def __init__(self, settings):
super(Trainer, self).__init__()
self.settings = settings
self.phase = settings.cmd
self.batch_size = settings.batch_size
self.data_dir = settings.data_dir
self.list_dir = settings.list_dir
self.checkpoint = settings.resume
self.load_checkpoint = (len(self.checkpoint) > 0)
self.num_epochs = settings.num_epochs
self.lr = float(settings.lr)
self.save = settings.save_on or settings.out_dir
self.from_pause = self.settings.continu
self.path_ctrl = settings.global_path
self.path = self.path_ctrl.get_path
log_dir = '' if settings.log_off else self.path_ctrl.get_dir('log')
self.logger = Logger(scrn=True, log_dir=log_dir, phase=self.phase)
for k, v in sorted(settings.__dict__.items()):
self.logger.show("{}: {}".format(k, v))
self.start_epoch = 0
self._init_max_acc = 0.0
self.model = None
self.criterion = None
def __init__(self,
data_dir,
ckp_path,
save_lr=False,
list_dir='',
out_dir='./',
log_dir=''):
super(Predictor, self).__init__()
self.data_dir = data_dir
self.list_dir = list_dir
self.out_dir = out_dir
self.checkpoint = ckp_path
self.save_lr = save_lr
self.logger = Logger(scrn=True, log_dir=log_dir, phase='test')
self.model = None
def set_gpc_and_logger(args):
gpc = OutPathGetter(root=os.path.join(args.exp_dir, args.tag),
suffix=args.suffix)
log_dir = '' if args.log_off else gpc.get_dir('log')
logger = Logger(scrn=True, log_dir=log_dir, phase=args.cmd)
register('GPC', gpc)
register('LOGGER', logger)
return gpc, logger
def __init__(self,
model=None,
mode='folder',
save_dir=None,
scrn=True,
log_dir=None,
cuda_off=False):
self.save_dir = save_dir
self.output = None
if not cuda_off and torch.cuda.is_available():
self.device = torch.device('cuda')
else:
self.device = torch.device('cpu')
assert model is not None, "The model must be assigned"
self.model = self._model_init(model)
if mode not in Predictor.modes:
raise NotImplementedError
self.logger = Logger(scrn=scrn, log_dir=log_dir, phase='predict')
if mode == 'dataloader':
self._predict = partial(self._predict_dataloader,
dataloader=None,
save_dir=save_dir)
elif mode == 'folder':
# self.suffix = ['.jpg', '.png', '.bmp', '.gif', '.npy'] # 支持的图像格式
self._predict = partial(self._predict_folder, save_dir=save_dir)
elif mode == 'list':
self._predict = partial(self._predict_list, save_dir=save_dir)
elif mode == 'file':
self._predict = partial(self._predict_file, save_dir=save_dir)
elif mode == 'data':
self._predict = partial(self._predict_data, save_dir=save_dir)
else:
raise NotImplementedError
# @FileName: main_wl.py
# @ProjectName :Facility_Location_WL
"""
from utils.util import DataHandler
from core.complex_model import FacilityLocation
from core.model import FacilityLocation
from core.cutoff_model import FacilityLocation
# from core.model import FacilityLocation
# from core.model_2 import FacilityLocation
from core.model_3 import FacilityLocation
from utils.misc import Logger
import pandas as pd
import os
# define the log file and log level
log = Logger(log_path='./log').logger
# define the configuration parameters
class Config(object):
"""
define all parameters
"""
# TODO: tune these capacity of cdc and rdc
rdc_capacity = 5000000000000
num_rdc = 1
num_cdc = 4
P_c = 0.95
P_b = 0.8
rr_cdc = 0.00
weight_avg = 100
class Predictor:
modes = ['dataloader', 'folder', 'list', 'file', 'data']
def __init__(self,
model=None,
mode='folder',
save_dir=None,
scrn=True,
log_dir=None,
cuda_off=False):
self.save_dir = save_dir
self.output = None
if not cuda_off and torch.cuda.is_available():
self.device = torch.device('cuda')
else:
self.device = torch.device('cpu')
assert model is not None, "The model must be assigned"
self.model = self._model_init(model)
if mode not in Predictor.modes:
raise NotImplementedError
self.logger = Logger(scrn=scrn, log_dir=log_dir, phase='predict')
if mode == 'dataloader':
self._predict = partial(self._predict_dataloader,
dataloader=None,
save_dir=save_dir)
elif mode == 'folder':
# self.suffix = ['.jpg', '.png', '.bmp', '.gif', '.npy'] # 支持的图像格式
self._predict = partial(self._predict_folder, save_dir=save_dir)
elif mode == 'list':
self._predict = partial(self._predict_list, save_dir=save_dir)
elif mode == 'file':
self._predict = partial(self._predict_file, save_dir=save_dir)
elif mode == 'data':
self._predict = partial(self._predict_data, save_dir=save_dir)
else:
raise NotImplementedError
def __call__(self, *args, **kwargs):
return self._predict(*args, **kwargs)
def _model_init(self, model):
model.to(self.device)
model.eval()
return model
def _load_data(self, path):
return io.imread(path)
def _to_tensor(self, arr):
return to_tensor(arr)
def _to_array(self, tensor):
return to_array(tensor)
def _normalize(self, tensor):
return normalize(tensor)
def _np2tensor(self, arr):
nor_tensor = self._normalize(self._to_tensor(arr))
assert isinstance(nor_tensor, torch.Tensor)
return nor_tensor
def _save_data_NTIRE2020(self, data, path):
s_dir = os.path.dirname(path)
if not os.path.exists(s_dir):
os.mkdir(s_dir)
path = path.replace('_clean.png',
'.mat').replace('_RealWorld.png', '.mat')
if isinstance(data, torch.Tensor):
data = self._to_array(data).squeeze()
content = {}
content['cube'] = data
content['bands'] = np.array([[
400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520,
530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650,
660, 670, 680, 690, 700
]])
# content['norm_factor'] =
hdf5.write(data=content,
filename=path,
store_python_metadata=True,
matlab_compatible=True)
def _save_data(self, data, path):
s_dir = os.path.dirname(path)
if not os.path.exists(s_dir):
os.mkdir(s_dir)
torchvision.utils.save_image(data, path)
def predict_base(self, model, data, path=None):
start = time.time()
with torch.no_grad():
output = model(data)
torch.cuda.synchronize()
su_time = time.time() - start
if path:
self._save_data_NTIRE2020(output, path)
self.output = output
return output, su_time
def _predict_dataloader(self, dataloader, save_dir=None):
assert dataloader is not None, \
"In 'dataloader' mode the input must be a valid dataloader!"
consume_time = AverageMeter()
pb = tqdm(dataloader)
for idx, (name, data) in enumerate(pb):
assert isinstance(data, torch.Tensor) and data.dim() == 4,\
"input data must be 4-dimention tensor"
data = data.to(self.device) # 4-d tensor
save_path = os.path.join(save_dir, name) if save_dir else None
_, su_time = self.predict_base(self.model, data, path=save_path)
consume_time.update(su_time, n=1)
# logger
description = (
"[{}/{}] speed: {time.val:.4f}s({time.avg:.4f}s)".format(
idx + 1, len(dataloader.dataset), time=consume_time))
pb.set_description(description)
self.logger.dump(description)
def _predict_folder(self, folder, save_dir=None):
assert folder is not None and os.path.isdir(folder),\
"In 'folder' mode the input must be a valid path of a folder!"
consume_time = AverageMeter()
file_list = glob.glob(os.path.join(folder, '*'))
assert not len(file_list) == 0, "The input folder is empty"
pb = tqdm(file_list) # processbar
for idx, file in enumerate(pb):
img = self._load_data(file)
name = os.path.basename(file)
img = self._np2tensor(img).unsqueeze(0).to(self.device)
save_path = os.path.join(save_dir, name) if save_dir else None
_, su_time = self.predict_base(model=self.model,
data=img,
path=save_path)
consume_time.update(su_time)
# logger
description = (
"[{}/{}] speed: {time.val:.4f}s({time.avg:.4f}s)".format(
idx + 1, len(file_list), time=consume_time))
pb.set_description(description)
self.logger.dump(description)
def _predict_list(self, file_list, save_dir=None):
assert isinstance(file_list, list),\
"In 'list' mode the input must be a valid file_path list!"
consume_time = AverageMeter()
assert not len(file_list) == 0, "The input file list is empty!"
pb = tqdm(file_list) # processbar
for idx, path in enumerate(pb):
data = self._load_data(path)
name = os.path.basename(path)
data = self._np2tensor(data).unsqueeze(0).to(self.device)
path = os.path.join(save_dir, name) if save_dir else None
_, su_time = self.predict_base(model=self.model,
data=data,
path=path)
consume_time.update(su_time, n=1)
# logger
description = (
"[{}/{}] speed: {time.val:.4f}s({time.avg:.4f}s)".format(
idx + 1, len(file_list), time=consume_time))
pb.set_description(description)
self.logger.dump(description)
def _predict_file(self, file_path, save_dir=None):
assert isinstance(file_path, str) and os.path.isfile(file_path), \
"In 'file' mode the input must a valid path of a file!"
consume_time = AverageMeter()
data = self._load_data(file_path)
name = os.path.basename(file_path)
data = self._np2tensor(data).unsqueeze(0).to(self.device)
path = os.path.join(save_dir, name) if save_dir else None
_, su_time = self.predict_base(model=self.model, data=data, path=path)
consume_time.update(su_time)
# logger
description = ("file: {} speed: {time.val:.4f}s".format(
name, time=consume_time))
self.logger.show(description)
def _predict_data(self, data):
"""
:return: tensor
"""
assert isinstance(data, torch.Tensor) and data.dim() == 4, \
"In 'data' mode the input must be a 4-d tensor"
consume_time = AverageMeter()
output, su_time = self.predict_base(model=self.model, data=data)
consume_time.update(su_time)
# logger
description = ("speed: {time.val:.4f}s".format(time=consume_time))
self.logger.dump(description)
return output
RESTORE_FROM = "/data/AutoPheno/green/200527/PatchNet/snapshots-fb/LEAF_UNET_B0064_S010700.pth"
SAVE_PRED_EVERY = 1000
SNAPSHOT_DIR = root_dir + 'PatchNet/snapshots'+postfix
IMGSHOT_DIR = root_dir + 'PatchNet/imgshots'+postfix
WEIGHT_DECAY = 0.0005
NUM_EXAMPLES_PER_EPOCH = 13862
NUM_STEPS_PER_EPOCH = math.ceil(NUM_EXAMPLES_PER_EPOCH / float(BATCH_SIZE))
MAX_ITER = max(NUM_EXAMPLES_PER_EPOCH * MAX_EPOCH + 1,
NUM_STEPS_PER_EPOCH * BATCH_SIZE * MAX_EPOCH + 1)
if not os.path.exists(SNAPSHOT_DIR):
os.makedirs(SNAPSHOT_DIR)
if not os.path.exists(IMGSHOT_DIR):
os.makedirs(IMGSHOT_DIR)
LOG_PATH = SNAPSHOT_DIR + "/B"+format(BATCH_SIZE, "04d")+"E"+format(MAX_EPOCH, "04d")+".log"
sys.stdout = Logger(LOG_PATH, sys.stdout)
print(DATA_LIST_PATH)
print("num of epoch:", MAX_EPOCH)
print("RESTORE_FROM:", RESTORE_FROM)
print(NUM_EXAMPLES_PER_EPOCH)
def get_arguments():
"""Parse all the arguments provided from the CLI.
Returns:
A list of parsed arguments.
"""
parser = argparse.ArgumentParser(description="UNet Network")
parser.add_argument("--set-start", default=False)
parser.add_argument("--start-step", default=0, type=int)
def run(try_num, config):
output_dir = f'./dae-out-{try_num}'
if not os.path.exists(output_dir):
os.mkdir(output_dir)
args = get_args()
train_features = pd.read_csv('../input/lish-moa/train_features.csv')
test_features = pd.read_csv('../input/lish-moa/test_features.csv')
if args.debug:
train_features = train_features.loc[:500]
config.update(dict(n_epochs=3, n_folds=2))
all_features = pd.concat([train_features,
test_features]).reset_index(drop=True)
g_features_columns = [
col for col in all_features.columns if col.startswith('g-')
]
c_features_columns = [
col for col in all_features.columns if col.startswith('c-')
]
feature_columns = g_features_columns + c_features_columns
n_features = len(feature_columns)
kfold = MultilabelStratifiedKFold(n_splits=config.n_folds,
random_state=42,
shuffle=True)
logger = Logger()
for fold_index, (train_idx, valid_idx) in enumerate(
kfold.split(all_features.values, all_features.values)):
print('Fold: ', fold_index + 1, flush=True)
x_train = all_features.loc[train_idx]
x_valid = all_features.loc[valid_idx]
model = new_autoencoder(config.model_kind,
n_features=n_features).to(DEVICE)
criterion = nn.MSELoss()
optimizer = torch.optim.Adam(model.parameters(),
lr=config.learning_rate,
weight_decay=1e-5)
scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer,
mode='min',
factor=0.1,
patience=3,
eps=1e-4,
verbose=True)
early_stopping = EarlyStopping(patience=10)
best_score = np.inf
for epoch in range(config.n_epochs):
dataset = DaeDataset(x_train,
feature_columns,
noise_ratio=config.noise_ratio)
dataloader = DataLoader(dataset,
batch_size=config.batch_size,
shuffle=True)
train_loss = loop_train(model, criterion, dataloader, optimizer)
dataset = DaeDataset(x_valid,
feature_columns,
noise_ratio=config.noise_ratio)
dataloader = DataLoader(dataset,
batch_size=config.valid_batch_size,
shuffle=False)
valid_loss, _ = loop_valid(model, criterion, dataloader)
scheduler.step(valid_loss)
logger.update({
'fold': fold_index,
'epoch': epoch + 1,
'train_loss': train_loss,
'val_loss': valid_loss
})
print(
f'epoch {epoch + 1}/{config.n_epochs} - train_loss: {train_loss:.5f} - '
+ f'valid_loss: {valid_loss:.5f}',
flush=True)
if valid_loss < best_score:
best_score = valid_loss
torch.save(model.state_dict(),
f'./{output_dir}/dae_fold_weight_{fold_index}.pt')
if early_stopping.should_stop(valid_loss):
print('Early stopping', flush=True)
break
logger.save(f'./{output_dir}/dae_log.csv')
oof_preds = []
for fold_index in range(config.n_folds):
model = new_autoencoder(config.model_kind,
n_features=n_features).to(DEVICE)
model.load_state_dict(
torch.load(f'./{output_dir}/dae_fold_weight_{fold_index}.pt'))
model.eval()
dataset = DaeDataset(all_features,
feature_columns,
noise_ratio=config.noise_ratio)
dataloader = DataLoader(dataset,
batch_size=config.valid_batch_size,
shuffle=False)
loss, preds = loop_valid(model, nn.MSELoss(), dataloader)
logger.update({'fold': fold_index, 'val_loss': loss})
print('Evaluation fold: {} - valid_loss: {:.5f}'.format(
fold_index, loss),
flush=True)
oof_preds.append(preds)
print('A Whole Evaluation Score: {:.5f}'.format(
mean_squared_error(all_features.loc[:, feature_columns].values,
np.mean(oof_preds, axis=0))),
flush=True)
# for i, preds in enumerate(oof_preds):
# create_pred_feature_df(preds, all_features).to_csv(f'./{output_dir}/dae_features_{i}.csv', index=False)
create_pred_feature_df(np.mean(oof_preds, axis=0), all_features).to_csv(
f'./{output_dir}/dae_features_mean.csv', index=False)
References
----------
[1] Narula, S. & Weistroffer,
H. A flexible method for nonlinear multicriteria decision-making problems Systems,
Man and Cybernetics, IEEE Transactions on, 1989 , 19 , 883-887.
'''
import sys,os
example_path=os.path.dirname(os.path.realpath(__file__))
sys.path.append(os.path.join(example_path,".."))
from utils.misc import Logger
sys.stdout = Logger(os.path.splitext(os.path.basename(__file__))[0])
from utils import tui
from method.NAUTILUS import NAUTILUSv1,ENAUTILUS
from optimization.OptimizationMethod import PointSearch
from problem.Problem import PreGeneratedProblem
if __name__ == '__main__':
# SciPy breaks box constraints
method = ENAUTILUS(PreGeneratedProblem(filename=os.path.join(example_path,"AuxiliaryServices.csv")), PointSearch)
zh=tui.iter_enautilus(method)
ci=method.current_iter
# -*- coding: UTF-8 -*- """ # @Time : 2020/11/17 18:57 # @Author : peng.wang # @Email : [email protected] # @FileName: main.py # @ProjectName :Prediction_Optimization """ import os import json from utils.util import DataHandler from utils.misc import Logger from core.model import Scheduler # define the log file and log level log = Logger(log_path='./log').logger # define the configuration parameters class Config(object): Dates = [] if not os.path.exists('results'): os.mkdir('results') # load the data filename = "data_input.xlsx" data_ins = DataHandler(file=filename, config=Config) mode = 'deterministic' mode = 'expected'
class Trainer:
def __init__(self, settings):
super(Trainer, self).__init__()
self.settings = settings
self.phase = settings.cmd
self.batch_size = settings.batch_size
self.data_dir = settings.data_dir
self.list_dir = settings.list_dir
self.checkpoint = settings.resume
self.load_checkpoint = (len(self.checkpoint) > 0)
self.num_epochs = settings.num_epochs
self.lr = float(settings.lr)
self.save = settings.save_on or settings.out_dir
self.from_pause = self.settings.continu
self.path_ctrl = settings.global_path
self.path = self.path_ctrl.get_path
log_dir = '' if settings.log_off else self.path_ctrl.get_dir('log')
self.logger = Logger(scrn=True, log_dir=log_dir, phase=self.phase)
for k, v in sorted(settings.__dict__.items()):
self.logger.show("{}: {}".format(k, v))
self.start_epoch = 0
self._init_max_acc = 0.0
self.model = None
self.criterion = None
def train_epoch(self):
raise NotImplementedError
def validate_epoch(self, epoch, store):
raise NotImplementedError
def train(self):
cudnn.benchmark = True
if self.load_checkpoint:
self._resume_from_checkpoint()
max_acc = self._init_max_acc
best_epoch = self.get_ckp_epoch()
self.model.cuda()
self.criterion.cuda()
end_epoch = self.num_epochs if self.from_pause else self.start_epoch + self.num_epochs
for epoch in range(self.start_epoch, end_epoch):
lr = self._adjust_learning_rate(epoch)
self.logger.show_nl("Epoch: [{0}]\tlr {1:.06f}".format(epoch, lr))
# Train for one epoch
self.train_epoch()
# Evaluate the model on validation set
self.logger.show_nl("Validate")
acc = self.validate_epoch(epoch=epoch, store=self.save)
is_best = acc > max_acc
if is_best:
max_acc = acc
best_epoch = epoch
self.logger.show_nl(
"Current: {:.6f} ({:03d})\tBest: {:.6f} ({:03d})\t".format(
acc, epoch, max_acc, best_epoch))
# The checkpoint saves next epoch
self._save_checkpoint(self.model.state_dict(), max_acc, epoch + 1,
is_best)
def validate(self):
if self.checkpoint:
if self._resume_from_checkpoint():
self.model.cuda()
self.criterion.cuda()
self.validate_epoch(self.get_ckp_epoch(), self.save)
else:
self.logger.warning("no checkpoint assigned!")
def _load_pretrained(self):
raise NotImplementedError
def _adjust_learning_rate(self, epoch):
# Note that this does not take effect for separate learning rates
start_epoch = 0 if self.from_pause else self.start_epoch
if self.settings.lr_mode == 'step':
lr = self.lr * (0.5**((epoch - start_epoch) // self.settings.step))
elif self.settings.lr_mode == 'poly':
lr = self.lr * (1 - (epoch - start_epoch) /
(self.num_epochs - start_epoch))**1.1
elif self.settings.lr_mode == 'const':
lr = self.lr
else:
raise ValueError('unknown lr mode {}'.format(
self.settings.lr_mode))
if lr == self.lr:
return self.lr
for param_group in self.optimizer.param_groups:
param_group['lr'] = lr
return lr
def _resume_from_checkpoint(self):
if not os.path.isfile(self.checkpoint):
self.logger.error("=> no checkpoint found at '{}'".format(
self.checkpoint))
return False
self.logger.show("=> loading checkpoint '{}'".format(self.checkpoint))
checkpoint = torch.load(self.checkpoint)
state_dict = self.model.state_dict()
ckp_dict = checkpoint.get('state_dict', checkpoint)
update_dict = {
k: v
for k, v in ckp_dict.items()
if k in state_dict and state_dict[k].shape == v.shape
}
num_to_update = len(update_dict)
if (num_to_update < len(state_dict)) or (len(state_dict) <
len(ckp_dict)):
if self.phase == 'val':
self.logger.error("=> mismatched checkpoint for validation")
return False
self.logger.warning(
"warning: trying to load an mismatched checkpoint")
if num_to_update == 0:
self.logger.error("=> no parameter is to be loaded")
return False
else:
self.logger.warning(
"=> {} params are to be loaded".format(num_to_update))
elif (not self.settings.anew) or (self.phase != 'train'):
# Note in the non-anew mode, it is not guaranteed that the contained field
# max_acc be the corresponding one of the loaded checkpoint.
self.start_epoch = checkpoint.get('epoch', self.start_epoch)
self._init_max_acc = checkpoint.get('max_acc', self._init_max_acc)
state_dict.update(update_dict)
self.model.load_state_dict(state_dict)
self.logger.show(
"=> loaded checkpoint '{}' (epoch {}, max_acc {:.4f})".format(
self.checkpoint, self.get_ckp_epoch(), self._init_max_acc))
return True
def _save_checkpoint(self, state_dict, max_acc, epoch, is_best):
state = {'epoch': epoch, 'state_dict': state_dict, 'max_acc': max_acc}
# Save history
history_path = self.path('weight',
CKP_COUNTED.format(e=epoch, s=self.scale),
underline=True)
if (epoch - self.start_epoch) % self.settings.trace_freq == 0:
torch.save(state, history_path)
# Save latest
latest_path = self.path('weight',
CKP_LATEST.format(s=self.scale),
underline=True)
torch.save(state, latest_path)
if is_best:
shutil.copyfile(
latest_path,
self.path('weight',
CKP_BEST.format(s=self.scale),
underline=True))
def get_ckp_epoch(self):
# Get current epoch of the checkpoint
# For dismatched ckp or no ckp, set to 0
return max(self.start_epoch - 1, 0)
class Predictor:
def __init__(self,
data_dir,
ckp_path,
save_lr=False,
list_dir='',
out_dir='./',
log_dir=''):
super(Predictor, self).__init__()
self.data_dir = data_dir
self.list_dir = list_dir
self.out_dir = out_dir
self.checkpoint = ckp_path
self.save_lr = save_lr
self.logger = Logger(scrn=True, log_dir=log_dir, phase='test')
self.model = None
def test_epoch(self):
raise NotImplementedError
def test(self):
if self.checkpoint:
if self._resume_from_checkpoint():
self.model.cuda()
self.model.eval()
self.test_epoch()
else:
self.logger.warning("no checkpoint assigned!")
def _resume_from_checkpoint(self):
if not os.path.isfile(self.checkpoint):
self.logger.error("=> no checkpoint found at '{}'".format(
self.checkpoint))
return False
self.logger.show("=> loading checkpoint '{}'".format(self.checkpoint))
checkpoint = torch.load(self.checkpoint)
state_dict = self.model.state_dict()
ckp_dict = checkpoint.get('state_dict', checkpoint)
try:
state_dict.update(ckp_dict)
self.model.load_state_dict(ckp_dict)
except KeyError as e:
self.logger.error("=> mismatched checkpoint for test")
self.logger.error(e)
return False
else:
self.epoch = checkpoint.get('epoch', 0)
self.logger.show("=> loaded checkpoint '{}'".format(self.checkpoint))
return True
# @Author : peng.wang # @Email : [email protected] # @FileName: util.py # @ProjectName :Facility_Location_FangTai """ import pandas as pd import os import xlwings as xw from utils.misc import Logger from pyecharts import options as opts from pyecharts.charts import Geo from pyecharts.globals import ChartType, SymbolType # define the log file RAW_DATA_PATH = os.path.dirname(os.path.dirname(__file__)) log = Logger(log_path=os.path.join(RAW_DATA_PATH, 'log')).logger class DataHandler(object): """ """ def __init__(self, file, config): """ file:文件名 :param file: :param config """ # 读数路径 self._PATH = os.path.join(os.path.join(RAW_DATA_PATH, 'data'), file) self._config = config
def run(try_num, config):
args = get_args()
print('args', args, flush=True)
print('config:', config.to_dict(), flush=True)
set_seed(config.rand_seed)
pretrained_model = f"tf_efficientnet_b3_ns"
model_dir = f'deepinsight-{try_num}'
if not os.path.exists(model_dir):
os.mkdir(model_dir)
train_features = pd.read_csv(f"../input/lish-moa/train_features.csv")
train_targets = pd.read_csv(f"../input/lish-moa/train_targets_scored.csv")
test_features = pd.read_csv(f"../input/lish-moa/test_features.csv")
if config.dae_path:
dae_features = pd.read_csv(config.dae_path)
if args.debug:
train_features = train_features.iloc[:500]
train_targets = train_targets.iloc[:500]
if config.dae_path:
dae_features = pd.concat([dae_features.iloc[:500], dae_features.iloc[-3982:]]).reset_index(drop=True)
config.update(dict(
kfolds=3,
n_epoch=3
))
train_features = train_features.sort_values(by=["sig_id"], axis=0, inplace=False).reset_index(drop=True)
train_targets = train_targets.sort_values(by=["sig_id"], axis=0, inplace=False).reset_index(drop=True)
cat_features_columns = ["cp_dose", 'cp_time']
num_feature_columns = [c for c in train_features.columns
if c != "sig_id" and c not in cat_features_columns + ['cp_type']]
all_features_columns = cat_features_columns + num_feature_columns
target_columns = [c for c in train_targets.columns if c != "sig_id"]
g_feature_columns = [c for c in num_feature_columns if c.startswith("g-")]
c_feature_columns = [c for c in num_feature_columns if c.startswith("c-")]
if config.dae_path:
if config.dae_strategy == 'replace':
train_features, test_features = assign_dae_features(
train_features, test_features, dae_features, len(num_feature_columns))
else:
train_features, test_features, dae_feature_columns = merge_dae_features(
train_features, test_features, dae_features, len(g_feature_columns), len(c_feature_columns))
all_features_columns += dae_feature_columns
train_targets = train_targets.loc[train_features['cp_type'] == 'trt_cp'].reset_index(drop=True)
train_features = train_features.loc[train_features['cp_type'] == 'trt_cp'].reset_index(drop=True)
if config.normalizer == 'rank':
train_features, test_features = normalize(train_features, test_features, num_feature_columns)
for df in [train_features, test_features]:
df['cp_type'] = df['cp_type'].map({'ctl_vehicle': 0, 'trt_cp': 1})
df['cp_dose'] = df['cp_dose'].map({'D1': 0, 'D2': 1})
df['cp_time'] = df['cp_time'].map({24: 0, 48: 0.5, 72: 1})
if config.variance_target_type == 1:
pickle_path = f'{model_dir}/variance_reduction.pkl'
variance_target_features = num_feature_columns
if config.dae_path and config.dae_strategy != 'replace':
variance_target_features += dae_feature_columns
if not os.path.exists(pickle_path):
vt = variance_reduction_fit(train_features, variance_target_features, config.variance_threshold)
save_pickle(vt, pickle_path)
vt = load_pickle(pickle_path)
train_features = variance_reduction_transform(vt, train_features, variance_target_features)
test_features = variance_reduction_transform(vt, test_features, variance_target_features)
print('(variance_reduction) Number of features after applying:', len(train_features.columns), flush=True)
all_features_columns = list(train_features.columns[1:])
skf = MultilabelStratifiedKFold(n_splits=config.kfolds, shuffle=True, random_state=config.rand_seed)
y_labels = np.sum(train_targets.drop("sig_id", axis=1), axis=0).index.tolist()
logger = Logger()
for fold_index, (train_index, val_index) in enumerate(skf.split(train_features, train_targets[y_labels])):
if args.only_pred:
print('Skip training', flush=True)
break
print(f'Fold: {fold_index}', train_index.shape, val_index.shape, flush=True)
X_train = train_features.loc[train_index, all_features_columns].copy().values
y_train = train_targets.iloc[train_index, 1:].copy().values
X_valid = train_features.loc[val_index, all_features_columns].copy().values
y_valid = train_targets.iloc[val_index, 1:].copy().values
if config.normalizer == 'log':
scaler = LogScaler()
if config.norm_apply_all:
scaler.fit(X_train)
X_train = scaler.transform(X_train)
X_valid = scaler.transform(X_valid)
else:
target_features = [i for i, c in enumerate(all_features_columns) if c in num_feature_columns]
non_target_features = [i for i, c in enumerate(all_features_columns) if c not in num_feature_columns]
scaler.fit(X_train[:, target_features])
X_train_tr = scaler.transform(X_train[:, target_features])
X_valid_tr = scaler.transform(X_valid[:, target_features])
X_train = np.concatenate([X_train[:, non_target_features], X_train_tr], axis=1)
X_valid = np.concatenate([X_valid[:, non_target_features], X_valid_tr], axis=1)
save_pickle(scaler, f'{model_dir}/scaler-{fold_index}.pkl')
transformer = DeepInsightTransformer(
feature_extractor=config.extractor,
pixels=config.resolution,
perplexity=config.perplexity,
random_state=config.rand_seed,
n_jobs=-1
).fit(X_train)
save_pickle(transformer, f'{model_dir}/transformer-{fold_index}.pkl')
model = MoAEfficientNet(
pretrained_model_name=pretrained_model,
fc_size=config.fc_size,
drop_rate=config.drop_rate,
drop_connect_rate=config.drop_connect_rate,
weight_init='goog',
).to(DEVICE)
if config.smoothing is not None:
if config.weighted_loss_weights is not None:
indices = get_minority_target_index(train_targets, threshold=config.weighted_loss_threshold)
indices = [int(i not in indices) for i, c in enumerate(target_columns)]
train_loss_function = SmoothBCEwLogits(
smoothing=config.smoothing,
weight=config.weighted_loss_weights,
weight_targets=indices,
n_labels=len(target_columns))
else:
train_loss_function = SmoothBCEwLogits(smoothing=config.smoothing)
else:
train_loss_function = bce_loss
eval_loss_function = bce_loss
optimizer = optim.Adam(model.parameters(), weight_decay=config.weight_decay, lr=config.learning_rate)
if config.scheduler_type == 'ca':
scheduler = optim.lr_scheduler.CosineAnnealingLR(optimizer, T_max=config.t_max, eta_min=0, last_epoch=-1)
elif config.scheduler_type == 'ms':
scheduler = optim.lr_scheduler.MultiStepLR(optimizer, milestones=config.ms_scheduler_milestones, gamma=0.1)
else:
scheduler = optim.lr_scheduler.ReduceLROnPlateau(
optimizer, mode='min', factor=0.1, patience=config.rp_patience, eps=1e-4, verbose=True)
early_stopping = EarlyStopping(patience=7)
best_score = np.inf
start_time = time.time()
for epoch in range(config.n_epoch):
if config.swap_enable:
dataset = MoAImageSwapDataset(
X_train,
y_train,
transformer,
image_size=config.image_size,
swap_prob=config.swap_prob,
swap_portion=config.swap_portion)
else:
dataset = MoAImageDataset(X_train, y_train, transformer, image_size=config.image_size)
dataloader = DataLoader(
dataset,
batch_size=config.batch_size,
shuffle=True,
num_workers=8,
pin_memory=True,
drop_last=False)
loss = loop_train(model, train_loss_function, dataloader, optimizer)
if config.scheduler_type == 'rp':
scheduler.step(loss)
else:
scheduler.step()
for param_group in optimizer.param_groups:
print('current learning rate:', param_group['lr'])
del dataset, dataloader
dataset = MoAImageDataset(X_valid, y_valid, transformer, image_size=config.image_size)
dataloader = DataLoader(
dataset,
batch_size=config.infer_batch_size,
shuffle=False,
num_workers=8,
pin_memory=True,
drop_last=False)
valid_loss, valid_preds = loop_valid(model, eval_loss_function, dataloader)
del dataset, dataloader
logger.update({'fold': fold_index, 'epoch': epoch + 1, 'train_loss': loss, 'val_loss': valid_loss})
print(f'epoch {epoch + 1}/{config.n_epoch} - train_loss: {loss:.5f} - ' +
f'valid_loss: {valid_loss:.5f} - elapsed: {time_format(time.time() - start_time)}', flush=True)
if valid_loss < best_score:
best_score = valid_loss
torch.save(model.state_dict(), f'./{model_dir}/deepinsight-{fold_index}.pt')
if early_stopping.should_stop(valid_loss):
print('Early stopping', flush=True)
break
print(f'Done -> Fold {fold_index}/{config.kfolds} - best_valid_loss: {best_score:.5f} - ' +
f'elapsed: {time_format(time.time() - start_time)}', flush=True)
torch.cuda.empty_cache()
gc.collect()
if args.return_first_fold:
logger.save(f'{model_dir}/log.csv')
return
test_preds = np.zeros((test_features.shape[0], len(target_columns)))
start_time = time.time()
print('Start infarence', flush=True)
oof_preds = np.zeros((len(train_features), len(target_columns)))
eval_loss_function = bce_loss
for fold_index, (train_index, val_index) in enumerate(skf.split(train_features, train_targets[y_labels])):
print(f'Infarence Fold: {fold_index}', train_index.shape, val_index.shape, flush=True)
X_valid = train_features.loc[val_index, all_features_columns].copy().values
y_valid = train_targets.iloc[val_index, 1:].copy().values
X_test = test_features[all_features_columns].values
if config.normalizer == 'log':
scaler = load_pickle(f'{model_dir}/scaler-{fold_index}.pkl')
X_valid = scaler.transform(X_valid)
X_test = scaler.transform(X_test)
transformer = load_pickle(f'{model_dir}/transformer-{fold_index}.pkl')
model = MoAEfficientNet(
pretrained_model_name=pretrained_model,
fc_size=config.fc_size,
drop_rate=config.drop_rate,
drop_connect_rate=config.drop_connect_rate,
weight_init='goog',
).to(DEVICE)
model.load_state_dict(torch.load(f'./{model_dir}/deepinsight-{fold_index}.pt'))
dataset = MoAImageDataset(X_valid, y_valid, transformer, image_size=config.image_size)
dataloader = DataLoader(
dataset,
batch_size=config.infer_batch_size,
shuffle=False,
num_workers=8,
pin_memory=True,
drop_last=False)
valid_loss, valid_preds = loop_valid(model, eval_loss_function, dataloader)
print(f'Fold {fold_index}/{config.kfolds} - fold_valid_loss: {valid_loss:.5f}', flush=True)
logger.update({'fold': fold_index, 'val_loss': valid_loss})
oof_preds[val_index, :] = valid_preds
dataset = TestDataset(X_test, None, transformer, image_size=config.image_size)
dataloader = DataLoader(
dataset,
batch_size=config.infer_batch_size,
shuffle=False,
num_workers=8,
pin_memory=True,
drop_last=False)
preds = loop_preds(model, dataloader)
test_preds += preds / config.kfolds
oof_preds_df = train_targets.copy()
oof_preds_df.loc[:, target_columns] = oof_preds.clip(0, 1)
oof_preds_df.to_csv(f'{model_dir}/oof_preds.csv', index=False)
oof_loss = mean_log_loss(train_targets.loc[:, target_columns].values, oof_preds)
print(f'OOF Validation Loss: {oof_loss:.6f}', flush=True)
print(f'Done infarence Elapsed {time_format(time.time() - start_time)}', flush=True)
logger.update({'fold': 'oof', 'val_loss': oof_loss})
logger.save(f'{model_dir}/log.csv')
submission = pd.DataFrame(data=test_features['sig_id'].values, columns=['sig_id'])
submission = submission.reindex(columns=['sig_id'] + target_columns)
submission.loc[:, target_columns] = test_preds.clip(0, 1)
submission.loc[test_features['cp_type'] == 0, submission.columns[1:]] = 0
submission.to_csv(f'{model_dir}/submission.csv', index=False)
def run(try_num, config):
logger = Logger()
args = get_args()
print('config:', config.to_dict(), flush=True)
print('args:', args, flush=True)
os.environ['KMP_DUPLICATE_LIB_OK'] = 'True'
model_dir = f'blending-01-nn-{try_num}'
if not os.path.exists(model_dir):
os.mkdir(model_dir)
train_features = pd.read_csv('../input/lish-moa/train_features.csv')
train_targets = pd.read_csv('../input/lish-moa/train_targets_scored.csv')
dae_features = pd.read_csv(config.dae_path)
test_features = pd.read_csv('../input/lish-moa/test_features.csv')
if args.debug:
train_features = train_features[:500]
train_targets = train_targets[:500]
dae_features = pd.concat(
[dae_features.iloc[:500],
dae_features.iloc[-3982:]]).reset_index(drop=True)
config.update(
dict(
n_folds=3,
seeds=[222],
n_epochs=3,
batch_size=128,
))
target_columns = [col for col in train_targets.columns if col != 'sig_id']
n_targets = len(target_columns)
train_features, train_targets, test_features = preprocess(
config, model_dir, train_features, train_targets, test_features,
dae_features)
features_columns = [
col for col in train_features.columns if col not in [
'sig_id', 'cp_type', 'cp_time', 'cp_dose', 'cp_type_ctl_vehicle',
'cp_type_trt_cp'
]
]
metric_loss_function = nn.BCELoss()
if config.weighted_loss_strategy == 1:
indices = get_minority_target_index(
train_targets, threshold=config.weighted_loss_threshold)
indices = [int(i not in indices) for i, c in enumerate(target_columns)]
smooth_loss_function = SmoothBCELoss(
smoothing=config.smoothing,
weight=config.weighted_loss_weights,
weight_targets=indices,
n_labels=n_targets)
else:
smooth_loss_function = SmoothBCELoss(smoothing=config.smoothing)
kfold = MultilabelStratifiedKFold(n_splits=config.n_folds,
random_state=42,
shuffle=True)
for seed_index, seed in enumerate(config.seeds):
if args.only_pred:
print('Skip training', flush=True)
break
print(f'Train seed {seed}', flush=True)
set_seed(seed)
for fold_index, (train_indices, val_indices) in enumerate(
kfold.split(train_targets[target_columns].values,
train_targets[target_columns].values)):
print(f'Train fold {fold_index + 1}', flush=True)
x_train = train_features.loc[train_indices, features_columns]
y_train = train_targets.loc[train_indices, target_columns]
x_val = train_features.loc[val_indices, features_columns]
y_val = train_targets.loc[val_indices, target_columns]
model = new_model(config.model_kind,
len(features_columns)).to(DEVICE)
checkpoint_path = f'{model_dir}/repeat-{seed}_Fold-{fold_index + 1}.pt'
optimizer = optim.Adam(model.parameters(),
weight_decay=config.weight_decay,
lr=config.learning_rate)
scheduler = optim.lr_scheduler.ReduceLROnPlateau(optimizer,
mode='min',
factor=0.1,
patience=3,
eps=1e-4,
verbose=True)
best_loss = np.inf
for epoch in range(config.n_epochs):
dataset = MoaDataset(x_train.values, y_train.values)
dataloader = DataLoader(dataset,
batch_size=config.batch_size,
shuffle=True,
drop_last=True)
train_loss = loop_train(model,
dataloader,
optimizer,
loss_functions=(
smooth_loss_function,
metric_loss_function,
))
dataset = MoaDataset(x_val.values, y_val.values)
dataloader = DataLoader(dataset,
batch_size=config.val_batch_size,
shuffle=False)
valid_loss, _ = loop_valid(model, dataloader,
metric_loss_function)
print(
'Epoch {}/{} - loss: {:5.5f} - val_loss: {:5.5f}'.
format(epoch + 1, config.n_epochs, train_loss, valid_loss),
flush=True)
logger.update({
'epoch': epoch + 1,
'loss': train_loss,
'val_loss': valid_loss
})
scheduler.step(valid_loss)
if valid_loss < best_loss:
best_loss = valid_loss
torch.save(model.state_dict(), checkpoint_path)
oof_preds = np.zeros((len(train_features), len(config.seeds), n_targets))
test_preds = np.zeros((len(test_features), n_targets))
for seed_index in range(len(config.seeds)):
seed = config.seeds[seed_index]
print(f'Inference for seed {seed}', flush=True)
_test_preds_in_seed = np.zeros((len(test_features), n_targets))
for fold_index, (_, valid_indices) in enumerate(
kfold.split(train_targets[target_columns].values,
train_targets[target_columns].values)):
x_val = train_features.loc[valid_indices, features_columns]
y_val = train_targets.loc[valid_indices, target_columns]
checkpoint_path = f'{model_dir}/repeat-{seed}_Fold-{fold_index + 1}.pt'
model = new_model(config.model_kind,
len(features_columns)).to(DEVICE)
model.load_state_dict(torch.load(checkpoint_path))
dataset = MoaDataset(x_val.values, y_val.values)
dataloader = DataLoader(dataset,
batch_size=config.val_batch_size,
shuffle=False)
preds = loop_pred(model, dataloader)
oof_preds[valid_indices, seed_index, :] = preds
dataset = MoaDataset(test_features[features_columns].values, None)
dataloader = DataLoader(dataset,
batch_size=config.val_batch_size,
shuffle=False)
preds = loop_pred(model, dataloader)
_test_preds_in_seed += preds / config.n_folds
score = mean_log_loss(train_targets.loc[:, target_columns].values,
oof_preds[:, seed_index, :],
n_targets=n_targets)
test_preds += _test_preds_in_seed / len(config.seeds)
print(f'Score for this seed {score:5.5f}', flush=True)
logger.update({'val_loss': score})
# Evalucate validation score
oof_preds = np.mean(oof_preds, axis=1)
score = mean_log_loss(train_targets.loc[:, target_columns].values,
oof_preds,
n_targets=n_targets)
print(f'Overall score is {score:5.5f}', flush=True)
# Save validation prediction
oof_pred_df = train_targets.copy()
oof_pred_df.iloc[:, 1:] = oof_preds
oof_pred_df.to_csv(f'{model_dir}/oof_pred.csv', index=False)
# Save log
logger.update({'val_loss': score})
logger.save(f'{model_dir}/log.csv')
# Save Test Prediction
test_features = pd.read_csv('../input/lish-moa/test_features.csv')
submission = create_submission(test_features, ['sig_id'] + target_columns)
submission[target_columns] = test_preds
submission.loc[test_features['cp_type'] == 'ctl_vehicle',
target_columns] = 0
submission.to_csv(f'{model_dir}/submission.csv', index=False)
import pandas as pd
import numpy as np
from sklearn.base import BaseEstimator
from sklearn.ensemble import GradientBoostingRegressor
from sklearn.ensemble import RandomForestRegressor
from sklearn.gaussian_process import GaussianProcessRegressor
from sklearn.gaussian_process.kernels import DotProduct, WhiteKernel
from sklearn.svm import SVR
from sklearn.linear_model import Lasso, Ridge
from sklearn.model_selection import GridSearchCV
#
from utils.misc import Logger
from utils.util import generate_cutoffs
from utils.misc import save_model_to_file, mean_abs_percentage_error, xgb_mape
log = Logger(log_path=os.path.join(os.path.dirname(os.path.dirname(__file__)),
'log')).logger
warnings.filterwarnings("ignore")
xgb_installed = False
lgt_installed = False
try:
import xgboost as xgb
xgb_installed = True
import lightgbm as lgt
lgt_installed = True
except ImportError:
pass
class TrainModel(BaseEstimator):
#!/usr/bin/python # -*- coding: UTF-8 -*- """ # @Time : 2019/9/9 9:55 # @Author : peng.wang # @Email : [email protected] # @FileName: model.py # @ProjectName :Facility_Location_FangTai """ from gurobipy import * from utils.misc import Logger import pandas as pd # define the log file log = Logger(log_path='../log').logger # define the facility location problem YEAR_DAY = 365 class FacilityLocation(object): """ this class is consist of attributes for problem construction some utils function for dealing with post-process one key function for building the detail model """ def __init__(self, data, config): """ :param data: class of data provide all data used
#!/usr/bin/python # -*- coding: UTF-8 -*- """ # @Time : 2019/10/8 22:34 # @Author : peng.wang # @Email : [email protected] # @FileName: util.py # @ProjectName :sh-demand-forecast-alg """ import pandas as pd import numpy as np import requests import json import os from utils.misc import Logger log = Logger(log_path='log').logger class DataLoader(object): """ Data loader. Combines a dataset and a sampler, and provides an iterable over the given dataset. """ def __init__(self, data, train_len, pred_len, feature_names, target_name, append_train=False): self.data = data
