.3)
classifier = engine.train_fn(X_train, y_train)
utils.save_model(classifier, config.MODEL_PATH)
predictions = engine.eval_fn(classifier, X_test)
accuracy = utils.accuracy_score(predictions, y_test)
print("Accuracy Score:", accuracy)
def test_unit():
print('\n===================================================================')
print('Unit test: Sparse Representation-based Classification (SRC)')
dataset = 'myYaleB'
N_train = 15
dataset, Y_train, Y_test, label_train, label_test = \
utils.train_test_split(dataset, N_train)
clf = SRC(lamb = 0.01)
clf.fit(Y_train, label_train)
clf.evaluate(Y_test, label_test)
def get_train_valid_dataset(data_dir): training_filenames, trainY = utils.load_train_filename_and_labels(data_dir) training_filenames, valid_filenames, trainY, validY = utils.train_test_split(training_filenames, trainY, split_ratio=0.1) trsfms = transforms.Compose([ transforms.RandomCrop(256, pad_if_needed=True, padding_mode='symmetric'), transforms.RandomHorizontalFlip(), transforms.RandomRotation(15), transforms.ToTensor(), ]) return MyDataset(os.path.join(data_dir, 'training'), transforms=trsfms), MyDataset(os.path.join(data_dir, 'validation'), transforms=trsfms)
def main():
print("Tesing the accuracy of NaiveBayes...")
# Load data
X, y = load_breast_cancer()
# Split data randomly, train set rate 70%
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=10)
# Train model
clf = GaussianNB()
clf.fit(X_train, y_train)
# Model accuracy
get_acc(clf, X_test, y_test)
def main():
parser = argparse.ArgumentParser("Preprocess the data")
parser.add_argument('task', nargs='?', type=str)
parser.add_argument('--path', '-p', dest='path', action='store', type=str)
parser.add_argument('--patch-size',
dest='patch_size',
action='store',
type=int,
default=[],
nargs='+')
parser.add_argument('--canny-sigma',
dest='canny_sigma',
action='store',
type=float)
parser.add_argument('--threshold', type=int)
parser.add_argument('--color', dest='color', action='store_true')
parser.add_argument('--binarized', dest='color', action='store_false')
parser.add_argument('--val-size', dest='val_size', type=float)
parser.set_defaults(color=True)
parser.add_argument('--patch-stride',
dest='patch_stride',
type=int,
default=256)
parser.add_argument('--padding', type=int, default=0)
args = parser.parse_args()
if args.task == 'patchify':
# split images into patches
utils.dataset_to_patches(args.path,
args.patch_size,
stride=args.patch_stride,
canny_sigma=args.canny_sigma,
threshold=args.threshold,
color=args.color,
padding=args.padding)
if args.task == 'split-writer-dirs':
utils.prepare_files_of_trainingset(args.path)
if args.task == 'train-val-split':
utils.train_test_split(args.path, args.val_size)
def test_unit():
print(
'\n==================================================================='
)
print('Mini Unit test: COPAR')
dataset = 'myYaleB'
N_train = 15
dataset, Y_train, Y_test, label_train, label_test = \
utils.train_test_split(dataset, N_train)
clf = COPAR(k=10, k0=5, lambd=0.001, eta=0.01)
clf.fit(Y_train, label_train, iterations=100, verbose=True)
clf.evaluate(Y_test, label_test)
def train_model():
Model = model.BertForFakeNewsDetection()
features, labels = Model.get_features(train=True)
X_train, X_test, y_train, y_test = utils.train_test_split(features,
labels,
test_size=0.3)
clf = svm.SVC()
clf.fit(features, labels)
print("Validation Accuracy:",
round(clf.score(X_test, y_test), 4) * 100, "%")
clf.fit(X_test, y_test)
utils.save_model(clf, config.MODEL_PATH)
def main():
data = datasets.load_digits()
X = data.data
y = data.target
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.4, seed=2)
print("X_train.shape:", X_train.shape)
print("Y_train.shape:", y_train.shape)
clf = RandomForest(n_estimators=100)
clf.fit(X_train, y_train)
y_pred = clf.predict(X_test)
accuracy = accuracy_score(y_test, y_pred)
print("Accuracy:", accuracy)
Plot().plot_in_2d(X_test, y_pred, title="Random Forest", accuracy=accuracy, legend_labels=data.target_names)
def main():
data = datasets.load_digits()
X = normalize(data.data)
y = data.target
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.4)
print("X_train",X_train.shape)
clf = NaiveBayes()
clf.fit(X_train, y_train)
y_pred = clf.predict(X_test)
accuracy = accuracy_score(y_test, y_pred)
print ("Accuracy:", accuracy)
# Reduce dimension to two using PCA and plot the results
Plot().plot_in_2d(X_test, y_pred, title="Naive Bayes", accuracy=accuracy, legend_labels=data.target_names)
def main():
# Load dataset
data = datasets.load_iris()
X = normalize(data.data[data.target != 0])
y = data.target[data.target != 0]
y[y == 1] = 0
y[y == 2] = 1
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.33, seed=1)
clf = LogisticRegression()
clf.fit(X_train, y_train)
y_pred = clf.predict(X_test)
y_pred = np.reshape(y_pred, y_test.shape)
accuracy = accuracy_score(y_test, y_pred)
print("Accuracy:", accuracy)
# Reduce dimension to two using PCA and plot the results
Plot().plot_in_2d(X_test, y_pred, title="Logistic Regression", accuracy=accuracy)
def main():
print ("-- Regression Tree --")
# Load temperature data
data = pd.read_csv('../TempLinkoping2016.txt', sep="\t")
time = np.atleast_2d(data["time"].as_matrix()).T
temp = np.atleast_2d(data["temp"].as_matrix()).T
X = standardize(time) # Time. Fraction of the year [0, 1]
y = temp[:, 0] # Temperature. Reduce to one-dim
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.3)
model = RegressionTree()
model.fit(X_train, y_train)
y_pred = model.predict(X_test)
y_pred_line = model.predict(X)
# Color map
cmap = plt.get_cmap('viridis')
mse = mean_squared_error(y_test, y_pred)
print ("Mean Squared Error:", mse)
# Plot the results
# Plot the results
m1 = plt.scatter(366 * X_train, y_train, color=cmap(0.9), s=10)
m2 = plt.scatter(366 * X_test, y_test, color=cmap(0.5), s=10)
m3 = plt.scatter(366 * X_test, y_pred, color='black', s=10)
plt.suptitle("Regression Tree")
plt.title("MSE: %.2f" % mse, fontsize=10)
plt.xlabel('Day')
plt.ylabel('Temperature in Celcius')
plt.legend((m1, m2, m3), ("Training data", "Test data", "Prediction"), loc='lower right')
plt.show()
def main():
print ("-- Classification Tree --")
data = datasets.load_iris()
X = data.data
y = data.target
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.4)
clf = ClassificationTree()
clf.fit(X_train, y_train)
y_pred = clf.predict(X_test)
accuracy = accuracy_score(y_test, y_pred)
print ("Accuracy:", accuracy)
Plot().plot_in_2d(X_test, y_pred,
title="Decision Tree",
accuracy=accuracy,
legend_labels=data.target_names)
def model(labels, data):
# set parameters:
# Training
batch_size = 100
nb_epoch = 100
train, test = train_test_split(
labels, data, batch_size=batch_size)
train_label, train_data = train
test_label, test_data = test
test_label_rep = test_label
shap=numpy.shape(train_data)
print('X_train shape: ',shap)
print('X_test shape: ',test_data.shape)
model = Sequential()
model.add(Dense(shap[1], activation='relu', input_dim=shap[1]))
model.add(Highway())
model.add(Dense(1,activation='sigmoid'))
print 'compiling model'
model.compile(loss='binary_crossentropy', optimizer='rmsprop', class_mode="binary")
print 'running at most 60 epochs'
checkpointer = ModelCheckpoint(filepath="bestmodel.hdf5", verbose=1, save_best_only=True)
earlystopper = EarlyStopping(monitor='val_loss', patience=5, verbose=1)
model.fit(train_data, train_label, batch_size=batch_size,nb_epoch=nb_epoch,shuffle=True, show_accuracy=True,
validation_split=0.3,callbacks=[checkpointer,earlystopper])
# # Loading saved weights
print 'Loading weights'
model.load_weights('bestmodel.hdf5')
pred_data = model.predict_classes(test_data, batch_size=batch_size)
# Saving the model
tresults = model.evaluate(test_data, test_label,show_accuracy=True)
print tresults
return classification_report(list(test_label_rep), pred_data)
def main():
print ("-- Gradient Boosting Classification --")
data = datasets.load_iris()
X = data.data
y = data.target
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.4)
print(y_train)
clf = GBDTClassifier()
clf.fit(X_train, y_train)
y_pred = clf.predict(X_test)
accuracy = accuracy_score(y_test, y_pred)
print ("Accuracy:", accuracy)
Plot().plot_in_2d(X_test, y_pred,
title="Gradient Boosting",
accuracy=accuracy,
legend_labels=data.target_names)
def model(labels, data, go_id):
# set parameters:
batch_size = 64
nb_epoch = 10
lstm_size = 128
data1, data2 = data
train1, test1 = train_test_split(
labels, data1, batch_size=batch_size)
train2, test2 = train_test_split(
labels, data2, batch_size=batch_size)
train_label, train1_data = train1
train_label, train2_data = train2
test_label, test1_data = test1
test_label, test2_data = test2
test_label_rep = test_label
# 256 0.5 256
model = Graph()
model.add_input(name='input1', batch_input_shape=(batch_size, 20))
model.add_input(name='input2', batch_input_shape=(batch_size, 3))
model.add_node(Convolution1D(
nb_filter=32,
filter_length=20,
border_mode='valid',
activation='relu',
subsample_length=1), name='conv1', input='input1')
model.add_node(MaxPooling1D(
pool_length=10, stride=10), name='pool1', input='conv1')
model.add_node(
LSTM(lstm_size), name='lstm1', input='pool1')
model.add_node(Convolution1D(
nb_filter=32,
filter_length=3,
border_mode='valid',
activation='relu',
subsample_length=1), name='conv2', input='input2')
model.add_node(MaxPooling1D(
pool_length=2), name='pool2', input='conv2')
model.add_node(
LSTM(lstm_size), name='lstm2', input='pool2')
model.add_node(
Dense(1024),
name='dense1', inputs=['lstm1', 'lstm2'])
model.add_node(Dropout(0.25), name='dropout', input='dense1')
model.add_node(Activation('relu'), name='relu', input='dropout')
model.add_node(
Dense(1, activation='sigmoid'), name='dense2', input='relu')
model.add_output(name='output', input='dense2')
# try using different optimizers and different optimizer configs
model.compile('adadelta', {'output': 'binary_crossentropy'})
model_path = DATA_ROOT + go_id + '.hdf5'
checkpointer = ModelCheckpoint(
filepath=model_path, verbose=1, save_best_only=True)
earlystopper = EarlyStopping(monitor='val_loss', patience=5, verbose=1)
model.fit(
{'input1': train1_data, 'input2': train2_data, 'output': train_label},
batch_size=batch_size,
nb_epoch=nb_epoch,
validation_split=0.2,
callbacks=[checkpointer, earlystopper])
print 'Loading weights'
model.load_weights(model_path)
pred_data = model.predict(
{'input1': test1_data, 'input2': test2_data}, batch_size=batch_size)
pred_data = numpy.round(numpy.array(pred_data['output']))
# Loading saved weights
# Saving the model
# print 'Saving the model for ' + go_id
# model.save_weights(DATA_ROOT + go_id + '.hdf5', overwrite=True)
return classification_report(list(test_label_rep), pred_data)
reload(utils)
reload(algo_param)
reload(param)
# TODO Add unlabeled subset functionality
# TODO Add parallelization
##################### PERFORM GRID SEARCH ########################
if param.optimize_params:
# parse data
all_X, all_Y = utils.parse(param.data_file, param.feature_file,
param.response_var, debug_limit=param.debug_limit)
X, Y = utils.labeled_subset(all_X, all_Y)
X, Y = utils.subsample((X, Y), param.labeled_subsample)
(X_train, X_test, Y_train, Y_test) = utils.train_test_split(X, Y, test_size=param.test_size)
# pickle data for use in other files
saved_data = (X_train, X_test, Y_train, Y_test)
utils.pickler(saved_data, param.optimization_data_pickle)
# make meta pipeline for grid searching
pipeline, parameter_space = make_meta_pipeline([
('imputer', param.imputer_params),
('scaler', param.scaler_params),
('dim_reducer', param.dim_reducer_params),
('regressor', param.regressor_params)
], all_X, all_Y)
print("Opening logfiles")
sys.stdout.flush()
def model(labels, data, parent_id, go_id):
# Convolution
filter_length = 20
nb_filter = 32
pool_length = 10
global nb_classes
# LSTM
lstm_output_size = 128
# Training
batch_size = 64
nb_epoch = 64
train, test = train_test_split(
labels, data, batch_size=batch_size)
train_label, train_data = train
# sample_weight = [1.0 if y == 1 else 1.0 for y in train_label]
# sample_wseight = numpy.array(sample_weight, dtype='float32')
test_label, test_data = test
test_label_rep = test_label
model = Sequential()
model.add(Convolution1D(input_dim=20,
input_length=MAXLEN,
nb_filter=nb_filter,
filter_length=filter_length,
border_mode='valid',
activation='relu',
subsample_length=1))
model.add(MaxPooling1D(pool_length=pool_length, stride=10))
model.add(Dropout(0.25))
model.add(Convolution1D(nb_filter=nb_filter,
filter_length=filter_length,
border_mode='valid',
activation='relu',
subsample_length=1))
model.add(MaxPooling1D(pool_length=pool_length, stride=10))
model.add(LSTM(lstm_output_size))
# model.add(Flatten())
model.add(Dense(1024))
model.add(Activation('relu'))
model.add(Dropout(0.5))
model.add(Dense(nb_classes))
model.add(Activation('softmax'))
model.compile(
loss='categorical_crossentropy',
optimizer='rmsprop')
model_path = DATA_ROOT + parent_id + '/' + go_id + '.hdf5'
# parent_model_path = DATA_ROOT + 'data/' + parent_id + '.hdf5'
# if os.path.exists(parent_model_path):
# print 'Loading parent model weights'
# model.load_weights(parent_model_path)
checkpointer = ModelCheckpoint(
filepath=model_path, verbose=1, save_best_only=True)
earlystopper = EarlyStopping(monitor='val_loss', patience=10, verbose=1)
model.fit(
X=train_data, y=train_label,
batch_size=batch_size, nb_epoch=nb_epoch,
show_accuracy=True, verbose=1,
validation_split=0.2,
callbacks=[checkpointer, earlystopper])
# Loading saved weights
print 'Loading weights'
model.load_weights(DATA_ROOT + parent_id + '/' + go_id + '.hdf5')
score = model.evaluate(
test_data, test_label, show_accuracy=True, verbose=1)
print 'Score: ', score[0]
print 'Accuracy: ', score[1]
def model(labels, data, parent_id, go_id):
# set parameters:
# Convolution
nb_filter = 64
nb_row = 5
nb_col = 1
pool_length = 3
# Training
batch_size = 64
nb_epoch = 24
lstm_size = 70
data1, data2 = data
train1, test1 = train_test_split(
labels, data1, batch_size=batch_size, split=0.8)
train_label, train1_data = train1
train2, test2 = train_test_split(
labels, data2, batch_size=batch_size, split=0.8)
train_label, train2_data = train2
if len(train1_data) < 100:
raise Exception("No training data for " + go_id)
test_label, test1_data = test1
test_label, test2_data = test2
test_label_rep = test_label
first = Sequential()
first.add(Convolution2D(
nb_filter, nb_row, nb_col,
border_mode='valid',
input_shape=(1, MAXLEN, 20)))
first.add(Activation('relu'))
first.add(Convolution2D(2 * nb_filter, nb_row, nb_col))
first.add(Activation('relu'))
# first.add(Convolution2D(nb_filter, nb_row, nb_col))
# first.add(Activation('relu'))
first.add(MaxPooling2D(pool_size=(pool_length, 1)))
first.add(Dropout(0.5))
first.add(Flatten())
second = Sequential()
second.add(
LSTM(lstm_size, return_sequences=True, input_shape=(MAXLEN, 20)))
second.add(Dropout(0.25))
# second.add(LSTM(lstm_size, return_sequences=True))
# second.add(Dropout(0.25))
second.add(LSTM(lstm_size, return_sequences=False))
second.add(Dropout(0.25))
second.add(Flatten())
model = Sequential()
model.add(Merge([first, second], mode='concat'))
model.add(Dense(256))
model.add(Activation('relu'))
model.add(Dropout(0.5))
model.add(Dense(128))
model.add(Activation('relu'))
model.add(Dropout(0.5))
model.add(Dense(1))
model.add(Activation('sigmoid'))
adam = Adam(lr=0.00001)
model.compile(
loss='binary_crossentropy', optimizer=adam, class_mode='binary')
model_path = DATA_ROOT + parent_id + '/' + go_id + '.hdf5'
checkpointer = ModelCheckpoint(
filepath=model_path, verbose=1, save_best_only=True)
earlystopper = EarlyStopping(monitor='val_loss', patience=5, verbose=1)
model.fit(
X=[train1_data, train2_data], y=train_label,
batch_size=batch_size, nb_epoch=nb_epoch,
show_accuracy=True, verbose=1,
validation_split=0.3,
callbacks=[checkpointer, earlystopper])
model.load_weights(model_path)
pred_data = model.predict_classes(
[test1_data, test2_data],
batch_size=batch_size)
return classification_report(list(test_label_rep), pred_data)
def model(labels, data, go_id):
# set parameters:
# Convolution
filter_length = 7
nb_filter = 64
pool_length = 2
k=7
# LSTM
lstm_output_size = 70
# Training
batch_size = 32
nb_epoch = 12
train, test = train_test_split(
labels, data, batch_size=batch_size)
train_label, train_data = train
test_label, test_data = test
test_label_rep = test_label
model = Sequential()
model.add(Convolution1D(
input_dim=20,
input_length=500,
nb_filter=320,
filter_length=20,
border_mode="valid",
activation="relu",
subsample_length=1))
model.add(MaxPooling1D(pool_length=10, stride=10))
model.add(Dropout(0.2))
model.add(Convolution1D(
nb_filter=320,
filter_length=20,
border_mode="valid",
activation="relu",
subsample_length=1))
model.add(MaxPooling1D(pool_length=10, stride=10))
model.add(Dropout(0.2))
model.add(Flatten())
model.add(Highway())
model.add(Dropout(0.5))
model.add(Dense(output_dim=1000))
model.add(Activation('relu'))
model.add(Dense(output_dim=1))
model.add(Activation('sigmoid'))
print 'compiling model'
model.compile(
loss='binary_crossentropy', optimizer='rmsprop', class_mode="binary")
print 'running at most 60 epochs'
model_path = DATA_ROOT + go_id + '.hdf5'
checkpointer = ModelCheckpoint(
filepath=model_path, verbose=1, save_best_only=True)
earlystopper = EarlyStopping(monitor='val_loss', patience=5, verbose=1)
model.fit(
train_data, train_label, batch_size=batch_size,
nb_epoch=60, shuffle=True, show_accuracy=True,
validation_split=0.3,
callbacks=[checkpointer, earlystopper])
# # Loading saved weights
print 'Loading weights'
model.load_weights(model_path)
pred_data = model.predict_classes(test_data, batch_size=batch_size)
# Saving the model
# tresults = model.evaluate(test_data, test_label,show_accuracy=True)
# print tresults
return classification_report(list(test_label_rep), pred_data)
def model(labels, data, go_id):
# set parameters:
# Convolution
filter_length = 7
nb_filter = 64
pool_length = 2
k=7
# LSTM
lstm_output_size = 70
# Training
batch_size = 30
nb_epoch = 12
train, test = train_test_split(
labels, data, batch_size=batch_size)
train_label, train_data = train
test_label, test_data = test
test_label_rep = test_label
nb_filters = 100
filter_lenghts = [7,10,12]
first = Sequential()
first.add(Convolution1D(input_dim=20,
input_length=500,
nb_filter=nb_filters,
filter_length=7,
border_mode="valid",
activation="relu",
subsample_length=1))
first.add(MaxPooling1D(pool_length=3, stride=3))
first.add(LSTM(input_dim=100, output_dim=100))
second = Sequential()
second.add(Convolution1D(input_dim=20,
input_length=500,
nb_filter=nb_filters,
filter_length=10,
border_mode="valid",
activation="relu",
subsample_length=1))
second.add(Activation('relu'))
second.add(MaxPooling1D(pool_length=5, stride=5))
second.add(LSTM(input_dim=100, output_dim=100))
third = Sequential()
third.add(Convolution1D(input_dim=20,
input_length=500,
nb_filter=nb_filters,
filter_length=12,
border_mode="valid",
activation="relu",
subsample_length=1))
third.add(Activation('relu'))
third.add(MaxPooling1D(pool_length=6, stride=6))
third.add(LSTM(input_dim=100, output_dim=100))
model = Sequential()
model.add(Merge([first, second, third], mode='concat'))
model.add(Dense(1000))
model.add(Activation('relu'))
model.add(Dropout(0.5))
model.add(Dense(1))
model.add(Activation('sigmoid'))
model.compile(loss='binary_crossentropy', optimizer='rmsprop', class_mode="binary")
checkpointer = ModelCheckpoint(filepath="bestmodel.hdf5", verbose=1, save_best_only=True)
earlystopper = EarlyStopping(monitor='val_loss', patience=5, verbose=1)
model.fit(X=[train_data, train_data, train_data], y=train_label, batch_size=100, nb_epoch=60, shuffle=True, show_accuracy=True,
validation_split=0.3, callbacks=[checkpointer,earlystopper])
#now concat all the results and do whatever you want with the new sentence_embedding :D
# # Loading saved weights
# print 'Loading weights'
# model.load_weights(DATA_ROOT + go_id + '.hdf5')
model.load_weights('bestmodel.hdf5')
pred_data = model.predict_classes(
[test_data, test_data, test_data], batch_size=batch_size)
# Saving the model
#tresults = model.evaluate(test_data, test_label,show_accuracy=True)
#print tresults
return classification_report(list(test_label_rep), pred_data)
print ("MLP")
print ("nb_epoch:{}".format(nb_epoch))
print ("Layer: {}/{}/{}".format(layer1,layer2,layer3))
Loop, Tap = utils.load_data_envelope()
Xloop, Xtap, target = utils.makeTrainingDataRegression(Loop, Tap)
# Xloop, Xtap, target = utils.makeTrainingDataRank(Loop, Tap)
# target = np_utils.to_categorical(target)
X = np.hstack((Xloop, Xtap))
X = np.float64(X)
if normFlag:
# X = X - np.mean(X, axis=1)[:, np.newaxis]
X = normalize(X, axis=1, norm='l2')
#X_train, X_test, target_train, target_test = cross_validation.train_test_split(X, target, test_size=test_split, random_state=0)
X_train, X_test, target_train, target_test = utils.train_test_split(X, target, test_split)
mlp = nn.MLP_regression(layer1=layer1, layer2=layer2, layer3=layer3, input_shape=X_train[0].shape)
checkpointer = ModelCheckpoint(filepath="./tmp/mlp_weights_l1{}l2{}l3{}.hdf5".format(layer1,layer2,layer3),\
verbose=1, save_best_only=True, monitor='val_loss')
mlp.fit(X_train, target_train, batch_size=batch_size, nb_epoch=nb_epoch,\
show_accuracy=True, verbose=2, shuffle=True, validation_data=(X_test, target_test), callbacks = [checkpointer])
# mlp.evaluate(X_test, target_test, show_accuracy=True, verbose=1)
#mlp.load_weights("./tmp/mlp_weights_l1{}l2{}l3{}.hdf5".format(layer1,layer2,layer3))
propagation = nn.Propagation(mlp)
utils.calculate_MRR(Loop, Tap, method='nn', model=mlp, prop=propagation)
# print("====test data====")
# for i in np.arange(len(target_test)):
# error = np.abs(y[i][0]-target_test[i])
# print("{:0.3f}, {:0.2f}, error= {:.2f}, {}").format(y[i][0], target_test[i], error, 'correct' if error < 0.5 else 'wrong')
nb_epoch = 200
test_split = 0.2
layer1 = 10
layer2 = None
layer3 = None
print ("GRU")
print ("nb_epoch:{}".format(nb_epoch))
print ("Layer: {}/{}/{}".format(layer1,layer2,layer3))
target = np.load('./target.npy')
Loop = pd.read_pickle('./Loop.pkl')
Tap = pd.read_pickle('./Tap.pkl')
X = np.load('./X.npy')
X_train, X_test, target_train, target_test =\
utils.train_test_split(X, target, test_split)
if normFlag:
Xloop = Xloop - np.mean(Xloop, axis=1)[:, np.newaxis]
Xtap = Xtap - np.mean(Xtap, axis=1)[:, np.newaxis]
Xloop = normalize(Xloop, axis=1, norm='l2')
Xtap = normalize(Xtap, axis=1, norm='l2')
rnn = nn.RNN_regression(\
layer1=layer1, layer2=layer2,\
layer3=layer3, input_length=(len(Xloop[0]),))
#X_train, X_test, target_train, target_test =\
# utils.train_test_split(X, target, test_split)
print("Train...")
checkpointer = ModelCheckpoint(\
filepath="./tmp/rnn_gru_weights_l1{}l2{}l3{}.hdf5".\
format(layer1,layer2,layer3),\
verbose=1, save_best_only=True, monitor='val_loss')
def model(go_id):
# set parameters:
# Convolution
filter_length = 20
nb_filter = 32
pool_length = 10
stride = 10
# LSTM
lstm_output_size = 96
# Training
batch_size = 100
nb_epoch = 60
patience = 5
#Encoding
maxlen = 500
dictn = 20
gram = 2
labels, data = load_data(go_id,maxlen,dictn,gram)
train, test = train_test_split(
labels, data, batch_size=batch_size)
train_label, train_data = train
test_label, test_data = test
test_label_rep = test_label
shap=numpy.shape(train_data)
print('X_train shape: ',shap)
print('X_test shape: ',test_data.shape)
model = Sequential()
model.add(Convolution1D(input_dim=shap[2],
input_length=shap[1],
nb_filter=nb_filter,
filter_length=filter_length,
border_mode="valid",
activation="relu",
subsample_length=1))
model.add(MaxPooling1D(pool_length=pool_length, stride=stride))
model.add(Dropout(0.75))
model.add(LSTM(lstm_output_size, return_sequences=True))
model.add(LSTM(lstm_output_size))
model.add(Dropout(0.75))
model.add(Dense(1000))
model.add(Dense(1,activation='sigmoid'))
print 'compiling model'
model.compile(loss='binary_crossentropy', optimizer='rmsprop', class_mode="binary")
print 'running at most 60 epochs'
checkpointer = ModelCheckpoint(filepath="bestmodel.hdf5", verbose=1, save_best_only=True)
earlystopper = EarlyStopping(monitor='val_loss', patience=patience, verbose=1)
model.fit(train_data, train_label, batch_size=batch_size, nb_epoch=nb_epoch, shuffle=True, show_accuracy=True,
validation_split=0.3,callbacks=[checkpointer,earlystopper])
# # Loading saved weights
print 'Loading weights'
model.load_weights('bestmodel.hdf5')
pred_data = model.predict_classes(test_data, batch_size=batch_size)
# Saving the model
tresults = model.evaluate(test_data, test_label,show_accuracy=True)
print tresults
return classification_report(list(test_label_rep), pred_data)
