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data.py
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import numpy as np
import csv
import scipy.io
from tensorflow.keras.datasets import mnist as mnist_keras, fashion_mnist as fashion_mnist_keras, \
cifar10 as cifar10_keras
data_dir = '/home/maksym/boost/data/'
def split_train_test(X_all, y_all, frac_train):
"""
The first X% of X_all, y_all become the training set, the rest (1-X)% become the test set.
Note that this assumes that the samples are already shuffled or if not (e.g. if we were to split MNIST) that
this behavior is intended.
"""
num_total = X_all.shape[0]
num_train = int(frac_train * num_total)
X_train, y_train = X_all[:num_train], y_all[:num_train]
X_test, y_test = X_all[num_train:], y_all[num_train:]
return X_train, y_train, X_test, y_test
def normalize_per_feature_0_1(X_train, X_test):
"""
We are not allowed to touch the test data, thus we do the normalization just based on the training data.
"""
X_train_max = X_train.max(axis=0, keepdims=True)
X_train_min = X_train.min(axis=0, keepdims=True)
X_train = (X_train - X_train_min) / (X_train_max - X_train_min)
X_test = (X_test - X_train_min) / (X_train_max - X_train_min)
return X_train, X_test
def split_train_validation(X_train_orig, y_train_orig, frac_valid, shuffle=True):
num_total = X_train_orig.shape[0]
n_valid = int(frac_valid*num_total)
idx = np.random.permutation(num_total) if shuffle else np.arange(num_total)
if shuffle:
X_valid, y_valid = X_train_orig[idx][:n_valid], y_train_orig[idx][:n_valid]
X_train, y_train = X_train_orig[idx][n_valid:], y_train_orig[idx][n_valid:]
else:
# If no shuffle, then one has to ensure that the classes are balanced
idx_valid, idx_train = [], []
for cls in np.unique(y_train_orig):
indices_cls = np.where(y_train_orig == cls)[0]
proportion_cls = len(indices_cls) / num_total
n_class_balanced_valid = int(proportion_cls * n_valid)
idx_valid.extend(list(indices_cls[:n_class_balanced_valid]))
idx_train.extend(list(indices_cls[n_class_balanced_valid:]))
idx_valid, idx_train = np.array(idx_valid), np.array(idx_train)
X_valid, y_valid = X_train_orig[idx_valid], y_train_orig[idx_valid]
X_train, y_train = X_train_orig[idx_train], y_train_orig[idx_train]
return X_train, y_train, X_valid, y_valid
def binary_from_multiclass(X_train, y_train, X_test, y_test, classes):
classes = np.array(classes) # for indexing only arrays work, not lists
idx_train1, idx_train2 = y_train == classes[0], y_train == classes[1]
idx_test1, idx_test2 = y_test == classes[0], y_test == classes[1]
X_train, X_test = X_train[idx_train1 + idx_train2], X_test[idx_test1 + idx_test2]
y_train = idx_train1 * 1 + idx_train2 * -1
y_test = idx_test1 * 1 + idx_test2 * -1
y_train, y_test = y_train[idx_train1 + idx_train2], y_test[idx_test1 + idx_test2]
return X_train, y_train, X_test, y_test
def transform_labels_one_vs_all(y_train_orig, y_valid_orig, y_test_orig):
n_cls = int(y_train_orig.max()) + 1
if n_cls == 2:
return y_train_orig[None, :], y_valid_orig[None, :], y_test_orig[None, :]
labels = np.unique(y_train_orig)
n_cls = len(labels)
n_train, n_valid, n_test = y_train_orig.shape[0], y_valid_orig.shape[0], y_test_orig.shape[0]
y_train, y_valid, y_test = np.zeros([n_cls, n_train]), np.zeros([n_cls, n_valid]), np.zeros([n_cls, n_test])
for i_cls in range(n_cls):
# convert from False/True to -1/1 compatible with One-vs-All formulation
y_train[i_cls] = 2 * (y_train_orig == i_cls) - 1
y_valid[i_cls] = 2 * (y_valid_orig == i_cls) - 1
y_test[i_cls] = 2 * (y_test_orig == i_cls) - 1
return y_train, y_valid, y_test
def toy_2d_stumps():
X = np.array([[0.38, 0.75], [0.50, 0.93], [0.05, 0.70], [0.30, 0.90], [0.15, 0.80],
# [0.15, 1.0], [0.125, 0.75], [0.1, 0.85], [0.045, 0.22], [0.725, 0.955], # small margin
# [0.15, 1.0], [0.125, 0.75], [0.1, 0.85], [0.075, 0.2], [0.775, 0.925], # small margin
[0.15, 1.0], [0.125, 0.5], [0.1, 0.85], [0.02, 0.25], [0.775, 0.975],
[0.05, 0.05], [0.2, 0.1], [0.4, 0.075], [0.6, 0.22], [0.8, 0.1],
[0.95, 0.05], [0.9, 0.2], [0.925, 0.4], [0.79, 0.6], [0.81, 0.8]])
y = np.array([-1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1])
eps_dataset = 0.075
return X, y, eps_dataset
def toy_2d_trees():
X = np.array([[0.38, 0.75], [0.50, 0.93], [0.05, 0.70], [0.30, 0.90], [0.15, 0.80],
[0.75, 0.38], [0.95, 0.48], [0.70, 0.05], [0.65, 0.30], [0.80, 0.30],
[0.05, 0.1], [0.35, 0.1], [0.45, 0.075], [0.3, 0.2], [0.25, 0.1],
[0.95, 0.65], [0.7, 0.9], [0.925, 0.7], [0.79, 0.55], [0.81, 0.8]])
y = np.array([-1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1])
eps_dataset = 0.075
return X, y, eps_dataset
def toy_2d_xor():
X = np.array([[0.05, 0.05], [0.95, 0.95], [0.05, 0.95], [0.95, 0.05]])
y = np.array([-1, -1, 1, 1])
eps_dataset = 0.15
return X, y, eps_dataset
def toy_2d_wong():
# random points at least 2r apart
m = 12
# seed=10 illustrates that by default the margin can be easily close to 0
# both plain and robust model have 0 train error, but the robust model additionally enforces a large margin
np.random.seed(10)
x = [np.random.uniform(size=2)]
r = 0.16
while len(x) < m:
p = np.random.uniform(size=2)
if min(np.abs(p - a).sum() for a in x) > 2 * r:
x.append(p)
eps_dataset = r / 2
X = np.array(x)
y = np.sign(np.random.uniform(-0.5, 0.5, size=m))
return X, y, eps_dataset
def breast_cancer():
"""
Taken from the UCI repository:
http://archive.ics.uci.edu/ml/datasets/breast+cancer+wisconsin+%28diagnostic%29 file: breast-cancer-wisconsin.data
After filtering the points with missing data, we have exactly the same as Chen et al, 2019
train: 546x10, test: 137x10
"""
eps_dataset = 0.3 # same as in Chen et al, 2019, worked well for them
path = data_dir + 'breast_cancer/breast-cancer-wisconsin.data'
lst = []
for line in csv.reader(open(path, 'r').readlines()):
if '?' not in line:
lst.append(line)
data_arr = np.array(lst, dtype=int)
X_all, y_all = data_arr[:, :10], data_arr[:, 10]
y_all[y_all == 2], y_all[y_all == 4] = -1, 1 # from 2, 4 to -1, 1
X_train, y_train, X_test, y_test = split_train_test(X_all, y_all, frac_train=0.8)
X_train, X_test = normalize_per_feature_0_1(X_train, X_test)
return X_train, y_train, X_test, y_test, eps_dataset
def diabetes():
"""
Taken from Kaggle:
https://www.kaggle.com/uciml/pima-indians-diabetes-database file: diabetes.csv
train: 614x8, test: 154x8
"""
eps_dataset = 0.05 # Chen et al, 2019 used 0.2, but it was too high
path = data_dir + 'diabetes/diabetes.csv'
data_arr = np.loadtxt(path, delimiter=',', skiprows=1) # loaded as float64
X_all, y_all = data_arr[:, :8], data_arr[:, 8]
y_all[y_all == 0], y_all[y_all == 1] = -1, 1 # from 0, 1 to -1, 1
X_train, y_train, X_test, y_test = split_train_test(X_all, y_all, frac_train=0.8)
X_train, X_test = normalize_per_feature_0_1(X_train, X_test)
return X_train, y_train, X_test, y_test, eps_dataset
def ijcnn1():
"""
Taken from LIBSVM data repository:
https://www.csie.ntu.edu.tw/~cjlin/libsvmtools/datasets/binary.html
train: 49990x22, test: 91701x22
note: imbalanced classes (-1: 90.3% vs 1: 9.7%)
"""
eps_dataset = 0.01 # Chen et al, 2019 used 0.1, but it was too high
folder = data_dir + 'ijcnn1/'
path_train, path_val, path_test = folder + 'ijcnn1.tr', folder + 'ijcnn1.val', folder + 'ijcnn1.t'
num_train, num_test, dim = 49990, 91701, 22
X_train = np.zeros((num_train, dim))
y_train = np.zeros(num_train)
num_train_orig = 0
for i, line in enumerate(open(path_train, 'r').readlines()):
y_train[i] = int(float(line.split(' ')[0])) # -1 or 1
for s in line.split(' ')[1:]:
coord_str, val_str = s.replace('\n', '').split(':')
coord, val = int(coord_str) - 1, float(val_str) # -1 is needed to have pythonic numeration from 0
X_train[i, coord] = val
num_train_orig += 1
num_val_orig = 0
for i, line in enumerate(open(path_val, 'r').readlines()):
y_train[num_train_orig + i] = int(float(line.split(' ')[0])) # -1 or 1
for s in line.split(' ')[1:]:
coord_str, val_str = s.replace('\n', '').split(':')
coord, val = int(coord_str) - 1, float(val_str)
X_train[num_train_orig + i, coord] = val
num_val_orig += 1
assert num_train == num_train_orig + num_val_orig # Check that we have not introduced extra zero rows
X_test = np.zeros((num_test, dim))
y_test = np.zeros(num_test)
num_test_orig = 0
for i, line in enumerate(open(path_test, 'r').readlines()):
y_test[i] = int(float(line.split(' ')[0])) # -1 or 1
for s in line.split(' ')[1:]:
coord_str, val_str = s.replace('\n', '').split(':')
coord, val = int(coord_str) - 1, float(val_str)
X_test[i, coord] = val
num_test_orig += 1
assert num_test == num_test_orig
X_train, X_test = normalize_per_feature_0_1(X_train, X_test)
return X_train, y_train, X_test, y_test, eps_dataset
def cod_rna():
"""
Taken from LIBSVM data repository:
https://www.csie.ntu.edu.tw/~cjlin/libsvmtools/datasets/binary.html
train: 59535x8, test: 271617x8
"""
eps_dataset = 0.025 # Chen et al, 2019 used 0.2, but it was too high
folder = data_dir + 'cod_rna/'
path_train, path_test = folder + 'cod-rna.tr', folder + 'cod-rna.t'
num_train, num_test, dim = 59535, 271617, 8
X_train = np.zeros((num_train, dim))
y_train = np.zeros(num_train)
num_train_orig = 0
for i, line in enumerate(open(path_train, 'r').readlines()):
y_train[i] = int(float(line.split(' ')[0])) # -1 or 1
for s in line.split(' ')[1:]:
coord_str, val_str = s.replace('\n', '').split(':')
coord, val = int(coord_str) - 1, float(val_str) # -1 is needed to have pythonic numeration from 0
X_train[i, coord] = val
num_train_orig += 1
assert num_train == num_train_orig # Check that we have not introduced extra zero rows
X_test = np.zeros((num_test, dim))
y_test = np.zeros(num_test)
num_test_orig = 0
for i, line in enumerate(open(path_test, 'r').readlines()):
y_test[i] = int(float(line.split(' ')[0])) # -1 or 1
for s in line.split(' ')[1:]:
coord_str, val_str = s.replace('\n', '').split(':')
coord, val = int(coord_str) - 1, float(val_str)
X_test[i, coord] = val
num_test_orig += 1
assert num_test == num_test_orig
X_train, X_test = normalize_per_feature_0_1(X_train, X_test)
# n_test_final = 10000 # take 10k test examples instead of all 270k
n_test_final = num_test
idx = np.random.permutation(num_test)[:n_test_final]
X_test, y_test = X_test[idx], y_test[idx]
return X_train, y_train, X_test, y_test, eps_dataset
def mnist_1_5():
"""
train: (12163, 784), test: (2027, 784)
"""
eps_dataset = 0.3
classes = [1, 5] # 2 is 1, 6 is -1 in the binary classification scheme
(X_train, y_train), (X_test, y_test) = mnist_keras.load_data()
X_train, X_test = X_train.astype(np.float64) / 255.0, X_test.astype(np.float64) / 255.0
X_train = np.reshape(X_train, [X_train.shape[0], -1])
X_test = np.reshape(X_test, [X_test.shape[0], -1])
X_train, y_train, X_test, y_test = binary_from_multiclass(X_train, y_train, X_test, y_test, classes)
return X_train, y_train, X_test, y_test, eps_dataset
def mnist_2_6():
"""
train: (11876, 784), test: (1990, 784)
"""
eps_dataset = 0.3
classes = [2, 6] # 2 is 1, 6 is -1 in the binary classification scheme
(X_train, y_train), (X_test, y_test) = mnist_keras.load_data()
X_train, X_test = X_train.astype(np.float64) / 255.0, X_test.astype(np.float64) / 255.0
X_train = np.reshape(X_train, [X_train.shape[0], -1])
X_test = np.reshape(X_test, [X_test.shape[0], -1])
X_train, y_train, X_test, y_test = binary_from_multiclass(X_train, y_train, X_test, y_test, classes)
return X_train, y_train, X_test, y_test, eps_dataset
def mnist():
"""
train: (60000, 784), test: (10000, 784)
"""
eps_dataset = 0.3
(X_train, y_train), (X_test, y_test) = mnist_keras.load_data()
X_train, X_test = X_train.astype(np.float64) / 255.0, X_test.astype(np.float64) / 255.0
X_train = np.reshape(X_train, [X_train.shape[0], -1])
X_test = np.reshape(X_test, [X_test.shape[0], -1])
return X_train, y_train, X_test, y_test, eps_dataset
def cifar10():
"""
train: (60000, 3072), test: (10000, 3072)
"""
eps_dataset = 8/255
(X_train, y_train), (X_test, y_test) = cifar10_keras.load_data()
X_train, X_test = X_train.astype(np.float64) / 255.0, X_test.astype(np.float64) / 255.0
X_train = np.reshape(X_train, [X_train.shape[0], -1])
X_test = np.reshape(X_test, [X_test.shape[0], -1])
y_train, y_test = y_train.flatten(), y_test.flatten()
return X_train, y_train, X_test, y_test, eps_dataset
def fmnist_sandal_sneaker():
"""
Classes:
0 T-shirt/top
1 Trouser
2 Pullover
3 Dress
4 Coat
5 Sandal
6 Shirt
7 Sneaker
8 Bag
9 Ankle boot
train: (12000, 784), test: (2000, 784)
"""
eps_dataset = 0.1
classes = [5, 7] # 5 is 1, 7 is -1 in the binary classification scheme
(X_train, y_train), (X_test, y_test) = fashion_mnist_keras.load_data()
X_train, X_test = X_train.astype(np.float64) / 255.0, X_test.astype(np.float64) / 255.0
X_train = np.reshape(X_train, [X_train.shape[0], -1])
X_test = np.reshape(X_test, [X_test.shape[0], -1])
X_train, y_train, X_test, y_test = binary_from_multiclass(X_train, y_train, X_test, y_test, classes)
return X_train, y_train, X_test, y_test, eps_dataset
def fmnist():
"""
train: (60000, 784), test: (10000, 784)
"""
eps_dataset = 0.1
(X_train, y_train), (X_test, y_test) = fashion_mnist_keras.load_data()
X_train, X_test = X_train.astype(np.float64) / 255.0, X_test.astype(np.float64) / 255.0
X_train = np.reshape(X_train, [X_train.shape[0], -1])
X_test = np.reshape(X_test, [X_test.shape[0], -1])
return X_train, y_train, X_test, y_test, eps_dataset
def gts_100_roadworks():
"""
the class ids can be checked in the original data folders, for example:
1: speed 30, 4: speed 70, 7: speed 100, 8: speed 120, 18: warning, 25: roadworks
train: (2940, 3072), test: (930, 3072)
"""
eps_dataset = 8 / 255 # following Madry et al, 2017 for cifar10
classes = [7, 25]
# Originally, all pixels values are uint8 values in [0, 255]
train = scipy.io.loadmat(data_dir + 'gts/gts_int_train.mat')
test = scipy.io.loadmat(data_dir + 'gts/gts_int_test.mat')
X_train, y_train, X_test, y_test = train['images'], train['labels'], test['images'], test['labels']
X_train, X_test = X_train.reshape(X_train.shape[0], -1), X_test.reshape(X_test.shape[0], -1)
X_train, X_test = X_train / 255.0, X_test / 255.0
y_train, y_test = y_train[0], y_test[0] # get rid of the extra dimension
X_train, y_train, X_test, y_test = binary_from_multiclass(X_train, y_train, X_test, y_test, classes)
return X_train, y_train, X_test, y_test, eps_dataset
def gts_30_70():
"""
the class ids can be checked in the original data folders, for example:
1: speed 30, 4: speed 70, 7: speed 100, 8: speed 120, 18: warning, 25: roadworks
train: 4200x3072, test: 1380x3072
"""
eps_dataset = 8 / 255 # following Madry et al, 2017 for cifar10
classes = [1, 4]
# Originally, all pixels values are uint8 values in [0, 255]
train = scipy.io.loadmat(data_dir + 'gts/gts_int_train.mat')
test = scipy.io.loadmat(data_dir + 'gts/gts_int_test.mat')
X_train, y_train, X_test, y_test = train['images'], train['labels'], test['images'], test['labels']
X_train, X_test = X_train.reshape(X_train.shape[0], -1), X_test.reshape(X_test.shape[0], -1)
X_train, X_test = X_train / 255.0, X_test / 255.0
y_train, y_test = y_train[0], y_test[0] # get rid of the extra dimension
X_train, y_train, X_test, y_test = binary_from_multiclass(X_train, y_train, X_test, y_test, classes)
return X_train, y_train, X_test, y_test, eps_dataset
def har():
"""
Human activity recognition dataset from https://archive.ics.uci.edu/ml/datasets/human+activity+recognition+using+smartphones
Note: Wong and Kolter, ICML 2018 used eps=0.05, but the data points were from -1 to 1.
We use equivalently eps=0.025, but data points from 0 to 1.
The labels are in {0, 1, 2, 3, 4, 5}.
train: (7352, 561), test: (2947, 561), n classes: 6.
"""
eps_dataset = 0.025
path_train, path_test = data_dir + 'har/train/', data_dir + 'har/test/'
X_train, X_test = np.loadtxt(path_train + 'X_train.txt'), np.loadtxt(path_test + 'X_test.txt')
y_train, y_test = np.loadtxt(path_train + 'y_train.txt'), np.loadtxt(path_test + 'y_test.txt')
y_train, y_test = y_train - 1, y_test - 1 # make the class numeration start from 0
X_train, X_test = (X_train + 1) / 2, (X_test + 1) / 2 # from [-1, 1] to [0, 1]
return X_train, y_train, X_test, y_test, eps_dataset
def convert_to_float32(X):
return X.astype(np.float32)
def random_crop(image, n_crop):
h, w, _ = image.shape
top = np.random.randint(0, n_crop)
left = np.random.randint(0, n_crop)
bottom = h - (n_crop - top)
right = w - (n_crop - left)
image = image[top:bottom, left:right, :]
return image
def horizontal_flip(images, prob=0.5):
if np.random.rand() < prob:
images = images[:, :, ::-1, :]
return images
def data_augment(X, dataset):
num, dim = X.shape
img_shape = datasets_img_shapes[dataset]
X_img = np.reshape(np.copy(X), [num, *img_shape])
if len(img_shape) == 2: # introduce a fake last dimension for grayscale datasets
X_img = X_img[:, :, :, None]
n_crop = 2
X_img_pad = np.pad(X_img, [(0, 0), (n_crop//2, n_crop//2), (n_crop//2, n_crop//2), (0, 0)], 'constant', constant_values=0) # zero padding
for i in range(num):
X_img[i] = random_crop(X_img_pad[i], n_crop=n_crop) # up to `n_crop` pixels are cropped
if dataset in ['cifar10']:
X_img = horizontal_flip(X_img)
return np.reshape(X_img, [num, dim])
def crop_batch(X_img, n_h, n_w, n_crop):
_, h, w, _ = X_img.shape
bottom, right = h - (n_crop - n_h), w - (n_crop - n_w)
return X_img[:, n_h:bottom, n_w:right, :]
def extend_dataset(X, dataset):
num, dim = X.shape
img_shape = datasets_img_shapes[dataset]
X_img = np.reshape(np.copy(X), [num, *img_shape])
if len(img_shape) == 2: # introduce a fake last dimension for grayscale datasets
X_img = X_img[:, :, :, None]
n_crop = 2
X_img_pad = np.pad(X_img, [(0, 0), (n_crop // 2, n_crop // 2), (n_crop // 2, n_crop // 2), (0, 0)], 'constant',
constant_values=0)
# Note: (1, 1) is the original image
X_img_l = crop_batch(X_img_pad, 1, 0, n_crop)
X_img_r = crop_batch(X_img_pad, 1, 2, n_crop)
X_img_t = crop_batch(X_img_pad, 0, 1, n_crop)
X_img_b = crop_batch(X_img_pad, 2, 1, n_crop)
X_img_extended = np.vstack([X_img, X_img_l, X_img_r, X_img_t, X_img_b])
# if dataset in ['cifar10']: # would lead to 10x expansion of the training data - might be too comp. expensive
# X_img_horiz_flip = X_img_extended[:, :, ::-1, :]
# X_img_extended = np.vstack([X_img_extended, X_img_horiz_flip])
X_final = np.reshape(X_img_extended, [-1, dim])
return X_final
all_datasets_dict = {
'toy_2d_stumps': toy_2d_stumps,
'toy_2d_trees': toy_2d_trees,
'toy_2d_xor': toy_2d_xor,
'toy_2d_wong': toy_2d_wong,
'breast_cancer': breast_cancer,
'diabetes': diabetes,
'ijcnn1': ijcnn1,
'cod_rna': cod_rna,
'mnist_1_5': mnist_1_5,
'mnist_2_6': mnist_2_6,
'fmnist_sandal_sneaker': fmnist_sandal_sneaker,
'gts_100_roadworks': gts_100_roadworks,
'gts_30_70': gts_30_70,
'har': har,
'mnist': mnist,
'fmnist': fmnist,
'cifar10': cifar10,
}
dataset_names_dict = {
'toy_2d_stumps': 'toy_2d_stumps',
'toy_2d_trees': 'toy_2d_trees',
'toy_2d_xor': 'toy_2d_xor',
'toy_2d_wong': 'toy_2d_wong',
'breast_cancer': 'breast-cancer',
'diabetes': 'diabetes',
'ijcnn1': 'IJCNN1',
'cod_rna': 'cod-rna',
'mnist_1_5': 'MNIST 1-5',
'mnist_2_6': 'MNIST 2-6',
'fmnist_sandal_sneaker': 'FMNIST shoes',
'gts_100_roadworks': 'GTS 100-rw',
'gts_30_70': 'GTS 30-70',
'har': 'har',
'mnist': 'mnist',
'fmnist': 'fmnist',
'cifar10': 'cifar10',
}
datasets_img_shapes = {
'mnist_1_5': (28, 28),
'mnist_2_6': (28, 28),
'mnist': (28, 28),
'fmnist': (28, 28),
'fmnist_sandal_sneaker': (28, 28),
'gts_100_roadworks': (32, 32, 3),
'gts_30_70': (32, 32, 3),
'cifar10': (32, 32, 3),
}
datasets_feature_names = {
'breast_cancer': ['radius', 'texture', 'perimeter', 'area', 'smoothness', 'compactness', 'concavity', 'concave points', 'symmetry', 'fractal dimension'],
'diabetes': ['# pregnancies', 'glucose', 'blood pressure', 'skin thickness', 'insulin', 'body mass index', 'diabetes pedigree', 'age'],
'cod_rna': ['Dynalign score', 'shorter seq. length', 'A freq. of seq. 1', 'U freq. of seq. 1', 'C freq. of seq. 1', 'A freq. of seq. 2', 'U freq. of seq. 2', 'C freq. of seq. 2'],
}