def train_net(model, loss, config, inputs, labels, batch_size, disp_freq,
current_iter_count):
iter_counter = 0
loss_value = 0
loss_values = []
for input, label in data_iterator(inputs, labels, batch_size):
target = onehot_encoding(label, 10)
iter_counter += 1
# forward net
output = model.forward(input)
# calculate loss
loss_value += loss.forward(output, target)
# generate gradient w.r.t loss
grad = loss.backward(output, target)
# backward gradient
model.backward(grad)
# update layers' weights
model.update(config)
if iter_counter % disp_freq == 0:
loss_values.append({
'iter': current_iter_count + iter_counter,
'loss': loss_value / disp_freq
})
loss_value = 0
current_iter_count += iter_counter
return current_iter_count, loss_values
def train_net(model, loss, config, inputs, labels, batch_size, disp_freq):
iter_counter = 0
loss_list = []
acc_list = []
for input, label in data_iterator(inputs, labels, batch_size):
target = onehot_encoding(label, 10)
iter_counter += 1
# forward net
output = model.forward(input)
# calculate loss
loss_value = loss.forward(output, target)
# generate gradient w.r.t loss
grad = loss.backward(output, target)
# backward gradient
model.backward(grad)
# update layers' weights
model.update(config)
acc_value = calculate_acc(output, label)
loss_list.append(loss_value)
acc_list.append(acc_value)
if iter_counter % disp_freq == 0:
msg = ' Training iter %d, batch loss %.4f, batch acc %.4f' % (iter_counter, np.mean(loss_list), np.mean(acc_list))
loss_list = []
acc_list = []
LOG_INFO(msg)
def test_net(model, loss, inputs, labels, batch_size, epoch, layer_name):
loss_list = []
acc_list = []
for input, label in data_iterator(inputs,
labels,
batch_size,
shuffle=False):
target = onehot_encoding(label, 10)
output, output_visualize = model.forward(input,
visualize=True,
layer_name=layer_name)
# collapse output_visualize into 1 channel
output_visualize = np.sum(output_visualize, axis=(1))
loss_value = loss.forward(output, target)
acc_value = calculate_acc(output, label)
loss_list.append(loss_value)
acc_list.append(acc_value)
msg = ' Testing, total mean loss %.5f, total acc %.5f' % (
np.mean(loss_list), np.mean(acc_list))
LOG_INFO(msg)
# save weights and biases
model.save_weights(loss.name, epoch)
return np.mean(loss_list), np.mean(
acc_list
), output_visualize # output_visualize: batch_size x height x width
def train_net(model, loss, config, inputs, labels, batch_size, disp_freq):
iter_counter = 0
loss_list = []
acc_list = []
for input, label in data_iterator(inputs, labels, batch_size):
target = onehot_encoding(label, 10)
iter_counter += 1
# forward net
output = model.forward(input)
# calculate loss
loss_value = loss.forward(output, target)
# generate gradient w.r.t loss
grad = loss.backward(output, target)
# backward gradient
model.backward(grad)
# update layers' weights
model.update(config)
acc_value = calculate_acc(output, label)
loss_list.append(loss_value)
acc_list.append(acc_value)
if iter_counter % disp_freq == 0:
msg = ' Training iter %d, batch loss %.4f, batch acc %.4f' % (
iter_counter, np.mean(loss_list), np.mean(acc_list))
loss_list = []
acc_list = []
LOG_INFO(msg)
def test_net(model, loss, input_feats, labels, test_mask, label_kind):
target = onehot_encoding(labels, label_kind)
output = model.forward(input_feats)
# set mask
output[~test_mask] = target[~test_mask]
loss_value = loss.forward(output, target)
acc_value = calculate_acc(output, labels, np.sum(test_mask))
msg = ' Testing, total mean loss %.5f, total acc %.5f' % (loss_value,
acc_value)
LOG_INFO(msg)
def train_net(model, loss, config, inputs, labels, batch_size, disp_freq, Loss,
Acur):
iter_counter = 0
loss_list = []
acc_list = []
ll = []
ac = []
for input, label in data_iterator(inputs, labels, batch_size):
target = onehot_encoding(label, 10)
iter_counter += 1
# forward net
output = model.forward(input)
# calculate loss
loss_value = loss.forward(output, target)
# generate gradient w.r.t loss
grad = loss.backward(output, target)
# backward gradient
model.backward(grad)
if loss_value > 1:
config['learning_rate'] = 0.2
elif loss_value > 0.5:
config['learning_rate'] = 0.1
elif loss_value > 0.2:
config['learning_rate'] = 0.05
else:
config['learning_rate'] = max(loss_value / 5.0, 0.005)
# update layers' weights
model.update(config)
acc_value = calculate_acc(output, label)
loss_list.append(loss_value)
acc_list.append(acc_value)
ll.append(loss_value)
ac.append(acc_value)
if iter_counter % disp_freq == 0:
msg = ' Training iter %d, batch loss %.4f, batch acc %.4f' % (
iter_counter, np.mean(loss_list), np.mean(acc_list))
Loss.append(np.mean(loss_list))
Acur.append(np.mean(acc_list))
loss_list = []
acc_list = []
LOG_INFO(msg)
Loss.append(np.mean(ll))
Acur.append(np.mean(ac))
def test_net(model, loss, inputs, labels, batch_size):
loss_list = []
acc_list = []
for input, label in data_iterator(inputs, labels, batch_size, shuffle=False):
target = onehot_encoding(label, 10)
output = model.forward(input)
loss_value = loss.forward(output, target)
acc_value = calculate_acc(output, label)
loss_list.append(loss_value)
acc_list.append(acc_value)
msg = ' Testing, total mean loss %.5f, total acc %.5f' % (np.mean(loss_list), np.mean(acc_list))
LOG_INFO(msg)
def test_net(model, loss, inputs, labels, batch_size):
loss_list = []
acc_list = []
for input, label in data_iterator(inputs, labels, batch_size, shuffle=False):
target = onehot_encoding(label, 10)
output = model.forward(input)
loss_value = loss.forward(output, target)
acc_value = calculate_acc(output, label)
loss_list.append(loss_value)
acc_list.append(acc_value)
msg = ' Testing, total mean loss %.5f, total acc %.5f' % (np.mean(loss_list), np.mean(acc_list))
LOG_INFO(msg)
def train_net(model, loss, config, inputs, labels, batch_size, disp_freq,
test_inputs, test_labels):
iter_counter = 0
train_loss_list, train_acc_list = [], []
test_loss_list, test_acc_list = [], []
# loss_list, acc_list = [], []
for input, label in data_iterator(inputs, labels, batch_size):
# train_loss_value, train_acc_value = test_net(model, loss, input, labels, 10000000)
# train_loss_list.append(train_loss_value)
# train_acc_list.append(train_acc_value)
test_loss_value, test_acc_value = test_net(model, loss, test_inputs,
test_labels, 10000000)
test_loss_list.append(test_loss_value)
test_acc_list.append(test_acc_value)
target = onehot_encoding(label, 10)
iter_counter += 1
# forward net
output = model.forward(input)
# calculate loss
loss_value = loss.forward(output, target)
# generate gradient w.r.t loss
grad = loss.backward(output, target)
# backward gradient
model.backward(grad)
# update layers' weights
model.update(config)
acc_value = calculate_acc(output, label)
# loss_list.append(loss_value)
# acc_list.append(acc_value)
train_loss_list.append(loss_value)
train_acc_list.append(acc_value)
# if iter_counter % disp_freq == 0:
# msg = ' Training iter %d, batch loss %.4f, batch acc %.4f' % (iter_counter, np.mean(loss_list), np.mean(acc_list))
# loss_list = []
# acc_list = []
# LOG_INFO(msg)
return train_loss_list, train_acc_list, test_loss_list, test_acc_list
def test_net(model, loss, inputs, labels, batch_size):
loss_list = []
acc_list = []
# test model with all the test data
for input, label in data_iterator(inputs, labels, batch_size, shuffle=False):
# get the expected value of this batch of input
target = onehot_encoding(label, 10)
output = model.forward(input)
# calculate loss of this batch
loss_value = loss.forward(output, target)
acc_value = calculate_acc(output, label)
loss_list.append(loss_value)
acc_list.append(acc_value)
# use the mean of all batch's loss and accuracy as the final result
msg = ' Testing, total mean loss %.5f, total acc %.5f' % (np.mean(loss_list), np.mean(acc_list))
LOG_INFO(msg)
def train_net(model, loss, config, inputs, labels, batch_size, disp_freq, loss_file):
iter_counter = 0
loss_list = []
acc_list = []
for input, label in data_iterator(inputs, labels, batch_size):
target = onehot_encoding(label, 10)
iter_counter += 1
# print "Debug: ", "input=", input.shape, " target=", target.shape
# forward net
output = model.forward(input)
# calculate loss
loss_value = loss.forward(output, target)
# generate gradient w.r.t loss
grad = loss.backward(output, target)
# backward gradient
model.backward(grad)
# update layers' weights
model.update(config)
acc_value = calculate_acc(output, label)
loss_list.append(loss_value)
acc_list.append(acc_value)
'''
outf = file(loss_file, "a")
outf.write(str(loss_value) + ' ' + str(acc_value) + '\n')
outf.close()
'''
if iter_counter % disp_freq == 0:
msg = ' Training iter %d, batch loss %.4f, batch acc %.4f' % (iter_counter, np.mean(loss_list), np.mean(acc_list))
outf = file(loss_file, "a")
outf.write(str(np.mean(loss_list)) + ' ' + str(np.mean(acc_list)) + '\n')
outf.close()
loss_list = []
acc_list = []
LOG_INFO(msg)
def train_net(model, loss, config, inputs, labels, batch_size, disp_freq, Loss, Acur):
iter_counter = 0
loss_list = []
acc_list = []
ll = []
ac = []
# train model with
for input, label in data_iterator(inputs, labels, batch_size):
target = onehot_encoding(label, 10)
iter_counter += 1
# forward net
output = model.forward(input)
# calculate loss value of the whole batch
loss_value = loss.forward(output, target)
# generate gradient w.r.t loss, this is actually the local gradient contribution of the output layer
grad = loss.backward(output, target)
# backward gradient
model.backward(grad)
# update layers' weights: recount after the whole backward procedure
model.update(config)
acc_value = calculate_acc(output, label)
loss_list.append(loss_value)
ll.append(loss_value)
acc_list.append(acc_value)
ac.append(acc_value)
if iter_counter % disp_freq == 0:
msg = ' Training iter %d, batch loss %.4f, batch acc %.4f' % (iter_counter, np.mean(loss_list), np.mean(acc_list))
loss_list = []
acc_list = []
LOG_INFO(msg)
Loss.append(np.mean(ll))
Acur.append(np.mean(ac))
def train_net(model, loss, config, input_feats, labels, train_mask,
label_kind):
target = onehot_encoding(labels, label_kind)
# forward net
output = model.forward(input_feats)
# set mask
output[~train_mask] = target[~train_mask]
# calculate loss
loss_value = loss.forward(output, target)
# generate gradient w.r.t loss
grad = loss.backward(output, target)
# backward gradient
model.backward(grad)
# update layers' weights
model.update(config)
acc_value = calculate_acc(output, labels, np.sum(train_mask))
msg = ' Training batch loss %.4f, batch acc %.4f' % (loss_value,
acc_value)
LOG_INFO(msg)
def test_net(model, loss, inputs, labels, batch_size, info):
# validation info = [validation, index, learning_rate, momentum, ...]
# test info = [test]
loss_list = []
acc_list = []
for input, label in data_iterator(inputs,
labels,
batch_size,
shuffle=False):
target = onehot_encoding(label, 10)
output = model.forward(input)
loss_value = loss.forward(output, target)
acc_value = np.sum(np.argmax(output, axis=1) == label)
loss_list.append(loss_value / 40)
acc_list.append(acc_value)
#msg = ' Testing, total mean loss %.5f, total acc %.5f' % (np.mean(loss_list), np.mean(acc_list))
#LOG_INFO(msg)
# write back to file...
if info[0] == 0: # validation
file = open('loss_info/loss.txt', 'a')
file.write(
'\n[{}]Val set: Avg. loss: {:.4f}, Accuracy: {}/{} ({:.0f}%), Learning_rate: {:.7f}, Momentum: {:.4f}, Weight Decay: {:.4f}\n---'
.format(info[1], np.mean(loss_list), np.sum(acc_list), batch_size,
100. * np.sum(acc_list) / batch_size, info[2], info[3],
info[4]))
else: # test
file = open('loss_info/loss.txt', 'a')
file.write(
'\nTest set: Avg. loss: {:.4f}, Accuracy: {}/{} ({:.0f}%)'.format(
np.mean(loss_list), np.sum(acc_list), batch_size,
100. * np.sum(acc_list) / batch_size))
return np.mean(loss_list)
def read_data_for_aspect(fname, pre_trained_vectors, embedding_size):
data_csv = pd.read_csv(fname,
sep='\t',
header=None,
index_col=None,
names=['text', 'aspect_l1', 'aspect_l2', 'score'])
data_csv = data_csv.sample(frac=1).reset_index(drop=True) # shuffle data
stop_words = [
',', '.', ':', ';', '?', '(', ')', '[', ']', '!', '@', '#', '%', '$',
'*', '-', '/', '&', '``', "''"
]
max_context_len = 0
word2idx = {} # Index 0 represents words we haven't met before
context = []
context_len = []
aspect_class = []
for index, row in data_csv.iterrows():
word_list = nltk.word_tokenize(row.text.strip())
context_words = [
word for word in word_list
if word not in stop_words and isinteger(word) is False
and isfloat(word) is False and word != 'T'
]
words_have_vector = [
word for word in context_words if word in pre_trained_vectors
]
# make sure most words can find their embedding vectors
if len(words_have_vector) / float(len(context_words)) < 0.8:
continue
max_context_len = max(max_context_len, len(words_have_vector))
idx = []
for word in words_have_vector:
if word not in word2idx:
word2idx[word] = len(
word2idx
) + 1 # Index 0 represents absent words, so start from 1
idx.append(word2idx[word])
context.append(idx)
context_len.append(len(words_have_vector))
aspect_class.append(row.aspect_l1 + '/' + row.aspect_l2)
# convert to numpy format
context_npy = np.zeros(shape=[len(context), max_context_len])
for i in range(len(context)):
context_npy[i, :len(context[i])] = context[i]
aspect_class_npy, onehot_mapping = onehot_encoding(aspect_class)
train_data = list()
train_data.append(context_npy) # [data_size, max_context_len]
train_data.append(np.array(context_len)) # [data_size,]
train_data.append(aspect_class_npy) # [data_size, aspect_class]
word_embeddings = np.zeros([len(word2idx) + 1, embedding_size])
for word in word2idx.keys():
word_embeddings[word2idx[word]] = pre_trained_vectors[word]
return train_data, word_embeddings, word2idx, max_context_len, onehot_mapping
def main(opt, save_dir):
os.environ['CUDA_VISIBLE_DEVICES'] = ','.join(
str(x) for x in opt.test['gpus'])
# img_dir = opt.test['img_dir']
ratio = opt.ratio
img_dir = './data/{:s}/images'.format(opt.dataset)
label_dir = './data/{:s}/labels_point'.format(opt.dataset)
label_instance_dir = './data/{:s}/labels_instance'.format(opt.dataset)
# save_dir = './data/{:s}/selected_masks'.format(opt.dataset)
if not os.path.exists(save_dir):
os.makedirs(save_dir, exist_ok=True)
model_path = opt.test['model_path']
# data transforms
test_transform = get_transforms(opt.transform['test'])
model = ResUNet34(pretrained=opt.model['pretrained'],
with_uncertainty=opt.with_uncertainty)
model = model.cuda()
cudnn.benchmark = True
# ----- load trained model ----- #
# print("=> loading trained model")
checkpoint = torch.load(model_path)
model.load_state_dict(checkpoint['state_dict'])
# print("=> loaded model at epoch {}".format(checkpoint['epoch']))
# switch to evaluate mode
model.eval()
apply_dropout(model)
with open('./data/{:s}/train_val_test.json'.format(opt.dataset),
'r') as file:
data_list = json.load(file)
train_list = data_list['train']
for img_name in tqdm(train_list):
# load test image
# print('=> Processing image {:s}'.format(img_name))
img_path = '{:s}/{:s}'.format(img_dir, img_name)
img = Image.open(img_path)
ori_h = img.size[1]
ori_w = img.size[0]
name = os.path.splitext(img_name)[0]
label_point = misc.imread('{:s}/{:s}_label_point.png'.format(
label_dir, name))
input = test_transform((img, ))[0].unsqueeze(0)
# print('\tComputing unertainty maps...')
mean_sigma = np.zeros((2, ori_h, ori_w))
mean_sigma_normalized = np.zeros((2, ori_h, ori_w))
mean_prob = np.zeros((2, ori_h, ori_w))
for _ in range(opt.T):
output, log_var = get_probmaps(input, model, opt)
output = output.astype(np.float64)
log_var = log_var.astype(np.float64)
sigma_map = np.exp(log_var / 2)
sigma_map_normalized = sigma_map / (np.exp(output) + 1e-8)
mean_prob += np.exp(output) / np.sum(np.exp(output), axis=0)
mean_sigma += sigma_map
mean_sigma_normalized += sigma_map_normalized
mean_prob /= opt.T
mean_sigma /= opt.T
mean_sigma_normalized /= opt.T
un_data_normalized = mean_sigma_normalized**2
pred = np.argmax(mean_prob, axis=0)
un_data_normalized = np.sum(un_data_normalized *
utils.onehot_encoding(pred),
axis=0)
# find the area of largest uncertainty for visualization
threshed = un_data_normalized > 1.0
large_unc_area = morph.opening(threshed, selem=morph.disk(1))
large_unc_area = morph.remove_small_objects(large_unc_area,
min_size=64)
un_data_smoothed = gaussian_filter(un_data_normalized * large_unc_area,
sigma=5)
# cmap = plt.cm.jet
# plt.imsave('{:s}/{:s}_uncertainty.png'.format(save_dir, name), cmap(un_data_normalized))
points = measure.label(label_point)
uncertainty_list = []
radius = 10
for k in range(1, np.max(points) + 1):
x, y = np.argwhere(points == k)[0]
r1 = x - radius if x - radius > 0 else 0
r2 = x + radius if x + radius < ori_h else ori_h
c1 = y - radius if y - radius > 0 else 0
c2 = y + radius if y + radius < ori_w else ori_w
uncertainty = np.mean(un_data_smoothed[r1:r2, c1:c2])
uncertainty_list.append([k, uncertainty])
uncertainty_list = np.array(uncertainty_list)
sorted_list = uncertainty_list[uncertainty_list[:, 1].argsort()[::-1]]
indices = sorted_list[:int(ratio * np.max(points)), 0]
# annotation
label_instance = misc.imread('{:s}/{:s}_label.png'.format(
label_instance_dir, name))
new_anno = np.zeros_like(label_instance)
counter = 1
for idx in indices:
nuclei_idx = np.unique(label_instance[points == idx])[0]
if nuclei_idx == 0:
continue
new_anno += (label_instance == nuclei_idx) * counter
counter += 1
# utils.show_figures((new_anno,))
misc.imsave('{:s}/{:s}_label_partial_mask.png'.format(save_dir, name),
new_anno.astype(np.uint8))
misc.imsave(
'{:s}/{:s}_label_partial_mask_binary.png'.format(save_dir, name),
(new_anno > 0).astype(np.uint8) * 255)
print('=> Processed all images')
seed=cfg_fe.seed,
runty=runty,
path=save_path)
elif runty == 'eval':
x_train, x_test = fe_cluster(x_train,
x_test,
genes_features,
cells_features,
n_cluster_g=cfg_fe.n_clusters_g,
n_cluster_c=cfg_fe.n_clusters_c,
seed=cfg_fe.seed,
runty=runty,
path=load_path)
# one-hot encoding
x_train = onehot_encoding(x_train)
x_test = onehot_encoding(x_test)
feature_cols = [
c for c in x_train.columns
if (str(c)[0:5] != 'kfold'
and c not in ['sig_id', 'drug_id', 'cp_type', 'cp_time', 'cp_dose'])
]
target_cols = [x for x in y_train.columns if x != 'sig_id']
# label smoothing
if cfg_fe.regularization_ls:
y_train = ls_manual(y_train, ls_rate=cfg_fe.ls_rate)
# merge drug_id and labels
x_train = x_train.merge(y_train, on='sig_id')
def main():
cfg_fe = Config_FeatureEngineer()
seed_everything(seed_value=cfg_fe.seed)
data_dir = '/kaggle/input/lish-moa/'
save_path = './'
load_path = '/kaggle/input/moatabnetmultimodekfold/'
runty = 'eval'
train = pd.read_csv(os.path.join(data_dir, 'train_features.csv'))
targets_scored = pd.read_csv(
os.path.join(data_dir, 'train_targets_scored.csv'))
test = pd.read_csv(os.path.join(data_dir, 'test_features.csv'))
train_drug = pd.read_csv(os.path.join(data_dir, 'train_drug.csv'))
submission = pd.read_csv(os.path.join(data_dir, 'sample_submission.csv'))
x_train = train.copy()
x_test = test.copy()
y_train = targets_scored.copy()
genes_features = [column for column in x_train.columns if 'g-' in column]
cells_features = [column for column in x_train.columns if 'c-' in column]
# scale the data, like RankGauss
x_train, x_test = scaling(x_train,
x_test,
scale=cfg_fe.scale,
n_quantiles=cfg_fe.scale_n_quantiles,
seed=cfg_fe.seed)
# decompose data, like PCA
if runty == 'traineval':
x_train, x_test = decompo_process(x_train,
x_test,
decompo=cfg_fe.decompo,
genes_variance=cfg_fe.genes_variance,
cells_variance=cfg_fe.cells_variance,
seed=cfg_fe.seed,
pca_drop_orig=cfg_fe.pca_drop_orig,
runty=runty,
path=save_path)
elif runty == 'eval':
x_train, x_test = decompo_process(x_train,
x_test,
decompo=cfg_fe.decompo,
genes_variance=cfg_fe.genes_variance,
cells_variance=cfg_fe.cells_variance,
seed=cfg_fe.seed,
pca_drop_orig=cfg_fe.pca_drop_orig,
runty=runty,
path=load_path)
# select feature, VarianceThreshold
x_train, x_test = feature_selection(
x_train,
x_test,
feature_select=cfg_fe.feature_select,
variancethreshold_for_FS=cfg_fe.variancethreshold_for_FS)
# fe_stats
x_train, x_test = fe_stats(x_train, x_test, genes_features, cells_features)
# group the drug using kmeans
if runty == 'traineval':
x_train, x_test = fe_cluster(x_train,
x_test,
genes_features,
cells_features,
n_cluster_g=cfg_fe.n_clusters_g,
n_cluster_c=cfg_fe.n_clusters_c,
seed=cfg_fe.seed,
runty=runty,
path=save_path)
elif runty == 'eval':
x_train, x_test = fe_cluster(x_train,
x_test,
genes_features,
cells_features,
n_cluster_g=cfg_fe.n_clusters_g,
n_cluster_c=cfg_fe.n_clusters_c,
seed=cfg_fe.seed,
runty=runty,
path=load_path)
# one-hot encoding
x_train = onehot_encoding(x_train)
x_test = onehot_encoding(x_test)
feature_cols = [
c for c in x_train.columns
if (str(c)[0:5] != 'kfold' and c not in
['sig_id', 'drug_id', 'cp_type', 'cp_time', 'cp_dose'])
]
target_cols = [x for x in y_train.columns if x != 'sig_id']
# label smoothing
if cfg_fe.regularization_ls:
y_train = ls_manual(y_train, ls_rate=cfg_fe.ls_rate)
# merge drug_id and labels
x_train = x_train.merge(y_train, on='sig_id')
x_train = x_train.merge(train_drug, on='sig_id')
# remove sig_id
# x_train, x_test, y_train = remove_ctl(x_train, x_test, y_train)
# make CVs
target_cols = [x for x in targets_scored.columns if x != 'sig_id']
x_train = make_cv_folds(x_train, cfg_fe.seeds, cfg_fe.nfolds,
cfg_fe.drug_thresh, target_cols)
begin_time = datetime.datetime.now()
if (runty == 'traineval'):
test_preds_all = train_tabnet(x_train, y_train, x_test, submission,
feature_cols, target_cols, cfg_fe.seeds,
cfg_fe.nfolds, save_path)
y_train = targets_scored[
train['cp_type'] != 'ctl_vehicle'].reset_index(drop=True)
test_pred_final = pred_tabnet(x_train,
y_train,
x_test,
submission,
feature_cols,
target_cols,
cfg_fe.seeds,
cfg_fe.nfolds,
load_path='./',
stacking=False)
elif (runty == 'eval'):
y_train = targets_scored[
train['cp_type'] != 'ctl_vehicle'].reset_index(drop=True)
test_pred_final = pred_tabnet(x_train,
y_train,
x_test,
submission,
feature_cols,
target_cols,
cfg_fe.seeds,
cfg_fe.nfolds,
load_path,
stacking=False)
time_diff = datetime.datetime.now() - begin_time
print(f'Total time is {time_diff}')
# make submission
all_feat = [col for col in submission.columns if col not in ["sig_id"]]
# To obtain the same lenght of test_preds_all and submission
# sig_id = test[test["cp_type"] != "ctl_vehicle"].sig_id.reset_index(drop=True)
sig_id = test.sig_id
tmp = pd.DataFrame(test_pred_final, columns=all_feat)
tmp["sig_id"] = sig_id
submission = pd.merge(test[["sig_id"]], tmp, on="sig_id", how="left")
submission.fillna(0, inplace=True)
submission[test["cp_type"] == "ctl_vehicle"] = 0.
submission.to_csv("submission_tabbet.csv", index=None)