I'm trying to work with RNN using Tensorflow. I use the following function from this repos:
def RNN(x, weights, biases):
# Prepare data shape to match `rnn` function requirements
# Current data input shape: (batch_size, timesteps, n_input)
# Required shape: 'timesteps' tensors list of shape (batch_size, n_input)
# Unstack to get a list of 'timesteps' tensors of shape (batch_size, n_input)
x = tf.unstack(x, timesteps, 1)
# Define a lstm cell with tensorflow
lstm_cell = rnn.BasicLSTMCell(num_hidden, forget_bias=1.0)
# Get lstm cell output
outputs, states = rnn.static_rnn(lstm_cell, x, dtype=tf.float32)
# Linear activation, using rnn inner loop last output
return tf.matmul(outputs[-1], weights['out']) + biases['out']
I understand that outputs is a list containing intermediate outputs in the unrolled neural network. I can verify that len(outputs) equals timesteps. However, I wonder why len(states) equals 2. I think I should contain only the final state of the network.
Could you please help explain?
Thanks.
To confirm the discussion in the comments: when constructing a static RNN using BasicLSTMCell, state is a two-tuple of (c, h), where c is the final cell state and h is the final hidden state. The final cell hidden state is in fact equal to the final output in outputs. You can corroborate this by reading the source code (see BasicLSTMCell's call method).
Related
I have been going through the implementation of neural network in openAI code for any Vanilla Policy Gradient (As a matter of fact, this part is used nearly everywhere). The code looks something like this :
def mlp_categorical_policy(x, a, hidden_sizes, activation, output_activation, action_space):
act_dim = action_space.n
logits = mlp(x, list(hidden_sizes) + [act_dim], activation, None)
logp_all = tf.nn.log_softmax(logits)
pi = tf.squeeze(tf.random.categorical(logits, 1), axis=1)
logp = tf.reduce_sum(tf.one_hot(a, depth=act_dim) * logp_all, axis=1)
logp_pi = tf.reduce_sum(tf.one_hot(pi, depth=act_dim) * logp_all, axis=1)
return pi, logp, logp_pi
and this multi-layered perceptron network is defined as follows :
def mlp(x, hidden_sizes=(32,), activation=tf.tanh, output_activation=None):
for h in hidden_sizes[:-1]:
x = tf.layers.dense(inputs=x, units=h, activation=activation)
return tf.layers.dense(inputs=x, units=hidden_sizes[-1], activation=output_activation)
My question is what is the return from this mlp function? I mean the structure or shape. Is it an N-dimentional tensor? If so, how is it given as an input to tf.random_categorical? If not, and its just has the shape [hidden_layer2, output], then what happened to the other layers? As per their website description about random_categorical it only takes a 2-D input. The complete code of openAI's VPG algorithm can be found here. The mlp is implemented here. I would be highly grateful if someone would just tell me what this mlp_categorical_policy() is doing?
Note: The hidden size is [64, 64], the action dimension is 3
Thanks and cheers
Note that this is a discrete action space - there are action_space.n different possible actions at every step, and the agent chooses one.
To do this the MLP is returning the logits (which are a function of the probabilities) of the different actions. This is specified in the code by + [act_dim] which is appending count of the action_space as the final MLP layer. Note that the last layer of an MLP is the output layer. The input layer is not specified in tensorflow, it is inferred from the inputs.
tf.random.categorical takes the logits and samples a policy action pi from them, which is returned as a number.
mlp_categorical_policy also returns logp, the log probability of the action a (used to assign credit), and logp_pi, the log probability of the policy action pi.
It seems your question is more about the return from the mlp.
The mlp creates a series of fully connected layers in a loop. In each iteration of the loop, the mlp is creating a new layer using the previous layer x as an input and assigning it's output to overwrite x, with this line x = tf.layers.dense(inputs=x, units=h, activation=activation).
So the output is not the same as the input, on each iteration x is overwritten with the value of the new layer. This is the same kind of coding trick as x = x + 1, which increments x by 1. This effectively chains the layers together.
The output of tf.layers.dense is a tensor of size [:,h] where : is the batch dimension (and can usually be ignored). The creation of the last layer happens outisde the loop, it can be seen that the number of nodes in this layer is act_dim (so shape is [:,3]). You can check the shape by doing this:
import tensorflow.compat.v1 as tf
import numpy as np
def mlp(x, hidden_sizes=(32,), activation=tf.tanh, output_activation=None):
for h in hidden_sizes[:-1]:
x = tf.layers.dense(x, units=h, activation=activation)
return tf.layers.dense(x, units=hidden_sizes[-1], activation=output_activation)
obs = np.array([[1.0,2.0]])
logits = mlp(obs, [64, 64, 3], tf.nn.relu, None)
print(logits.shape)
result: TensorShape([1, 3])
Note that the observation in this case is [1.,2.], it is nested inside a batch of size 1.
I'm studying LSTM with CNN in tensorflow.
I want to put some scalar label into LSTM network as a condition.
Does anybody know which LSTM is what I meant?
If available, please let me know the usage of that
Thank you.
This thread might interest you: Adding Features To Time Series Model LSTM.
You have basically 3 possible ways:
Let's take an example with weather data from two different cities: Paris and San Francisco. You want to predict the next temperature based on historical data. But at the same time, you expect the weather to change based on the city. You can either:
Combine the auxiliary features with the time series data, at the beginning or at the end (ugly!).
Concatenate the auxiliary features with the output of the RNN layer. It's some kind of post-RNN adjustment since the RNN layer won't see this auxiliary info.
Or just initialize the RNN states with a learned representation of the condition (e.g. Paris or San Francisco).
I wrote a library to condition on auxiliary inputs. It abstracts all the complexity and has been designed to be as user-friendly as possible:
https://github.com/philipperemy/cond_rnn/
The implementation is in tensorflow (>=1.13.1) and Keras.
Hope it helps!
Heres an example of applying CNN and LSTM over the output probabilities of a sequence, like you asked:
def build_model(inputs):
BATCH_SIZE = 4
NUM_CLASSES = 2
NUM_UNITS = 128
H = 224
W = 224
C = 3
TIME_STEPS = 4
# inputs is assumed to be of shape (BATCH_SIZE, TIME_STEPS, H, W, C)
# reshape your input such that you can apply the CNN for all images
input_cnn_reshaped = tf.reshape(inputs, (-1, H, W, C))
# define CNN, for instance vgg 16
cnn_logits_output, _ = vgg_16(input_cnn_reshaped, num_classes=NUM_CLASSES)
cnn_probabilities_output = tf.nn.softmax(cnn_logits_output)
# reshape back to time series convention
cnn_probabilities_output = tf.reshape(cnn_probabilities_output, (BATCH_SIZE, TIME_STEPS, NUM_CLASSES))
# perform LSTM over the probabilities per image
cell = tf.contrib.rnn.LSTMCell(NUM_UNITS)
_, state = tf.nn.dynamic_rnn(cell, cnn_probabilities_output)
# employ FC layer over the last state
logits = tf.layers.dense(state, NUM_UNITS)
# logits is of shape (BATCH_SIZE, NUM_CLASSES)
return logits
By the way, a better approach would be to employ the LSTM over the last hidden layer, i.e to use the CNN as feature extractor and make the prediction over sequences of features.
I have been trying to learn how to code up an RNN and LSTM in tensorflow. I found an example online on this blog post
http://r2rt.com/recurrent-neural-networks-in-tensorflow-ii.html
Below are the snippets which I am having trouble understanding for an LSTM network to be used eventually for char-rnn generation
x = tf.placeholder(tf.int32, [batch_size, num_steps], name='input_placeholder')
y = tf.placeholder(tf.int32, [batch_size, num_steps], name='labels_placeholder')
embeddings = tf.get_variable('embedding_matrix', [num_classes, state_size])
rnn_inputs = [tf.squeeze(i) for i in tf.split(1,
num_steps, tf.nn.embedding_lookup(embeddings, x))]
Different Section of the Code Now where the weights are defined
with tf.variable_scope('softmax'):
W = tf.get_variable('W', [state_size, num_classes])
b = tf.get_variable('b', [num_classes], initializer=tf.constant_initializer(0.0))
logits = [tf.matmul(rnn_output, W) + b for rnn_output in rnn_outputs]
y_as_list = [tf.squeeze(i, squeeze_dims=[1]) for i in tf.split(1, num_steps, y)]
x is the data to be fed, and y is the set of labels. In the lstm equations we have a series of gates, x(t) gets multiplied by a series and prev_hidden_state gets multiplied by some set of weights, biases are added and non-liniearities are applied.
Here are the doubts I have
In this case only one weight matrix is defined does that mean that
works for both x(t) and prev_hidden_state as well.
For the embeddings matrix I know it has to be multiplied by the
weight matrix but why is the first dimension num_classes
For the rnn_inputs we are using squeeze which removes dimensions of 1
but why would I want to do that in a one-hot-encoding.
Also from the splits I understand that we are unrolling the x of
dimension (batch_size X num_steps) into discrete (batch_size X 1)
vectors and then passing these values through the network is this
right
May I help you.
In this case only one weight matrix is defined does that mean that works for both x(t) and prev_hidden_state as well.
There are more weights as you call tf.nn.rnn_cell.LSTMCell. They are the internal weights of the RNN cell, which tensorflow created it implicitly when you call the cell.
The weight matrix you explicitly defined is the transform from the hidden state to the vocabulary space.
You can view the implicit weights accounting for the recurrent parts, taking the previous hidden state and current input and output the new hidden state. And the weight matrix you defined transform the hidden states(i.e. state_size = 200) to the higher vocabulary space.(i.e. vocab_size = 2000)
For further information, maybe you can view this tutorial : http://colah.github.io/posts/2015-08-Understanding-LSTMs/
For the embeddings matrix I know it has to be multiplied by the weight matrix but why is the first dimension num_classes
The num_classes accounts for the vocab_size, the embedding matrix is transforming the vocabulary to the required embedding size(in this example is equal to the state_size).
For the rnn_inputs we are using squeeze which removes dimensions of 1 but why would I want to do that in a one-hot-encoding.
You need to get rid of the extra dimension because tf.nn.rnn takes inputs as (batch_size, input_size) instead of (batch_size, 1, input_size).
Also from the splits I understand that we are unrolling the x of dimension (batch_size X num_steps) into discrete (batch_size X 1) vectors and then passing these values through the network is this right?
Being more precise, after embedding. (batch_size, num_steps, state_size) turns into a list of num_step elements, each of size (batch_size, 1, state_size).
The flow goes like this :
The embedding matrix embed each word as a state_size dimension vector(a row of the matrix), making the size (vocab_size, state_size).
Retrieve the the indices specified by the x placeholder and get the rnn input, which is size (batch_size, num_steps, state_size).
tf.split split the inputs to (batch_size, 1, state_size)
tf.squeeze sqeeze them to (batch_size, state_size), forming the desired input format for tf.nn.rnn.
If there's any problem with the tensorflow methods, maybe you can search them in the tensorflow API for more detailed introduction.
I'm trying to use the Tensorflow's CTC implementation under contrib package (tf.contrib.ctc.ctc_loss) without success.
First of all, anyone know where can I read a good step-by-step tutorial? Tensorflow's documentation is very poor on this topic.
Do I have to provide to ctc_loss the labels with the blank label interleaved or not?
I could not be able to overfit my network even using a train dataset of length 1 over 200 epochs. :(
How can I calculate the label error rate using tf.edit_distance?
Here is my code:
with graph.as_default():
max_length = X_train.shape[1]
frame_size = X_train.shape[2]
max_target_length = y_train.shape[1]
# Batch size x time steps x data width
data = tf.placeholder(tf.float32, [None, max_length, frame_size])
data_length = tf.placeholder(tf.int32, [None])
# Batch size x max_target_length
target_dense = tf.placeholder(tf.int32, [None, max_target_length])
target_length = tf.placeholder(tf.int32, [None])
# Generating sparse tensor representation of target
target = ctc_label_dense_to_sparse(target_dense, target_length)
# Applying LSTM, returning output for each timestep (y_rnn1,
# [batch_size, max_time, cell.output_size]) and the final state of shape
# [batch_size, cell.state_size]
y_rnn1, h_rnn1 = tf.nn.dynamic_rnn(
tf.nn.rnn_cell.LSTMCell(num_hidden, state_is_tuple=True, num_proj=num_classes), # num_proj=num_classes
data,
dtype=tf.float32,
sequence_length=data_length,
)
# For sequence labelling, we want a prediction for each timestamp.
# However, we share the weights for the softmax layer across all timesteps.
# How do we do that? By flattening the first two dimensions of the output tensor.
# This way time steps look the same as examples in the batch to the weight matrix.
# Afterwards, we reshape back to the desired shape
# Reshaping
logits = tf.transpose(y_rnn1, perm=(1, 0, 2))
# Get the loss by calculating ctc_loss
# Also calculates
# the gradient. This class performs the softmax operation for you, so inputs
# should be e.g. linear projections of outputs by an LSTM.
loss = tf.reduce_mean(tf.contrib.ctc.ctc_loss(logits, target, data_length))
# Define our optimizer with learning rate
optimizer = tf.train.RMSPropOptimizer(learning_rate).minimize(loss)
# Decoding using beam search
decoded, log_probabilities = tf.contrib.ctc.ctc_beam_search_decoder(logits, data_length, beam_width=10, top_paths=1)
Thanks!
Update (06/29/2016)
Thank you, #jihyeon-seo! So, we have at input of RNN something like [num_batch, max_time_step, num_features]. We use the dynamic_rnn to perform the recurrent calculations given the input, outputting a tensor of shape [num_batch, max_time_step, num_hidden]. After that, we need to do an affine projection in each tilmestep with weight sharing, so we've to reshape to [num_batch*max_time_step, num_hidden], multiply by a weight matrix of shape [num_hidden, num_classes], sum a bias undo the reshape, transpose (so we will have [max_time_steps, num_batch, num_classes] for ctc loss input), and this result will be the input of ctc_loss function. Did I do everything correct?
This is the code:
cell = tf.nn.rnn_cell.MultiRNNCell([cell] * num_layers, state_is_tuple=True)
h_rnn1, self.last_state = tf.nn.dynamic_rnn(cell, self.input_data, self.sequence_length, dtype=tf.float32)
# Reshaping to share weights accross timesteps
x_fc1 = tf.reshape(h_rnn1, [-1, num_hidden])
self._logits = tf.matmul(x_fc1, self._W_fc1) + self._b_fc1
# Reshaping
self._logits = tf.reshape(self._logits, [max_length, -1, num_classes])
# Calculating loss
loss = tf.contrib.ctc.ctc_loss(self._logits, self._targets, self.sequence_length)
self.cost = tf.reduce_mean(loss)
Update (07/11/2016)
Thank you #Xiv. Here is the code after the bug fix:
cell = tf.nn.rnn_cell.MultiRNNCell([cell] * num_layers, state_is_tuple=True)
h_rnn1, self.last_state = tf.nn.dynamic_rnn(cell, self.input_data, self.sequence_length, dtype=tf.float32)
# Reshaping to share weights accross timesteps
x_fc1 = tf.reshape(h_rnn1, [-1, num_hidden])
self._logits = tf.matmul(x_fc1, self._W_fc1) + self._b_fc1
# Reshaping
self._logits = tf.reshape(self._logits, [-1, max_length, num_classes])
self._logits = tf.transpose(self._logits, (1,0,2))
# Calculating loss
loss = tf.contrib.ctc.ctc_loss(self._logits, self._targets, self.sequence_length)
self.cost = tf.reduce_mean(loss)
Update (07/25/16)
I published on GitHub part of my code, working with one utterance. Feel free to use! :)
I'm trying to do the same thing.
Here's what I found you may be interested in.
It was really hard to find the tutorial for CTC, but this example was helpful.
And for the blank label, CTC layer assumes that the blank index is num_classes - 1, so you need to provide an additional class for the blank label.
Also, CTC network performs softmax layer. In your code, RNN layer is connected to CTC loss layer. Output of RNN layer is internally activated, so you need to add one more hidden layer (it could be output layer) without activation function, then add CTC loss layer.
See here for an example with bidirectional LSTM, CTC, and edit distance implementations, training a phoneme recognition model on the TIMIT corpus. If you train on that corpus's training set, you should be able to get phoneme error rates down to 20-25% after 120 epochs or so.
I am trying the create a recurrent neural network in tensor flow. The input to the network is a sequence of vectors. The sequence length is different for all the inputs. I want to do this with batch of inputs.
Can anyone help me on how exactly to do this? I have gone through the tutorials on the tensorflow site, but it is still not clear to me.
You can use the rnn function defined here
One of the arguments it takes is sequence_length
sequence_length: Specifies the length of each sequence in inputs.
An int32 or int64 vector (tensor) size [batch_size]. Values in [0, T).
Here is how to implement complete loop
# x, state, sequence_length are placeholders
outputs, final_state = tf.nn.rnn(lstm_cell, x, state, sequence_length = sequence_lengths)
# add softmax layer, define loss, training method, etc
...
# code for one epoch
iterations = total_data_length / batch_size
max_sequence_length = max(all_possible_sequence_lengths)
cur_state = initial_state
for i in range(iterations):
# x is of dimension [max_sequence_length, batch_size, input_size]
# sequence_lengths is of dimension [batch_size]
x_data, sequence_data, y_data = mini_batch(batch_size)
feed_dict = {k: v for k, v in zip(x, x_data)}
feed_dict.append(sequence_lengths: sequence_data, ...)
outs, cur_state, _ = session.run([outputs, final_state, train], feed_dict)
This method was bit confusing to me for couple of reasons:
Input shape is [sequence_length, batch_size, input_size] and not [batch_size, sequence_length, input_size]. However, this totally makes sense if you go through the code and see how rnn() is implemented. This also means you need to reshape your outputs (having dimension same as inputs) in order to pass them to matmul and then softmax for example.
Parameter inputs in function rnn() is a python list. And you cannot pass this in feed_dict as {x: x_data}, you will get an error saying "Not able to hash type: 'list'". Instead see how i used comprehension in code above.
It depends on your data set, but you can do:
Use the max length in your dataset, or
Use a reasonable size (e.g., 256) and splits the input data up to the size if they are longer than the size.