def split_patients(patients, valid_percent, test_percent, rng=(2014, 10, 22)):
if isinstance(rng, (list, tuple)):
rng = make_np_rng(None, rng, which_method='uniform')
vals = np.asarray(patients.values())
keys = np.asarray(patients.keys())
sss = StratifiedShuffleSplit(
vals, n_iter=1, test_size=test_percent, random_state=rng)
remaining_idx, test_idx = sss.__iter__().next()
if valid_percent > 0:
# Rate of samples required to build validation set
valid_rate = valid_percent / (1 - test_percent)
sss = StratifiedShuffleSplit(
vals[remaining_idx], n_iter=1, test_size=valid_rate, random_state=rng)
tr_idx, val_idx = sss.__iter__().next()
valid_idx = remaining_idx[val_idx]
train_idx = remaining_idx[tr_idx]
else:
train_idx = remaining_idx
valid_idx = []
train_patients = dict(zip(keys[train_idx], vals[train_idx]))
valid_patients = dict(zip(keys[valid_idx], vals[valid_idx]))
test_patients = dict(zip(keys[test_idx], vals[test_idx]))
return train_patients, valid_patients, test_patients
def simple_classification(n_samples=100, n_features=10, random_state=33):
"""
Generate simple classification task for training.
Parameters
----------
n_samples : int
Number of samples in dataset.
n_features : int
Number of features for each sample.
random_state : int
Random state to make results reproducible.
Returns
-------
tuple
Returns tuple that contains 4 variables. There are input train,
input test, target train, target test respectevly.
"""
X, y = datasets.make_classification(n_samples=n_samples,
n_features=n_features,
random_state=random_state)
shuffle_split = StratifiedShuffleSplit(y, 1, train_size=0.6,
random_state=random_state)
train_index, test_index = next(shuffle_split.__iter__())
x_train, x_test = X[train_index], X[test_index]
y_train, y_test = y[train_index], y[test_index]
return x_train, x_test, y_train, y_test
def simple_classification(n_samples=100, n_features=10, random_state=33):
""" Generate simple classification task for training.
Parameters
----------
n_samples : int
Number of samples in dataset.
n_features : int
Number of features for each sample.
random_state : int
Random state to make results reproducible.
Returns
-------
tuple
Returns tuple that contains 4 variables. There are input train,
input test, target train, target test respectevly.
"""
X, y = datasets.make_classification(n_samples=n_samples,
n_features=n_features,
random_state=random_state)
shuffle_split = StratifiedShuffleSplit(y,
1,
train_size=0.6,
random_state=random_state)
train_index, test_index = next(shuffle_split.__iter__())
x_train, x_test = X[train_index], X[test_index]
y_train, y_test = y[train_index], y[test_index]
return x_train, x_test, y_train, y_test
def setUp(self):
super(QuasiNewtonTestCase, self).setUp()
X, y = datasets.make_classification(n_samples=100, n_features=10, random_state=33)
shuffle_split = StratifiedShuffleSplit(y, 1, train_size=0.6, random_state=33)
train_index, test_index = next(shuffle_split.__iter__())
x_train, x_test = X[train_index], X[test_index]
y_train, y_test = y[train_index], y[test_index]
self.X, self.y = X, y
self.data = (x_train, x_test, y_train, y_test)
def get_rows_msr(data):
conf = get_config()
rng = get_rng()
train = [data[1][idx] for idx in data[3]]
test = [data[1][idx] for idx in data[2]]
# test = [data[1][idx] for idx in data[4]]
shuffle(train, rng.rand)
train_y = [y for y, o, p in train]
# build dev set
sss = StratifiedShuffleSplit(
train_y, 1, train_size=0.8, test_size=0.2, random_state=rng)
train_index, dev_index = sss.__iter__().next()
return [train[i] for i in train_index], [train[i] for i in dev_index], test
def setUp(self):
super(QuasiNewtonTestCase, self).setUp()
X, y = datasets.make_classification(n_samples=100,
n_features=10,
random_state=33)
shuffle_split = StratifiedShuffleSplit(y,
1,
train_size=0.6,
random_state=33)
train_index, test_index = next(shuffle_split.__iter__())
x_train, x_test = X[train_index], X[test_index]
y_train, y_test = y[train_index], y[test_index]
self.X, self.y = X, y
self.data = (x_train, x_test, y_train, y_test)
dataset = task.get_dataset()
# Impute the values - While values would be imputed when calculating some meta-features anyway, this gives more control.
X, y, categorical = dataset.get_data(target = task.target_feature, return_categorical_indicator = True)
#X, categorical = remove_zero_columns(impute_values(X, categorical), categorical)
# Subsample landmarker need folds, the train+test set of subsample landmarkers should be 500 instances,
# since that is the size of our smallest dataset.
# We first create a fold for 500 stratified samples, and then again divide that selection to 10 folds.
max_size = 500
number_of_classes = len(np.unique(y))
if y.shape[0] < (max_size + number_of_classes):
subset_indices = np.arange(max_size)
else:
subset_split = StratifiedShuffleSplit(y, n_iter=1, test_size=500, random_state = 0)
_, subset_indices = next(subset_split.__iter__())
mapped_folds = StratifiedShuffleSplit(y[subset_indices], n_iter=10, test_size=0.2, random_state = 0)
subsample_folds = [(subset_indices[train],subset_indices[test]) for train, test in mapped_folds]
# Because the subsamples are of constant size, always 500, we just calculate them once per dataset,
# not once for every subsample of every dataset (those are stratified anyway)
log("subsample-mf")
subsample_features = subsample_metafeatures(X, y, categorical, subsample_folds)
# We also take subsets of the original dataset, because it creates a bigger metadataset to learn from
for i in np.arange(0.1, 1.01, 0.1):
# We want a minimum size of 500, otherwise predicting runtime is not that useful anyway,
# and it avoids some issues with train/test splits being too small and timing not being accurately measured
if(int(i*len(y)) >= 500):