def __init__(self, node_dim, embedding_vec, gpu_device, **kwargs):
self.node_dim = node_dim
self.embedding_vec = embedding_vec
self.vocab_size = embedding_vec.shape[0]
self.gpu_device = gpu_device
# hyperparams
self.units = kwargs.get('units', 32)
self.layers = kwargs.get('layers', 10)
self.pool_steps = kwargs.get('pool_steps', 10)
self.dropout_rate = kwargs.get('dropout_rate', 0.2)
self.learning_rate = kwargs.get('learning_rate', 2e-4)
self.use_clr = kwargs.get('use_clr', False)
self.use_momentum = kwargs.get('use_momentum', False)
self.use_bn = kwargs.get('use_bn', False)
self.reuse_weights = kwargs.get('reuse_weights', False)
self.lstm_ggnn = kwargs.get('lstm_ggnn', False)
self.probabilistic = kwargs.get('probabilistic', True)
self.use_attention = kwargs.get('use_attention', False)
self.mixing_ratio = kwargs.get('mixing_ratio', 0.)
self.use_ghm = kwargs.get('use_ghm', False)
self.g = tf.Graph()
with self.g.as_default():
self._placeholders()
if self.use_momentum:
self.optimizer = tf.contrib.opt.MomentumWOptimizer(
1e-4, self.learning_rate * self.lr_multiplier,
0.9, use_nesterov=True
)
else:
self.optimizer = AMSGrad(
learning_rate=self.learning_rate * self.lr_multiplier,
beta2=0.999
)
with tf.variable_scope('Classifier', reuse=tf.AUTO_REUSE):
self._build_ggnn()
self._loss()
self._train()
self._merge()
with tf.control_dependencies(tf.get_collection(tf.GraphKeys.UPDATE_OPS)):
self.train_op = self.optimizer.apply_gradients(self.gv)
_stats('Joint_SMRGCN', self.gv)
self.saver = tf.train.Saver(max_to_keep=5)
self.init = tf.global_variables_initializer()
self.local_init = tf.local_variables_initializer()
self._init_session()
def __init__(self, args, adj_mx, **kwargs):
self._kwargs = kwargs
self._data_kwargs = kwargs.get('data')
self._model_kwargs = kwargs.get('model')
self._train_kwargs = kwargs.get('train')
# logging.
self._log_dir = self._get_log_dir(kwargs)
log_level = self._kwargs.get('log_level', 'INFO')
self._logger = utils.get_logger(self._log_dir,
__name__,
kwargs['name'] + '_info.log',
level=log_level)
self._writer = tf.summary.FileWriter(self._log_dir)
self._logger.info(kwargs)
# Data preparation
if self._data_kwargs.get('data_type') == 'npz':
self._data = utils.load_dataset(**self._data_kwargs)
elif self._data_kwargs.get('data_type') == 'csv':
self._data = utils.load_dataset_from_csv(**self._data_kwargs)
for k, v in self._data.items():
if hasattr(v, 'shape'):
self._logger.info((k, v.shape))
# Build models.
scaler = self._data['scaler']
with tf.name_scope('Train'):
with tf.variable_scope('DCRNN', reuse=False):
self._train_model = DCRNNModel(
args=args,
is_training=True,
scaler=scaler,
batch_size=self._data_kwargs['batch_size'],
adj_mx=adj_mx,
**self._model_kwargs)
with tf.name_scope('Test'):
with tf.variable_scope('DCRNN', reuse=True):
self._test_model = DCRNNModel(
args=args,
is_training=False,
scaler=scaler,
batch_size=self._data_kwargs['test_batch_size'],
adj_mx=adj_mx,
**self._model_kwargs)
# Learning rate.
self._lr = tf.get_variable('learning_rate',
shape=(),
initializer=tf.constant_initializer(0.01),
trainable=False)
self._new_lr = tf.placeholder(tf.float32,
shape=(),
name='new_learning_rate')
self._lr_update = tf.assign(self._lr, self._new_lr, name='lr_update')
# Configure optimizer
optimizer_name = self._train_kwargs.get('optimizer', 'adam').lower()
epsilon = float(self._train_kwargs.get('epsilon', 1e-3))
optimizer = tf.train.AdamOptimizer(self._lr, epsilon=epsilon)
if optimizer_name == 'sgd':
optimizer = tf.train.GradientDescentOptimizer(self._lr, )
elif optimizer_name == 'amsgrad':
optimizer = AMSGrad(self._lr, epsilon=epsilon)
# Calculate loss
output_dim = self._model_kwargs.get('output_dim')
preds = self._train_model.outputs
labels = self._train_model.labels[..., :output_dim]
null_val = 0.
self._loss_fn = masked_mae_loss(scaler, null_val)
self._mape_fn = masked_mape(scaler, null_val)
self._rmse_fn = masked_rmse_loss(scaler, null_val)
self._train_loss = self._loss_fn(preds=preds, labels=labels)
tvars = tf.trainable_variables()
grads = tf.gradients(self._train_loss, tvars)
max_grad_norm = kwargs['train'].get('max_grad_norm', 1.)
grads, _ = tf.clip_by_global_norm(grads, max_grad_norm)
global_step = tf.train.get_or_create_global_step()
self._train_op = optimizer.apply_gradients(zip(grads, tvars),
global_step=global_step,
name='train_op')
max_to_keep = self._train_kwargs.get('max_to_keep', 100)
self._epoch = 0
self._saver = tf.train.Saver(tf.global_variables(),
max_to_keep=max_to_keep)
# Log model statistics.
total_trainable_parameter = utils.get_total_trainable_parameter_size()
self._logger.info('Total number of trainable parameters: {:d}'.format(
total_trainable_parameter))
for var in tf.global_variables():
self._logger.debug('{}, {}'.format(var.name, var.get_shape()))
def __init__(self, is_training=False, **kwargs):
super(DCRNNSupervisor, self).__init__(**kwargs)
self._data = utils.load_dataset_dcrnn(
seq_len=self._model_kwargs.get('seq_len'),
horizon=self._model_kwargs.get('horizon'),
input_dim=self._model_kwargs.get('input_dim'),
mon_ratio=self._mon_ratio,
scaler_type=self._kwargs.get('scaler'),
is_training=is_training,
**self._data_kwargs)
for k, v in self._data.items():
if hasattr(v, 'shape'):
self._logger.info((k, v.shape))
# Build models.
scaler = self._data['scaler']
if is_training:
self.model = DCRNNModel(scaler=scaler,
batch_size=self._data_kwargs['batch_size'],
adj_mx=self._data['adj_mx'],
**self._model_kwargs)
else:
self.model = DCRNNModel(scaler=scaler,
batch_size=1,
adj_mx=self._data['adj_mx'],
**self._model_kwargs)
# Learning rate.
self._lr = tf.get_variable('learning_rate',
shape=(),
initializer=tf.constant_initializer(0.01),
trainable=False)
self._new_lr = tf.placeholder(tf.float32,
shape=(),
name='new_learning_rate')
self._lr_update = tf.assign(self._lr, self._new_lr, name='lr_update')
# Configure optimizer
optimizer_name = self._train_kwargs.get('optimizer', 'adam').lower()
epsilon = float(self._train_kwargs.get('epsilon', 1e-3))
optimizer = tf.train.AdamOptimizer(
self._lr,
epsilon=epsilon,
)
if optimizer_name == 'sgd':
optimizer = tf.train.GradientDescentOptimizer(self._lr, )
elif optimizer_name == 'amsgrad':
optimizer = AMSGrad(self._lr, epsilon=epsilon)
# Calculate loss
output_dim = self._model_kwargs.get('output_dim')
preds = self.model.outputs
labels = self.model.labels[..., :output_dim]
null_val = 0.
self._loss_fn = masked_mse_loss(scaler, null_val)
# self._loss_fn = masked_mae_loss(scaler, null_val)
self._train_loss = self._loss_fn(preds=preds, labels=labels)
tvars = tf.trainable_variables()
grads = tf.gradients(self._train_loss, tvars)
max_grad_norm = kwargs['train'].get('max_grad_norm', 1.)
grads, _ = tf.clip_by_global_norm(grads, max_grad_norm)
global_step = tf.train.get_or_create_global_step()
self._train_op = optimizer.apply_gradients(zip(grads, tvars),
global_step=global_step,
name='train_op')
max_to_keep = self._train_kwargs.get('max_to_keep', 100)
self._epoch = 0
self._saver = tf.train.Saver(tf.global_variables(),
max_to_keep=max_to_keep)
# Log model statistics.
total_trainable_parameter = utils.get_total_trainable_parameter_size()
self._logger.info('Total number of trainable parameters: {:d}'.format(
total_trainable_parameter))
for var in tf.global_variables():
self._logger.debug('{}, {}'.format(var.name, var.get_shape()))
def __init__(self, **kwargs):
self._kwargs = kwargs
self._data_kwargs = kwargs.get('data')
self._model_kwargs = kwargs.get('model')
self._train_kwargs = kwargs.get('train')
# logging.
self._log_dir = self._get_log_dir(kwargs)
log_level = self._kwargs.get('log_level', 'INFO')
self._logger = utils.get_logger(self._log_dir,
__name__,
'info.log',
level=log_level)
self._writer = tf.summary.FileWriter(self._log_dir)
self._logger.info(kwargs)
# Data preparation
# load data set
self._data = utils.load_dataset(**self._data_kwargs)
# print(self._data.keys())
# print(len(self._data))
# print(self._data['x_train'].shape)
# print(self._data['y_train'].shape)
# print(self._data['x_val'].shape)
# print(self._data['y_val'].shape)
# print(self._data['x_test'].shape)
# print(self._data['y_test'].shape)
# exit()
# (23974, 12, 207, 2)
# (23974, 12, 207, 2)
# (3425, 12, 207, 2)
# (3425, 12, 207, 2)
# (6850, 12, 207, 2)
# (6850, 12, 207, 2)
# import our node2vec data and replace
# but how do we comply with the dimensions
# we can plant the same into every time step, but what about the same dimension
# exit()
# I think we just need to attach our node to vector here
for k, v in self._data.items():
if hasattr(v, 'shape'):
self._logger.info((k, v.shape))
# Build models.
scaler = self._data['scaler']
# scaler is the mean and standard deviation pre-computed and stored
# used to normalize data and de-normalize data
# print(scaler)
# exit()
with tf.name_scope('Train'):
# Batch size is a term used in machine learning and refers to the number of training examples utilised in one iteration.
with tf.variable_scope('DCRNN', reuse=False):
self._train_model = DCRNNModel(
is_training=True,
scaler=scaler,
batch_size=self._data_kwargs['batch_size'],
adj_matrix_file=self._data_kwargs['graph_pkl_filename'],
**self._model_kwargs)
with tf.name_scope('Test'):
with tf.variable_scope('DCRNN', reuse=True):
self._test_model = DCRNNModel(
is_training=False,
scaler=scaler,
batch_size=self._data_kwargs['test_batch_size'],
adj_matrix_file=self._data_kwargs['graph_pkl_filename'],
**self._model_kwargs)
# Learning rate.
self._lr = tf.get_variable('learning_rate',
shape=(),
initializer=tf.constant_initializer(0.01),
trainable=False)
self._new_lr = tf.placeholder(tf.float32,
shape=(),
name='new_learning_rate')
self._lr_update = tf.assign(self._lr, self._new_lr, name='lr_update')
# Configure optimizer
optimizer_name = self._train_kwargs.get('optimizer', 'adam').lower()
epsilon = float(self._train_kwargs.get('epsilon', 1e-3))
optimizer = tf.train.AdamOptimizer(self._lr, epsilon=epsilon)
if optimizer_name == 'sgd':
optimizer = tf.train.GradientDescentOptimizer(self._lr, )
elif optimizer_name == 'amsgrad':
optimizer = AMSGrad(self._lr, epsilon=epsilon)
# Calculate loss
output_dim = self._model_kwargs.get('output_dim')
# preds is a placeholder of outputs, which is a stacked tensor
preds = self._train_model.outputs
# print(preds.eval())
# exit()
# You must feed a value for placeholder tensor
labels = self._train_model.labels[..., :output_dim]
null_val = 0.
self._loss_fn = masked_mae_loss(scaler, null_val)
self._train_loss = self._loss_fn(preds=preds, labels=labels)
tvars = tf.trainable_variables()
grads = tf.gradients(self._train_loss, tvars)
max_grad_norm = kwargs['train'].get('max_grad_norm', 1.)
grads, _ = tf.clip_by_global_norm(grads, max_grad_norm)
global_step = tf.train.get_or_create_global_step()
self._train_op = optimizer.apply_gradients(zip(grads, tvars),
global_step=global_step,
name='train_op')
# print(type(self._train_op))
# exit()
max_to_keep = self._train_kwargs.get('max_to_keep', 100)
self._epoch = 0
self._saver = tf.train.Saver(tf.global_variables(),
max_to_keep=max_to_keep)
# Log model statistics.
total_trainable_parameter = utils.get_total_trainable_parameter_size()
self._logger.info('Total number of trainable parameters: {:d}'.format(
total_trainable_parameter))
for var in tf.global_variables():
self._logger.debug('{}, {}'.format(var.name, var.get_shape()))
def __init__(self, sess, adj_mx, dataloaders, kwargs):
self._kwargs = kwargs
self._data_kwargs = kwargs.get('data')
self._model_kwargs = kwargs.get('model')
self._train_kwargs = kwargs.get('train')
self._paths_kwargs = kwargs.get('paths')
self._save_tensors = kwargs.get('tf_config').get('save_tensors', False) \
if kwargs.get('tf_config') else False
self._trace = kwargs.get('tf_config').get('trace', False) \
if kwargs.get('tf_config') else False
self._save_graph = kwargs.get('tf_config').get('save_graph', False) \
if kwargs.get('tf_config') else False
self._log_dir = self._get_log_dir(kwargs)
self._writer = tf.summary.FileWriter(self._log_dir, sess.graph) \
if self._save_graph else tf.summary.FileWriter(self._log_dir)
# Data preparation
self._data = dataloaders
# for k, v in self._data.items():
# if hasattr(v, 'shape'):
# self._kwargs.logger.info((k, v.shape))
# Build models.
scaler = self._data['scaler']
with tf.name_scope('Train'):
with tf.variable_scope('DCRNN', reuse=False):
train_batch_size = dataloaders['train_loader'].batch_size
self._train_model = DCRNNModel(is_training=True,
scaler=scaler,
batch_size=train_batch_size,
adj_mx=adj_mx,
**self._model_kwargs)
with tf.name_scope('Val'):
with tf.variable_scope('DCRNN', reuse=True):
val_batch_size = dataloaders['val_loader'].batch_size
self._val_model = DCRNNModel(is_training=False,
scaler=scaler,
batch_size=val_batch_size,
adj_mx=adj_mx,
**self._model_kwargs)
with tf.name_scope('Test'):
with tf.variable_scope('DCRNN', reuse=True):
test_batch_size = dataloaders['test_loader'].batch_size
self._test_model = DCRNNModel(is_training=False,
scaler=scaler,
batch_size=test_batch_size,
adj_mx=adj_mx,
**self._model_kwargs)
# Learning rate.
self._lr = tf.get_variable('learning_rate',
shape=(),
initializer=tf.constant_initializer(0.01),
trainable=False)
self._new_lr = tf.placeholder(tf.float32,
shape=(),
name='new_learning_rate')
self._lr_update = tf.assign(self._lr, self._new_lr, name='lr_update')
# Configure optimizer
optimizer_name = self._train_kwargs.get('optimizer', 'adam').lower()
epsilon = float(self._train_kwargs.get('epsilon', 1e-3))
optimizer = tf.train.AdamOptimizer(self._lr, epsilon=epsilon)
if optimizer_name == 'sgd':
optimizer = tf.train.GradientDescentOptimizer(self._lr, )
elif optimizer_name == 'amsgrad':
optimizer = AMSGrad(self._lr, epsilon=epsilon)
# Calculate loss
output_dim = self._model_kwargs.get('output_dim')
preds = self._train_model.outputs
labels = self._train_model.labels[..., :output_dim]
null_val = 0. if kwargs['model'].get('exclude_zeros_in_metric',
True) else np.nan
loss_func_dict = {
'mae': masked_mae_loss(scaler, null_val),
'rmse': masked_rmse_loss(scaler, null_val),
'mse': masked_mse_loss(scaler, null_val)
}
self._loss_fn = loss_func_dict.get(kwargs['train'].get(
'loss_func', 'mae'))
self._metric_fn = loss_func_dict.get(kwargs['train'].get(
'metric_func', 'mae'))
self._train_loss = self._loss_fn(preds=preds, labels=labels)
tvars = tf.trainable_variables()
grads = tf.gradients(self._train_loss, tvars)
max_grad_norm = kwargs['train'].get('max_grad_norm', 1.)
grads, _ = tf.clip_by_global_norm(grads, max_grad_norm)
self._train_op = optimizer.apply_gradients(
zip(grads, tvars),
global_step=tf.train.get_or_create_global_step(),
name='train_op')
max_to_keep = self._train_kwargs.get('max_to_keep', 100)
self._saver = tf.train.Saver(tf.global_variables(),
max_to_keep=max_to_keep)
# load model
model_filename = self._paths_kwargs.get('model_filename')
if model_filename is not None:
self._saver.restore(sess, model_filename)
self._kwargs.logger.info(
'Pretrained model was loaded from : {}'.format(model_filename))
else:
sess.run(tf.global_variables_initializer())
# Log model statistics.
total_trainable_parameter = utils.get_total_trainable_parameter_size()
self._kwargs.logger.info('Total number of trainable parameters: {:d}'.\
format(total_trainable_parameter))
for var in tf.global_variables():
self._kwargs.logger.debug('{}, {}'.format(var.name,
var.get_shape()))
class JointAdaModel:
def __init__(self, node_dim, embedding_vec, gpu_device, **kwargs):
self.node_dim = node_dim
self.embedding_vec = embedding_vec
self.vocab_size = embedding_vec.shape[0]
self.gpu_device = gpu_device
# hyperparams
self.units = kwargs.get('units', 32)
self.layers = kwargs.get('layers', 10)
self.pool_steps = kwargs.get('pool_steps', 10)
self.dropout_rate = kwargs.get('dropout_rate', 0.2)
self.learning_rate = kwargs.get('learning_rate', 2e-4)
self.use_clr = kwargs.get('use_clr', False)
self.use_momentum = kwargs.get('use_momentum', False)
self.use_bn = kwargs.get('use_bn', False)
self.reuse_weights = kwargs.get('reuse_weights', False)
self.lstm_ggnn = kwargs.get('lstm_ggnn', False)
self.probabilistic = kwargs.get('probabilistic', True)
self.use_attention = kwargs.get('use_attention', False)
self.mixing_ratio = kwargs.get('mixing_ratio', 0.)
self.use_ghm = kwargs.get('use_ghm', False)
self.g = tf.Graph()
with self.g.as_default():
self._placeholders()
if self.use_momentum:
self.optimizer = tf.contrib.opt.MomentumWOptimizer(
1e-4, self.learning_rate * self.lr_multiplier,
0.9, use_nesterov=True
)
else:
self.optimizer = AMSGrad(
learning_rate=self.learning_rate * self.lr_multiplier,
beta2=0.999
)
with tf.variable_scope('Classifier', reuse=tf.AUTO_REUSE):
self._build_ggnn()
self._loss()
self._train()
self._merge()
with tf.control_dependencies(tf.get_collection(tf.GraphKeys.UPDATE_OPS)):
self.train_op = self.optimizer.apply_gradients(self.gv)
_stats('Joint_SMRGCN', self.gv)
self.saver = tf.train.Saver(max_to_keep=5)
self.init = tf.global_variables_initializer()
self.local_init = tf.local_variables_initializer()
self._init_session()
def _placeholders(self):
self.node_input_ph = tf.placeholder(tf.int32, shape=[None, None, ]) # batch_size x nb_nodes
self.adj_mat_ph = tf.sparse_placeholder(tf.float32, shape=[None, None, None])
# batch_size x nb_nodes x nb_nodes
self.labels = tf.placeholder(tf.int32, shape=[None, None, ]) # batch_size x nb_nodes
self.mask_offset = tf.placeholder(tf.int32, shape=[None, ]) # batch_size
self.is_training_ph = tf.placeholder(tf.bool, ())
self.global_step = tf.placeholder(tf.int32, ())
self.hf_iters_per_epoch = tf.placeholder(tf.int32, ())
if self.use_clr:
print('using cyclic learning rate')
self.lr_multiplier = lib.clr. \
cyclic_learning_rate(self.global_step, 0.5, 5.,
self.hf_iters_per_epoch, mode='exp_range')
else:
print('using constant learning rate')
self.lr_multiplier = 1.
def _build_ggnn(self):
embedding = tf.get_variable('embedding_layer', shape=(self.vocab_size, self.node_dim),
initializer=tf.constant_initializer(self.embedding_vec), trainable=False)
node_tensor = tf.nn.embedding_lookup(embedding, self.node_input_ph)
self.node_tensor = node_tensor
if self.reuse_weights:
if self.node_dim < self.units:
node_tensor = tf.pad(node_tensor,
[[0, 0], [0, 0], [0, self.units - self.node_dim]])
elif self.node_dim > self.units:
print('Changing \'self.units\' to %d!' % (self.node_dim))
self.units = self.node_dim
hidden_tensor = None
with tf.variable_scope('gated-rgcn', reuse=tf.AUTO_REUSE):
if self.lstm_ggnn:
cell = tf.nn.rnn_cell.LSTMCell(self.units, name='lstm_cell')
cell = tf.nn.rnn_cell.DropoutWrapper(
cell,
output_keep_prob=tf.cond(self.is_training_ph, lambda: 1 - self.dropout_rate, lambda: 1.)
# keep prob
)
memory = None
else:
cell = tf.contrib.rnn.GRUCell(self.units)
adj_mat = tf.sparse.to_dense(self.adj_mat_ph, validate_indices=False)
self.dense_adj_mat = adj_mat
for i in range(self.layers):
name = 'joint_convolutional' if self.reuse_weights else 'joint_convolutional_%d' % (i + 1)
# variables for sparse implementation default placement to gpu
msg_tensor = joint_layer(name, (adj_mat, hidden_tensor, node_tensor),
self.units, reuse=self.reuse_weights, batch_axis=True,
use_attention=self.use_attention)
msg_tensor = normalize('Norm' if self.reuse_weights else 'Norm%d' % (i + 1),
msg_tensor, self.use_bn, self.is_training_ph)
msg_tensor = tf.nn.leaky_relu(msg_tensor)
msg_tensor = tf.layers.dropout(msg_tensor, self.dropout_rate, training=self.is_training_ph)
# reshaping msg_tensor to two dimensions
original_shape = tf.shape(msg_tensor) # batch_size, nb_nodes, units
msg_tensor = tf.reshape(msg_tensor, (-1, self.units))
if hidden_tensor is None: # hidden_state
state = node_tensor
else:
state = hidden_tensor
state = tf.reshape(state, (-1, self.units))
if self.lstm_ggnn:
if i == 0:
memory = tf.zeros(tf.shape(state), tf.float32)
# state becomes the hidden tensor
hidden_tensor, (memory, _) = cell(msg_tensor, tf.nn.rnn_cell.LSTMStateTuple(memory, state))
else:
hidden_tensor, _ = cell(msg_tensor, state)
# [batch_size, length, u]
hidden_tensor = tf.reshape(hidden_tensor, original_shape)
hidden_tensor *= (1. - tf.sequence_mask(self.mask_offset, maxlen=original_shape[1], dtype=tf.float32))[
:, :, None]
# the original nucleotide embeddings learnt by GNN
output = hidden_tensor
self.gnn_embedding = output
# we have dummies padded to the front
with tf.variable_scope('set2set_pooling'):
output = lib.ops.LSTM.set2set_pooling('set2set_pooling', output, self.pool_steps, self.dropout_rate,
self.is_training_ph, True, self.mask_offset,
variables_on_cpu=False)
self.bilstm_embedding = tf.get_collection('nuc_emb')[0]
# [batch_size, max_len, 2]
self.gnn_output = lib.ops.Linear.linear('gnn_nuc_output', self.units, 2, self.gnn_embedding)
self.bilstm_output = lib.ops.Linear.linear('bilstm_nuc_output', self.units * 2, 2,
self.bilstm_embedding)
self.output = lib.ops.Linear.linear('OutputMapping', output.get_shape().as_list()[-1],
2, output, variables_on_cpu=False) # categorical logits
def _loss(self):
self.prediction = tf.nn.softmax(self.output)
self.gnn_prediction = tf.nn.softmax(self.gnn_output)
self.bilstm_prediction = tf.nn.softmax(self.bilstm_output)
# graph level loss
self.graph_cost = tf.reduce_mean(
tf.nn.softmax_cross_entropy_with_logits(
logits=self.output, # reduce along the RNA sequence to a graph label
labels=tf.one_hot(tf.reduce_max(self.labels, axis=1), depth=2),
))
# nucleotide level loss
# dummies are padded to the front...
self.mask = 1.0 - tf.sequence_mask(self.mask_offset, maxlen=tf.shape(self.labels)[1], dtype=tf.float32)
if self.use_ghm:
self.gnn_cost = tf.reduce_sum(
get_ghm_weights(self.gnn_prediction, self.labels, self.mask,
bins=10, alpha=0.75, name='GHM_GNN') * \
tf.nn.softmax_cross_entropy_with_logits(
logits=self.gnn_output,
labels=tf.one_hot(self.labels, depth=2),
) / tf.cast(tf.reduce_sum(self.mask), tf.float32)
)
self.bilstm_cost = tf.reduce_sum(
get_ghm_weights(self.bilstm_prediction, self.labels, self.mask,
bins=10, alpha=0.75, name='GHM_BILSTM') * \
tf.nn.softmax_cross_entropy_with_logits(
logits=self.bilstm_output,
labels=tf.one_hot(self.labels, depth=2),
) / tf.cast(tf.reduce_sum(self.mask), tf.float32)
)
else:
self.gnn_cost = tf.reduce_sum(
self.mask * \
tf.nn.softmax_cross_entropy_with_logits(
logits=self.gnn_output,
labels=tf.one_hot(self.labels, depth=2),
)) / tf.cast(tf.reduce_sum(self.mask), tf.float32)
self.bilstm_cost = tf.reduce_sum(
self.mask * \
tf.nn.softmax_cross_entropy_with_logits(
logits=self.bilstm_output,
labels=tf.one_hot(self.labels, depth=2),
)) / tf.cast(tf.reduce_sum(self.mask), tf.float32)
self.cost = self.mixing_ratio * self.graph_cost + (1. - self.mixing_ratio) * self.bilstm_cost
def _train(self):
self.gv = self.optimizer.compute_gradients(self.cost,
var_list=[var for var in tf.trainable_variables()],
colocate_gradients_with_ops=True)
def _merge(self):
# graph level accuracy
self.seq_acc_val, self.seq_acc_update_op = tf.metrics.accuracy(
labels=tf.reduce_max(self.labels, axis=-1),
predictions=tf.to_int32(tf.argmax(self.prediction, axis=-1)),
)
# nucleotide level accuracy of containing a binding site
self.gnn_acc_val, self.gnn_acc_update_op = tf.metrics.accuracy(
labels=tf.reduce_max(self.labels, axis=-1),
predictions=tf.to_int32(tf.reduce_max(
tf.argmax(self.gnn_prediction, axis=-1), axis=-1)),
)
self.bilstm_acc_val, self.bilstm_acc_update_op = tf.metrics.accuracy(
labels=tf.reduce_max(self.labels, axis=-1),
predictions=tf.to_int32(tf.reduce_max(
tf.argmax(self.bilstm_prediction, axis=-1), axis=-1)),
)
self.acc_val = [self.seq_acc_val, self.gnn_acc_val, self.bilstm_acc_val]
self.acc_update_op = [self.seq_acc_update_op, self.gnn_acc_update_op, self.bilstm_acc_update_op]
# graph level ROC AUC
self.auc_val, self.auc_update_op = tf.metrics.auc(
labels=tf.reduce_max(self.labels, axis=-1),
predictions=self.prediction[:, 1],
)
self.g_nodes = tf.gradients(self.prediction[:, 1], self.node_tensor)[0]
self.g_adj_mat = tf.gradients(self.prediction[:, 1], self.dense_adj_mat)[0]
def _init_session(self):
gpu_options = tf.GPUOptions()
gpu_options.per_process_gpu_memory_fraction = 0.3
if type(self.gpu_device) is list:
gpu_options.visible_device_list = ','.join([device[-1] for device in self.gpu_device])
else:
gpu_options.visible_device_list = self.gpu_device[-1]
self.sess = tf.Session(graph=self.g, config=tf.ConfigProto(gpu_options=gpu_options))
self.sess.run(self.init)
self.sess.run(self.local_init)
def reset_session(self):
del self.saver
with self.g.as_default():
self.saver = tf.train.Saver(max_to_keep=5)
self.sess.run(self.init)
self.sess.run(self.local_init)
lib.plot.reset()
@classmethod
def _merge_sparse_submatrices(cls, data, row_col, segments, merge_mode='stack'):
'''
merge sparse submatrices to 3 dimensional sparse tensor
take note that padding has to be made in the beginning of each submatrix
'''
all_data, all_row_col = [], []
if merge_mode == 'concat':
# concatenate submatrices along existing dimensions
size = 0
for _data, _row_col, _segment in zip(data, row_col, segments):
all_data.append(_data[2])
all_data.append(_data[3])
all_row_col.append(np.array(_row_col[2]).reshape((-1, 2)) + size)
all_row_col.append(np.array(_row_col[3]).reshape((-1, 2)) + size)
size += _segment
return tf.compat.v1.SparseTensorValue(
np.concatenate(all_row_col),
np.concatenate(all_data),
(size, size)
)
elif merge_mode == 'stack':
max_size = np.max(segments)
for i, (_data, _row_col, _segment) in enumerate(zip(data, row_col, segments)):
all_data.append(_data[2])
all_data.append(_data[3])
all_row_col.append(np.concatenate([(np.ones((len(_row_col[2]), 1)) * i).astype(np.int32),
(np.array(_row_col[2]) + max_size - _segment).reshape(-1, 2)],
axis=-1))
all_row_col.append(np.concatenate([(np.ones((len(_row_col[3]), 1)) * i).astype(np.int32),
(np.array(_row_col[3]) + max_size - _segment).reshape(-1, 2)],
axis=-1))
return tf.compat.v1.SparseTensorValue(
np.concatenate(all_row_col),
np.concatenate(all_data),
(len(segments), max_size, max_size)
)
else:
raise ValueError('merge mode only supports stack and concat')
@classmethod
def graph_sampler(cls, batch_data, batch_row_col, batch_segment, neighbourhood_size):
# adj_mat in dense form adopting a shape of batch_size x nb_nodes x nb_nodes
# adj_mat may have paddings in the beginning
# from top layer to bottom layer
all_adj_mat = []
res = cls._merge_sparse_submatrices(batch_data, batch_row_col, batch_segment, merge_mode='concat')
whole_mat = sp.coo_matrix((res.values, (res.indices[:, 0], res.indices[:, 1])), shape=res.dense_shape)
for ng_idx, ng_size in enumerate(neighbourhood_size):
# iterate each graph
sampled_data, sampled_row_col, sampled_segment = [], [], []
for i, segment in enumerate(batch_segment):
offset = int(np.sum(batch_segment[:i]))
idx = np.arange(offset, offset + segment)
local_mat = whole_mat[idx, :][:, idx]
column_norm = norm(local_mat, axis=0)
proposal_dist = column_norm / np.sum(column_norm)
sampled_idx = np.random.choice(proposal_dist, ng_size, replace=False, p=proposal_dist)
# if ng_idx == 0
@classmethod
def indexing_iterable(cls, iterable, idx):
return [item[idx] for item in iterable]
def fit(self, X, y, epochs, batch_size, output_dir, logging=False, epoch_to_start=0):
checkpoints_dir = os.path.join(output_dir, 'checkpoints/')
if not os.path.exists(checkpoints_dir):
os.makedirs(checkpoints_dir)
# split validation set
row_sum = np.array(list(map(lambda label: np.sum(label), y)))
pos_idx, neg_idx = np.where(row_sum > 0)[0], np.where(row_sum == 0)[0]
dev_idx = np.array(list(np.random.choice(pos_idx, int(len(pos_idx) * 0.1), False)) + \
list(np.random.choice(neg_idx, int(len(neg_idx) * 0.1), False)))
train_idx = np.delete(np.arange(len(y)), dev_idx)
dev_data = self.indexing_iterable(X, dev_idx)
dev_targets = y[dev_idx]
X = self.indexing_iterable(X, train_idx)
train_targets = y[train_idx]
best_dev_cost = np.inf
# best_dev_auc = 0.
lib.plot.set_output_dir(output_dir)
if logging:
logger = lib.logger.CSVLogger('run.csv', output_dir,
['epoch', 'cost', 'graph_cost', 'gnn_cost', 'bilstm_cost',
'seq_acc', 'gnn_acc', 'bilstm_acc', 'auc',
'dev_cost', 'dev_graph_cost', 'dev_gnn_cost', 'dev_bilstm_cost',
'dev_seq_acc', 'dev_gnn_acc', 'dev_bilstm_acc', 'dev_auc'])
train_generator = BackgroundGenerator(X, train_targets, batch_size, random_crop=False)
val_generator = BackgroundGenerator(dev_data, dev_targets, batch_size)
iters_per_epoch = train_generator.iters_per_epoch
for epoch in range(epoch_to_start, epochs):
prepro_time = 0.
training_time = 0.
for i in range(iters_per_epoch):
prepro_start = time.time()
_node_tensor, _mask_offset, all_adj_mat, _labels = train_generator.next()
feed_dict = {
self.node_input_ph: _node_tensor,
self.adj_mat_ph: all_adj_mat,
self.labels: _labels,
self.mask_offset: _mask_offset,
self.global_step: i + epoch * iters_per_epoch,
self.hf_iters_per_epoch: iters_per_epoch // 2,
self.is_training_ph: True,
}
prepro_end = time.time()
prepro_time += (prepro_end - prepro_start)
self.sess.run(self.train_op, feed_dict)
training_time += (time.time() - prepro_end)
print('preprocessing time: %.4f, training time: %.4f' % (prepro_time / (i + 1), training_time / (i + 1)))
train_cost, train_acc, train_auc = self.evaluate_with_generator(train_generator)
lib.plot.plot('train_cost', train_cost[0])
lib.plot.plot('train_graph_cost', train_cost[1])
lib.plot.plot('train_gnn_cost', train_cost[2])
lib.plot.plot('train_bilstm_cost', train_cost[3])
lib.plot.plot('train_seq_acc', train_acc[0])
lib.plot.plot('train_gnn_acc', train_acc[1])
lib.plot.plot('train_bilstm_acc', train_acc[2])
lib.plot.plot('train_auc', train_auc)
dev_cost, dev_acc, dev_auc = self.evaluate_with_generator(val_generator)
lib.plot.plot('dev_cost', dev_cost[0])
lib.plot.plot('dev_graph_cost', dev_cost[1])
lib.plot.plot('dev_gnn_cost', dev_cost[2])
lib.plot.plot('dev_bilstm_cost', dev_cost[3])
lib.plot.plot('dev_seq_acc', dev_acc[0])
lib.plot.plot('dev_gnn_acc', dev_acc[1])
lib.plot.plot('dev_bilstm_acc', dev_acc[2])
lib.plot.plot('dev_auc', dev_auc)
logger.update_with_dict({
'epoch': epoch, 'cost': train_cost[0], 'graph_cost': train_cost[1], 'gnn_cost': train_cost[2],
'bilstm_cost': train_cost[3], 'seq_acc': train_acc[0], 'gnn_acc': train_acc[1],
'bilstm_acc': train_acc[2], 'auc': train_auc,
'dev_cost': dev_cost[0], 'dev_graph_cost': dev_cost[1], 'dev_gnn_cost': dev_cost[2],
'dev_bilstm_cost': dev_cost[3], 'dev_seq_acc': dev_acc[0], 'dev_gnn_acc': dev_acc[1],
'dev_bilstm_acc': dev_acc[2], 'dev_auc': dev_auc,
})
lib.plot.flush()
lib.plot.tick()
if dev_cost[0] < best_dev_cost and epoch - epoch_to_start >= 10: # unstable loss in the beginning
best_dev_cost = dev_cost[0]
save_path = self.saver.save(self.sess, checkpoints_dir, global_step=epoch)
print('Validation sample cost improved. Saved to path %s\n' % (save_path), flush=True)
else:
print('\n', flush=True)
print('Loading best weights %s' % (save_path), flush=True)
self.saver.restore(self.sess, save_path)
if logging:
logger.close()
train_generator.kill.set()
val_generator.kill.set()
train_generator.next()
val_generator.next()
train_generator.join()
val_generator.join()
def evaluate_with_generator(self, generator):
all_cost, all_graph_cost, all_gnn_nuc_cost, all_bilstm_nuc_cost = 0., 0., 0., 0.
for i in range(generator.iters_per_epoch):
_node_tensor, _mask_offset, all_adj_mat, _labels = generator.next()
feed_dict = {
self.node_input_ph: _node_tensor,
self.adj_mat_ph: all_adj_mat,
self.labels: _labels,
self.mask_offset: _mask_offset,
self.is_training_ph: False
}
cost, graph_cost, gnn_nuc_cost, bilstm_nuc_cost, _, _ = self.sess.run(
[self.cost, self.graph_cost, self.gnn_cost, self.bilstm_cost, self.acc_update_op,
self.auc_update_op], feed_dict)
all_cost += cost * _labels.shape[0]
all_graph_cost += graph_cost * _labels.shape[0]
all_gnn_nuc_cost += gnn_nuc_cost * _labels.shape[0]
all_bilstm_nuc_cost += bilstm_nuc_cost * _labels.shape[0]
acc, auc = self.sess.run([self.acc_val, self.auc_val])
self.sess.run(self.local_init)
return (all_cost / generator.size_train, all_graph_cost / generator.size_train,
all_gnn_nuc_cost / generator.size_train, all_bilstm_nuc_cost / generator.size_train), acc, auc
def evaluate(self, X, y, batch_size):
node_tensor, all_rel_data, all_row_col, segment_length, raw_seq = X
all_cost, all_graph_cost, all_gnn_nuc_cost, all_bilstm_nuc_cost = 0., 0., 0., 0.
iters_per_epoch = len(node_tensor) // batch_size + (0 if len(node_tensor) % batch_size == 0 else 1)
for i in range(iters_per_epoch):
_node_tensor, _rel_data, _row_col, _segment, _labels \
= node_tensor[i * batch_size: (i + 1) * batch_size], \
all_rel_data[i * batch_size: (i + 1) * batch_size], \
all_row_col[i * batch_size: (i + 1) * batch_size], \
segment_length[i * batch_size: (i + 1) * batch_size], \
y[i * batch_size: (i + 1) * batch_size]
_max_len = max(_segment)
_mask_offset = np.array([_max_len - _seg for _seg in _segment])
_node_tensor = np.array([np.pad(seq, [_max_len - len(seq), 0], mode='constant') for seq in _node_tensor])
_labels = np.array([np.pad(label, [_max_len - len(label), 0], mode='constant') for label in _labels])
all_adj_mat = self._merge_sparse_submatrices(_rel_data, _row_col, _segment)
feed_dict = {
self.node_input_ph: _node_tensor,
self.adj_mat_ph: all_adj_mat,
self.labels: _labels,
self.mask_offset: _mask_offset,
self.is_training_ph: False
}
cost, graph_cost, gnn_nuc_cost, bilstm_nuc_cost, _, _ = self.sess.run(
[self.cost, self.graph_cost, self.gnn_cost, self.bilstm_cost, self.acc_update_op,
self.auc_update_op], feed_dict)
all_cost += cost * len(_node_tensor)
all_graph_cost += graph_cost * len(_node_tensor)
all_gnn_nuc_cost += gnn_nuc_cost * len(_node_tensor)
all_bilstm_nuc_cost += bilstm_nuc_cost * len(_node_tensor)
acc, auc = self.sess.run([self.acc_val, self.auc_val])
self.sess.run(self.local_init)
return (all_cost / len(node_tensor), all_graph_cost / len(node_tensor),
all_gnn_nuc_cost / len(node_tensor), all_bilstm_nuc_cost / len(node_tensor)), acc, auc
def predict(self, X, batch_size):
node_tensor, all_rel_data, all_row_col, segment_length, raw_seq = X
preds = []
iters_per_epoch = len(node_tensor) // batch_size + (0 if len(node_tensor) % batch_size == 0 else 1)
for i in range(iters_per_epoch):
_node_tensor, _rel_data, _row_col, _segment \
= node_tensor[i * batch_size: (i + 1) * batch_size], \
all_rel_data[i * batch_size: (i + 1) * batch_size], \
all_row_col[i * batch_size: (i + 1) * batch_size], \
segment_length[i * batch_size: (i + 1) * batch_size]
_max_len = max(_segment)
_mask_offset = np.array([_max_len - _seg for _seg in _segment])
_node_tensor = np.array([np.pad(seq, [_max_len - len(seq), 0], mode='constant') for seq in _node_tensor])
all_adj_mat = self._merge_sparse_submatrices(_rel_data, _row_col, _segment)
feed_dict = {
self.node_input_ph: _node_tensor,
self.adj_mat_ph: all_adj_mat,
self.mask_offset: _mask_offset,
self.is_training_ph: False
}
preds.append(self.sess.run(self.prediction, feed_dict))
return np.concatenate(np.array(preds), axis=0)
def integrated_gradients(self, X, y, ids, interp_steps=100, save_path=None, max_plots=np.inf):
counter = 0
for _node_tensor, _rel_data, _row_col, _segment, _, _label, _id in zip(*X, y, ids):
if np.max(_label) == 0:
continue
if counter >= max_plots:
break
_meshed_node_tensor = np.array([self.embedding_vec[idx] for idx in _node_tensor])
_meshed_reference_input = np.zeros_like(_meshed_node_tensor)
new_node_tensor = []
for i in range(0, interp_steps + 1):
new_node_tensor.append(
_meshed_reference_input + i / interp_steps * (_meshed_node_tensor - _meshed_reference_input))
all_adj_mat = self._merge_sparse_submatrices([_rel_data] * (interp_steps + 1),
[_row_col] * (interp_steps + 1),
[_segment] * (interp_steps + 1))
feed_dict = {
self.node_tensor: np.array(new_node_tensor),
self.adj_mat_ph: all_adj_mat,
self.mask_offset: np.zeros((interp_steps + 1,), np.int32),
self.is_training_ph: False
}
grads = self.sess.run(self.g_nodes, feed_dict).reshape((interp_steps + 1, _segment, 4))
grads = (grads[:-1] + grads[1:]) / 2.0
node_scores = np.average(grads, axis=0) * (_meshed_node_tensor - _meshed_reference_input)
pos_idx = np.where(_label == 1)[0]
extended_start = max(pos_idx[0] - 50, 0)
extended_end = min(pos_idx[-1] + 50, _segment)
extended_region = [extended_start, extended_end]
viewpoint_region = [pos_idx[0] - extended_start, pos_idx[-1] - extended_start + 1]
if save_path is not None:
saveto = os.path.join(save_path, '%s.jpg' % (_id))
else:
saveto = None
lib.plot.plot_weights(node_scores[range(*extended_region)],
subticks_frequency=10, highlight={'r': [viewpoint_region]},
save_path=saveto)
counter += 1
def rank_extract_motifs(self, X, interp_steps=100, save_path=None, max_examples=400,
mer_size=12, p=None):
counter = 0
all_scores, all_mers, all_struct_context = [], [], []
tmp_f = open(os.path.join(save_path, 'output.txt'), 'a')
for _node_tensor, _segment, _raw_seq in zip(*X):
if counter >= max_examples:
break
# only keep the binding site portion
# pos_idx = np.where(np.array(list(_raw_seq)) <= 'Z')[0]
# extended_start = max(pos_idx[0] - 50, 0)
# extended_end = min(pos_idx[-1] + 50, _segment)
# extended_region = list(range(extended_start, extended_end))
# _raw_seq = ''.join(np.array(list(_raw_seq))[extended_region])
# _segment = len(_raw_seq)
# _node_tensor = np.array(_node_tensor)[extended_region]
# viewpoint_idx = (np.array(list(_raw_seq)) <= 'Z').astype(np.int32)
# _raw_seq = ''.join(np.array(list(_raw_seq))[viewpoint_idx == 1])
# _segment = len(_raw_seq)
# _node_tensor = np.array(_node_tensor)[viewpoint_idx == 1]
# for each nucleic sequence we consider 10000 random folding hypothesis
cmd = 'echo "%s" | RNAsubopt --stochBT=%d' % (_raw_seq, 300000)
struct_list = subprocess.check_output(cmd, shell=True). \
decode('utf-8').rstrip().split('\n')[1:]
struct_list = list(set(struct_list)) # all unique structures
if '.' * _segment in struct_list:
struct_list.remove('.' * _segment)
if len(struct_list) > 4000:
viewpoint_idx = (np.array(list(_raw_seq)) <= 'Z').astype(np.int32)
len_pos_idx = np.sum(viewpoint_idx)
# sample 2000 based on the number of unpaired nucleotides
unpaired_proportion = np.array(
list(map(lambda st: np.sum(np.array(list(st))[viewpoint_idx == 1] == '.'),
struct_list))) / len_pos_idx
prob = unpaired_proportion / np.sum(unpaired_proportion)
struct_list = np.random.choice(struct_list, 4000, replace=False, p=prob)
if p is None:
all_data, all_row_col, all_segment = [], [], []
for _struct in struct_list:
row_col = []
bg = fgb.BulgeGraph.from_dotbracket(_struct)
for i, ele in enumerate(_struct):
if ele == '(':
row_col.append((i, bg.pairing_partner(i + 1) - 1))
row_col = np.array(row_col)
row_col = [None, None, row_col, row_col[:, ::-1]]
all_row_col.append(row_col)
all_data.append([None, None, np.ones(len(row_col[2])), np.ones(len(row_col[3]))])
all_segment.append(len(_struct))
all_row_col = np.array(all_row_col)
all_data = np.array(all_data)
all_segment = np.array(all_segment)
else:
res = np.array(list(p.imap(mesh_struct, struct_list)))
all_data = res[:, 0]
all_row_col = res[:, 1]
all_segment = res[:, 2]
_meshed_node_tensor = np.array([self.embedding_vec[idx] for idx in _node_tensor])
_meshed_reference_input = np.zeros_like(_meshed_node_tensor)
new_node_tensor = []
for i in range(0, interp_steps + 1):
new_node_tensor.append(
_meshed_reference_input + i / interp_steps * (_meshed_node_tensor - _meshed_reference_input))
new_node_tensor = np.array(new_node_tensor)
seq_scores, seq_mers, seq_struct_context = [], [], []
for struct_idx in range(len(struct_list)):
_struct = struct_list[struct_idx]
all_adj_mat = self._merge_sparse_submatrices(
[all_data[struct_idx]] * (interp_steps + 1),
[all_row_col[struct_idx]] * (interp_steps + 1),
[all_segment[struct_idx]] * (interp_steps + 1))
feed_dict = {
self.node_tensor: new_node_tensor,
self.adj_mat_ph: all_adj_mat,
self.mask_offset: np.zeros((interp_steps + 1,), np.int32),
self.is_training_ph: False
}
grads = self.sess.run(self.g_nodes, feed_dict).reshape((interp_steps + 1, _segment, 4))
grads = (grads[:-1] + grads[1:]) / 2.0
node_scores = np.sum(np.average(grads, axis=0) * (_meshed_node_tensor - _meshed_reference_input),
axis=-1)
mer_scores = []
# for start in range(max(pos_idx[0] - mer_size + 1, 0), min(pos_idx[-1], len(node_scores)-mer_size+1)):
for start in range(len(node_scores) - mer_size + 1):
mer_scores.append(np.sum(node_scores[start: start + mer_size]))
slicing_idx = np.argmax(mer_scores)
seq_scores.append(np.max(mer_scores))
seq_mers.append(_raw_seq[slicing_idx: slicing_idx + mer_size].upper().replace('T', 'U'))
seq_struct_context.append(fgb.BulgeGraph.from_dotbracket(_struct).to_element_string()
[slicing_idx: slicing_idx + mer_size].upper())
top_idx = np.argsort(seq_scores)[::-1]
print(np.array(seq_scores)[top_idx[:50]], file=tmp_f)
print(np.array(seq_mers)[top_idx[:50]], file=tmp_f)
print(np.array(seq_struct_context)[top_idx[:50]], file=tmp_f)
tmp_f.flush()
all_scores.extend(seq_scores)
all_mers.extend(seq_mers)
all_struct_context.extend(seq_struct_context)
counter += 1
np.save(os.path.join(save_path, 'all_scores.npy'), all_scores)
np.save(os.path.join(save_path, 'all_mers.npy'), all_mers)
np.save(os.path.join(save_path, 'all_struct_context.npy'), all_struct_context)
FNULL = open(os.devnull, 'w')
ranked_idx = np.argsort(all_scores)[::-1]
for top_rank in [1000, 2000, 3000, 4000, 5000, 6000]:
# align top_rank mers
best_mers = np.array(all_mers)[ranked_idx[:top_rank]]
best_struct = np.array(all_struct_context)[ranked_idx[:top_rank]]
fasta_path = os.path.join(save_path, 'top%d_mers.fa' % (top_rank))
with open(fasta_path, 'w') as f:
for i, seq in enumerate(best_mers):
print('>{}'.format(i), file=f)
print(seq, file=f)
# multiple sequence alignment
out_fasta_path = os.path.join(save_path, 'aligned_top%d_mers.fa' % (top_rank))
cline = ClustalwCommandline("clustalw2", infile=fasta_path, type="DNA", outfile=out_fasta_path,
output="FASTA")
subprocess.call(str(cline), shell=True, stdout=FNULL)
motif_path = os.path.join(save_path, 'top%d_sequence_motif.jpg' % (top_rank))
lib.plot.plot_weblogo(out_fasta_path, motif_path)
aligned_seq = {}
with open(out_fasta_path, 'r') as f:
for line in f:
if line.startswith('>'):
seq_id = int(line.rstrip()[1:])
else:
aligned_seq[seq_id] = line.rstrip()
aligned_seq[seq_id] = line.rstrip()
# structural motifs
fasta_path = os.path.join(save_path, 'aligned_top%d_struct.fa' % (top_rank))
with open(fasta_path, 'w') as f:
for i, struct_context in enumerate(best_struct):
print('>{}'.format(i), file=f)
struct_context = list(struct_context)
seq = aligned_seq[i]
for j in range(len(seq)):
if seq[j] == '-':
struct_context = struct_context[:j] + ['-'] + struct_context[j:]
print(''.join(struct_context), file=f)
motif_path = os.path.join(save_path, 'top%d_struct_motif.jpg' % (top_rank))
lib.plot.plot_weblogo(fasta_path, motif_path)
def integrated_gradients_2d(self, X, y, ids, interp_steps=100, save_path=None, max_plots=np.inf):
counter = 0
all_acc_hl, all_acc_nonhl = [], []
for _node_tensor, _raw_seq, _label, _id in zip(*X, y, ids):
if np.max(_label) == 0:
continue
if counter >= max_plots:
break
_struct, _mfe_adj_mat = lib.rna_utils.fold_seq_rnafold(_raw_seq)
_struct = ''.join(['.()'[c] for c in np.argmax(_struct, axis=-1)])
# convert to undirected base pairing probability matrix
_mfe_adj_mat = (_mfe_adj_mat > 2).astype(np.float32)
_mfe_adj_mat = np.array(_mfe_adj_mat.todense())
_node_tensor = np.array([self.embedding_vec[idx] for idx in _node_tensor])
feed_dict = {
self.node_tensor: _node_tensor[None, :, ],
self.dense_adj_mat: _mfe_adj_mat[None, :, :],
self.mask_offset: np.array([0]),
self.is_training_ph: False
}
pos_pred = self.sess.run(self.prediction, feed_dict)[0][1]
if pos_pred < 0.95:
# we only visualize strongly predicted candidates
continue
array_mfe_adj_mat = np.stack([_mfe_adj_mat] * (interp_steps + 1), axis=0)
array_node_tensor = np.stack([_node_tensor] * (interp_steps + 1), axis=0)
interp_ratio = []
for i in range(0, interp_steps + 1):
interp_ratio.append(i / interp_steps)
interp_ratio = np.array(interp_ratio)[:, None, None]
new_adj_mat = array_mfe_adj_mat * interp_ratio
new_node_tensor = array_node_tensor * interp_ratio
# interpolating sequence while having its structure fixed
feed_dict = {
self.node_tensor: new_node_tensor,
self.dense_adj_mat: array_mfe_adj_mat,
self.mask_offset: np.zeros((interp_steps + 1,), np.int32),
self.is_training_ph: False
}
node_grads = self.sess.run(self.g_nodes, feed_dict)
avg_node_grads = np.average((node_grads[:-1] + node_grads[1:]) / 2.0, axis=0)
node_scores = np.sum(avg_node_grads * _node_tensor, -1)
# interpolating structure while having its sequence fixed
feed_dict = {
self.node_tensor: array_node_tensor,
self.dense_adj_mat: new_adj_mat,
self.mask_offset: np.zeros((interp_steps + 1,), np.int32),
self.is_training_ph: False
}
adj_mat_grads = self.sess.run(self.g_adj_mat, feed_dict)
avg_adj_mat_grads = np.average((adj_mat_grads[:-1] + adj_mat_grads[1:]) / 2.0, axis=0)
adj_mat_scores = avg_adj_mat_grads * _mfe_adj_mat
# select the top 20 most highly activated nucleotides and basepairs
hl_nt_idx = np.argsort(node_scores)[-30:]
row_col = np.array(list(zip(*np.nonzero(adj_mat_scores))))
hl_bp_idx = row_col[np.argsort(adj_mat_scores[row_col[:, 0], row_col[:, 1]])[-30:]]
if save_path is not None:
saveto = os.path.join(save_path, '%s.jpg' % (_id))
else:
saveto = '%s.jpg' % (_id)
try:
lib.plot.plot_rna_struct(_raw_seq, _struct, highlight_nt_idx=hl_nt_idx, highlight_bp_idx=hl_bp_idx,
saveto=saveto)
except StopIteration as e:
print(e)
continue
counter += 1
bp_access = np.sum(avg_adj_mat_grads, axis=-1)
all_acc_hl.extend(bp_access[hl_nt_idx])
all_acc_nonhl.extend(bp_access[list(set(range(len(node_scores))).difference(hl_nt_idx))])
import matplotlib.pyplot as plt
figure = plt.figure(figsize=(10, 10))
plt.hist(all_acc_hl, label='structural accessibility of sequence motifs', density=True, alpha=0.7)
plt.hist(all_acc_nonhl, label='structural accessibility of background sequence', density=True, alpha=0.5)
legend = plt.legend()
plt.setp(legend.texts, **{'fontname': 'Times New Roman'})
if save_path is not None:
saveto = os.path.join(save_path, 'struct_access.jpg')
else:
saveto = 'struct_access.jpg'
plt.savefig(saveto, dpi=350)
plt.close(figure)
def delete(self):
tf.reset_default_graph()
self.sess.close()
def load(self, chkp_path):
self.saver.restore(self.sess, chkp_path)
class JMRT:
def __init__(self, node_dim, embedding_vec, gpu_device, **kwargs):
self.node_dim = node_dim
self.embedding_vec = embedding_vec
self.vocab_size = embedding_vec.shape[0]
self.gpu_device = gpu_device
# hyperparams
self.units = kwargs.get('units', 32)
self.pool_steps = kwargs.get('pool_steps', 10)
self.lstm_encoder = kwargs.get('lstm_encoder', True)
self.dropout_rate = kwargs.get('dropout_rate', 0.2)
self.learning_rate = kwargs.get('learning_rate', 2e-4)
self.use_clr = kwargs.get('use_clr', False)
self.use_momentum = kwargs.get('use_momentum', False)
self.use_bn = kwargs.get('use_bn', False)
self.mixing_ratio = kwargs.get('mixing_ratio', 0.)
self.use_ghm = kwargs.get('use_ghm', False)
self.g = tf.Graph()
with self.g.as_default():
self._placeholders()
if self.use_momentum:
self.optimizer = tf.contrib.opt.MomentumWOptimizer(
1e-4,
self.learning_rate * self.lr_multiplier,
0.9,
use_nesterov=True)
else:
self.optimizer = AMSGrad(self.learning_rate *
self.lr_multiplier,
beta2=0.999)
with tf.variable_scope('Classifier', reuse=tf.AUTO_REUSE):
self._build_ggnn()
self._loss()
self._train()
self._merge()
with tf.control_dependencies(
tf.get_collection(tf.GraphKeys.UPDATE_OPS)):
self.train_op = self.optimizer.apply_gradients(self.gv)
_stats('Joint_MRT', self.gv)
self.saver = tf.train.Saver(max_to_keep=5)
self.init = tf.global_variables_initializer()
self.local_init = tf.local_variables_initializer()
self.g.finalize()
self._init_session()
def _placeholders(self):
self.node_input_ph = tf.placeholder(tf.int32, shape=[
None,
]) # nb_nodes
# nb_nodes x nb_nodes
self.labels = tf.placeholder(tf.int32, shape=[
None,
None,
])
self.max_len = tf.placeholder(tf.int32, shape=())
self.segment_length = tf.placeholder(tf.int32, shape=[
None,
])
self.is_training_ph = tf.placeholder(tf.bool, ())
self.global_step = tf.placeholder(tf.int32, ())
self.hf_iters_per_epoch = tf.placeholder(tf.int32, ())
if self.use_clr:
self.lr_multiplier = lib.clr. \
cyclic_learning_rate(self.global_step, 0.5, 5.,
self.hf_iters_per_epoch, mode='exp_range')
else:
self.lr_multiplier = 1.
def _build_ggnn(self):
embedding = tf.get_variable('embedding_layer',
shape=(self.vocab_size, self.node_dim),
initializer=tf.constant_initializer(
self.embedding_vec),
trainable=False)
output = tf.nn.embedding_lookup(embedding, self.node_input_ph)
self.node_tensor = output
# while loop to recover batch size
batch_output = tf.TensorArray(tf.float32,
size=tf.shape(self.segment_length)[0],
infer_shape=True,
dynamic_size=True)
mask_offset = tf.TensorArray(tf.int32,
size=tf.shape(self.segment_length)[0],
infer_shape=True,
dynamic_size=True)
i = tf.constant(0)
start_idx = tf.constant(0)
while_condition = lambda i, _1, _2, _3: tf.less(
i,
tf.shape(self.segment_length)[0])
def body(i, start_idx, batch_output, mask_offset):
end_idx = start_idx + self.segment_length[i]
segment = output[start_idx:end_idx]
# pad segment to max len
segment = tf.pad(
segment, [[self.max_len - self.segment_length[i], 0], [0, 0]])
batch_output = batch_output.write(i, segment)
mask_offset = mask_offset.write(
i, self.max_len - self.segment_length[i])
return [tf.add(i, 1), end_idx, batch_output, mask_offset]
_, _, batch_output, mask_offset = tf.while_loop(
while_condition, body, [i, start_idx, batch_output, mask_offset])
output = batch_output.stack()
mask_offset = mask_offset.stack()
self.mask_offset = mask_offset
with tf.variable_scope('seq_scan'):
# paddings will influence the prediction results, even unavoidable if batch norm is used
# but the influence will be very small, enough to ignore it
output = lib.ops.Conv1D.conv1d('conv1',
self.node_dim,
self.units,
10,
output,
biases=False,
pad_mode='SAME',
variables_on_cpu=False)
output = normalize('bn1', output, self.use_bn, self.is_training_ph)
output = tf.nn.relu(output)
output = tf.layers.dropout(output,
self.dropout_rate,
training=self.is_training_ph)
output = lib.ops.Conv1D.conv1d('conv2',
self.units,
self.units,
10,
output,
biases=False,
pad_mode='SAME',
variables_on_cpu=False)
output = normalize('bn2', output, self.use_bn, self.is_training_ph)
output = tf.nn.relu(output)
output = tf.layers.dropout(output,
self.dropout_rate,
training=self.is_training_ph)
with tf.variable_scope('set2set_pooling'):
output = lib.ops.LSTM.set2set_pooling('set2set_pooling',
output,
self.pool_steps,
self.dropout_rate,
self.is_training_ph,
self.lstm_encoder,
mask_offset,
variables_on_cpu=False)
self.nuc_embedding = tf.get_collection('nuc_emb')[
0] # will depend on if bilstm encoder is used or not
self.nuc_output = lib.ops.Linear.linear(
'bilstm_nuc_output',
self.units * 2 if self.lstm_encoder else self.units, 2,
self.nuc_embedding)
self.output = lib.ops.Linear.linear(
'OutputMapping',
output.get_shape().as_list()[-1],
2,
output,
variables_on_cpu=False) # categorical logits
def _loss(self):
self.prediction = tf.nn.softmax(self.output)
self.nuc_prediction = tf.nn.softmax(self.nuc_output)
# graph level loss
self.graph_cost = tf.reduce_mean(
tf.nn.softmax_cross_entropy_with_logits(
logits=self.
output, # reduce along the RNA sequence to a graph label
labels=tf.one_hot(tf.reduce_max(self.labels, axis=1), depth=2),
))
# nucleotide level loss
# dummies are padded to the front...
self.mask = 1.0 - tf.sequence_mask(
self.mask_offset, maxlen=self.max_len, dtype=tf.float32)
if self.use_ghm:
self.nuc_cost = tf.reduce_sum(
get_ghm_weights(self.nuc_prediction, self.labels, self.mask,
bins=10, alpha=0.75, name='GHM_NUC_EMB') * \
tf.nn.softmax_cross_entropy_with_logits(
logits=self.nuc_output,
labels=tf.one_hot(self.labels, depth=2),
) / tf.cast(tf.reduce_sum(self.segment_length), tf.float32)
)
else:
self.nuc_cost = tf.reduce_sum(
self.mask * \
tf.nn.softmax_cross_entropy_with_logits(
logits=self.nuc_output,
labels=tf.one_hot(self.labels, depth=2),
)) / tf.cast(tf.reduce_sum(self.segment_length), tf.float32)
self.cost = self.mixing_ratio * self.graph_cost + (
1. - self.mixing_ratio) * self.nuc_cost
def _train(self):
self.gv = self.optimizer.compute_gradients(
self.cost,
var_list=[var for var in tf.trainable_variables()],
colocate_gradients_with_ops=True)
def _merge(self):
# If the example contains a binding site: more global
self.seq_acc_val, self.seq_acc_update_op = tf.metrics.accuracy(
labels=tf.reduce_max(self.labels, axis=-1),
predictions=tf.to_int32(tf.argmax(self.prediction, axis=-1)),
)
# nucleotide level accuracy of containing a binding site
self.nuc_acc_val, self.nuc_acc_update_op = tf.metrics.accuracy(
labels=tf.reduce_max(self.labels, axis=-1),
predictions=tf.to_int32(
tf.reduce_max(tf.argmax(self.nuc_prediction, axis=-1),
axis=-1)),
)
self.acc_val = [self.seq_acc_val, self.nuc_acc_val]
self.acc_update_op = [self.seq_acc_update_op, self.nuc_acc_update_op]
# graph level ROC AUC
self.auc_val, self.auc_update_op = tf.metrics.auc(
labels=tf.reduce_max(self.labels, axis=-1),
predictions=self.prediction[:, 1],
)
self.g_nodes = tf.gradients(self.prediction[:, 1], self.node_tensor)[0]
def _init_session(self):
gpu_options = tf.GPUOptions()
gpu_options.per_process_gpu_memory_fraction = 0.2
if type(self.gpu_device) is list:
gpu_options.visible_device_list = ','.join(
[device[-1] for device in self.gpu_device])
else:
gpu_options.visible_device_list = self.gpu_device[-1]
self.sess = tf.Session(graph=self.g,
config=tf.ConfigProto(gpu_options=gpu_options))
self.sess.run(self.init)
self.sess.run(self.local_init)
def reset_session(self):
del self.saver
with self.g.as_default():
self.saver = tf.train.Saver(max_to_keep=5)
self.sess.run(self.init)
self.sess.run(self.local_init)
lib.plot.reset()
@classmethod
def indexing_iterable(cls, iterable, idx):
return [item[idx] for item in iterable]
@classmethod
def random_crop(cls, node_tensor, raw_seq, y, pos_read_retention_rate=0.5):
m_seq, m_label, m_sg, m_data, m_row_col = [], [], [], [], []
for seq, _raw_seq, label in zip(node_tensor, raw_seq, y):
if np.max(label) == 0:
# negative sequence
pseudo_label = (np.array(list(_raw_seq)) <= 'Z').astype(
np.int32)
pos_idx = np.where(pseudo_label == 1)[0]
else:
pos_idx = np.where(label == 1)[0]
# keep more than 3/4 of the sequence (length), and random start
read_length = len(pos_idx)
rate = min(max(pos_read_retention_rate, np.random.rand()), 0.9)
winsize = int(rate * read_length)
surplus = read_length - winsize + 1
start_idx = np.random.choice(
range(int(surplus / 4), math.ceil(surplus * 3 / 4)))
label = [0] * (pos_idx[0] + start_idx) + [1] * winsize + [0] * \
(len(seq) - winsize - start_idx - pos_idx[0])
left_truncate = int(np.random.rand() * pos_idx[0])
right_truncate = int(np.random.rand() *
(len(seq) - pos_idx[-1] - 1))
if not right_truncate > 0:
right_truncate = -len(seq)
seq = seq[left_truncate:-right_truncate]
label = label[left_truncate:-right_truncate]
m_seq.append(seq)
m_sg.append(len(seq))
m_label.append(label)
return np.array(m_seq), np.array(m_sg), np.array(m_label)
def fit(self,
X,
y,
epochs,
batch_size,
output_dir,
logging=False,
epoch_to_start=0,
random_crop=False):
checkpoints_dir = os.path.join(output_dir, 'checkpoints/')
if not os.path.exists(checkpoints_dir):
os.makedirs(checkpoints_dir)
# split validation set
row_sum = np.array(list(map(lambda label: np.sum(label), y)))
pos_idx, neg_idx = np.where(row_sum > 0)[0], np.where(row_sum == 0)[0]
dev_idx = np.array(list(np.random.choice(pos_idx, int(len(pos_idx) * 0.1), False)) + \
list(np.random.choice(neg_idx, int(len(neg_idx) * 0.1), False)))
train_idx = np.delete(np.arange(len(y)), dev_idx)
dev_data = self.indexing_iterable(X, dev_idx)
dev_targets = y[dev_idx]
X = self.indexing_iterable(X, train_idx)
train_targets = y[train_idx]
size_train = train_targets.shape[0]
iters_per_epoch = size_train // batch_size + (0 if size_train %
batch_size == 0 else 1)
best_dev_cost = np.inf
lib.plot.set_output_dir(output_dir)
if logging:
logger = lib.logger.CSVLogger('run.csv', output_dir, [
'epoch', 'cost', 'graph_cost', 'nuc_cost', 'seq_acc',
'nuc_acc', 'auc', 'dev_cost', 'dev_graph_cost', 'dev_nuc_cost',
'dev_seq_acc', 'dev_nuc_acc', 'dev_auc'
])
for epoch in range(epoch_to_start, epochs):
permute = np.random.permutation(size_train)
node_tensor, segment_length, raw_seq = self.indexing_iterable(
X, permute)
y = train_targets[permute]
if random_crop:
# augmentation
node_tensor, segment_length, y = \
self.random_crop(node_tensor, raw_seq, y)
prepro_time = 0.
training_time = 0.
for i in range(iters_per_epoch):
prepro_start = time.time()
_node_tensor, _segment, _labels \
= node_tensor[i * batch_size: (i + 1) * batch_size], \
segment_length[i * batch_size: (i + 1) * batch_size], \
y[i * batch_size: (i + 1) * batch_size]
_max_len = max(_segment)
_labels = np.array([
np.pad(label, [_max_len - len(label), 0], mode='constant')
for label in _labels
])
feed_dict = {
self.node_input_ph: np.concatenate(_node_tensor, axis=0),
self.labels: _labels,
self.max_len: _max_len,
self.segment_length: _segment,
self.global_step: i,
self.hf_iters_per_epoch: iters_per_epoch // 2,
self.is_training_ph: True
}
prepro_end = time.time()
prepro_time += (prepro_end - prepro_start)
self.sess.run(self.train_op, feed_dict)
training_time += (time.time() - prepro_end)
print('preprocessing time: %.4f, training time: %.4f' %
(prepro_time / (i + 1), training_time / (i + 1)))
train_cost, train_acc, train_auc = self.evaluate(
X, train_targets, batch_size)
lib.plot.plot('train_cost', train_cost[0])
lib.plot.plot('train_graph_cost', train_cost[1])
lib.plot.plot('train_nuc_cost', train_cost[2])
lib.plot.plot('train_seq_acc', train_acc[0])
lib.plot.plot('train_nuc_acc', train_acc[1])
lib.plot.plot('train_auc', train_auc)
dev_cost, dev_acc, dev_auc = self.evaluate(dev_data, dev_targets,
batch_size)
lib.plot.plot('dev_cost', dev_cost[0])
lib.plot.plot('dev_graph_cost', dev_cost[1])
lib.plot.plot('dev_nuc_cost', dev_cost[2])
lib.plot.plot('dev_seq_acc', dev_acc[0])
lib.plot.plot('dev_nuc_acc', dev_acc[1])
lib.plot.plot('dev_auc', dev_auc)
logger.update_with_dict({
'epoch': epoch,
'cost': train_cost[0],
'graph_cost': train_cost[1],
'nuc_cost': train_cost[2],
'seq_acc': train_acc[0],
'nuc_acc': train_acc[1],
'auc': train_auc,
'dev_cost': dev_cost[0],
'dev_graph_cost': dev_cost[1],
'dev_nuc_cost': dev_cost[2],
'dev_seq_acc': dev_acc[0],
'dev_nuc_acc': dev_acc[1],
'dev_auc': dev_auc,
})
lib.plot.flush()
lib.plot.tick()
if dev_cost[
0] < best_dev_cost and epoch - epoch_to_start >= 10: # unstable loss in the beginning
best_dev_cost = dev_cost[0]
save_path = self.saver.save(self.sess,
checkpoints_dir,
global_step=epoch)
print('Validation sample cost improved. Saved to path %s\n' %
(save_path),
flush=True)
else:
print('\n', flush=True)
print('Loading best weights %s' % (save_path), flush=True)
self.saver.restore(self.sess, save_path)
if logging:
logger.close()
def evaluate(self, X, y, batch_size, random_crop=False):
node_tensor, segment_length, raw_seq = X
if random_crop:
# augmentation
node_tensor, segment_length, y = \
self.random_crop(node_tensor, raw_seq, y)
all_cost = 0.
all_graph_cost = 0.
all_bilstm_nuc_cost = 0.
iters_per_epoch = len(node_tensor) // batch_size + (
0 if len(node_tensor) % batch_size == 0 else 1)
for i in range(iters_per_epoch):
_node_tensor, _segment, _labels \
= node_tensor[i * batch_size: (i + 1) * batch_size], \
segment_length[i * batch_size: (i + 1) * batch_size], \
y[i * batch_size: (i + 1) * batch_size]
_max_len = max(_segment)
_labels = np.array([
np.pad(label, [_max_len - len(label), 0], mode='constant')
for label in _labels
])
feed_dict = {
self.node_input_ph: np.concatenate(_node_tensor, axis=0),
self.labels: _labels,
self.max_len: _max_len,
self.segment_length: _segment,
self.is_training_ph: False
}
cost, graph_cost, bilstm_nuc_cost, _, _ = self.sess.run([
self.cost, self.graph_cost, self.nuc_cost, self.acc_update_op,
self.auc_update_op
], feed_dict)
all_cost += cost * len(_node_tensor)
all_graph_cost += graph_cost * len(_node_tensor)
all_bilstm_nuc_cost += bilstm_nuc_cost * len(_node_tensor)
acc, auc = self.sess.run([self.acc_val, self.auc_val])
self.sess.run(self.local_init)
return (all_cost / len(node_tensor), all_graph_cost / len(node_tensor),
all_bilstm_nuc_cost / len(node_tensor)), acc, auc
def predict(self, X, batch_size):
node_tensor, segment_length, raw_seq = X
preds = []
iters_per_epoch = len(node_tensor) // batch_size + (
0 if len(node_tensor) % batch_size == 0 else 1)
for i in range(iters_per_epoch):
_node_tensor, _segment \
= node_tensor[i * batch_size: (i + 1) * batch_size], \
segment_length[i * batch_size: (i + 1) * batch_size]
_max_len = max(_segment)
feed_dict = {
self.node_input_ph: np.concatenate(_node_tensor, axis=0),
self.max_len: _max_len,
self.segment_length: _segment,
self.is_training_ph: False
}
preds.append(self.sess.run(self.prediction, feed_dict))
return np.concatenate(np.array(preds), axis=0)
def integrated_gradients(self,
X,
y,
ids,
interp_steps=100,
save_path=None,
max_plots=np.inf):
counter = 0
for _node_tensor, _segment, _, _label, _id in zip(*X, y, ids):
if np.max(_label) == 0:
continue
if counter >= max_plots:
break
_meshed_node_tensor = np.array(
[self.embedding_vec[idx] for idx in _node_tensor])
_meshed_reference_input = np.zeros_like(_meshed_node_tensor)
new_node_tensor = []
for i in range(0, interp_steps + 1):
new_node_tensor.append(
_meshed_reference_input + i / interp_steps *
(_meshed_node_tensor - _meshed_reference_input))
feed_dict = {
self.node_tensor: np.concatenate(np.array(new_node_tensor),
axis=0),
self.max_len: _segment,
self.segment_length: [_segment] * (interp_steps + 1),
self.is_training_ph: False
}
grads = self.sess.run(self.g_nodes, feed_dict).reshape(
(interp_steps + 1, _segment, 4))
grads = (grads[:-1] + grads[1:]) / 2.0
node_scores = np.average(grads, axis=0) * (_meshed_node_tensor -
_meshed_reference_input)
pos_idx = np.where(_label == 1)[0]
extended_start = max(pos_idx[0] - 50, 0)
extended_end = min(pos_idx[-1] + 50, _segment)
extended_region = [extended_start, extended_end]
viewpoint_region = [
pos_idx[0] - extended_start, pos_idx[-1] - extended_start + 1
]
if save_path is not None:
saveto = os.path.join(save_path, '%s.jpg' % (_id))
else:
saveto = None
lib.plot.plot_weights(node_scores[range(*extended_region)],
subticks_frequency=10,
highlight={'r': [viewpoint_region]},
save_path=saveto)
counter += 1
def extract_sequence_motifs(self,
X,
interp_steps=100,
save_path=None,
max_examples=4000,
mer_size=12):
counter = 0
all_mers = []
all_scores = []
for _node_tensor, _segment, _raw_seq in zip(*X):
if counter >= max_examples:
break
_meshed_node_tensor = np.array(
[self.embedding_vec[idx] for idx in _node_tensor])
_meshed_reference_input = np.zeros_like(_meshed_node_tensor)
new_node_tensor = []
for i in range(0, interp_steps + 1):
new_node_tensor.append(
_meshed_reference_input + i / interp_steps *
(_meshed_node_tensor - _meshed_reference_input))
feed_dict = {
self.node_tensor: np.concatenate(np.array(new_node_tensor),
axis=0),
self.max_len: _segment,
self.segment_length: [_segment] * (interp_steps + 1),
self.is_training_ph: False
}
grads = self.sess.run(self.g_nodes, feed_dict).reshape(
(interp_steps + 1, _segment, 4))
grads = (grads[:-1] + grads[1:]) / 2.0
node_scores = np.sum(
np.average(grads, axis=0) *
(_meshed_node_tensor - _meshed_reference_input),
axis=-1)
mer_scores = []
for start in range(len(node_scores) - mer_size + 1):
mer_scores.append(np.sum(node_scores[start:start + mer_size]))
max_scores = np.max(node_scores)
all_mers.append(
_raw_seq[np.argmax(mer_scores):np.argmax(mer_scores) +
mer_size].upper().replace('T', 'U'))
all_scores.append(max_scores)
counter += 1
FNULL = open(os.devnull, 'w')
for top_rank in [100, 500, 1000, 2000]:
# align top_rank mers
best_mers = np.array(all_mers)[:top_rank]
fasta_path = os.path.join(save_path, 'top%d_mers.fa' % (top_rank))
with open(fasta_path, 'w') as f:
for i, seq in enumerate(best_mers):
print('>{}'.format(i), file=f)
print(seq, file=f)
# multiple sequence alignment
out_fasta_path = os.path.join(save_path,
'aligned_top%d_mers.fa' % (top_rank))
cline = ClustalwCommandline("clustalw2",
infile=fasta_path,
type="DNA",
outfile=out_fasta_path,
output="FASTA")
sp.call(str(cline), shell=True, stdout=FNULL)
motif_path = os.path.join(save_path,
'top%d-sequence_motif.jpg' % (top_rank))
lib.plot.plot_weblogo(out_fasta_path, motif_path)
even_mers = all_mers[::2]
fasta_path = os.path.join(save_path, 'even_mers.fa')
with open(fasta_path, 'w') as f:
for i, seq in enumerate(even_mers):
print('>{}'.format(i), file=f)
print(seq, file=f)
# multiple sequence alignment
out_fasta_path = os.path.join(save_path, 'aligned_even_mers.fa')
cline = ClustalwCommandline("clustalw2",
infile=fasta_path,
type="DNA",
outfile=out_fasta_path,
output="FASTA")
sp.call(str(cline), shell=True, stdout=FNULL)
motif_path = os.path.join(save_path, 'top1000-even-sequence_motif.jpg')
lib.plot.plot_weblogo(out_fasta_path, motif_path)
odd_mers = all_mers[1::2]
fasta_path = os.path.join(save_path, 'odd_mers.fa')
with open(fasta_path, 'w') as f:
for i, seq in enumerate(odd_mers):
print('>{}'.format(i), file=f)
print(seq, file=f)
# multiple sequence alignment
out_fasta_path = os.path.join(save_path, 'aligned_odd_mers.fa')
cline = ClustalwCommandline("clustalw2",
infile=fasta_path,
type="DNA",
outfile=out_fasta_path,
output="FASTA")
sp.call(str(cline), shell=True, stdout=FNULL)
motif_path = os.path.join(save_path, 'top1000-odd-sequence_motif.jpg')
lib.plot.plot_weblogo(out_fasta_path, motif_path)
def delete(self):
tf.reset_default_graph()
self.sess.close()
def load(self, chkp_path):
self.saver.restore(self.sess, chkp_path)
def __init__(self, **kwargs):
self._kwargs = kwargs
self._data_kwargs = kwargs.get('data')
self._model_kwargs = kwargs.get('model')
self._train_kwargs = kwargs.get('train')
self._test_kwargs = kwargs.get('test')
# logging.
self._log_dir = _get_log_dir(kwargs)
log_level = self._kwargs.get('log_level', 'INFO')
self._logger = utils.get_logger(self._log_dir,
__name__,
'info.log',
level=log_level)
self._writer = tf.summary.FileWriter(self._log_dir)
self._logger.info(kwargs)
self._mon_ratio = float(self._kwargs.get('mon_ratio'))
# Model's args
self._seq_len = int(self._model_kwargs.get('seq_len'))
self._horizon = int(self._model_kwargs.get('horizon'))
self._input_dim = int(self._model_kwargs.get('input_dim'))
self._nodes = int(self._model_kwargs.get('num_nodes'))
self._r = int(self._model_kwargs.get('r'))
# Test's args
self._flow_selection = self._test_kwargs.get('flow_selection')
self._run_times = self._test_kwargs.get('run_times')
self._lamda = []
self._lamda.append(self._test_kwargs.get('lamda_0'))
self._lamda.append(self._test_kwargs.get('lamda_1'))
self._lamda.append(self._test_kwargs.get('lamda_2'))
# Data preparation
self._day_size = self._data_kwargs.get('day_size')
self.data = utils.load_dataset_dcrnn_fwbw(
seq_len=self._model_kwargs.get('seq_len'),
horizon=self._model_kwargs.get('horizon'),
input_dim=self._model_kwargs.get('input_dim'),
mon_ratio=self._mon_ratio,
**self._data_kwargs)
for k, v in self.data.items():
if hasattr(v, 'shape'):
self._logger.info((k, v.shape))
# Build models.
scaler = self.data['scaler']
with tf.name_scope('Train'):
with tf.variable_scope('DCRNN', reuse=False):
self.train_model = DCRNNModel(
is_training=True,
scaler=scaler,
batch_size=self._data_kwargs['batch_size'],
adj_mx=self.data['adj_mx'],
**self._model_kwargs)
with tf.name_scope('Val'):
with tf.variable_scope('DCRNN', reuse=True):
self.val_model = DCRNNModel(
is_training=False,
scaler=scaler,
batch_size=self._data_kwargs['val_batch_size'],
adj_mx=self.data['adj_mx'],
**self._model_kwargs)
with tf.name_scope('Eval'):
with tf.variable_scope('DCRNN', reuse=True):
self.eval_model = DCRNNModel(
is_training=False,
scaler=scaler,
batch_size=self._data_kwargs['eval_batch_size'],
adj_mx=self.data['adj_mx'],
**self._model_kwargs)
with tf.name_scope('Test'):
with tf.variable_scope('DCRNN', reuse=True):
self.test_model = DCRNNModel(
is_training=False,
scaler=scaler,
batch_size=self._data_kwargs['test_batch_size'],
adj_mx=self.data['adj_mx'],
**self._model_kwargs)
# Learning rate.
self._lr = tf.get_variable('learning_rate',
shape=(),
initializer=tf.constant_initializer(0.01),
trainable=False)
self._new_lr = tf.placeholder(tf.float32,
shape=(),
name='new_learning_rate')
self._lr_update = tf.assign(self._lr, self._new_lr, name='lr_update')
# Configure optimizer
optimizer_name = self._train_kwargs.get('optimizer', 'adam').lower()
epsilon = float(self._train_kwargs.get('epsilon', 1e-3))
optimizer = tf.train.AdamOptimizer(
self._lr,
epsilon=epsilon,
)
if optimizer_name == 'sgd':
optimizer = tf.train.GradientDescentOptimizer(self._lr, )
elif optimizer_name == 'amsgrad':
optimizer = AMSGrad(self._lr, epsilon=epsilon)
# Calculate loss
output_dim = self._model_kwargs.get('output_dim')
# fw decoder
preds_fw = self.train_model.outputs_fw
labels_fw = self.train_model.labels_fw[..., :output_dim]
# bw encoder
enc_preds_bw = self.train_model.enc_outputs_bw
enc_labels_bw = self.train_model.enc_labels_bw[..., :output_dim]
null_val = 0.
self._loss_fn = masked_mse_loss(scaler, null_val)
self._train_loss_dec = self._loss_fn(preds=preds_fw, labels=labels_fw)
# backward loss
self._train_loss_enc_bw = self._loss_fn(preds=enc_preds_bw,
labels=enc_labels_bw)
self._train_loss = self._train_loss_dec + self._train_loss_enc_bw
tvars = tf.trainable_variables()
grads = tf.gradients(self._train_loss, tvars)
max_grad_norm = kwargs['train'].get('max_grad_norm', 1.)
grads, _ = tf.clip_by_global_norm(grads, max_grad_norm)
global_step = tf.train.get_or_create_global_step()
self._train_op = optimizer.apply_gradients(zip(grads, tvars),
global_step=global_step,
name='train_op')
max_to_keep = self._train_kwargs.get('max_to_keep', 100)
self._epoch = 0
self._saver = tf.train.Saver(tf.global_variables(),
max_to_keep=max_to_keep)
# Log model statistics.
total_trainable_parameter = utils.get_total_trainable_parameter_size()
self._logger.info('Total number of trainable parameters: {:d}'.format(
total_trainable_parameter))
for var in tf.global_variables():
self._logger.debug('{}, {}'.format(var.name, var.get_shape()))
def __init__(self, adj_mx, **kwargs):
self._kwargs = kwargs
self._data_kwargs = kwargs.get('data')
self._model_kwargs = kwargs.get('model')
self._train_kwargs = kwargs.get('train')
# logging.
self._log_dir = self._get_log_dir(kwargs)
log_level = self._kwargs.get('log_level', 'INFO')
self._logger = utils.get_logger(self._log_dir,
__name__,
'info.log',
level=log_level)
self._writer = tf.summary.FileWriter(self._log_dir)
self._logger.info(kwargs)
# Data preparation
self._data = utils.load_dataset(
**self._data_kwargs) # return 3 DataLoaders and 1 scaler
for k, v in self._data.items():
if hasattr(v, 'shape'):
self._logger.info((k, v.shape))
# Build models.
scaler = self._data['scaler']
with tf.name_scope(
'Train'
): # reuse、variable_scope讲解：https://www.jianshu.com/p/ab0d38725f88
with tf.variable_scope(
'DCRNN', reuse=False): # reuse==False的含义: 该作用域下创建的变量不会重用
self._train_model = DCRNNModel(
is_training=True,
scaler=scaler,
batch_size=self._data_kwargs['batch_size'],
adj_mx=adj_mx,
**self._model_kwargs)
with tf.name_scope('Test'):
with tf.variable_scope('DCRNN', reuse=True): # 测试时创建的变量可以重用
self._test_model = DCRNNModel(
is_training=False,
scaler=scaler,
batch_size=self._data_kwargs['test_batch_size'],
adj_mx=adj_mx,
**self._model_kwargs)
# Learning rate.
self._lr = tf.get_variable('learning_rate',
shape=(),
initializer=tf.constant_initializer(0.01),
trainable=False)
self._new_lr = tf.placeholder(tf.float32,
shape=(),
name='new_learning_rate')
self._lr_update = tf.assign(self._lr, self._new_lr, name='lr_update')
# Configure optimizer
optimizer_name = self._train_kwargs.get('optimizer',
'adam').lower() # 默认是'adam'
epsilon = float(self._train_kwargs.get('epsilon', 1e-3))
optimizer = tf.train.AdamOptimizer(self._lr, epsilon=epsilon)
if optimizer_name == 'sgd':
optimizer = tf.train.GradientDescentOptimizer(self._lr, )
elif optimizer_name == 'amsgrad':
optimizer = AMSGrad(self._lr, epsilon=epsilon)
# Calculate loss
output_dim = self._model_kwargs.get(
'output_dim') # output_dim在配置文件里写的1，指只预测speed这一个特征
preds = self._train_model.outputs
labels = self._train_model.labels[..., :output_dim]
null_val = 0.
self._loss_fn = masked_mae_loss(scaler, null_val)
self._train_loss = self._loss_fn(preds=preds, labels=labels)
tvars = tf.trainable_variables()
grads = tf.gradients(self._train_loss, tvars)
max_grad_norm = kwargs['train'].get('max_grad_norm', 1.)
grads, _ = tf.clip_by_global_norm(
grads, max_grad_norm
) # 在一次迭代更新中，所有权重的梯度的平方和在一个设定范围以内，这个范围就是clip_gradient.
global_step = tf.train.get_or_create_global_step()
self._train_op = optimizer.apply_gradients(zip(grads, tvars),
global_step=global_step,
name='train_op')
max_to_keep = self._train_kwargs.get('max_to_keep', 100)
self._epoch = 0
self._saver = tf.train.Saver(
tf.global_variables(),
max_to_keep=max_to_keep) # Saver将保存最近的max_to_keep个模型
# Log model statistics.
total_trainable_parameter = utils.get_total_trainable_parameter_size()
self._logger.info('Total number of trainable parameters: {:d}'.format(
total_trainable_parameter))
for var in tf.global_variables():
self._logger.debug('{}, {}'.format(var.name, var.get_shape()))
def __init__(self, **kwargs):
self._kwargs = kwargs
self._data_kwargs = kwargs.get('data')
self._train_kwargs = kwargs.get('train')
self._test_kwargs = kwargs.get('test')
self._model_kwargs = kwargs.get('model')
self._alg_name = self._kwargs.get('alg')
# logging.
self._log_dir = self._get_log_dir(kwargs)
log_level = self._kwargs.get('log_level', 'INFO')
self._logger = utils.get_logger(self._log_dir,
__name__,
'info.log',
level=log_level)
self._writer = tf.summary.FileWriter(self._log_dir)
self._logger.info(kwargs)
# Data's args
self._day_size = self._data_kwargs.get('day_size')
# Model's Args
self._rnn_units = self._model_kwargs.get('rnn_units')
self._seq_len = self._model_kwargs.get('seq_len')
self._horizon = self._model_kwargs.get('horizon')
self._input_dim = self._model_kwargs.get('input_dim')
self._input_shape = (self._seq_len, self._input_dim)
self._output_dim = self._model_kwargs.get('output_dim')
self._nodes = self._model_kwargs.get('num_nodes')
self._n_rnn_layers = self._model_kwargs.get('n_rnn_layers')
# Train's args
self._drop_out = self._train_kwargs.get('dropout')
self._epochs = self._train_kwargs.get('epochs')
self._batch_size = self._data_kwargs.get('batch_size')
# Test's args
self._run_times = self._test_kwargs.get('run_times')
self._flow_selection = self._test_kwargs.get('flow_selection')
self._test_size = self._test_kwargs.get('test_size')
self._results_path = self._test_kwargs.get('results_path')
self._mon_ratio = self._kwargs.get('mon_ratio')
# Load data
self._data = utils.load_dataset_lstm(seq_len=self._seq_len,
horizon=self._horizon,
input_dim=self._input_dim,
mon_ratio=self._mon_ratio,
test_size=self._test_size,
**self._data_kwargs)
for k, v in self._data.items():
if hasattr(v, 'shape'):
self._logger.info((k, v.shape))
scaler = self._data['scaler']
# Model
with tf.name_scope('Train'):
with tf.variable_scope('LSTM', reuse=False):
self._train_model = EncoderDecoderLSTM(
is_training=True,
scaler=self._data['scaler'],
batch_size=self._batch_size,
**self._model_kwargs)
with tf.name_scope('Val'):
with tf.variable_scope('LSTM', reuse=True):
self._val_model = EncoderDecoderLSTM(
is_training=True,
scaler=self._data['scaler'],
batch_size=self._data_kwargs['val_batch_size'],
**self._model_kwargs)
with tf.name_scope('Eval'):
with tf.variable_scope('LSTM', reuse=True):
self._eval_model = EncoderDecoderLSTM(
is_training=True,
scaler=self._data['scaler'],
batch_size=self._data_kwargs['eval_batch_size'],
**self._model_kwargs)
with tf.name_scope('Test'):
with tf.variable_scope('LSTM', reuse=True):
self._test_model = EncoderDecoderLSTM(
is_training=True,
scaler=self._data['scaler'],
batch_size=self._data_kwargs['test_batch_size'],
**self._model_kwargs)
# Learning rate
self._lr = tf.get_variable('learning_rate',
shape=(),
initializer=tf.constant_initializer(0.01),
trainable=False)
self._new_lr = tf.placeholder(tf.float32,
shape=(),
name='new_learning_rate')
self._lr_update = tf.assign(self._lr, self._new_lr, name='lr_update')
# Configure optimizer
optimizer_name = self._train_kwargs.get('optimizer', 'adam').lower()
epsilon = float(self._train_kwargs.get('epsilon', 1e-3))
optimizer = tf.train.AdamOptimizer(
self._lr,
epsilon=epsilon,
)
if optimizer_name == 'sgd':
optimizer = tf.train.GradientDescentOptimizer(self._lr, )
elif optimizer_name == 'amsgrad':
optimizer = AMSGrad(self._lr, epsilon=epsilon)
# Calculate loss
output_dim = self._model_kwargs.get('output_dim')
preds = self._train_model.outputs
labels = self._train_model.labels[..., :output_dim]
null_val = 0.
self._loss_fn = masked_mse_loss(scaler, null_val)
# self._loss_fn = masked_mae_loss(scaler, null_val)
self._train_loss = self._loss_fn(preds=preds, labels=labels)
tvars = tf.trainable_variables()
grads = tf.gradients(self._train_loss, tvars)
max_grad_norm = kwargs['train'].get('max_grad_norm', 1.)
grads, _ = tf.clip_by_global_norm(grads, max_grad_norm)
global_step = tf.train.get_or_create_global_step()
self._train_op = optimizer.apply_gradients(zip(grads, tvars),
global_step=global_step,
name='train_op')
max_to_keep = self._train_kwargs.get('max_to_keep', 100)
self._epoch = 0
self._saver = tf.train.Saver(tf.global_variables(),
max_to_keep=max_to_keep)
# Log model statistics.
total_trainable_parameter = utils.get_total_trainable_parameter_size()
self._logger.info('Total number of trainable parameters: {:d}'.format(
total_trainable_parameter))
for var in tf.global_variables():
self._logger.debug('{}, {}'.format(var.name, var.get_shape()))