Freeze sublayers in tensorflow 2 - tensorflow

I have a model which is composed of custom layers. Each custom layer contains many tf.keras.layers. The problem is that if I want to freeze those layers after defining my model, the loop:
for i, layer in enumerate(model.layers):
print(i, layer.name)
only prints the "outer" custom layers and not those who exist inside. Is there any way to access the inner layers so I can freeze them?
an example of a custom layer from the official tf docs:
class MLPBlock(layers.Layer):
def __init__(self):
super(MLPBlock, self).__init__()
self.linear_1 = Linear(32)
self.linear_2 = Linear(32)
self.linear_3 = Linear(1)
def call(self, inputs):
x = self.linear_1(inputs)
x = tf.nn.relu(x)
x = self.linear_2(x)
x = tf.nn.relu(x)
return self.linear_3(x)

You can use keras callbacks. If you want to freeze your first layer after some certain amount of epochs, add this callback
class FreezeCallback(tf.keras.callbacks.Callback):
def __init__(self, n_epochs=10):
super().__init__()
self.n_epochs = n_epochs
def on_epoch_end(self, epoch, logs=None):
if epoch == self.n_epochs:
l = self.model.get_layer('first')
l.trainable = False

What you are doing in your update function is to replace the first Dense() layer with another Dense() layer, this time setting trainable = false.
While this works, I would update the 'update' function as following:
def updt(self):
self.dense1.trainable = False

Ok i came up with a solution.
An "update" function must be implemented inside the custom layer, which updates the inner layers so that they become non trainable.
Here is a sample code:
import tensorflow as tf
import numpy as np
layers = tf.keras.layers
seq_model = tf.keras.models.Sequential
class MDBlock(layers.Layer):
def __init__(self):
super(MDBlock, self).__init__()
self.dense1 = layers.Dense(784, name="first")
self.dense2 = layers.Dense(32, name="second")
self.dense3 = layers.Dense(32, name="third")
self.dense4 = layers.Dense(1, activation='sigmoid', name="outp")
def call(self, inputs):
x = self.dense1(inputs)
x = tf.nn.relu(x)
x = self.dense2(x)
x = tf.nn.relu(x)
x = self.dense3(x)
x = tf.nn.relu(x)
x = self.dense4(x)
return x
def updt(self):
self.dense1.trainable = False
def __str__(self):
return "\nd1:{0}\nd2:{1}\nd3:{2}\nd4:{3}".format(self.dense1.trainable, self.dense2.trainable,
self.dense3.trainable, self.dense4.trainable)
# define layer block
layer = MDBlock()
model = seq_model()
model.add(layers.Input(shape=(784,)))
model.add(layer)
# Use updt function to make layers non-trainable
for i, layer in enumerate(model.layers):
layer.updt()
model.compile(optimizer='rmsprop',
loss='binary_crossentropy',
metrics=['accuracy'])
# Generate dummy data
data = np.random.random((1000, 784))
labels = np.random.randint(2, size=(1000, 1))
# Train the model, iterating on the data in batches of 32 samples
model.fit(data, labels, epochs=10, batch_size=32)
# print block's layers state
for i, layer in enumerate(model.layers):
print(i, layer)

Related

How to write a custom call function for a Tensorflow LSTM class?

I have defined a custom LSTM Layer as follows:
class LSTMModel(tf.keras.Model):
def __init__(self, CNN_model, num_classes):
super().__init__()
self.cnn_model = CNN_model
self.lstm = tf.keras.layers.LSTM(units=64, return_state=True, dropout=0.3)
self.dense = tf.keras.layers.Dense(num_classes, activation="softmax")
def call(self, input):
pass
However, I am unclear what needs too occur in the call function here. I also wrote a generic CNN class like below:
class generic_vns_function(tf.keras.Model):
# Where would we use layer_units here?
def __init__(self, input_shape, layers, layer_units):
super().__init__()
self.convolutions = []
# Dynamically create Convolutional layers and MaxPools
for layer in range(len(layers)):
self.convolutions.append(tf.keras.layers.Conv2D(layer, 3, padding="same",
input_shape=input_shape, activation="relu"))
# Add MaxPooling layer
self.convolutions.append(tf.keras.layers.MaxPooling2D((2,2)))
# Flatten
self.flatten = tf.keras.layers.Flatten()
# Dense layer
self.dense1 = tf.keras.layers.Dense(1024, activation="relu")
def call(self, input):
x = input
for layer in self.convolutions:
x = layer(x)
x = self.flatten(x)
x = self.dense1(x)
return x
but here the required structure makes a lot more sense to me. I am just initializing all of the layers. What do I need to do to initialize my LSTM layers?
You could write it like this:
import tensorflow as tf
from tensorflow.keras.layers import Dense
from tensorflow.keras.layers import LSTM
from tensorflow.keras import Model
class LSTMModel(Model):
def __init__(self, num_classes, num_units=64, drop_prob=0.3):
super().__init__()
self.num_classes = num_classes
self.num_units = num_units
self.drop_prob = drop_prob
self.lstm = LSTM(
units=self.num_units,
return_state=True,
dropout=self.drop_prob)
self.dense = Dense(
num_classes,
activation="softmax")
def call(self, x, training=True):
x, *state = self.lstm(x, training=training)
x = self.dense(x)
return x
And then you would use it like:
model = LSTMModel(num_classes=2)
time_series = tf.random.normal((32, 64, 128))
x_pred = model(time_series)
# loss and gradients calculations ...
It is a common tensorflow idom to instantiate layers when initializing a custom layer/model, and then execute their call() methods by passing data through them in your custom call implementation.

How to connect a single neuron in one layer with the single neuron in another layer

I am new to Tensorflow. I want to connect a layer with another layer in which only the corresponding neurons are connected with weights to each other as shown below. This means all the neurons in the previous layer are not connected to a neuron in the next layer.
Now I get 4 neurons with wixi. Further, I need to add all these outputs to get a single value. Now I want to pass this single value to a dense layer of size 4 for the autoencoder operation to complete.
I have created my custom layer for the wixi operation and I am correctly getting it but when I apply normal dense layer after addition I get the following error:
'''
ValueError: Input 0 of layer dense_15 is incompatible with the layer: : expected min_ndim=2, found ndim=1. Full shape received: [100]
'''
Following is my code for custom layer and model-
class Layer_w_x(tf.keras.layers.Layer):
def __init__(self):
super(Layer_w_x, self).__init__()
def build(self, input_shape):
self.w = self.add_weight(shape=(input_shape[-1],),
initializer="random_normal", trainable=True)
def call(self, inputs):
return tf.multiply(inputs, self.w)
class MyModel(Model):
def __init__(self, **kwargs):
super(MyModel, self).__init__(**kwargs)
self.layer_1 = Layer_w_x()
self.dense = Dense(4,activation = 'sigmoid')
def call(self, inputs):
# CALCULATION FOR FIRST NEURON
h1 = self.layer_1(inputs)
h4 = tf.reduce_sum(h1,1)
encoded = self.dense(h4)
return encoded
model = MyModel()
output =model(my_train_data1)
my_train_data1 has size (100,4)
You can make your own layer by subclassing from tf.keras.layers.Layer.
Creating custom layers is described in https://www.tensorflow.org/guide/keras/custom_layers_and_models
and https://www.tensorflow.org/tutorials/customization/custom_layers.
I created the layer for you.
import tensorflow as tf
class DirectLayer(tf.keras.layers.Layer):
def __init__(self):
super(DirectLayer, self).__init__()
def build(self, input_shape):
self.w = self.add_weight(
shape=input_shape,
initializer="random_normal",
trainable=True,
)
self.b = self.add_weight(
shape=(input_shape[-1],), initializer="random_normal", trainable=True
)
def call(self, inputs):
# outputs shape
return tf.multiply(inputs, self.w) + self.b
layer1 = DirectLayer()
layer2 = DirectLayer()
x = tf.ones([16,2])
y = layer1(x)
y = layer2(y)
tf.print(y.shape)
It outputs TensorShape([16, 2]), which means that it maintains the input's dimensions, which, I believe, is what you want. Notice I used tf.multiply (multiply elementwise) as opposed to what the Dense layer does—tf.matmul (matrix multiplication).

How to apply Monte Carlo Dropout, in tensorflow, for an LSTM if batch normalization is part of the model?

I have a model composed of 3 LSTM layers followed by a batch norm layer and finally dense layer. Here is the code:
def build_uncomplied_model(hparams):
inputs = tf.keras.Input(shape=(None, hparams["n_features"]))
x = return_RNN(hparams["rnn_type"])(hparams["cell_size_1"], return_sequences=True, recurrent_dropout=hparams['dropout'])(inputs)
x = return_RNN(hparams["rnn_type"])(hparams["cell_size_2"], return_sequences=True)(x)
x = return_RNN(hparams["rnn_type"])(hparams["cell_size_3"], return_sequences=True)(x)
x = layers.BatchNormalization()(x)
outputs = layers.TimeDistributed(layers.Dense(hparams["n_features"]))(x)
model = tf.keras.Model(inputs, outputs, name=RNN_type + "_model")
return model
Now I am aware that to apply MCDropout, we can apply the following code:
y_predict = np.stack([my_model(X_test, training=True) for x in range(100)])
y_proba = y_predict.mean(axis=0)
However, setting training = True will force the batch norm layer to overfit the testing dataset.
Additionally, building a custom Dropout layer while setting training to True isn't a solution in my case because I am using LSTM.
class MCDropout(tf.keras.layers.Dropout):
def call(self, inputs):
return super().call(inputs, training=True)
Any help is much appreciated!!
A possible solution could be to create a custom LSTM layer. You should override the call method to force the training flag to be True
class MCLSTM(keras.layers.LSTM):
def __init__(self, units, **kwargs):
super(MCLSTM, self).__init__(units, **kwargs)
def call(self, inputs, mask=None, training=None, initial_state=None):
return super(MCLSTM, self).call(
inputs,
mask=mask,
training=True,
initial_state=initial_state,
)
Then you can use it in your code
def build_uncomplied_model(hparams):
inputs = tf.keras.Input(shape=(None, hparams["n_features"]))
x = MCLSTM(hparams["cell_size_1"], return_sequences=True, recurrent_dropout=hparams['dropout'])(inputs)
x = return_RNN(hparams["rnn_type"])(hparams["cell_size_2"], return_sequences=True)(x)
x = return_RNN(hparams["rnn_type"])(hparams["cell_size_3"], return_sequences=True)(x)
x = layers.BatchNormalization()(x)
outputs = layers.TimeDistributed(layers.Dense(hparams["n_features"]))(x)
model = tf.keras.Model(inputs, outputs, name=RNN_type + "_model")
return model
or add it to your return_RNN factory (a more elegant way)
===== EDIT =====
Another solution could be to add the training flag when creating the model. Something like this:
def build_uncomplied_model(hparams):
inputs = tf.keras.Input(shape=(None, hparams["n_features"]))
# This the Monte Carlo LSTM
x = LSTM(hparams["cell_size_1"], return_sequences=True, recurrent_dropout=hparams['dropout'])(inputs, training=True)
x = return_RNN(hparams["rnn_type"])(hparams["cell_size_2"], return_sequences=True)(x)
x = return_RNN(hparams["rnn_type"])(hparams["cell_size_3"], return_sequences=True)(x)
x = layers.BatchNormalization()(x)
outputs = layers.TimeDistributed(layers.Dense(hparams["n_features"]))(x)
model = tf.keras.Model(inputs, outputs, name=RNN_type + "_model")
return model

Tensorflow 2.0 Keras Model subclassing

I'm trying to implement a simple UNet-like model using the model subclassing method. Here's my code:
import tensorflow as tf
from tensorflow import keras as K
class Enc_block(K.layers.Layer):
def __init__(self, in_dim):
super(Enc_block, self).__init__()
self.conv_layer = K.layers.SeparableConv2D(in_dim,3, padding='same', activation='relu')
self.batchnorm_layer = K.layers.BatchNormalization()
self.pool_layer = K.layers.SeparableConv2D(in_dim,3, padding='same',strides=2, activation='relu')
def call(self, x):
x = self.conv_layer(x)
x = self.batchnorm_layer(x)
x = self.conv_layer(x)
x = self.batchnorm_layer(x)
return self.pool_layer(x), x
class Dec_block(K.layers.Layer):
def __init__(self, in_dim):
super(Dec_block, self).__init__()
self.conv_layer = K.layers.SeparableConv2D(in_dim,3, padding='same', activation='relu')
self.batchnorm_layer = K.layers.BatchNormalization()
def call(self, x):
x = self.conv_layer(x)
x = self.batchnorm_layer(x)
x = self.conv_layer(x)
x = self.batchnorm_layer(x)
return x
class Bottleneck(K.layers.Layer):
def __init__(self, in_dim):
super(Bottleneck, self).__init__()
self.conv_1layer = K.layers.SeparableConv2D(in_dim,1, padding='same', activation='relu')
self.conv_3layer = K.layers.SeparableConv2D(in_dim,3, padding='same', activation='relu')
self.batchnorm_layer = K.layers.BatchNormalization()
def call(self, x):
x = self.conv_1layer(x)
x = self.batchnorm_layer(x)
x = self.conv_3layer(x)
x = self.batchnorm_layer(x)
return x
class Output_block(K.layers.Layer):
def __init__(self, in_dim):
super(Output_block, self).__init__()
self.logits = K.layers.SeparableConv2D(in_dim,3, padding='same', activation=None)
self.out = K.layers.Softmax()
def call(self, x):
x_logits = self.logits(x)
x = self.out(x_logits)
return x_logits, x
class UNetModel(K.Model):
def __init__(self,in_dim):
super(UNetModel, self).__init__()
self.encoder_block = Enc_block(in_dim)
self.bottleneck = Bottleneck(in_dim)
self.decoder_block = Dec_block(in_dim)
self.output_block = Output_block(in_dim)
def call(self, inputs, training=None):
x, x_skip1 = self.encoder_block(32)(inputs)
x, x_skip2 = self.encoder_block(64)(x)
x, x_skip3 = self.encoder_block(128)(x)
x, x_skip4 = self.encoder_block(256)(x)
x = self.bottleneck(x)
x = K.layers.UpSampling2D(size=(2,2))(x)
x = K.layers.concatenate([x,x_skip4],axis=-1)
x = self.decoder_block(256)(x)
x = K.layers.UpSampling2D(size=(2,2))(x) #56x56
x = K.layers.concatenate([x,x_skip3],axis=-1)
x = self.decoder_block(128)(x)
x = K.layers.UpSampling2D(size=(2,2))(x) #112x112
x = K.layers.concatenate([x,x_skip2],axis=-1)
x = self.decoder_block(64)(x)
x = K.layers.UpSampling2D(size=(2,2))(x) #224x224
x = K.layers.concatenate([x,x_skip1],axis=-1)
x = self.decoder_block(32)(x)
x_logits, x = self.output_block(2)(x)
return x_logits, x
I am getting the following error:
ValueError: Input 0 of layer separable_conv2d is incompatible with the layer: expected ndim=4, found ndim=0. Full shape received: []
I'm not sure if this is the correct way to implement a network in tf.keras
The idea was to implement encoder and decoder blocks by subclassing keras layers and subclassing the Model later.
Take a look at this line from UNetModel class:
x, x_skip1 = self.encoder_block(32)(inputs)
where self.encoder_block() is defined by
self.encoder_block = Enc_block(in_dim)
encoder_block is an instance of class. By doing self.encoder_block(32) you are invoking a __call__() method of the End_block class which expect to receive an iterable of image inputs of rank=4. Instead you're passing an integer number 32 of rank=0 and you get ValueError which says exactly what I've just explained: expected ndim=4, found ndim=0. What probably you intended to do is:
x, x_skip1 = self.encoder_block(inputs)
You repeat the same mistake in the subsequent lines as well. There are additional errors where you define the same in_dim for every custom layer:
self.encoder_block = Enc_block(in_dim)
self.bottleneck = Bottleneck(in_dim)
self.decoder_block = Dec_block(in_dim)
self.output_block = Output_block(in_dim)
The input shape for Bottleneck layer should be the same shape as output of the Enc_Block layer and so one. I suggest you first to understand simple example before you're trying to implement more complicated ones. Take a look at this example. It has two custom layers:
import tensorflow as tf
import numpy as np
from tensorflow.keras import layers
class CustomLayer1(layers.Layer):
def __init__(self, outshape=4):
super(CustomLayer1, self).__init__()
self.outshape = outshape
def build(self, input_shape):
self.kernel = self.add_weight(name='kernel',
shape=(int(input_shape[1]), self.outshape),
trainable=True)
super(CustomLayer1, self).build(input_shape)
def call(self, inputs):
return tf.matmul(inputs, self.kernel)
class CustomLayer2(layers.Layer):
def __init__(self):
super(CustomLayer2, self).__init__()
def call(self, inputs):
return inputs / tf.reshape(tf.reduce_sum(inputs, 1), (-1, 1))
Now I will use both of these layers in the new CombinedLayers class:
class CombinedLayers(layers.Layer):
def __init__(self, units=3):
super(CombinedLayers, self).__init__()
# `units` defines a number of units in the layer. It is the
# output shape of the `CustomLayer`
self.layer1 = CustomLayer1(units)
# The input shape is inferred dynamically in the `build()`
# method of the `CustomLayer1` class
self.layer2 = CustomLayer1(units)
# Some layers such as this one do not need to know the shape
self.layer3 = CustomLayer2()
def call(self, inputs):
x = self.layer1(inputs)
x = self.layer2(x)
x = self.layer3(x)
return x
Note that the input shape of CustomLayer1 is inferred dynamically in the build() method. Now let's test it with some input:
x_train = [np.random.normal(size=(3, )) for _ in range(5)]
x_train_tensor = tf.convert_to_tensor(x_train)
combined = CombinedLayers(3)
result = combined(x_train_tensor)
result.numpy()
# array([[ 0.50822063, -0.0800476 , 0.57182697],
# [ -0.76052217, 0.50127872, 1.25924345],
# [-19.5887986 , 9.23529798, 11.35350062],
# [ -0.33696137, 0.22741248, 1.10954888],
# [ 0.53079047, -0.08941536, 0.55862488]])
This is how you should approach it. Create layers one by one. Each time you add a new layer test everything with some input to verify that you are doing things correctly.

How do I load a checkpoint using tensorflow in eager execution mode?

I am using tensorflow 1.7.0 in eager execution mode. I have the model working, but none of the examples that I have found for saving the model work.
This is the code that I am using:
checkpoint_directory ='./JokeWords/'
checkpoint_prefix = os.path.join(checkpoint_directory, "ckpt")
checkpoint = tfe.Checkpoint(model=model,optimizer=optimizer) # save as "x"
checkpoint.restore(tf.train.latest_checkpoint(checkpoint_directory))
evaluate(model,jokes,2,32)
....
checkpoint.save(file_prefix=checkpoint_prefix)
I have trained the model and use evaluate to check the results when loading from a restart. Each time I get a random result from evaluate, meaning that the model is not loading from the data, but instead only having random weights.
How do I save the model? It can take days to train one of these.
Edit. Here is the model:
class EagerRNN(tfe.Network):
def __init__(self,embedding, hidden_dim, num_layers, keep_ratio):
super(EagerRNN, self).__init__()
self.keep_ratio = keep_ratio
self.cells = self._add_cells([
tf.nn.rnn_cell.BasicLSTMCell(num_units=hidden_dim)
for _ in range(num_layers)
])
self.backcells = self._add_cells([
tf.nn.rnn_cell.BasicLSTMCell(num_units=hidden_dim)
for _ in range(num_layers)
])
self.linear = layers.Dense(embedding. vocab_size, kernel_initializer=tf.random_uniform_initializer(-0.1, 0.1))
self.backlinear = layers.Dense(embedding. vocab_size, kernel_initializer=tf.random_uniform_initializer(-0.1, 0.1))
self.attension = layers.Dense(hidden_dim, kernel_initializer=tf.random_uniform_initializer(-0.1, 0.1))
def call(self, input_seq,seq_lengths, training):
lengths=[i[0] for i in seq_lengths]
nRotations=max(lengths)
batchSize=input_seq.shape[0]
input_seq2 = tf.unstack(input_seq, num=int(input_seq.shape[1]), axis=1)
atten = None
state = self.cells[0].zero_state(batchSize, tf.float32)
for i in range(0,nRotations):
for j in range(0,len(self.cells)):
c=self.cells[j]
inp=input_seq2[i]
output, state = c(inp, state)
#input_seq2[i]=(output)
if atten==None:
atten =self.linear(output)
else:
atten=atten+self.linear(output)
for i in range(nRotations-1,-1,-1):
for j in range(0,len(self.backcells)):
c=self.backcells[j]
inp=input_seq2[i]
output, state = c(inp, state)
#input_seq2[i]=(output)
atten=atten+self.backlinear(output)
#input_seq = tf.stack(input_seq2[0:nRotations], axis=1)
atten=self.attension(atten)
if training:
input_seq = tf.nn.dropout(input_seq, self.keep_ratio)
# Returning a list instead of a single tensor so that the line:
# y = self.rnn(y, ...)[0]
# in PTBModel.call works for both this RNN and CudnnLSTM (which returns a
# tuple (output, output_states).
return input_seq,state,atten
def _add_cells(self, cells):
# "Magic" required for keras.Model classes to track all the variables in
# a list of Layer objects.
# TODO(ashankar): Figure out API so user code doesn't have to do this.
for i, c in enumerate(cells):
setattr(self, "cell-%d" % i, c)
return cells
class EagerLSTM_Model(tfe.Network):
"""LSTM for word language modeling.
Model described in:
(Zaremba, et. al.) Recurrent Neural Network Regularization
http://arxiv.org/abs/1409.2329
See also:
https://github.com/tensorflow/models/tree/master/tutorials/rnn/ptb
"""
def __init__(self,
embedding,
hidden_dim,
num_layers,
dropout_ratio,
use_cudnn_rnn=True):
super(EagerLSTM_Model, self).__init__()
self.keep_ratio = 1 - dropout_ratio
self.use_cudnn_rnn = use_cudnn_rnn
self.embedding = embedding
if self.use_cudnn_rnn:
self.rnn = cudnn_rnn.CudnnLSTM(
num_layers, hidden_dim, dropout=dropout_ratio)
else:
self.rnn = EagerRNN(embedding,hidden_dim, num_layers, self.keep_ratio)
self.unrnn = EagerUnRNN(embedding,hidden_dim, num_layers, self.keep_ratio)
def callRNN(self, input_seq,seq_lengths, training):
y = self.embedding.callbatchword(input_seq)
if training:
y = tf.nn.dropout(y, self.keep_ratio)
y,state,atten = self.rnn.call(y,seq_lengths, training=training)
return state,atten
def callUnRNN (self,state,atten,seq_lengths, training ):
x,state = self.unrnn(state,atten,seq_lengths,training=training)
#b=tf.reshape(y, self._output_shape)
#c=self.linear(b)
return x
tfe.Network is not (easily) Checkpointable and it will soon be deprecated. Prefer to subclass tf.Keras.Model instead. So if you change class EagerRNN(tfe.Network) to class EagerRNN(tf.keras.Model) and class EagerLSTM_Model(tfe.Network) to class EagerLSTM_Model(tf.keras.Model), checkpoint.save(file_prefix=checkpoint_prefix) should actually save all your variables and checkpoint.restore(tf.train.latest_checkpoint(checkpoint_directory)) should restore them.