def fit(self,
X_train: ndarray,
y_train: ndarray,
X_test: ndarray,
y_test: ndarray,
epochs: int = 100,
eval_every: int = 10,
batch_size: int = 32,
seed: int = 1,
restart: bool = True) -> None:
'''
Fits the neural network on the training data for a certain number of epochs.
Every 'eval_every' epochs, evaluates the network on testing data
'''
setattr(self.optim, 'max_epochs', epochs)
self.optim._setup_decay()
np.random.seed(seed)
if restart:
for layer in self.net.layers:
layer.first = True
self.best_loss = 1e9
for epoch in range(epochs):
if (epoch + 1) % eval_every == 0:
# for early stopping
last_model = deepcopy(self.net)
X_train, y_train = permute_data(X_train, y_train)
batch_generator = self.generate_batches(X_train, y_train,
batch_size)
pbar = tqdm(enumerate(batch_generator),
total=len(list(batch_generator)))
for i, (X_batch, y_batch) in pbar:
pbar.set_postfix({"Epoch": epoch + 1, "Batch": i + 1})
self.net.train_batch(X_batch, y_batch)
self.optim.step()
if (epoch + 1) % eval_every == 0:
test_preds = self.net.forward(X_test, inference=True)
loss = self.net.loss.forward(test_preds, y_test)
if loss < self.best_loss:
print(
f'Validation loss after {epoch + 1} epochs is {loss:.3f}'
)
self.best_loss = loss
else:
print(
f'Loss increased after {epoch + 1}, final loss was {self.best_loss:.3f}, using the model from epoch {epoch + 1 - eval_every}'
)
self.net = last_model
setattr(self.optim, 'net', self.net)
break
if self.optim.final_lr:
self.optim._decay_lr()
def split_huuskonsen():
train_file_path = 'ugrnn/data/huuskonsen/train.smi'
test1_file_path = 'ugrnn/data/huuskonsen/test1.smi'
test2_file_path = 'ugrnn/data/huuskonsen/test2.smi'
smile_col_name = "smiles"
target_col_name = "solubility"
logp_col_name = "logp"
dtype = [(smile_col_name, 'S200'), (target_col_name, 'f8'),
(logp_col_name, 'f8')]
data = np.genfromtxt(train_file_path,
usecols=(6, 3, 5),
dtype=dtype,
comments=None)
data_perm = permute_data(data)
l = len(data)
train_end = int(l * .9)
train_data = data_perm[:train_end]
val_data = data_perm[train_end:]
test1_data = np.genfromtxt(test1_file_path, usecols=(6, 3, 5), dtype=dtype)
test2_data = np.genfromtxt(test2_file_path, usecols=(6, 3, 5), dtype=dtype)
test_data = np.concatenate((test1_data, test2_data))
train_file_path = 'ugrnn/data/huuskonsen/train_huuskonsen.csv'
validate_file_path = 'ugrnn/data/huuskonsen/validate_huuskonsen.csv'
test_file_path = 'ugrnn/data/huuskonsen/test_huuskonsen.csv'
header = "{:},{:},{:}".format(smile_col_name, target_col_name,
logp_col_name)
fmt = ('%s', '%4f', '%4f')
np.savetxt(train_file_path,
train_data,
header=header,
fmt=fmt,
comments='',
delimiter=',')
np.savetxt(validate_file_path,
val_data,
header=header,
fmt=fmt,
comments='',
delimiter=',')
np.savetxt(test_file_path,
test_data,
header=header,
fmt=fmt,
comments='',
delimiter=',')
def split_delaney():
csv_file_path = 'ugrnn/data/DILI/DILI.csv'
smile_col_name = "smiles"
target_col_name = "solubility"
logp_col_name = "logp"
data = read_csv(csv_file_path, smile_col_name, target_col_name, logp_col_name)
data_perm = permute_data(data)
traindata, valdata, testdata = cross_validation_split(data_perm, crossval_split_index=1, crossval_total_num_splits=10)
train_file_path = './data/DILI/train_DILI.csv'
validate_file_path = './data/DILI/validate_DILI.csv'
test_file_path = './data/DILI/test_DILI.csv'
header = "{:},{:},{:}".format(smile_col_name, target_col_name, logp_col_name )
fmt = ('%s', '%4f', '%4f')
np.savetxt(train_file_path, traindata, header=header, fmt=fmt, comments='', delimiter=',')
np.savetxt(validate_file_path, valdata, header=header, fmt=fmt, comments='', delimiter=',')
np.savetxt(test_file_path, testdata, header=header, fmt=fmt, comments='', delimiter=',')
def split_karthikeyan():
csv_file_path = 'ugrnn/data/karthikeyan/melting_points.csv'
smile_col_name = "SMILES"
target_col_name = "MTP"
data = read_csv(csv_file_path, smile_col_name, target_col_name)
bool_arr = np.array([valid_smile(row[0]) for row in data])
print(bool_arr)
filter_data = data[bool_arr]
data_perm = permute_data(filter_data)
traindata, valdata, testdata = cross_validation_split(data_perm, crossval_split_index=1, crossval_total_num_splits=10)
train_file_path = 'ugrnn/data/karthikeyan/train_karthikeyan.csv'
validate_file_path = 'ugrnn/data/karthikeyan/validate_karthikeyan.csv'
test_file_path = 'ugrnn/data/karthikeyan/test_karthikeyan.csv'
header = "{:},{:}".format(smile_col_name, target_col_name)
fmt = ('%s', '%4f')
np.savetxt(train_file_path, traindata, header=header, fmt=fmt, comments='', delimiter=',')
np.savetxt(validate_file_path, valdata, header=header, fmt=fmt, comments='', delimiter=',')
np.savetxt(test_file_path, testdata, header=header, fmt=fmt, comments='', delimiter=',')
def main(output_dir='output/',
model_name='my_model',
training_file='delaney_train.csv',
validation_file='delaney_validate.csv',
smile_col='smiles',
target_col='solubility',
crossval_total_num_splits=10,
initial_crossvalidation_index=0,
weight_decay_factor=0,
*args,
**kwargs):
'''
valid kwargs:
experiment_name, regression,
binary_classification, batch_size,
clip_gradient, model_params,
contract_rings, learning_rate,
max_epochs, enable_plotting
'''
log_format = '%(asctime)s - %(name)s - %(levelname)s - %(message)s'
logging.basicConfig(level=logging.INFO, format=log_format)
logger = logging.getLogger(__name__)
print('output_dir', output_dir)
output_dir = os.path.join(output_dir, model_name)
# if tf.gfile.Exists(output_dir):
# tf.gfile.DeleteRecursively(output_dir)
tf.gfile.MakeDirs(output_dir)
with tf.Graph().as_default():
# Create a session for running Ops on the Graph.
# select CPU (as it is faster than GPUs)
config = tf.ConfigProto(device_count={'GPU': 0})
session = tf.Session(config=config)
logger.info('Loading data set from {:}'.format(training_file))
csv_file_path = training_file
smile_col_name = smile_col
target_col_name = target_col
data = utils.read_csv(csv_file_path, None, smile_col_name,
target_col_name)
assert len(data[0]) > 0, 'no data loaded!'
smiles, labels = utils.permute_data(data[0], data[1])
if kwargs['regression']:
# normalize regression targets to be in a reasonable value-range
labels_mean = labels.mean()
labels_range = np.max(labels) - np.min(labels)
labels = (labels - labels_mean) / labels_range
#this function will be applied to predictions of the model and to targets when computing metrics
def Targets_UnNormalization_fn(targets):
return targets * labels_range + labels_mean
def Targets_Normalization_fn(targets):
return (targets - labels_mean) / labels_range
else:
if labels.ndim == 1:
labels = labels.reshape((len(labels), 1))
Targets_UnNormalization_fn = lambda x: x
Targets_Normalization_fn = lambda x: x
if validation_file != '' and validation_file is not None:
# train single model
logger.info(
'Loading validation dataset from {:}'.format(validation_file))
valid_data = utils.read_csv(validation_file, None, smile_col_name,
target_col_name)
if kwargs['regression'] == 0 and labels.ndim == 1:
labels = labels.reshape(
(len(labels), 1)) #binary classification
train_data = (smiles, labels)
valid_data = (valid_data[0],
Targets_Normalization_fn(valid_data[1]))
training_scores_dict, validation_scores_dict = build_and_train(
logger,
session,
output_dir,
train_data,
valid_data,
model_name=model_name,
Targets_UnNormalization_fn=Targets_UnNormalization_fn,
weight_decay_factor=weight_decay_factor,
**kwargs)
else:
# cross validation
assert initial_crossvalidation_index < crossval_total_num_splits, 'INVALID VALUE GIVEN for initial_crossvalidation_index or crossval_total_num_splits!'
training_scores_dict, validation_scores_dict = [], []
for crossval_split_index in range(initial_crossvalidation_index,
crossval_total_num_splits):
print('crossval_split: {} of {}'.format(
crossval_split_index + 1, crossval_total_num_splits))
assert len(smiles) == len(labels)
train_data, valid_data, testdata = utils.cross_validation_split(
smiles,
labels,
crossval_split_index,
crossval_total_num_splits=crossval_total_num_splits,
validation_data_ratio=1. / crossval_total_num_splits)
#merge "test" and train -- validation part used for testing
train_data = (np.concatenate((train_data[0], testdata[0])),
np.concatenate((train_data[1], testdata[1])))
print('CV: # train samples:', len(train_data[0]),
'# validation samples:', len(valid_data[0]))
td, vd = build_and_train(
logger,
session,
output_dir + '_CV_{}'.format(crossval_split_index),
train_data,
valid_data,
model_name=model_name,
Targets_UnNormalization_fn=Targets_UnNormalization_fn,
weight_decay_factor=weight_decay_factor,
**kwargs)
training_scores_dict.append(td)
validation_scores_dict.append(vd)
if isinstance(training_scores_dict,
list) and len(training_scores_dict) == 1 and len(
validation_scores_dict) == 1:
return training_scores_dict[0], validation_scores_dict[0]
return training_scores_dict, validation_scores_dict