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two_dim_resnet.py
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from absl import logging
import tensorflow as tf # pylint: disable=g-explicit-tensorflow-version-import
from alphafold_casp13 import two_dim_convnet
def make_sep_res_layer(
input_node,
in_channels,
out_channels,
layer_name,
filter_size,
filter_size_2=None,
batch_norm=False,
is_training=True,
divide_channels_by=2,
atrou_rate=1,
channel_multiplier=0,
data_format='NHWC',
stddev=0.01,
dropout_keep_prob=1.0):
"""A separable resnet block."""
with tf.name_scope(layer_name):
input_times_almost_1 = input_node
h_conv = input_times_almost_1
if batch_norm:
h_conv = two_dim_convnet.batch_norm_layer(
h_conv, layer_name=layer_name, is_training=is_training,
data_format=data_format)
h_conv = tf.nn.elu(h_conv)
if filter_size_2 is None:
filter_size_2 = filter_size
# 1x1 with half size
h_conv = two_dim_convnet.make_conv_layer(
h_conv,
in_channels=in_channels,
out_channels=in_channels / divide_channels_by,
layer_name=layer_name + '_1x1h',
filter_size=1,
filter_size_2=1,
non_linearity=True,
batch_norm=batch_norm,
is_training=is_training,
data_format=data_format,
stddev=stddev)
# 3x3 with half size
if channel_multiplier == 0:
h_conv = two_dim_convnet.make_conv_layer(
h_conv,
in_channels=in_channels / divide_channels_by,
out_channels=in_channels / divide_channels_by,
layer_name=layer_name + '_%dx%dh' % (filter_size, filter_size_2),
filter_size=filter_size,
filter_size_2=filter_size_2,
non_linearity=True,
batch_norm=batch_norm,
is_training=is_training,
atrou_rate=atrou_rate,
data_format=data_format,
stddev=stddev)
else:
# We use separable convolution for 3x3
h_conv = two_dim_convnet.make_conv_sep2d_layer(
h_conv,
in_channels=in_channels / divide_channels_by,
channel_multiplier=channel_multiplier,
out_channels=in_channels / divide_channels_by,
layer_name=layer_name + '_sep%dx%dh' % (filter_size, filter_size_2),
filter_size=filter_size,
filter_size_2=filter_size_2,
batch_norm=batch_norm,
is_training=is_training,
atrou_rate=atrou_rate,
data_format=data_format,
stddev=stddev)
# 1x1 back to normal size without relu
h_conv = two_dim_convnet.make_conv_layer(
h_conv,
in_channels=in_channels / divide_channels_by,
out_channels=out_channels,
layer_name=layer_name + '_1x1',
filter_size=1,
filter_size_2=1,
non_linearity=False,
batch_norm=False,
is_training=is_training,
data_format=data_format,
stddev=stddev)
if dropout_keep_prob < 1.0:
logging.info('dropout keep prob %f', dropout_keep_prob)
h_conv = tf.nn.dropout(h_conv, keep_prob=dropout_keep_prob)
return h_conv + input_times_almost_1
def make_two_dim_resnet(
input_node,
num_residues=50,
num_features=40,
num_predictions=1,
num_channels=32,
num_layers=2,
filter_size=3,
filter_size_2=None,
final_non_linearity=False,
name_prefix='',
fancy=True,
batch_norm=False,
is_training=False,
atrou_rates=None,
channel_multiplier=0,
divide_channels_by=2,
resize_features_with_1x1=False,
data_format='NHWC',
stddev=0.01,
dropout_keep_prob=1.0):
"""Two dim resnet towers."""
del num_residues # Unused.
if atrou_rates is None:
atrou_rates = [1]
if not fancy:
raise ValueError('non fancy deprecated')
logging.info('atrou rates %s', atrou_rates)
logging.info('name prefix %s', name_prefix)
x_image = input_node
previous_layer = x_image
non_linearity = True
for i_layer in range(num_layers):
in_channels = num_channels
out_channels = num_channels
curr_atrou_rate = atrou_rates[i_layer % len(atrou_rates)]
if i_layer == 0:
in_channels = num_features
if i_layer == num_layers - 1:
out_channels = num_predictions
non_linearity = final_non_linearity
if i_layer == 0 or i_layer == num_layers - 1:
layer_name = name_prefix + 'conv%d' % (i_layer + 1)
initial_filter_size = filter_size
if resize_features_with_1x1:
initial_filter_size = 1
previous_layer = two_dim_convnet.make_conv_layer(
input_node=previous_layer,
in_channels=in_channels,
out_channels=out_channels,
layer_name=layer_name,
filter_size=initial_filter_size,
filter_size_2=filter_size_2,
non_linearity=non_linearity,
atrou_rate=curr_atrou_rate,
data_format=data_format,
stddev=stddev)
else:
layer_name = name_prefix + 'res%d' % (i_layer + 1)
previous_layer = make_sep_res_layer(
input_node=previous_layer,
in_channels=in_channels,
out_channels=out_channels,
layer_name=layer_name,
filter_size=filter_size,
filter_size_2=filter_size_2,
batch_norm=batch_norm,
is_training=is_training,
atrou_rate=curr_atrou_rate,
channel_multiplier=channel_multiplier,
divide_channels_by=divide_channels_by,
data_format=data_format,
stddev=stddev,
dropout_keep_prob=dropout_keep_prob)
y = previous_layer
return y