def make_train_loader(small=False):
#TODO update with new amounts of tensors
if small:
# equal amount of patients from each class = |smallest class|
train_indices = list(range(26750, 29876)) # class 1 & 2
train_indices.extend(random.sample(range(0, 26750), 1600)) # class 0
train_indices.extend(random.sample(range(29876, 32750),
1600)) # class 3
train_indices.extend(random.sample(range(32750, 36798),
1400)) # class 4
train_data = Dataset(train_indices, train_path)
return DataLoader(train_data,
batch_size=args.batch,
shuffle=True,
collate_fn=collate_fn)
else:
# equal amount of patients from each class = |largest class|
train_indices = list(range(26750, 29876)) * 3 # class 1 & 2
train_indices.extend(random.sample(range(0, 26750), 2505)) # class 0
train_indices.extend(list(range(29876, 32750))) # class 3
train_indices.extend(random.sample(range(29876, 32750),
762)) # class 3
train_indices.extend(list(range(32750, 36798))) # class 4
train_data = Dataset(train_indices, train_path)
return DataLoader(train_data,
batch_size=args.batch,
shuffle=True,
collate_fn=collate_fn)
def validation(database_img, query_img, config):
model = DVSQ(config)
img_database = Dataset(database_img, config['output_dim'],
config['n_subspace'] * config['n_subcenter'])
img_query = Dataset(query_img, config['output_dim'],
config['n_subspace'] * config['n_subcenter'])
model.validation(img_query, img_database, config['R'])
return
def load_x(ds, preset):
feature_parts = [Dataset.load_part(ds, part) for part in preset.get('features', [])]
prediction_parts = [load_prediction(ds, p, mode=preset.get('predictions_mode', 'fulltrain')) for p in preset.get('predictions', [])]
prediction_parts = [p.clip(lower=0.1).values.reshape((p.shape[0], 1)) for p in prediction_parts]
if 'prediction_transform' in preset:
prediction_parts = map(preset['prediction_transform'], prediction_parts)
return hstack(feature_parts + prediction_parts)
def experiment(p, trainData, validData, testData, eps, hparams, run,
resultRep):
trainS, trainX1, trainX2, trainY = copy.deepcopy(trainData)
validS, validX1, validX2, validY = copy.deepcopy(validData)
testS, testX1, testX2, testY = copy.deepcopy(testData)
dataset = Dataset(trainS, trainX1, trainX2, trainY)
dataset.add_validdata(validS, validX1, validX2, validY)
dataset.add_testdata(testS, testX1, testX2, testY)
avails = []
for j in range(len(testS[0])):
vals = set()
vals = vals.union(set([s[j] for s in trainS]))
#print "trainS=",trainS
vals = vals.union(set([s[j] for s in validS]))
#print "validS=",trainS
vals = vals.union(set([s[j] for s in testS]))
#print "testS=",trainS
avails.append(vals == set([0, 1]))
#print "j,vals=",j,vals
result_unfair_train, result_unfair_valid, result_unfair_test = dataset.Unfair_Prediction(
p.kernel or p.rff, hparams["lmd"], hparams["gamma"], avails)
title = {}
result_train, result_valid, result_test = dataset.EpsFair_Prediction(
p.dataset, eps, hparams, avails, p)
title["hparam"] = hparams
title["preprocessing"] = p.preprocessing
title["run"] = run
if p.kernel:
title["kernel"] = "kernel"
elif p.rff and p.nonlinears:
title["kernel"] = "rff-ns"
elif p.rff:
title["kernel"] = "rff"
else:
title["kernel"] = "no"
title["eps"] = eps
title["dataset"] = "train"
resultRep.add_run(copy.deepcopy(title), result_train)
title["dataset"] = "valid"
resultRep.add_run(copy.deepcopy(title), result_valid)
title["dataset"] = "test"
resultRep.add_run(copy.deepcopy(title), result_test)
title["eps"] = "unfair"
title["dataset"] = "train"
resultRep.add_run(copy.deepcopy(title), result_unfair_train)
title["dataset"] = "valid"
resultRep.add_run(copy.deepcopy(title), result_unfair_valid)
title["dataset"] = "test"
resultRep.add_run(copy.deepcopy(title), result_unfair_test)
def extract_feature_names(preset):
x = []
for part in preset.get('features', []):
x += Dataset.get_part_features(part)
lp = 1
for pred in preset.get('predictions', []):
if type(pred) is list:
x.append('pred_%d' % lp)
lp += 1
else:
x.append(pred)
return x
X_train = data['X'][:split_train_test]
Y_train = data['Y'][:split_train_test]
X_test = data['X'][split_train_test:last_divisible_index]
Y_test = data['Y'][split_train_test:last_divisible_index]
#Y_train = np.expand_dims(Y_train, axis=-1)
#Y_test = np.expand_dims(Y_test, axis=-1)
print('Y_train:', Y_test[0:10])
n_samples = X_train.shape[0]
n_timesteps = X_train.shape[1]
n_input = X_train.shape[2]
n_output = 2 # rise or fall
n_iters = int(n_epochs * n_samples / batch_size)
print('number of iterations %d' %n_iters)
# Convert to Dataset instance
train_dataset = Dataset(X_train, Y_train, batch_size)
def dense(x, n_out):
return tf.contrib.layers.fully_connected(x, n_out, activation_fn=tf.nn.relu)
def dense2d(x, n_out):
x_sequence = tf.unstack(x, n_timesteps, 1)
#print(tf.unstack(x_sequence[0], batch_size, 0)[0].get_shape())
timesteps = [dense(x_sequence[t], n_out) for t in range(n_timesteps)]
return timesteps
def model(is_train):
x = tf.placeholder('float', [None, n_timesteps, n_input])
y = tf.placeholder('float', [None, n_output])
if is_train:
# Save column names
num_columns = [
'ApplicantIncome', 'CoapplicantIncome', 'LoanAmount',
'Loan_Amount_Term'
]
cat_columns = [
c for c in data.columns if (c not in [*num_columns, target, id])
]
cData_mode = data[cat_columns].copy()
cData_mode.Credit_History.fillna(1.0, inplace=True)
cData_mode.fillna("X", inplace=True)
cData_mode = cData_mode.apply(LabelEncoder().fit_transform)
Dataset.save_part_features('categorical_na_new',
Dataset.get_part_features('categorical_mode'))
Dataset(categorical_na_new=cData_mode.values).save(name)
Dataset(id=data[id]).save(name)
if target in data.columns:
le = LabelEncoder()
le.fit(data[target])
print(le.transform(data[target]))
Dataset(target=le.transform(data[target])).save(name)
Dataset(target_labels=le.classes_).save(name)
print("Done.")
import pandas as pd
import numpy as np
from util import Dataset
for name in ['train', 'test']:
print "Processing %s..." % name
data = pd.read_csv('../input/lin_%s.csv' % name)
# Save column names
if name == 'train':
num_columns = [c for c in data.columns if c.startswith('cont')]
Dataset.save_part_features('numeric_lin', num_columns)
Dataset(numeric_lin=data[num_columns].values.astype(np.float32)).save(name)
print "Done."
p_loc[p_loc < 0.2] = 0.3
polar_labels(theta, groups, 1.3)
polar_labels(theta, probs1, p_loc)
plt.subplots_adjust(wspace=0.35)
plt.show()
if __name__ == '__main__':
path = '/home/osvald/Projects/Diagnostics/github/srtr_data/multi_label/backup/n_train_tensors/'
groups = ['survival/', 'cardiac/', 'graft/', 'cancer/', 'infection/']
#load model
indices = list(range(4804))
data = Dataset(indices, path)
loader = DataLoader(data,
batch_size=1,
shuffle=True,
collate_fn=collate_fn)
model_folder = '/home/osvald/Projects/Diagnostics/github/models/TCN/normalized/search/[64, 64]_fcl32_att0/lr0.0007787054002686635_b1_0.7982063652094732_b2_0.6107009808891577_gamma0.8319009616491654_drop0.2357377200377962_l2_0.006814594805294124/'
model = DynamicTCN(input_size=267,
output_size=10,
num_channels=[64, 64],
fcl=32,
attention=0,
kernel_size=2,
dropout=0)
model.load_state_dict(torch.load(model_folder + '/best_auc_model'))
model.eval()
import numpy as np
import scipy.sparse as sp
from tqdm import tqdm
from util import Dataset
print("Loading data...")
min_freq = 10
train_cat = Dataset.load_part('train', 'cat_manual')
test_cat = Dataset.load_part('test', 'cat_manual')
train_cat_enc = []
test_cat_enc = []
cats = Dataset.get_part_features('categorical')
features = []
with tqdm(total=len(cats), desc=' Encoding', unit='cols') as pbar:
for col, cat in enumerate(cats):
value_counts = dict(
zip(*np.unique(train_cat[:, col], return_counts=True)))
train_rares = np.zeros(train_cat.shape[0], dtype=np.uint8)
test_rares = np.zeros(test_cat.shape[0], dtype=np.uint8)
for val in value_counts:
if value_counts[val] >= min_freq:
features.append('%s_%s' % (cat, val))
train_cat_enc.append(
import numpy as np
from scipy.stats import skew, boxcox
from tqdm import tqdm
from util import Dataset
print("Loading data...")
train_num = Dataset.load_part('train', 'numeric_mean')
test_num = Dataset.load_part('test', 'numeric_mean')
train_num_enc = np.zeros(train_num.shape, dtype=np.float32)
test_num_enc = np.zeros(test_num.shape, dtype=np.float32)
with tqdm(total=train_num.shape[1], desc=' Transforming', unit='cols') as pbar:
for col in range(train_num.shape[1]):
values = np.hstack((train_num[:, col], test_num[:, col]))
print(values)
sk = skew(values)
if sk > 0.25:
values_enc, lam = boxcox(values+1)
train_num_enc[:, col] = values_enc[:train_num.shape[0]]
test_num_enc[:, col] = values_enc[train_num.shape[0]:]
else:
train_num_enc[:, col] = train_num[:, col]
test_num_enc[:, col] = test_num[:, col]
pbar.update(1)
data = pd.read_csv('input/%s.csv' % name)
target = "Loan_Status"
id = "Loan_ID"
# Save column names
if name == 'train':
num_columns = [
'ApplicantIncome', 'CoapplicantIncome', 'LoanAmount',
'Loan_Amount_Term'
]
cat_columns = [
c for c in data.columns if (c not in [*num_columns, target, id])
]
print(cat_columns)
print(num_columns)
Dataset.save_part_features('categorical_mode', cat_columns)
Dataset.save_part_features('numeric_mean', num_columns)
Dataset.save_part_features('numeric_median', num_columns)
cData_mode = data[cat_columns].copy()
cat_mode = cData_mode.mode().ix[0]
cData_mode.fillna(cat_mode, inplace=True)
cData_mode = cData_mode.apply(LabelEncoder().fit_transform)
#print(cat_data.isnull().sum())
numData_mean = data[num_columns].copy()
num_mean = numData_mean.mean()
numData_mean.fillna(num_mean, inplace=True)
numData_median = data[num_columns].copy()
def calculate_error_with_real_price(sess, predict_op, X, Y, real_last_one,
real_last_two, statistcs):
# Predict prices
dataset = Dataset(X, Y, batch_size)
n_batch = int(X.shape[0] / batch_size)
for i in range(n_batch):
next_x, next_y = dataset.next_batch()
if i == 0:
predict_log_return = sess.run(predict,
feed_dict={
x: next_x,
y: next_y
}).tolist()
else:
predict_log_return = np.append(predict_log_return,
sess.run(predict,
feed_dict={
x: next_x,
y: next_y
}).tolist(),
axis=0)
predict_last_one = np.exp(predict_log_return + np.log(real_last_two))
# Export prices to statistcs_file
statistcs['real_price'] = real_last_one.tolist()
statistcs['predict_price'] = predict_last_one.tolist()
# Show last 5 statistics
print('last price is: ', real_last_two[-5:])
print('predict price is: ', predict_last_one[-5:])
print('real price is: ', real_last_one[-5:])
# Calculate MSE
MSE = np.mean((real_last_one - predict_last_one)**2)
statistcs['MSE'] = MSE
print('MSE = %.10f' % MSE)
# Caluculate Variance
mean_real = np.mean(real_last_one)
var_real = np.var(real_last_one)
print('Real mean=%.4f, var=%.5f' % (mean_real, var_real))
mean_predict = np.mean(predict_last_one)
var_predict = np.var(predict_last_one)
print('Predict mean=%.4f, var=%.5f' % (mean_predict, var_predict))
length = real_last_one.shape[0]
real_last_one = np.reshape(real_last_one, length)
real_last_two = np.reshape(real_last_two, length)
predict_last_one = np.reshape(predict_last_one, length)
# Calculate sign accuracy
real_diff = real_last_one - real_last_two
predict_diff = predict_last_one - real_last_two
real_diff_sign = np.sign(real_diff)
predict_diff_sign = np.sign(predict_diff)
print('real_diff: ', real_diff[-20:])
print('predict_diff: ', predict_diff[-20:])
num_correct_sign = np.count_nonzero(
np.equal(real_diff_sign, predict_diff_sign))
sign_accuracy = num_correct_sign / real_diff_sign.shape[0]
statistcs['sign_accuracy'] = sign_accuracy
print('Sign Accuracy = %.10f' % sign_accuracy)
import pandas as pd
import numpy as np
from tqdm import tqdm
from util import Dataset
print "Loading data..."
train_cat = Dataset.load_part('train', 'categorical')
test_cat = Dataset.load_part('test', 'categorical')
train_cat_enc = np.zeros(train_cat.shape, dtype=np.uint8)
test_cat_enc = np.zeros(test_cat.shape, dtype=np.uint8)
with tqdm(total=train_cat.shape[1], desc=' Encoding', unit='cols') as pbar:
for col in xrange(train_cat.shape[1]):
values = np.hstack((train_cat[:, col], test_cat[:, col]))
values = np.unique(values)
values = sorted(values, key=lambda x: (len(x), x))
encoding = dict(zip(values, range(len(values))))
train_cat_enc[:, col] = pd.Series(train_cat[:,
col]).map(encoding).values
test_cat_enc[:, col] = pd.Series(test_cat[:, col]).map(encoding).values
pbar.update(1)
print "Saving..."
Dataset.save_part_features('categorical_encoded',
import numpy as np
from scipy.stats.mstats import rankdata
from scipy.special import erfinv
from sklearn.preprocessing import scale, minmax_scale
from tqdm import tqdm
from util import Dataset
print "Loading data..."
lim = 0.999
train_num = Dataset.load_part('train', 'numeric')
test_num = Dataset.load_part('test', 'numeric')
train_num_enc = np.zeros(train_num.shape, dtype=np.float32)
test_num_enc = np.zeros(test_num.shape, dtype=np.float32)
with tqdm(total=train_num.shape[1], desc=' Transforming',
unit='cols') as pbar:
for col in xrange(train_num.shape[1]):
values = np.hstack((train_num[:, col], test_num[:, col]))
# Apply rank transformation
values = rankdata(values).astype(np.float64)
# Scale into range (-1, 1)
values = minmax_scale(values, feature_range=(-lim, lim))
import numpy as np
import scipy.sparse as sp
from scipy.stats import boxcox
import pandas as pd
from sklearn.preprocessing import scale
from tqdm import tqdm
from util import Dataset
print("Loading data...")
idx = Dataset.load_part("train", 'id')
train_num = pd.DataFrame(Dataset.load_part("train", 'numeric_mean'), columns=Dataset.get_part_features('numeric_mean'), index=idx)
idx = Dataset.load_part("test", 'id')
test_num = pd.DataFrame(Dataset.load_part("test", 'numeric_mean'), columns=Dataset.get_part_features('numeric_mean'), index=idx)
all_nData = train_num.append(test_num)
print(all_nData.head())
all_num_norm = pd.DataFrame()
all_num_norm["ApplicantIncome"] = np.log1p(all_nData.ApplicantIncome)
all_num_norm["CoapplicantIncome"] = np.log1p(all_nData.CoapplicantIncome)
all_num_norm["LoanAmount"] = (np.log1p(all_nData.LoanAmount))
all_num_norm["Loan_Amount_Term"] = np.log1p(all_nData.Loan_Amount_Term)
train_custom = all_num_norm[:train_num.shape[0]]
test_custom = all_num_norm[train_num.shape[0]:]
def evaluate(self, x, y, batch_size):
'''
input:
FloatTensor/ndarray x: data
list[str] y: targets
int batch_size: batch size, x and y should be dividable with this
output:
seq_acc: mean accuracy, per sequence
dig_acc: mean accuracy, per digit
loss: mean ctc loss
dist: mean Levenshtein edit distance
'''
print ("evaluating...", end="\r")
with torch.no_grad():
loss = 0
dist = 0
seq_acc = 0
dig_acc = 0
if type(x) is not torch.FloatTensor:
x = torch.FloatTensor(x)
eval_set = Dataset(x, y, normalize=True, augment=False)
params = {'batch_size':batch_size, 'shuffle':False, 'num_workers':6}
eval_generator = data.DataLoader(eval_set, **params)
for x_batch, y_batch in eval_generator:
x_batch = x_batch.to(self.device)
y, p, out_sizes = self.predict(x_batch)
y_batch_no_pad, target_sizes = self.remove_padding(y_batch, p.shape[0])
# ------ LOSS CALCULATION ------
loss += self.loss_fcn(p, y_batch_no_pad, out_sizes, target_sizes).numpy()
# ------ ACCURACY CALCULATION ------
y_batch = self.decoder.convert_to_strings(y_batch)
for i in range(len(y_batch)):
chars_pred = list(y[i][0])
chars_true = list(y_batch[i][0])
len_diff = len(chars_pred) - len(chars_true)
if len_diff < 0:
chars_pred += ["_"]*(-len_diff)
elif len_diff > 0:
chars_true += ["_"]*len_diff
dist += levenshtein(chars_pred , chars_true)
seq_acc += accuracy_score(y[i], y_batch[i])
dig_acc += accuracy_score(chars_pred, chars_true)
torch.cuda.empty_cache()
# average over sequences
loss /= x.shape[0]
dist /= x.shape[0]
seq_acc /= x.shape[0]
dig_acc /= x.shape[0]
return seq_acc, dig_acc, loss, dist
def fit(self, training_data, validation_data, optimizer,
epochs=100, batch_size=10, logger=None):
'''
Training loop
input:
tuple training_data: (features, labels), as numpy.ndarray
tuple validation_data: (features, labels), as numpy.ndarray
optimizer: a PyTorch optimizer object
logger: a HistoryLogger object, for visualizing training
'''
# Learning-rate is reduced on plateau, parameters might need tweaking depending on data
scheduler = lr_reducer(optimizer, factor=0.5, patience=5, min_lr=1e-6)
logger.on_train_begin()
self.to(self.device)
# Data to tensors
x_tr = torch.tensor(training_data[0]).type(torch.FloatTensor)
y_tr = torch.IntTensor(training_data[1])
x_te = torch.tensor(validation_data[0]).type(torch.FloatTensor)
y_te = torch.IntTensor(validation_data[1])
print("\nTraining with {} examples, validating with {} examples"\
.format(x_tr.shape[0], x_te.shape[0]))
best_acc = 0 # for determining best checkpoint
training_set = Dataset(x_tr, y_tr, normalize=True, augment=True)
params = {'batch_size':batch_size, 'shuffle':True, 'num_workers':6}
train_generator = data.DataLoader(training_set, **params)
for e in range(self.last_epoch, epochs):
print("\nStarting epoch {}/{} ...".format(e+1, epochs))
loss = 0
# Progress bar
with tqdm(train_generator,
total = (x_tr.shape[0]//batch_size)+1,
unit_scale = batch_size,
postfix = "loss: {}".format(loss)) as t:
for x_batch, y_batch in t:
# one batch at a time to GPU, uses less GPU memory
x_batch = x_batch.to(self.device)
optimizer.zero_grad()
y = self(x_batch) # predict on batch
# Output strings are all the same length, but warp-ctc needs
# these lengths as a tensor to work.
out_sizes = torch.IntTensor([y.shape[0]]*batch_size)
out_sizes = torch.autograd.Variable(out_sizes, requires_grad=False)
y_batch, target_sizes = self.remove_padding(y_batch, y.shape[0])
# predictions are needed without softmax in the loss function
loss = self.loss_fcn(y, y_batch, out_sizes, target_sizes)
loss.backward()
optimizer.step()
t.postfix = "loss: {:8.4f}".format(loss.cpu().detach().numpy()[0])
torch.cuda.empty_cache()
if logger is not None:
seq_acc, _, loss, _ = logger.on_epoch_end(e)
else:
seq_acc, _, loss, _ = self.evaluate(x_te, y_te, batch_size)
scheduler.step(loss)
# Save checkpoint
most_accurate = False
if seq_acc > best_acc:
best_acc = seq_acc
most_accurate = True
checkpointer({'epoch' : e+1,
'model_states' : self.state_dict(),
'optimizer' : optimizer.state_dict(),
'accuracy' : best_acc,
'model_params' : self.modelparams},
most_accurate, self.out_path)
print("validation accuracy: {:4.2f}, validation loss: {:6.4f}"\
.format(float(seq_acc), float(loss)))
#
# all_s["app_s"] = all_s["ApplicantIncome"] * all_s["Self_Employed"]
# all_s["ci_s"] = all_s["CoapplicantIncome"] * all_s["Self_Employed"]
# all_s["la_s"] = all_s["LoanAmount"] * all_s["Self_Employed"]
# all_s["lat_s"] = all_s["Loan_Amount_Term"] * all_s["Self_Employed"]
features_to_drop = ['Gender', 'Married', 'Dependents','Education', 'Self_Employed','ApplicantIncome','CoapplicantIncome','LoanAmount','Loan_Amount_Term']
all_filtered = all_s.drop(features_to_drop,axis=1)
print(train.columns)
# ['Loan_ID', 'Gender', 'Married', 'Dependents', 'Education',
# 'Self_Employed', 'ApplicantIncome', 'CoapplicantIncome', 'LoanAmount',
# 'Loan_Amount_Term', 'Credit_History', 'Property_Area', 'Loan_Status']
train_cust = all_filtered[:ntrain]
test_cust = all_filtered[ntrain:]
print(all_s.columns)
#
# train_cat_enc = sp.hstack(train_cat_enc, format='csr')
# test_cat_enc = sp.hstack(test_cat_enc, format='csr')
Dataset.save_part_features('fSelect', list(all_filtered.columns))
Dataset(fSelect=train_cust.values).save('train')
Dataset(fSelect=test_cust.values).save('test')
#
# print("Done.")
import numpy as np
from util import Dataset
from sklearn.preprocessing import scale
print("Loading data...")
train_num = Dataset.load_part('train', 'numeric_mean')
test_num = Dataset.load_part('test', 'numeric_mean')
print("Scaling...")
all_scaled = scale(np.vstack((train_num, test_num)))
print("Saving...")
Dataset.save_part_features('numeric_mean_scaled',
Dataset.get_part_features('numeric'))
Dataset(numeric_mean_scaled=all_scaled[:train_num.shape[0]]).save('train')
Dataset(numeric_mean_scaled=all_scaled[train_num.shape[0]:]).save('test')
print("Done.")
help='Resume from the given checkpoint.')
opt = args.parse_args()
tokenizer = BertTokenizer.from_pretrained('bert-base-chinese')
if (opt.checkpoint != None):
print('Load model from checkpoints')
model = BertForNextSentencePrediction.from_pretrained(
join('checkpoints', opt.checkpoint))
else:
model = BertForNextSentencePrediction.from_pretrained('bert-base-chinese')
optimizer = torch.optim.Adam(model.parameters(), lr=1e-5)
dataset = Dataset(tokenizer)
dataloader = data.DataLoader(dataset=dataset,
batch_size=opt.batch_size,
shuffle=True,
collate_fn=custom_collate(tokenizer))
task_name = '{}-{}'.format(opt.name, time.strftime("%Y-%m-%d-%H-%M-%S"))
writer = SummaryWriter('runs/{}'.format(task_name))
if not os.path.exists(join('checkpoints', task_name)):
os.mkdir(join('checkpoints', task_name))
model.to('cuda')
model.train()
acc_loss = [] # accumulated loss, refreshed when it is plotted
import numpy as np
from util import Dataset, vstack, hstack
from sklearn.preprocessing import scale
from sklearn.decomposition import TruncatedSVD
n_components = 500 # 500 components explain 99.8% of variance
print "Loading data..."
train_num = Dataset.load_part('train', 'numeric')
train_cat = Dataset.load_part('train', 'categorical_dummy')
test_num = Dataset.load_part('test', 'numeric')
test_cat = Dataset.load_part('test', 'categorical_dummy')
train_cnt = train_num.shape[0]
print "Combining data..."
all_data = hstack((scale(vstack(
(train_num, test_num)).astype(np.float64)).astype(np.float32),
vstack((train_cat, test_cat))))
del train_num, train_cat, test_num, test_cat
print "Fitting svd..."
svd = TruncatedSVD(n_components)
res = svd.fit_transform(all_data)
import numpy as np
import pandas as pd
from scipy.stats import skew, boxcox
from sklearn.preprocessing import scale
from tqdm import tqdm
from util import Dataset
import itertools
print("Loading data...")
train_num = Dataset.load_part('train', 'numeric_mean')
test_num = Dataset.load_part('test', 'numeric_mean')
ntrain = train_num.shape[0]
train_test = np.vstack([train_num, test_num])
num_features = Dataset.get_part_features('numeric')
num_comb_df = pd.DataFrame()
with tqdm(total=train_num.shape[1], desc=' Transforming',
unit='cols') as pbar:
for comb in itertools.combinations(num_features, 2):
feat = comb[0] + "_" + comb[1]
num_comb_df[
feat] = train_test[:, num_features.index(comb[0]) -
1] + train_test[:,
num_features.index(comb[1]) - 1]
print('Combining Columns:', feat)
# Replace category label with their counts
import numpy as np
import pandas as pd
from tqdm import tqdm
from util import Dataset
print("Loading data...")
train_cat = Dataset.load_part('train', 'categorical_mode')
test_cat = Dataset.load_part('test', 'categorical_mode')
train_cat_counts = np.zeros(train_cat.shape, dtype=np.float32)
test_cat_counts = np.zeros(test_cat.shape, dtype=np.float32)
with tqdm(total=train_cat.shape[1], desc=' Counting', unit='cols') as pbar:
for col in range(train_cat.shape[1]):
train_series = pd.Series(train_cat[:, col])
test_series = pd.Series(test_cat[:, col])
counts = pd.concat((train_series, test_series)).value_counts()
train_cat_counts[:, col] = train_series.map(counts).values
test_cat_counts[:, col] = test_series.map(counts).values
pbar.update(1)
print("Saving...")
print(train_cat_counts)
Dataset.save_part_features('categorical_counts',
Dataset.get_part_features('categorical'))
from keras.optimizers import SGD, Adam, Adadelta
from keras.callbacks import ModelCheckpoint
from keras import regularizers
#from keras_util import ExponentialMovingAverage, batch_generator
from statsmodels.regression.quantile_regression import QuantReg
from pylightgbm.models import GBMRegressor
from scipy.stats import boxcox
from bayes_opt import BayesianOptimization
from util import Dataset, load_prediction, hstack
categoricals = Dataset.get_part_features('categorical')
class DenseTransformer(BaseEstimator):
def transform(self, X, y=None, **fit_params):
return X.todense()
def fit_transform(self, X, y=None, **fit_params):
self.fit(X, y, **fit_params)
return self.transform(X)
def fit(self, X, y=None, **fit_params):
return self
class BaseAlgo(object):
import numpy as np
import scipy.sparse as sp
import pandas as pd
from sklearn.preprocessing import scale
from tqdm import tqdm
from util import Dataset
print("Loading data...")
idx = Dataset.load_part("train", 'id')
train_cat = pd.DataFrame(Dataset.load_part("train", 'categorical_mode'),
columns=Dataset.get_part_features('categorical_mode'),
index=idx)
train_num = pd.DataFrame(Dataset.load_part("train", 'numeric_mean'),
columns=Dataset.get_part_features('numeric_mean'),
index=idx)
train = pd.concat([train_cat, train_num], axis=1)
idx = Dataset.load_part("test", 'id')
test_cat = pd.DataFrame(Dataset.load_part("test", 'categorical_mode'),
columns=Dataset.get_part_features('categorical_mode'),
index=idx)
test_num = pd.DataFrame(Dataset.load_part("test", 'numeric_mean'),
columns=Dataset.get_part_features('numeric_mean'),
index=idx)
test = pd.concat([test_cat, test_num], axis=1)
def y_decode(y):
og = Dataset.load_part("train", "target_labels")
le = LabelEncoder()
le.classes_ = og
z = [int(i) for i in y]
return le.inverse_transform(z)
'discriminator_loss': [],
'encoded_feature_vector': [],
'original_images': [],
'encoded_images': [],
'reconstruct_images': [],
'reconstruct_from_random': [],
}
statistics_file = 'statistics/' + eid
print('id: ', eid)
print('number of epochs = {:d}'.format(n_epochs))
print('batch_size = {:d}'.format(batch_size))
# Load data
X_train = load_data('../data/data.npy') # (2000, 784)
label_train = load_data('../data/label.npy') # (2000,)
train_dataset = Dataset(X_train, label_train, batch_size)
n_train_samples = X_train.shape[0]
n_iters = int(n_epochs * n_train_samples / batch_size)
print('number of iterations = {:d}'.format(n_iters))
def weight_variable(shape):
initial = tf.random_normal(shape, stddev=0.01)
return tf.Variable(initial)
def bias_variable(shape):
initial = tf.fill(shape, 0.1)
return tf.Variable(initial)
import pandas as pd
from util import Dataset
for name in ['train', 'test']:
print "Processing %s..." % name
num = pd.DataFrame(Dataset.load_part(name, 'numeric'),
columns=Dataset.get_part_features('numeric'))
df = pd.DataFrame(index=num.index)
df['diff_1_6'] = num['cont1'] - num['cont6']
df['diff_1_9'] = num['cont1'] - num['cont9']
df['diff_1_10'] = num['cont1'] - num['cont10']
df['diff_6_9'] = num['cont6'] - num['cont9']
df['diff_6_10'] = num['cont6'] - num['cont10']
df['diff_6_11'] = num['cont6'] - num['cont11']
df['diff_6_12'] = num['cont6'] - num['cont12']
df['diff_6_13'] = num['cont6'] - num['cont13']
df['diff_7_11'] = num['cont7'] - num['cont11']
df['diff_7_12'] = num['cont7'] - num['cont12']
df['diff_11_12'] = num['cont11'] - num['cont12']
if name == 'train':
Dataset.save_part_features('numeric_combinations', list(df.columns))
Dataset(numeric_combinations=df.values).save(name)
print "Done."
import numpy as np
import pandas as pd
from util import Dataset
from sklearn.preprocessing import minmax_scale
print "Loading data..."
train_num = Dataset.load_part('train', 'numeric')
test_num = Dataset.load_part('test', 'numeric')
print "Scaling..."
numeric = pd.DataFrame(np.vstack((train_num, test_num)),
columns=Dataset.get_part_features('numeric'))
df = pd.DataFrame(index=numeric.index)
df["cont1"] = np.sqrt(minmax_scale(numeric["cont1"]))
df["cont4"] = np.sqrt(minmax_scale(numeric["cont4"]))
df["cont5"] = np.sqrt(minmax_scale(numeric["cont5"]))
df["cont8"] = np.sqrt(minmax_scale(numeric["cont8"]))
df["cont10"] = np.sqrt(minmax_scale(numeric["cont10"]))
df["cont11"] = np.sqrt(minmax_scale(numeric["cont11"]))
df["cont12"] = np.sqrt(minmax_scale(numeric["cont12"]))
df["cont6"] = np.log(minmax_scale(numeric["cont6"]) + 0000.1)
df["cont7"] = np.log(minmax_scale(numeric["cont7"]) + 0000.1)
df["cont9"] = np.log(minmax_scale(numeric["cont9"]) + 0000.1)
df["cont13"] = np.log(minmax_scale(numeric["cont13"]) + 0000.1)
df["cont14"] = (np.maximum(numeric["cont14"] - 0.179722, 0) / 0.665122)**0.25
print "Saving..."