My problem:
I have a sequence of complex states and I want to predict the future states.
Input:
I have a sequence of states. Each sequence can be of variable length. Each state is a moment in time and is described by several attributes: [att1, att2, ...]. Where each attribute is a number between an interval [[0..5], [1..3651], ...]
The example (and paper) of Seq2Seq is based on that each state (word) is taken from their dictionary. So each state has around 80.000 possibilities. But how would you represent each state when it is taken from a set of vectors and the set is just each possible combination of the attributes.
Is there any method to work with more complex states with TensorFlow? Also, what is a good method do decide the boundaries of your buckets when the relation between input length and output length is unclear?
May I suggest a rephrasing and splitting of your question into two parts? The first is really a general machine learning/LSTM question that's independent of tensorflow: How to use an LSTM to predict when the sequence elements are general vectors, and the second is how to represent this in tensorflow. For the former - there's nothing really magical to do there.
But a very quick answer: You've really just skipped the embedding lookup part of seq2seq. You can feed dense tensors in to a suitably modified version of it -- your state is just a dense vector representation of the state. That's the same thing that comes out of an embedding lookup.
The vector representation tutorial discusses the preprocessing that turns, e.g., words into embeddings for use in later parts of the learning pipeline.
If you look at line 139 of seq2seq.py you'll see that the embedding_rnn_decoder takes in a 1D batch of things to decide (the dimension is elements in the batch), but then uses the embedding lookup to turn it into a batch_size * cell.input_size tensor. You want to directly input a batch_size * cell.input_size tensor into the RNN, skipping the embedding step.
Related
As part of my thesis, I am trying to build a recurrent Neural Network Language Model.
From theory, I know that the input layer should be a one-hot vector layer with a number of neurons equal to the number of words of our Vocabulary, followed by an Embedding layer, which, in Keras, it apparently translates to a single Embedding layer in a Sequential model. I also know that the output layer should also be the size of our vocabulary so that each output value maps 1-1 to each vocabulary word.
However, in both the Keras documentation for the Embedding layer (https://keras.io/layers/embeddings/) and in this article (https://machinelearningmastery.com/how-to-develop-a-word-level-neural-language-model-in-keras/#comment-533252), the vocabulary size is arbitrarily augmented by one for both the input and the output layers! Jason gives an explenation that this is due to the implementation of the Embedding layer in Keras but that doesn't explain why we would also use +1 neuron in the output layer. I am at the point of wanting to order the possible next words based on their probabilities and I have one probability too many that I do not know to which word to map it too.
Does anyone know what is the correct way of acheiving the desired result? Did Jason just forget to subtrack one from the output layer and the Embedding layer just needs a +1 for implementation reasons (I mean it's stated in the official API)?
Any help on the subject would be appreciated (why is Keras API documentation so laconic?).
Edit:
This post Keras embedding layer masking. Why does input_dim need to be |vocabulary| + 2? made me think that Jason does in fact have it wrong and that the size of the Vocabulary should not be incremented by one when our word indices are: 0, 1, ..., n-1.
However, when using Keras's Tokenizer our word indices are: 1, 2, ..., n. In this case, the correct approach is to:
Set mask_zero=True, to treat 0 differently, as there is never a
0 (integer) index input in the Embedding layer and keep the
vocabulary size the same as the number of vocabulary words (n)?
Set mask_zero=True but augment the vocabulary size by one?
Not set mask_zero=True and keep the vocabulary size the same as the
number of vocabulary words?
the reason why we add +1 leads to the possibility that we can encounter a chance to see an unseen word(out of our vocabulary) during testing or in production, it is common to consider a generic term for those UNKNOWN and that is why we add a OOV word in front which resembles all out of vocabulary words.
Check this issue on github which explains it in detail:
https://github.com/keras-team/keras/issues/3110#issuecomment-345153450
Correct me if I am wrong but according to the official Keras documentation, by default, the fit function has the argument 'shuffle=True', hence it shuffles the whole training dataset on each epoch.
However, the point of using recurrent neural networks such as LSTM or GRU is to use the precise order of each data so that the state of the previous data influence the current one.
If we shuffle all the data, all the logical sequences are broken. Thus I don't understand why there are so much examples of LSTM where the argument is not set to False. What is the point of using RNN without sequences ?
Also, when I set the shuffle option to False, my LSTM model is less performant eventhought there are dependencies between the data: I use the KDD99 dataset where the connections are linked.
If we shuffle all the data, all the logical sequences are broken.
No, the shuffling happens on the batches axis, not on the time axis.
Usually, your data for an RNN has a shape like this: (batch_size, timesteps, features)
Usually, you give your network not only one sequence to learn from, but many sequences. Only the order in which these many sequences are being trained on gets shuffled. The sequences themselves stay intact.
Shuffling is usually always a good idea because your network shall only learn the training examples themselves, not their order.
This being said, there are cases where you have indeed only one huge sequence to learn from. In that case you have the option to still divide your sequence into several batches. If this is the case, you are absolutely right with your concern that shuffling would have a huge negative impact, so don't do that in this case!
Note: RNNs have a stateful parameter that you can set to True. In that case the last state of the previous batch will be passed to the following one which effectively makes your RNN see all batches as one huge sequence. So, absolutely do this, if you have a huge sequence over multiple batches.
I'm trying to predict sequences of 2D coordinates. But I don't want only the most probable future path but all the most probable paths to visualize it in a grid map.
For this I have traning data consisting of 40000 sequences. Each sequence consists of 10 2D coordinate pairs as input and 6 2D coordinate pairs as labels.
All the coordinates are in a fixed value range.
What would be my first step to predict all the probable paths? To get all probable paths I have to apply a softmax in the end, where each cell in the grid is one class right? But how to process the data to reflect this grid like structure? Any ideas?
A softmax activation won't do the trick I'm afraid; if you have an infinite number of combinations, or even a finite number of combinations that do not already appear in your data, there is no way to turn this into a multi-class classification problem (or if you do, you'll have loss of generality).
The only way forward I can think of is a recurrent model employing variational encoding. To begin with, you have a lot of annotated data, which is good news; a recurrent network fed with a sequence X (10,2,) will definitely be able to predict a sequence Y (6,2,). But since you want not just one but rather all probable sequences, this won't suffice. Your implicit assumption here is that there is some probability space hidden behind your sequences, which affects how they play out over time; so to model the sequences properly, you need to model that latent probability space. A Variational Auto-Encoder (VAE) does just that; it learns the latent space, so that during inference the output prediction depends on sampling over that latent space. Multiple predictions over the same input can then result in different outputs, meaning that you can finally sample your predictions to empirically approximate the distribution of potential outputs.
Unfortunately, VAEs can't really be explained within a single paragraph over stackoverflow, and even if they could I wouldn't be the most qualified person to attempt it. Try searching the web for LSTM-VAE and arm yourself with patience; you'll probably need to do some studying but it's definitely worth it. It might also be a good idea to look into Pyro or Edward, which are probabilistic network libraries for python, better suited to the task at hand than Keras.
Here is my understanding of a basic Sequence to Sequence LSTMs. Suppose we are tackling a question-answer setting.
You have two set of LSTMs (green and blue below). Each set respectively sharing weights (i.e. each of the 4 green cells have the same weights and similarly with the blue cells). The first is a many to one LSTM, which summarises the question at the last hidden layer/ cell memory.
The second set (blue) is a Many to Many LSTM which has different weights to the first set of LSTMs. The input is simply the answer sentence while the output is the same sentence shifted by one.
The question is two fold:
1. Are we passing the last hidden state only to the blue LSTMs as the initial hidden state. Or is it last hidden state and cell memory.
2. Is there a way to set the initial hiddden state and cell memory in Keras or Tensorflow? If so reference?
(image taken from suriyadeepan.github.io)
Are we passing the last hidden state only to the blue LSTMs as the initial hidden state. Or is it last hidden state and cell memory.
Both hidden state h and cell memory c are passed to the decoder.
TensorFlow
In seq2seq source code, you can find the following code in basic_rnn_seq2seq():
_, enc_state = rnn.static_rnn(enc_cell, encoder_inputs, dtype=dtype)
return rnn_decoder(decoder_inputs, enc_state, cell)
If you use an LSTMCell, the returned enc_state from the encoder will be a tuple (c, h). As you can see, the tuple is passed directly to the decoder.
Keras
In Keras, the "state" defined for an LSTMCell is also a tuple (h, c) (note that the order is different from TF). In LSTMCell.call(), you can find:
h_tm1 = states[0]
c_tm1 = states[1]
To get the states returned from an LSTM layer, you can specify return_state=True. The returned value is a tuple (o, h, c). The tensor o is the output of this layer, which will be equal to h unless you specify return_sequences=True.
Is there a way to set the initial hiddden state and cell memory in Keras or Tensorflow? If so reference?
###TensorFlow###
Just provide the initial state to an LSTMCell when calling it. For example, in the official RNN tutorial:
lstm = tf.contrib.rnn.BasicLSTMCell(lstm_size)
...
output, state = lstm(current_batch_of_words, state)
There's also an initial_state argument for functions such as tf.nn.static_rnn. If you use the seq2seq module, provide the states to rnn_decoder as have been shown in the code for question 1.
###Keras###
Use the keyword argument initial_state in the LSTM function call.
out = LSTM(32)(input_tensor, initial_state=(h, c))
You can actually find this usage on the official documentation:
###Note on specifying the initial state of RNNs###
You can specify the initial state of RNN layers symbolically by
calling them with the keyword argument initial_state. The value of
initial_state should be a tensor or list of tensors representing the
initial state of the RNN layer.
EDIT:
There's now an example script in Keras (lstm_seq2seq.py) showing how to implement basic seq2seq in Keras. How to make prediction after training a seq2seq model is also covered in this script.
(Edit: this answer is incomplete and hasn't considered actual possibilities of state transfering. See the accepted answer).
From a Keras point of view, that picture has only two layers.
The green group is one LSTM layer.
The blue group is another LSTM layer.
There isn't any communication between green and blue other than passing the outputs. So, the answer for 1 is:
Only the thought vector (which is the actual output of the layer) is passed to the other layer.
Memory and state (not sure if these are two different entities) are totally contained inside a single layer and are not initially intended to be seen or shared with any other layer.
Each individual block in that image is totally invisible in keras. They are considered "time steps", something that only appears in the shape of the input data. It's rarely important to worry about them (unless for very advanced usages).
In keras, it's like this:
Easily, you have access only to the external arrows (including "thought vector").
But having access to each step (each individual green block in your picture) is not an exposed thing. So...
Passing the states from one layer to the other is also not expected in Keras. You will probably have to hack things. (See this: https://github.com/fchollet/keras/issues/2995)
But considering a thought vector big enough, you could say it will learn a way to carry what is important in itself.
The only notion you have from the steps is:
You have to input things shaped like (sentences, length, wordIdFeatures)
The steps will be performed considering that each slice in the length dimension is an input to each green block.
You may choose to have a single output (sentences, cells), for which you completely lose track of steps. Or...
Outputs like (sentences, length, cells), from which you know the output of each block through the length dimension.
One to many or many to many?
Now, the first layer is many to one (but nothing prevents it from being many to many too if you want).
But the second... that's complicated.
If the thought vector was made by a many to one. You will have to manage a way of creating a one to many. (That's not trivial in keras, but you could think of repeating the thought vector for the expected length, making it be the input to all steps. Or maybe fill an entire sequence with zeros or ones, keeping only the first element as the thought vector)
If the thought vector was made by a many to many, you can take advantage of this and keep an easy many to many, if you're willing to accept that the output has exactly the same number of steps as the input.
Keras doesn't have a ready solution for 1 to many cases. (From a single input predict a whole sequence).
I am confused about what dynamic RNN (i.e. dynamic_rnn) is. It returns an output and a state in TensorFlow. What are these state and output? What is dynamic in a dynamic RNN, in TensorFlow?
Dynamic RNN's allow for variable sequence lengths. You might have an input shape (batch_size, max_sequence_length), but this will allow you to run the RNN for the correct number of time steps on those sequences that are shorter than max_sequence_length.
In contrast, there are static RNNs, which expect to run the entire fixed RNN length. There are cases where you might prefer to do this, such as if you are padding your inputs to max_sequence_length anyway.
In short, dynamic_rnn is usually what you want for variable length sequential data. It has a sequence_length parameter, and it is your friend.
While AlexDelPiero's answer was what I was googling for, the original question was different. You can take a look at this detailed description about LSTMs and intuition behind them. LSTM is the most common example of an RNN.
http://colah.github.io/posts/2015-08-Understanding-LSTMs/
The short answer is: the state is an internal detail that is passed from one timestep to another. The output is a tensor of outputs on each timestep. You usually need to pass all outputs to the next RNN layer or the last output for the last RNN layer. To get the last output you can use output[:,-1,:]