def main():
# Parse the arguments.
args = parse_arguments()
if args.label:
labels = args.label
class_num = len(labels) if isinstance(labels, list) else 1
else:
raise ValueError('No target label was specified.')
# Dataset preparation. Postprocessing is required for the regression task.
def postprocess_label(label_list):
return numpy.asarray(label_list, dtype=numpy.float32)
# Apply a preprocessor to the dataset.
print('Preprocessing dataset...')
preprocessor = preprocess_method_dict[args.method]()
parser = CSVFileParser(preprocessor, postprocess_label=postprocess_label,
labels=labels, smiles_col='SMILES')
dataset = parser.parse(args.datafile)['dataset']
# Scale the label values, if necessary.
if args.scale == 'standardize':
scaler = StandardScaler()
scaler.fit(dataset.get_datasets()[-1])
else:
scaler = None
# Split the dataset into training and validation.
train_data_size = int(len(dataset) * args.train_data_ratio)
train, _ = split_dataset_random(dataset, train_data_size, args.seed)
# Set up the predictor.
predictor = set_up_predictor(
args.method, args.unit_num,
args.conv_layers, class_num, label_scaler=scaler)
# Set up the regressor.
device = chainer.get_device(args.device)
metrics_fun = {'mae': F.mean_absolute_error, 'rmse': rmse}
regressor = Regressor(predictor, lossfun=F.mean_squared_error,
metrics_fun=metrics_fun, device=device)
print('Training...')
run_train(regressor, train, valid=None,
batch_size=args.batchsize, epoch=args.epoch,
out=args.out, extensions_list=None,
device=device, converter=concat_mols,
resume_path=None)
# Save the regressor's parameters.
model_path = os.path.join(args.out, args.model_filename)
print('Saving the trained model to {}...'.format(model_path))
# TODO(nakago): ChainerX array cannot be sent to numpy array when internal
# state has gradients.
if hasattr(regressor.predictor.graph_conv, 'reset_state'):
regressor.predictor.graph_conv.reset_state()
regressor.save_pickle(model_path, protocol=args.protocol)
def main():
args = parse_arguments()
# Set up some useful variables that will be used later on.
dataset_name = args.dataset
method = args.method
num_data = args.num_data
n_unit = args.unit_num
conv_layers = args.conv_layers
task_type = molnet_default_config[dataset_name]['task_type']
model_filename = {
'classification': 'classifier.pkl',
'regression': 'regressor.pkl'
}
print('Using dataset: {}...'.format(dataset_name))
# Set up some useful variables that will be used later on.
if args.label:
labels = args.label
cache_dir = os.path.join(
'input', '{}_{}_{}'.format(dataset_name, method, labels))
class_num = len(labels) if isinstance(labels, list) else 1
else:
labels = None
cache_dir = os.path.join('input',
'{}_{}_all'.format(dataset_name, method))
class_num = len(molnet_default_config[args.dataset]['tasks'])
# Load the train and validation parts of the dataset.
filenames = [
dataset_part_filename(p, num_data) for p in ['train', 'valid']
]
paths = [os.path.join(cache_dir, f) for f in filenames]
if all([os.path.exists(path) for path in paths]):
dataset_parts = []
for path in paths:
print('Loading cached dataset from {}.'.format(path))
dataset_parts.append(NumpyTupleDataset.load(path))
else:
dataset_parts = download_entire_dataset(dataset_name, num_data, labels,
method, cache_dir)
train, valid = dataset_parts[0], dataset_parts[1]
# Scale the label values, if necessary.
scaler = None
if args.scale == 'standardize':
if task_type == 'regression':
print('Applying standard scaling to the labels.')
scaler = fit_scaler(dataset_parts)
else:
print('Label scaling is not available for classification tasks.')
else:
print('No label scaling was selected.')
# Set up the predictor.
predictor = set_up_predictor(method,
n_unit,
conv_layers,
class_num,
label_scaler=scaler)
# Set up the iterators.
train_iter = iterators.SerialIterator(train, args.batchsize)
valid_iter = iterators.SerialIterator(valid,
args.batchsize,
repeat=False,
shuffle=False)
# Load metrics for the current dataset.
metrics = molnet_default_config[dataset_name]['metrics']
metrics_fun = {
k: v
for k, v in metrics.items() if isinstance(v, types.FunctionType)
}
loss_fun = molnet_default_config[dataset_name]['loss']
device = chainer.get_device(args.device)
if task_type == 'regression':
model = Regressor(predictor,
lossfun=loss_fun,
metrics_fun=metrics_fun,
device=device)
elif task_type == 'classification':
model = Classifier(predictor,
lossfun=loss_fun,
metrics_fun=metrics_fun,
device=device)
else:
raise ValueError('Invalid task type ({}) encountered when processing '
'dataset ({}).'.format(task_type, dataset_name))
# Set up the optimizer.
optimizer = optimizers.Adam()
optimizer.setup(model)
# Save model-related output to this directory.
model_dir = os.path.join(args.out, os.path.basename(cache_dir))
if not os.path.exists(model_dir):
os.makedirs(model_dir)
# Set up the updater.
updater = training.StandardUpdater(train_iter,
optimizer,
device=device,
converter=concat_mols)
# Set up the trainer.
trainer = training.Trainer(updater, (args.epoch, 'epoch'), out=model_dir)
trainer.extend(
E.Evaluator(valid_iter, model, device=device, converter=concat_mols))
trainer.extend(E.snapshot(), trigger=(args.epoch, 'epoch'))
trainer.extend(E.LogReport())
# TODO: consider go/no-go of the following block
# # (i) more reporting for val/evalutaion
# # (ii) best validation score snapshot
# if task_type == 'regression':
# metric_name_list = list(metrics.keys())
# if 'RMSE' in metric_name_list:
# trainer.extend(E.snapshot_object(model, "best_val_" + model_filename[task_type]),
# trigger=training.triggers.MinValueTrigger('validation/main/RMSE'))
# elif 'MAE' in metric_name_list:
# trainer.extend(E.snapshot_object(model, "best_val_" + model_filename[task_type]),
# trigger=training.triggers.MinValueTrigger('validation/main/MAE'))
# else:
# print("[WARNING] No validation metric defined?")
#
# elif task_type == 'classification':
# train_eval_iter = iterators.SerialIterator(
# train, args.batchsize, repeat=False, shuffle=False)
# trainer.extend(ROCAUCEvaluator(
# train_eval_iter, predictor, eval_func=predictor,
# device=args.gpu, converter=concat_mols, name='train',
# pos_labels=1, ignore_labels=-1, raise_value_error=False))
# # extension name='validation' is already used by `Evaluator`,
# # instead extension name `val` is used.
# trainer.extend(ROCAUCEvaluator(
# valid_iter, predictor, eval_func=predictor,
# device=args.gpu, converter=concat_mols, name='val',
# pos_labels=1, ignore_labels=-1, raise_value_error=False))
#
# trainer.extend(E.snapshot_object(
# model, "best_val_" + model_filename[task_type]),
# trigger=training.triggers.MaxValueTrigger('val/main/roc_auc'))
# else:
# raise NotImplementedError(
# 'Not implemented task_type = {}'.format(task_type))
trainer.extend(AutoPrintReport())
trainer.extend(E.ProgressBar())
trainer.run()
# Save the model's parameters.
model_path = os.path.join(model_dir, model_filename[task_type])
print('Saving the trained model to {}...'.format(model_path))
model.save_pickle(model_path, protocol=args.protocol)
def main():
# Parse the arguments.
args = parse_arguments()
# Set up some useful variables that will be used later on.
method = args.method
if args.label != 'all':
labels = args.label
cache_dir = os.path.join('input', '{}_{}'.format(method, labels))
class_num = len(labels) if isinstance(labels, list) else 1
else:
labels = None
cache_dir = os.path.join('input', '{}_all'.format(method))
class_num = len(D.get_qm9_label_names())
# Get the filename corresponding to the cached dataset, based on the amount
# of data samples that need to be parsed from the original dataset.
num_data = args.num_data
if num_data >= 0:
dataset_filename = 'data_{}.npz'.format(num_data)
else:
dataset_filename = 'data.npz'
# Load the cached dataset.
dataset_cache_path = os.path.join(cache_dir, dataset_filename)
dataset = None
if os.path.exists(dataset_cache_path):
print('Loading cached dataset from {}.'.format(dataset_cache_path))
dataset = NumpyTupleDataset.load(dataset_cache_path)
if dataset is None:
print('Preprocessing dataset...')
preprocessor = preprocess_method_dict[method]()
if num_data >= 0:
# Select the first `num_data` samples from the dataset.
target_index = numpy.arange(num_data)
dataset = D.get_qm9(preprocessor,
labels=labels,
target_index=target_index)
else:
# Load the entire dataset.
dataset = D.get_qm9(preprocessor, labels=labels)
# Cache the laded dataset.
if not os.path.exists(cache_dir):
os.makedirs(cache_dir)
NumpyTupleDataset.save(dataset_cache_path, dataset)
# Scale the label values, if necessary.
if args.scale == 'standardize':
print('Fit StandardScaler to the labels.')
scaler = StandardScaler()
scaler.fit(dataset.get_datasets()[-1])
else:
print('No standard scaling was selected.')
scaler = None
# Split the dataset into training and validation.
train_data_size = int(len(dataset) * args.train_data_ratio)
train, valid = split_dataset_random(dataset, train_data_size, args.seed)
# Set up the predictor.
predictor = set_up_predictor(method, args.unit_num, args.conv_layers,
class_num, scaler)
# Set up the regressor.
device = chainer.get_device(args.device)
metrics_fun = {'mae': F.mean_absolute_error, 'rmse': rmse}
regressor = Regressor(predictor,
lossfun=F.mean_squared_error,
metrics_fun=metrics_fun,
device=device)
print('Training...')
run_train(regressor,
train,
valid=valid,
batch_size=args.batchsize,
epoch=args.epoch,
out=args.out,
extensions_list=None,
device=device,
converter=concat_mols,
resume_path=None)
# Save the regressor's parameters.
model_path = os.path.join(args.out, args.model_filename)
print('Saving the trained model to {}...'.format(model_path))
regressor.save_pickle(model_path, protocol=args.protocol)
def main():
# Parse the arguments.
args = parse_arguments()
# Set up some useful variables that will be used later on.
method = args.method
if args.label != 'all':
labels = args.label
cache_dir = os.path.join('input', '{}_{}'.format(method, labels))
class_num = len(labels) if isinstance(labels, list) else 1
else:
labels = None
cache_dir = os.path.join('input', '{}_all'.format(method))
class_num = len(D.get_qm9_label_names())
# Get the filename corresponding to the cached dataset, based on the amount
# of data samples that need to be parsed from the original dataset.
num_data = args.num_data
if num_data >= 0:
dataset_filename = 'data_{}.npz'.format(num_data)
else:
dataset_filename = 'data.npz'
# Load the cached dataset.
dataset_cache_path = os.path.join(cache_dir, dataset_filename)
dataset = None
if os.path.exists(dataset_cache_path):
print('Loading cached dataset from {}.'.format(dataset_cache_path))
dataset = NumpyTupleDataset.load(dataset_cache_path)
if dataset is None:
print('Preprocessing dataset...')
preprocessor = preprocess_method_dict[method]()
if num_data >= 0:
# Select the first `num_data` samples from the dataset.
target_index = numpy.arange(num_data)
dataset = D.get_qm9(preprocessor, labels=labels,
target_index=target_index)
else:
# Load the entire dataset.
dataset = D.get_qm9(preprocessor, labels=labels)
# Cache the laded dataset.
if not os.path.exists(cache_dir):
os.makedirs(cache_dir)
NumpyTupleDataset.save(dataset_cache_path, dataset)
# Scale the label values, if necessary.
if args.scale == 'standardize':
print('Applying standard scaling to the labels.')
scaler = StandardScaler()
scaled_t = scaler.fit_transform(dataset.get_datasets()[-1])
dataset = NumpyTupleDataset(*(dataset.get_datasets()[:-1]
+ (scaled_t,)))
else:
print('No standard scaling was selected.')
scaler = None
# Split the dataset into training and validation.
train_data_size = int(len(dataset) * args.train_data_ratio)
train, valid = split_dataset_random(dataset, train_data_size, args.seed)
# Set up the predictor.
predictor = set_up_predictor(method, args.unit_num, args.conv_layers,
class_num, scaler)
# Set up the iterators.
train_iter = iterators.SerialIterator(train, args.batchsize)
valid_iter = iterators.SerialIterator(valid, args.batchsize, repeat=False,
shuffle=False)
# Set up the regressor.
device = args.gpu
metrics_fun = {'mae': MeanAbsError(scaler=scaler),
'rmse': RootMeanSqrError(scaler=scaler)}
regressor = Regressor(predictor, lossfun=F.mean_squared_error,
metrics_fun=metrics_fun, device=device)
# Set up the optimizer.
optimizer = optimizers.Adam()
optimizer.setup(regressor)
# Set up the updater.
updater = training.StandardUpdater(train_iter, optimizer, device=device,
converter=concat_mols)
# Set up the trainer.
trainer = training.Trainer(updater, (args.epoch, 'epoch'), out=args.out)
trainer.extend(E.Evaluator(valid_iter, regressor, device=device,
converter=concat_mols))
trainer.extend(E.snapshot(), trigger=(args.epoch, 'epoch'))
trainer.extend(E.LogReport())
trainer.extend(E.PrintReport([
'epoch', 'main/loss', 'main/mae', 'main/rmse', 'validation/main/loss',
'validation/main/mae', 'validation/main/rmse', 'elapsed_time']))
trainer.extend(E.ProgressBar())
trainer.run()
# Save the regressor's parameters.
model_path = os.path.join(args.out, args.model_filename)
print('Saving the trained model to {}...'.format(model_path))
regressor.save_pickle(model_path, protocol=args.protocol)
def main():
# Parse the arguments.
args = parse_arguments()
if args.label:
labels = args.label
class_num = len(labels) if isinstance(labels, list) else 1
else:
raise ValueError('No target label was specified.')
# Dataset preparation. Postprocessing is required for the regression task.
def postprocess_label(label_list):
return numpy.asarray(label_list, dtype=numpy.float32)
# Apply a preprocessor to the dataset.
print('Preprocessing dataset...')
preprocessor = preprocess_method_dict[args.method]()
parser = CSVFileParser(preprocessor,
postprocess_label=postprocess_label,
labels=labels,
smiles_col='SMILES')
dataset = parser.parse(args.datafile)['dataset']
# Scale the label values, if necessary.
if args.scale == 'standardize':
scaler = StandardScaler()
labels = scaler.fit_transform(dataset.get_datasets()[-1])
dataset = NumpyTupleDataset(*(dataset.get_datasets()[:-1] +
(labels, )))
else:
scaler = None
# Split the dataset into training and validation.
train_data_size = int(len(dataset) * args.train_data_ratio)
train, _ = split_dataset_random(dataset, train_data_size, args.seed)
# Set up the predictor.
predictor = set_up_predictor(args.method, args.unit_num, args.conv_layers,
class_num)
# Set up the iterator.
train_iter = SerialIterator(train, args.batchsize)
# Set up the regressor.
metrics_fun = {
'mean_abs_error': MeanAbsError(scaler=scaler),
'root_mean_sqr_error': RootMeanSqrError(scaler=scaler)
}
regressor = Regressor(predictor,
lossfun=F.mean_squared_error,
metrics_fun=metrics_fun,
device=args.gpu)
# Set up the optimizer.
optimizer = optimizers.Adam()
optimizer.setup(regressor)
# Set up the updater.
updater = training.StandardUpdater(train_iter,
optimizer,
device=args.gpu,
converter=concat_mols)
# Set up the trainer.
print('Training...')
trainer = training.Trainer(updater, (args.epoch, 'epoch'), out=args.out)
trainer.extend(E.snapshot(), trigger=(args.epoch, 'epoch'))
trainer.extend(E.LogReport())
trainer.extend(
E.PrintReport([
'epoch', 'main/loss', 'main/mean_abs_error',
'main/root_mean_sqr_error', 'elapsed_time'
]))
trainer.extend(E.ProgressBar())
trainer.run()
# Save the regressor's parameters.
model_path = os.path.join(args.out, args.model_filename)
print('Saving the trained model to {}...'.format(model_path))
regressor.save_pickle(model_path, protocol=args.protocol)
# Save the standard scaler's parameters.
if scaler is not None:
with open(os.path.join(args.out, 'scaler.pkl'), mode='wb') as f:
pickle.dump(scaler, f, protocol=args.protocol)
def main():
# Supported preprocessing/network list
method_list = [
'nfp', 'ggnn', 'schnet', 'weavenet', 'rsgcn', 'relgcn', 'relgat'
]
label_names = D.get_tox21_label_names()
iterator_type = ['serial', 'balanced']
parser = argparse.ArgumentParser(
description='Multitask Learning with Tox21.')
parser.add_argument('--method',
'-m',
type=str,
choices=method_list,
default='nfp',
help='graph convolution model to use '
'as a predictor.')
parser.add_argument('--label',
'-l',
type=str,
choices=label_names,
default='',
help='target label for logistic '
'regression. Use all labels if this option '
'is not specified.')
parser.add_argument('--iterator-type',
type=str,
choices=iterator_type,
default='serial',
help='iterator type. If `balanced` '
'is specified, data is sampled to take same number of'
'positive/negative labels during training.')
parser.add_argument('--eval-mode',
type=int,
default=1,
help='Evaluation mode.'
'0: only binary_accuracy is calculated.'
'1: binary_accuracy and ROC-AUC score is calculated')
parser.add_argument('--conv-layers',
'-c',
type=int,
default=4,
help='number of convolution layers')
parser.add_argument('--batchsize',
'-b',
type=int,
default=32,
help='batch size')
parser.add_argument(
'--device',
type=str,
default='-1',
help='Device specifier. Either ChainerX device specifier or an '
'integer. If non-negative integer, CuPy arrays with specified '
'device id are used. If negative integer, NumPy arrays are used')
parser.add_argument('--out',
'-o',
type=str,
default='result',
help='path to output directory')
parser.add_argument('--epoch',
'-e',
type=int,
default=10,
help='number of epochs')
parser.add_argument('--unit-num',
'-u',
type=int,
default=16,
help='number of units in one layer of the model')
parser.add_argument('--resume',
'-r',
type=str,
default='',
help='path to a trainer snapshot')
parser.add_argument('--frequency',
'-f',
type=int,
default=-1,
help='Frequency of taking a snapshot')
parser.add_argument('--protocol',
type=int,
default=2,
help='protocol version for pickle')
parser.add_argument('--model-filename',
type=str,
default='classifier.pkl',
help='file name for pickled model')
parser.add_argument('--num-data',
type=int,
default=-1,
help='Number of data to be parsed from parser.'
'-1 indicates to parse all data.')
args = parser.parse_args()
method = args.method
if args.label:
labels = args.label
class_num = len(labels) if isinstance(labels, list) else 1
else:
labels = None
class_num = len(label_names)
# Dataset preparation
train, val, _ = data.load_dataset(method, labels, num_data=args.num_data)
# Network
predictor_ = set_up_predictor(method, args.unit_num, args.conv_layers,
class_num)
iterator_type = args.iterator_type
if iterator_type == 'serial':
train_iter = I.SerialIterator(train, args.batchsize)
elif iterator_type == 'balanced':
if class_num > 1:
raise ValueError('BalancedSerialIterator can be used with only one'
'label classification, please specify label to'
'be predicted by --label option.')
train_iter = BalancedSerialIterator(train,
args.batchsize,
train.features[:, -1],
ignore_labels=-1)
train_iter.show_label_stats()
else:
raise ValueError('Invalid iterator type {}'.format(iterator_type))
device = chainer.get_device(args.device)
classifier = Classifier(predictor_,
lossfun=F.sigmoid_cross_entropy,
metrics_fun=F.binary_accuracy,
device=device)
extensions_list = []
eval_mode = args.eval_mode
if eval_mode == 1:
train_eval_iter = I.SerialIterator(train,
args.batchsize,
repeat=False,
shuffle=False)
extensions_list.append(
ROCAUCEvaluator(train_eval_iter,
classifier,
eval_func=predictor_,
device=device,
converter=concat_mols,
name='train',
pos_labels=1,
ignore_labels=-1,
raise_value_error=False))
# extension name='validation' is already used by `Evaluator`,
# instead extension name `val` is used.
val_iter = I.SerialIterator(val,
args.batchsize,
repeat=False,
shuffle=False)
extensions_list.append(
ROCAUCEvaluator(val_iter,
classifier,
eval_func=predictor_,
device=device,
converter=concat_mols,
name='val',
pos_labels=1,
ignore_labels=-1))
run_train(classifier,
train_iter,
valid=val,
batch_size=args.batchsize,
epoch=args.epoch,
out=args.out,
device=device,
converter=concat_mols,
extensions_list=extensions_list,
resume_path=args.resume)
# frequency = args.epoch if args.frequency == -1 else max(1, args.frequency)
# trainer.extend(E.snapshot(), trigger=(frequency, 'epoch'))
# trainer.run()
config = {
'method': args.method,
'conv_layers': args.conv_layers,
'unit_num': args.unit_num,
'labels': args.label
}
save_json(os.path.join(args.out, 'config.json'), config)
classifier.save_pickle(os.path.join(args.out, args.model_filename),
protocol=args.protocol)
def main():
# Supported preprocessing/network list
method_list = [
'nfp', 'ggnn', 'schnet', 'weavenet', 'rsgcn', 'relgcn', 'relgat'
]
label_names = D.get_tox21_label_names()
iterator_type = ['serial', 'balanced']
parser = argparse.ArgumentParser(
description='Multitask Learning with Tox21.')
parser.add_argument('--method',
'-m',
type=str,
choices=method_list,
default='nfp',
help='graph convolution model to use '
'as a predictor.')
parser.add_argument('--label',
'-l',
type=str,
choices=label_names,
default='',
help='target label for logistic '
'regression. Use all labels if this option '
'is not specified.')
parser.add_argument('--iterator-type',
type=str,
choices=iterator_type,
default='serial',
help='iterator type. If `balanced` '
'is specified, data is sampled to take same number of'
'positive/negative labels during training.')
parser.add_argument('--eval-mode',
type=int,
default=1,
help='Evaluation mode.'
'0: only binary_accuracy is calculated.'
'1: binary_accuracy and ROC-AUC score is calculated')
parser.add_argument('--conv-layers',
'-c',
type=int,
default=4,
help='number of convolution layers')
parser.add_argument('--batchsize',
'-b',
type=int,
default=32,
help='batch size')
parser.add_argument('--gpu',
'-g',
type=int,
default=-1,
help='GPU ID to use. Negative value indicates '
'not to use GPU and to run the code in CPU.')
parser.add_argument('--out',
'-o',
type=str,
default='result',
help='path to output directory')
parser.add_argument('--epoch',
'-e',
type=int,
default=10,
help='number of epochs')
parser.add_argument('--unit-num',
'-u',
type=int,
default=16,
help='number of units in one layer of the model')
parser.add_argument('--resume',
'-r',
type=str,
default='',
help='path to a trainer snapshot')
parser.add_argument('--frequency',
'-f',
type=int,
default=-1,
help='Frequency of taking a snapshot')
parser.add_argument('--protocol',
type=int,
default=2,
help='protocol version for pickle')
parser.add_argument('--model-filename',
type=str,
default='classifier.pkl',
help='file name for pickled model')
parser.add_argument('--num-data',
type=int,
default=-1,
help='Number of data to be parsed from parser.'
'-1 indicates to parse all data.')
args = parser.parse_args()
method = args.method
if args.label:
labels = args.label
class_num = len(labels) if isinstance(labels, list) else 1
else:
labels = None
class_num = len(label_names)
# Dataset preparation
train, val, _ = data.load_dataset(method, labels, num_data=args.num_data)
# Network
predictor_ = set_up_predictor(method, args.unit_num, args.conv_layers,
class_num)
iterator_type = args.iterator_type
if iterator_type == 'serial':
train_iter = I.SerialIterator(train, args.batchsize)
elif iterator_type == 'balanced':
if class_num > 1:
raise ValueError('BalancedSerialIterator can be used with only one'
'label classification, please specify label to'
'be predicted by --label option.')
train_iter = BalancedSerialIterator(train,
args.batchsize,
train.features[:, -1],
ignore_labels=-1)
train_iter.show_label_stats()
else:
raise ValueError('Invalid iterator type {}'.format(iterator_type))
val_iter = I.SerialIterator(val,
args.batchsize,
repeat=False,
shuffle=False)
classifier = Classifier(predictor_,
lossfun=F.sigmoid_cross_entropy,
metrics_fun=F.binary_accuracy,
device=args.gpu)
optimizer = O.Adam()
optimizer.setup(classifier)
updater = training.StandardUpdater(train_iter,
optimizer,
device=args.gpu,
converter=concat_mols)
trainer = training.Trainer(updater, (args.epoch, 'epoch'), out=args.out)
trainer.extend(
E.Evaluator(val_iter,
classifier,
device=args.gpu,
converter=concat_mols))
trainer.extend(E.LogReport())
eval_mode = args.eval_mode
if eval_mode == 0:
trainer.extend(
E.PrintReport([
'epoch', 'main/loss', 'main/accuracy', 'validation/main/loss',
'validation/main/accuracy', 'elapsed_time'
]))
elif eval_mode == 1:
train_eval_iter = I.SerialIterator(train,
args.batchsize,
repeat=False,
shuffle=False)
trainer.extend(
ROCAUCEvaluator(train_eval_iter,
classifier,
eval_func=predictor_,
device=args.gpu,
converter=concat_mols,
name='train',
pos_labels=1,
ignore_labels=-1,
raise_value_error=False))
# extension name='validation' is already used by `Evaluator`,
# instead extension name `val` is used.
trainer.extend(
ROCAUCEvaluator(val_iter,
classifier,
eval_func=predictor_,
device=args.gpu,
converter=concat_mols,
name='val',
pos_labels=1,
ignore_labels=-1))
trainer.extend(
E.PrintReport([
'epoch', 'main/loss', 'main/accuracy', 'train/main/roc_auc',
'validation/main/loss', 'validation/main/accuracy',
'val/main/roc_auc', 'elapsed_time'
]))
else:
raise ValueError('Invalid accfun_mode {}'.format(eval_mode))
trainer.extend(E.ProgressBar(update_interval=10))
frequency = args.epoch if args.frequency == -1 else max(1, args.frequency)
trainer.extend(E.snapshot(), trigger=(frequency, 'epoch'))
if args.resume:
chainer.serializers.load_npz(args.resume, trainer)
trainer.run()
config = {
'method': args.method,
'conv_layers': args.conv_layers,
'unit_num': args.unit_num,
'labels': args.label
}
with open(os.path.join(args.out, 'config.json'), 'w') as o:
o.write(json.dumps(config))
classifier.save_pickle(os.path.join(args.out, args.model_filename),
protocol=args.protocol)
def main():
# Parse the arguments.
args = parse_arguments()
args.model_folder_name = os.path.join(theme_name, 'chainer')
base_epoch = complexity_degree[high_low]
args.epoch = int(base_epoch * 60 / method_complexity[method_name])
args.epoch = max(args.epoch, 5)
#args.epoch = int(float(t_epochs.get()))
args.out = parent_path / 'models' / theme_name / method_name / high_low
args.method = method_name
if t_model_path != "":
args.source_transferlearning = Path(t_model_path.get())
print(theme_name)
if args.label:
labels = args.label
class_num = len(labels) if isinstance(labels, list) else 1
else:
raise ValueError('No target label was specified.')
# Dataset preparation. Postprocessing is required for the regression task.
def postprocess_label(label_list):
return numpy.asarray(label_list, dtype=numpy.float32)
# Apply a preprocessor to the dataset.
print('Preprocessing dataset...')
preprocessor = preprocess_method_dict[args.method]()
smiles_col_name = t_smiles.get()
parser = CSVFileParser(preprocessor,
postprocess_label=postprocess_label,
labels=labels,
smiles_col=smiles_col_name)
args.datafile = t_csv_filepath.get()
dataset = parser.parse(args.datafile)['dataset']
# Scale the label values, if necessary.
if args.scale == 'standardize':
scaler = StandardScaler()
scaler.fit(dataset.get_datasets()[-1])
else:
scaler = None
# Split the dataset into training and validation.
train_data_size = int(len(dataset) * args.train_data_ratio)
trainset, testset = split_dataset_random(dataset, train_data_size,
args.seed)
print((args.source_transferlearning / method_name / high_low /
'regressor.pickle'))
print((args.source_transferlearning / method_name / high_low /
'regressor.pickle').exists())
# Set up the predictor.
if Booleanvar_transfer_learning.get() == True \
and (args.source_transferlearning / method_name / high_low /'regressor.pickle').exists() == True:
# refer https://github.com/pfnet-research/chainer-chemistry/issues/407
with open(
args.source_transferlearning / method_name / high_low /
'regressor.pickle', 'rb') as f:
regressor = cloudpickle.loads(f.read())
pre_predictor = regressor.predictor
predictor = GraphConvPredictor(pre_predictor.graph_conv,
MLP(out_dim=1, hidden_dim=16))
else:
predictor = set_up_predictor(args.method,
args.unit_num,
args.conv_layers,
class_num,
label_scaler=scaler)
# Set up the regressor.
device = chainer.get_device(args.device)
metrics_fun = {'mae': functions.mean_absolute_error, 'rmse': rmse}
regressor = Regressor(predictor,
lossfun=functions.mean_squared_error,
metrics_fun=metrics_fun,
device=device)
print('Training... : ', method_name)
run_train(regressor,
trainset,
valid=None,
batch_size=args.batchsize,
epoch=args.epoch,
out=args.out,
extensions_list=None,
device=device,
converter=concat_mols,
resume_path=None)
# Save the regressor's parameters.
args.model_foldername = t_theme_name.get()
model_path = os.path.join(args.out, args.model_foldername,
args.model_filename)
print('Saving the trained model to {}...'.format(model_path))
# TODO(nakago): ChainerX array cannot be sent to numpy array when internal
# state has gradients.
if hasattr(regressor.predictor.graph_conv, 'reset_state'):
regressor.predictor.graph_conv.reset_state()
with open(
parent_path / 'models' / theme_name / method_name / high_low /
('regressor.pickle'), 'wb') as f:
cloudpickle.dump(regressor, f)
#with open(parent_path / 'models' / theme_name / method_name / high_low /('predictor.pickle'), 'wb') as f:
# cloudpickle.dump(predictor, f)
print('Evaluating... : ', method_name)
test_iterator = SerialIterator(testset,
16,
repeat=False,
shuffle=False)
eval_result = Evaluator(test_iterator,
regressor,
converter=concat_mols,
device=device)()
print('Evaluation result: : ', method_name)
print(eval_result)
@chainer.dataset.converter()
def extract_inputs(batch, device=None):
return concat_mols(batch, device=device)[:-1]
pred_train = regressor.predict(trainset, converter=extract_inputs)
pred_train = [i[0] for i in pred_train]
pred_test = regressor.predict(testset, converter=extract_inputs)
pred_test = [i[0] for i in pred_test]
y_train = [i[2][0] for i in trainset]
y_test = [i[2][0] for i in testset]
title = args.label
save_path = parent_path / 'results' / theme_name / method_name / high_low / 'scatter.png'
save_scatter(y_train, pred_train, y_test, pred_test, title, save_path)
global image_score
image_score_open = Image.open(parent_path / 'results' / theme_name /
method_name / high_low / 'scatter.png')
image_score = ImageTk.PhotoImage(image_score_open, master=frame1)
canvas.create_image(200, 200, image=image_score)
from sklearn.metrics import mean_squared_error, mean_absolute_error
from sklearn.metrics import r2_score
train_mse = mean_squared_error(y_train, pred_train)
test_mse = mean_squared_error(y_test, pred_test)
train_rmse = np.sqrt(train_mse)
test_rmse = np.sqrt(test_mse)
train_mae = mean_absolute_error(y_train, pred_train)
test_mae = mean_absolute_error(y_test, pred_test)
train_r2score = r2_score(y_train, pred_train)
test_r2score = r2_score(y_test, pred_test)
print('train_mse : ', train_mse)
print('test_mse : ', test_mse)
print('train_rmse : ', train_rmse)
print('test_rmse : ', test_rmse)
print('train_mae : ', train_mae)
print('test_mae : ', train_mae)
print('train_r2score : ', train_r2score)
print('test_r2score : ', test_r2score)
def main():
# Parse the arguments.
args = parse_arguments()
args.out = os.path.join(args.out, args.method)
save_args(args, args.out)
if args.label:
labels = args.label
class_num = len(labels) if isinstance(labels, list) else 1
else:
raise ValueError('No target label was specified.')
# Dataset preparation. Postprocessing is required for the regression task.
def postprocess_label_float(label_list):
return numpy.asarray(label_list, dtype=numpy.float32)
def postprocess_label_int(label_list):
return numpy.asarray(label_list, dtype=numpy.int64)
# Apply a preprocessor to the dataset.
if args.train:
## training data
fn,ext = os.path.splitext(args.train)
if ext==".npz":
print('Loading training dataset...')
train = NumpyTupleDataset.load(args.train)
else:
print('Preprocessing training dataset...')
preprocessor = preprocess_method_dict[args.method]()
if args.classification:
parser = CSVFileParser(preprocessor, postprocess_label=postprocess_label_int,labels=labels, smiles_col='SMILES')
else:
parser = CSVFileParser(preprocessor, postprocess_label=postprocess_label_float,labels=labels, smiles_col='SMILES')
train = parser.parse(args.train)['dataset']
NumpyTupleDataset.save(os.path.join(args.out,os.path.split(fn)[1]), train)
# Scale the label values, if necessary.
if args.scale == 'standardize':
scaler = StandardScaler()
scaler.fit(train.get_datasets()[-1])
else:
scaler = None
## test data
fn,ext = os.path.splitext(args.val)
if ext==".npz":
print('Loading test dataset...')
test = NumpyTupleDataset.load(args.val)
else:
print('Preprocessing test dataset...')
preprocessor = preprocess_method_dict[args.method]()
if args.classification:
parser = CSVFileParser(preprocessor, postprocess_label=postprocess_label_int,labels=labels, smiles_col='SMILES')
else:
parser = CSVFileParser(preprocessor, postprocess_label=postprocess_label_float,labels=labels, smiles_col='SMILES')
test = parser.parse(args.val)['dataset']
NumpyTupleDataset.save(os.path.join(args.out,os.path.split(fn)[1]), test)
# Set up the model.
device = chainer.get_device(args.device)
converter = converter_method_dict[args.method]
metrics_fun = {'mae': F.mean_absolute_error, 'rmse': rmse}
if args.classification:
if args.load_model:
model = Classifier.load_pickle(args.load_model, device=device)
print("model file loaded: ",args.load_model)
else:
predictor = set_up_predictor(args.method, args.unit_num, args.conv_layers, class_num)
model = Classifier(predictor,
lossfun=F.sigmoid_cross_entropy,
metrics_fun=F.binary_accuracy,
device=device)
else:
if args.load_model:
model = Regressor.load_pickle(args.load_model, device=device)
print("model file loaded: ",args.load_model)
else:
predictor = set_up_predictor(
args.method+args.method_suffix, args.unit_num,
args.conv_layers, class_num, label_scaler=scaler)
model = Regressor(predictor, lossfun=F.mean_squared_error,
metrics_fun=metrics_fun, device=device)
if args.train:
if args.balanced_iter:
train = BalancedSerialIterator(train, args.batchsize, train.features[:, -1], ignore_labels=-1)
train.show_label_stats()
print('Training...')
log_keys = ['main/mae','main/rmse','validation/main/mae','validation/main/rmse','validation/main/roc_auc']
extensions_list = [extensions.PlotReport(log_keys, 'iteration', trigger=(100, 'iteration'), file_name='loss.png')]
if args.eval_roc and args.classification:
extensions_list.append(ROCAUCEvaluator(
test, model, eval_func=predictor,
device=device, converter=converter, name='validation',
pos_labels=1, ignore_labels=-1, raise_value_error=False))
save_json(os.path.join(args.out, 'args.json'), vars(args))
run_train(model, train, valid=test,
batch_size=args.batchsize, epoch=args.epoch,
out=args.out, extensions_list=extensions_list,
device=device, converter=converter) #, resume_path=args.resume)
# Save the model's parameters.
model_path = os.path.join(args.out, args.model_filename)
print('Saving the trained model to {}...'.format(model_path))
if hasattr(model.predictor.graph_conv, 'reset_state'):
model.predictor.graph_conv.reset_state()
model.save_pickle(model_path, protocol=args.protocol)
## prediction
it = SerialIterator(test, args.batchsize, repeat=False, shuffle=False)
result = []
for batch in it:
in_arrays = convert._call_converter(converter, batch, device)
with chainer.using_config('train', False), chainer.function.no_backprop_mode():
if isinstance(in_arrays, tuple):
res = model(*in_arrays)
elif isinstance(in_arrays, dict):
res = model(**in_arrays)
else:
res = model(in_arrays)
result.extend(model.y.array.get())
numpy.savetxt(os.path.join(args.out,"result.csv"), numpy.array(result))
eval_result = Evaluator(it, model, converter=converter,device=device)()
print('Evaluation result: ', eval_result)
