The encoder-decoder model provides a pattern for using recurrent neural networks to address challenging sequence-to-sequence prediction problems such as machine translation.
Encoder-decoder models can be developed in the Keras Python deep learning library and an example of a neural machine translation system developed with this model has been described on the Keras blog, with sample code distributed with the Keras project.
This example can provide the basis for developing encoder-decoder LSTM models for your own sequence-to-sequence prediction problems.
In this tutorial, you will discover how to develop a sophisticated encoder-decoder recurrent neural network for sequence-to-sequence prediction problems with Keras.
After completing this tutorial, you will know:
How to correctly define a sophisticated encoder-decoder model in Keras for sequence-to-sequence prediction.
How to define a contrived yet scalable sequence-to-sequence prediction problem that you can use to evaluate the encoder-decoder LSTM model.
How to apply the encoder-decoder LSTM model in Keras to address the scalable integer sequence-to-sequence prediction problem.
The encoder-decoder model is a way of organizing recurrent neural networks for sequence-to-sequence prediction problems.
It was originally developed for machine translation problems, although it has proven successful at related sequence-to-sequence prediction problems such as text summarization and question answering.
The approach involves two recurrent neural networks, one to encode the source sequence, called the encoder, and a second to decode the encoded source sequence into the target sequence, called the decoder.
Using the code in that example as a starting point, we can develop a generic function to define an encoder-decoder recurrent neural network. Below is this function named define_models().
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# returns train, inference_encoder and inference_decoder models
n_input: The cardinality of the input sequence, e.g. number of features, words, or characters for each time step.
n_output: The cardinality of the output sequence, e.g. number of features, words, or characters for each time step.
n_units: The number of cells to create in the encoder and decoder models, e.g. 128 or 256.
The function then creates and returns 3 models, as follows:
train: Model that can be trained given source, target, and shifted target sequences.
inference_encoder: Encoder model used when making a prediction for a new source sequence.
inference_decoder Decoder model use when making a prediction for a new source sequence.
The model is trained given source and target sequences where the model takes both the source and a shifted version of the target sequence as input and predicts the whole target sequence.
For example, one source sequence may be [1,2,3] and the target sequence [4,5,6]. The inputs and outputs to the model during training would be:
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Input1: ['1', '2', '3']
Input2: ['_', '4', '5']
Output: ['4', '5', '6']
The model is intended to be called recursively when generating target sequences for new source sequences.
The source sequence is encoded and the target sequence is generated one element at a time, using a “start of sequence” character such as ‘_’ to start the process. Therefore, in the above case, the following input-output pairs would occur during training:
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t, Input1, Input2, Output
1, ['1', '2', '3'], '_', '4'
2, ['1', '2', '3'], '4', '5'
3, ['1', '2', '3'], '5', '6'
Here you can see how the recursive use of the model can be used to build up output sequences.
During prediction, the inference_encoder model is used to encode the input sequence once which returns states that are used to initialize the inference_decoder model. From that point, the inference_decoder model is used to generate predictions step by step.
The function below named predict_sequence() can be used after the model is trained to generate a target sequence given a source sequence.
infenc: Encoder model used when making a prediction for a new source sequence.
infdec: Decoder model use when making a prediction for a new source sequence.
source:Encoded source sequence.
n_steps: Number of time steps in the target sequence.
cardinality: The cardinality of the output sequence, e.g. the number of features, words, or characters for each time step.
The function then returns a list containing the target sequence.
Scalable Sequence-to-Sequence Problem
In this section, we define a contrived and scalable sequence-to-sequence prediction problem.
The source sequence is a series of randomly generated integer values, such as [20, 36, 40, 10, 34, 28], and the target sequence is a reversed pre-defined subset of the input sequence, such as the first 3 elements in reverse order [40, 36, 20].
The length of the source sequence is configurable; so is the cardinality of the input and output sequence and the length of the target sequence.
We will use source sequences of 6 elements, a cardinality of 50, and target sequences of 3 elements.
Below are some more examples to make this concrete.
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Source, Target
[13, 28, 18, 7, 9, 5] [18, 28, 13]
[29, 44, 38, 15, 26, 22] [38, 44, 29]
[27, 40, 31, 29, 32, 1] [31, 40, 27]
...
You are encouraged to explore larger and more complex variations. Post your findings in the comments below.
Let’s start off by defining a function to generate a sequence of random integers.
We will use the value of 0 as the padding or start of sequence character, therefore it is reserved and we cannot use it in our source sequences. To achieve this, we will add 1 to our configured cardinality to ensure the one-hot encoding is large enough (e.g. a value of 1 maps to a ‘1’ value in index 1).
For example:
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n_features=50+1
We can use the randint() python function to generate random integers in a range between 1 and 1-minus the size of the problem’s cardinality. The generate_sequence() below generates a sequence of random integers.
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# generate a sequence of random integers
def generate_sequence(length,n_unique):
return[randint(1,n_unique-1)for_inrange(length)]
Next, we need to create the corresponding output sequence given the source sequence.
To keep thing simple, we will select the first n elements of the source sequence as the target sequence and reverse them.
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# define target sequence
target=source[:n_out]
target.reverse()
We also need a version of the output sequence shifted forward by one time step that we can use as the mock target generated so far, including the start of sequence value in the first time step. We can create this from the target sequence directly.
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# create padded input target sequence
target_in=[0]+target[:-1]
Now that all of the sequences have been defined, we can one-hot encode them, i.e. transform them into sequences of binary vectors. We can use the Keras built in to_categorical() function to achieve this.
We can put all of this into a function named get_dataset() that will generate a specific number of sequences that we can use to train a model.
Finally, we need to be able to decode a one-hot encoded sequence to make it readable again.
This is needed for both printing the generated target sequences but also for easily comparing whether the full predicted target sequence matches the expected target sequence. The one_hot_decode() function will decode an encoded sequence.
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# decode a one hot encoded string
def one_hot_decode(encoded_seq):
return[argmax(vector)forvector inencoded_seq]
We can tie all of this together and test these functions.
Running the example first prints the shape of the generated dataset, ensuring the 3D shape required to train the model matches our expectations.
The generated sequence is then decoded and printed to screen demonstrating both that the preparation of source and target sequences matches our intention and that the decode operation is working.
We are now ready to develop a model for this sequence-to-sequence prediction problem.
Encoder-Decoder LSTM for Sequence Prediction
In this section, we will apply the encoder-decoder LSTM model developed in the first section to the sequence-to-sequence prediction problem developed in the second section.
The first step is to configure the problem.
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# configure problem
n_features=50+1
n_steps_in=6
n_steps_out=3
Next, we must define the models and compile the training model.
Once the model is trained, we can evaluate it. We will do this by making predictions for 100 source sequences and counting the number of target sequences that were predicted correctly. We will use the numpy array_equal() function on the decoded sequences to check for equality.
Finally, we will generate some predictions and print the decoded source, target, and predicted target sequences to get an idea of whether the model is working as expected.
Putting all of these elements together, the complete code example is listed below.
Next, the model is evaluated and the accuracy printed.
Note: Your results may vary given the stochastic nature of the algorithm or evaluation procedure, or differences in numerical precision. Consider running the example a few times and compare the average outcome.
We can see that the model achieves 100% accuracy on new randomly generated examples.
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Accuracy: 100.00%
Finally, 10 new examples are generated and target sequences are predicted. Again, we can see that the model correctly predicts the output sequence in each case and the expected value matches the reversed first 3 elements of the source sequences.
It provides self-study tutorials on topics like: CNN LSTMs, Encoder-Decoder LSTMs, generative models, data preparation, making predictions and much more...
Finally Bring LSTM Recurrent Neural Networks to
Your Sequence Predictions Projects
Hi, thank you for your post. I am new to LSTM. It looks like the target should always be a subset of the source, could we use LSTM to predict the target which is not a subset of the source? For example, the source is [0.123,0.234,0.345], and the target is [0.564, 0.923, 0.667]? Thanks in advance.
Could you give some more detail as to how it would need to be modified to have multiple LSTM layers in the decoder? I am working on something similar and looking to add layers to the decoder.
Thanks for the wonderful tutorial, Jason!
I am facing an issue, though: I tried to execute your code as is (copy-pasted it), but it throws an error:
Using TensorFlow backend.
Traceback (most recent call last):
File “C:\Users\User\Documents\pystuff\keras_auto.py”, line 91, in
train, infenc, infdec = define_models(n_features, n_features, 128)
File “C:\Users\User\Documents\pystuff\keras_auto.py”, line 40, in define_models
encoder = LSTM(n_units, return_state=True)
File “C:\Users\User\Anaconda3\envs\py35\lib\site-packages\keras\legacy\interfaces.py”, line 88, in wrapper
return func(*args, **kwargs)
File “C:\Users\User\Anaconda3\envs\py35\lib\site-packages\keras\layers\recurrent.py”, line 949, in __init__
super(LSTM, self).__init__(**kwargs)
File C:\Users\User\Anaconda3\envs\py35\lib\site-packages\keras\layers\recurrent.py”, line 191, in __init__
super(Recurrent, self).__init__(**kwargs)
File “C:\Users\User\Anaconda3\envs\py35\lib\site-packages\keras\engine\topology.py”, line 281, in __init__
raise TypeError(‘Keyword argument not understood:’, kwarg)
TypeError: (‘Keyword argument not understood:’, ‘return_state’)
I am using an anaconda environment (python 3.5.3). What could have possibly gone wrong?
I had the same problem, and updated Keras (to version 2.1.2) and TensorFlow (to version 1.4.0). The problem above was solved. However, I now see that the shapes of X1, X2, and y are ((100000, 1, 6, 51), (100000, 1, 3, 51), (100000, 1, 3, 51)) instead of ((100000, 6, 51), (100000, 3, 51), (100000, 3, 51)). Why could this be?
Notice instead of returning array(X1), array(X2), array(y), we now return arrays that have been squeezed – one axis has been removed. We remove axis 1 because it’s the wrong shape for what we need.
The output is now as it should be (although I’m getting 98% accuracy instead of 100%).
yes, we have to reshape the model and then everything works fine
what is(n_in, cardinality)?
I am facing difficulty in using it with a user-defined variable.for random what should be the input and input shape for the arguments
I removed the brackets [ ] in the parameters to to_categorical instead. I think because parameters like target etc are already arrays the brackets are not necessary.
I also had to do that to get the data in the right format. There’s also a function tensorflow.one_hot which I prefer over to_categorical. They do the same thing.
Thanks Jason, for writing blogs for machinelearningmastery.com. I have seen no. of blogs.
I have one query – –
In my dataset —-
no. of columns are 5 (inputs),
No. of outputs – 3 (feature , which I want to predict) and
number of rows – 34079.
Then how to put these parameters in your code –
n_features = 34079
n_steps_in = 5
n_steps_out = 3
# generate training dataset
X1, X2, y = get_dataset(n_steps_in, n_steps_out, n_features, 1)
print(X1.shape,X2.shape,y.shape)
I am getting error like ——–>>> Your session crashed after using all available RAM. View runtime logs. I am using 14Gb RAM. please suggest me how to arrange my parameters as per your code.. thanks in advance.
Hi Jason,
running the get_dataset the function returns one additional row in the Arrays X1, X2, y:
(1,1,6,51) (1,1,3,51)(1,1,3,51).
This results form numpy.array(), before the X1, X2, y are lists with the correct sizes:
(1,6,51) (1,3,51)(1,3,51).
It seems the comand array() adds an additional dimension. Could you help on solving this problem?
Could you please give me a tutorial for a case where we are input to the seq2seq model is word embeddings and outputs is also word embeddings. I find it frustrating to see a Dense layer at the end. this is what is stopping a fully seq2seq model with input as well as output word embeddings.
If embeddings are coming in, we’d want to have embeddings going out (auto-encoder). Imagine input = category (cat, dog, frog, wale, human). These animals are quite different, so we represent w/ embedding. Rather than having a dense output of 5 OHE, if an embedding is used for output, the assumption is that, especially if weights are shared between inputs + outputs, we could train the net with and give it more detail about what exactly each class is… rather than use something like cross entropy.
I am trying to put embedding layer at encoder and decoder input with dense layer as it as you mentioned in the above code.
Later in the prediction function call, when I give 3D input to target_seq, it throws dimensional error: Error when checking input: expected Decoder_input to have 2 dimensions, but got array with shape (1, 1, 341), here 341 is my original feature dimension which is compressed to 32 by embedding layer.
Thanks Jason. Just wanted to get an idea in scenarios when decoder_input and decoder_output have different dimensions, what happens to your prediction function (target_seq) shape?
Hi ! When adding dropout and recurrent_dropout as LSTM arguments on line 40 of the last complete code example with everything else being the same, the code went wrong. So how can I add dropout in this case? Thanks!
Hi Jason! Thanks for your great effort to put encoder decoder implementations here. As Dinter mentioned, when dropout is added, the code runs well for training phase but gives following error during prediction.
InvalidArgumentError (see above for traceback): You must feed a value for placeholder tensor ‘lstm_1/keras_learning_phase’ with dtype bool
[[Node: lstm_1/keras_learning_phase = Placeholder[dtype=DT_BOOL, shape=, _device=”/job:localhost/replica:0/task:0/cpu:0″]()]]
How to fix the problem in this particular implementation?
[Note: Your worked example of dropout however worked for me, but the difference is you are adding layer by layer in sequential model there which is different than this example of encoder decoder]
When I tried with exactly the same network in the example you presented and added dropout=0.0 in line 10 and line 15 of define_models function, the program runs but for other values of dropout it gives error. Also changing the size of network, for example, number of units to 5, 10, 20 does give the same error.
Any idea to add dropout?
line 5: encoder = LSTM(n_units, return_state=True,dropout=0.0)
line 10: decoder_lstm = LSTM(n_units, return_sequences=True, return_state=True,dropout=0.0)
Hi Jason,
what is the difference between specifying the model input:
Model( [decoder_inputs] + decoder_states_inputs,….)
and this
Model([decoder_inputs,decoder_states_inputs],…)
Does the 1st version add the elements of decoder_states_inputs array to corresponding elements of decoder_inputs
It is a silly question but why n_features in this case is used for the n_input and for the n_output instead of n_input equal to 6 and n_output equal to 3 ?
Traceback (most recent call last):
File “”, line 1, in
File “E:\ProgramData\Anaconda3\lib\site-packages\keras\models.py”, line 965, in fit
validation_steps=validation_steps)
File “E:\ProgramData\Anaconda3\lib\site-packages\keras\engine\training.py”, line 1593, in fit
batch_size=batch_size)
File “E:\ProgramData\Anaconda3\lib\site-packages\keras\engine\training.py”, line 1430, in _standardize_user_data
exception_prefix=’target’)
File “E:\ProgramData\Anaconda3\lib\site-packages\keras\engine\training.py”, line 110, in _standardize_input_data
‘with shape ‘ + str(data_shape))
ValueError: Error when checking target: expected dense_24 to have 3 dimensions, but got array with shape (94, 1)
How can I make this model work, and also how can I view the hidden states for each of the input samples (should be 96 hidden states).
Hi Jason,
I like your blog posts. I have some code based on this post, but I get this error message all the time. There’s something wrong with my dense layer. Can you point it out? Here units is 300 and tokens_per_sentence is 25.
an error message:
ValueError: Error when checking target: expected dense_layer_b to have 2 dimensions, but got array with shape (1, 25, 300)
Do you think that this algorithm works for weather prediction? For example, by having the input integer variables as dew point, humidity, and temperature, to predict rainfall as output
I would like tou ask you, how could I use this model with float numbers? Yours training data seems like this:
[[
[0,0,0,0,1,0,0]
[0,0,1,0,0,1,0]
[0,1,0,0,0,0,0]]
.
.
.
]]
I would need something like this:
[[
[0.12354,0.9854,5875, 0.0659]
[0.12354,0.9854,5875, 0.0659]
[0.12354,0.9854,5875, 0.0659]
[0.12354,0.9854,5875, 0.0659]
]]
Whan i run your model with float numbers, the network doesn’t learn. Should I use some different LOSS function?
# Set up the decoder, using encoder_states as initial state.
decoder_inputs = Input(shape=(None,))
x = Embedding(num_decoder_tokens, latent_dim)(decoder_inputs)
x = LSTM(latent_dim, return_sequences=True)(x, initial_state=encoder_states)
decoder_outputs = Dense(num_decoder_tokens, activation=’softmax’)(x)
# Define the model that will turn
# encoder_input_data & decoder_input_data into decoder_target_data
model = Model([encoder_inputs, decoder_inputs], decoder_outputs)
Whan i try to train the model, i get this error: expected dense_1 to have 3 dimensions, but got array with shape (10, 15). Could you help me with that please?
I am trying to do seq2seq problem using Keras – LSTM. Predicted output words matches with most frequent words of the vocabulary built using the dataset. Not sure what could be the reason. After training is completed while trying to predict the output for the given input sequence model is predicting same output irrespective of the input seq. Also using separate embedding layer for both encoder and decoder.
Could you help me with my problem? I think that a lot of required logic is implemented in your code but I am very beginner in python. I want to predict numbers according to input test sequence (seq2seq) so output of my decoder should by sequence of 6 numbers (1-7). U can imagine it as lottery prediction. I have very long input vector of numbers 1-7 (contains sequenses of 6 numbers) so I don’t need to generate test data. I just need to predict next 6 numbers which should be generated. 1,1,2,2,3 -> 3,4,4,5,5,6
Thank you Jason, it was very helpful for me. And can you give me advice or link how to correctly initiate and train network with multiple input sequences?
Thank you Jason for this tutorial it gets me started. I tried to use larger sequence where input is 400 series of numbers and output is 40 numbers. I have problem with categorical because of index error and i don’t know how to set or get the the value for cardinality/n_features. Can you give me an idea on this?
Im also not clear if this is a classification type of model. Can you please confirm. Thanks
Hi,
thank you for this totu, please i receive this error when i run your example :
ValueError: Error when checking input: expected input_1 to have 3 dimensions, but got array with shape (100000, 1, 6, 51)
Hi Jason, thank you very much for the tutorial. Is it possible to decode many sequences simultaneously instead of decoding a single sequence one character at a time? The inference for my project takes too long and I thought that doing it in larger batches may help.
Hi im just wondering why do we need to use to_categorical if the sequence is already numbers. On my case i have a series of input features(numbers) and another series of output features(number). Should i still use to_categorical method?
I am working on word boundary detection problem where dataset containing .wav files in which a sentence is spoken are given, and corresponding to each .wav file a .wrd file is also given which contains the words spoken in a sentence and also its boundaries (starting and end boundaries).
Our task is to identify word boundaries in test .wav file (words spoken will also be given).
I want to do this with sequential models .
What I have tried is:
I have read .wav files using librosa module in numpy array (made it equal to max size using padding)
Its output is like 3333302222213333022221333302222133333 (for i/p ex: I am hero)
where (0:start of word, 1:end of word, 2:middle, 3:space)
means I want to solve this as supervised learning problem, can I train such model with RNN?
Hello.
I’ve tried this example for word-level chatbot. Everything works great, on a small data (5000 sentences)
When I use dataset of 50 000 sentences something is wrong. Model accuracy is 95% but when i try to chat with this chatbot, responses are generated randomly. Chatbot is capable of learning sentences from dataset, but it use them randomly to respond to users questions.
How it is possible, when accuracy is so hight?
Thanks
Sir, how to create confusion matrix, evaluated and the accuracy printed for this model :
# Define an input sequence and process it.
encoder_inputs = Input(shape=(None, num_encoder_tokens))
encoder = LSTM(latent_dim, return_state=True)
encoder_outputs, state_h, state_c = encoder(encoder_inputs)
# We discard encoder_outputs and only keep the states.
encoder_states = [state_h, state_c]
# Set up the decoder, using encoder_states as initial state.
decoder_inputs = Input(shape=(None, num_decoder_tokens))
# We set up our decoder to return full output sequences,
# and to return internal states as well. We don’t use the
# return states in the training model, but we will use them in inference.
decoder_lstm = LSTM(latent_dim, return_sequences=True, return_state=True)
decoder_outputs, _, _ = decoder_lstm(decoder_inputs,
initial_state=encoder_states)
decoder_dense = Dense(num_decoder_tokens, activation=’softmax’)
decoder_outputs = decoder_dense(decoder_outputs)
# Define the model that will turn
# encoder_input_data & decoder_input_data into decoder_target_data
model = Model([encoder_inputs, decoder_inputs], decoder_outputs)
Thanks for all the wonderful tutorial ..great work.
i have question,
in time series prediction does multivariate give better result then uni-variate.
eg.- for “Beijing PM2.5 Data Set” we have multivariate data will the multivariate give better results, or by taking the single pollution data for uni-variate will give better result.
2 – what is better encoder-decoder or normal RNN for time series prediction.
Thank you very much! I would like to ask a question which seems silly…When training the model, we store the weights in training model. Are the inference encoder and inference decoder empty? At predict stage, the training model is not used, so how are the training model weights used to predict?
(great post, btw) I could also use a bit more. Here is my misunderstanding, 3 models were instantiated (train, infenc, infdec). One was trained (train) and developed weights that (hopefully) would generate accurate predictions.
Then the other two models are used to test the predictive power, but I do not understand where the weights from train were parsed and transferred to infenc and infdec, respectively. (and, I suspect I fundamentally am missing something about the keras infrastructure which informs this)
I recommend reviewing the define_models() function, you can see that model weights are shared between the models – but each model provides a different use case.
Hi Jason how to deal and implement this model if you have time series data with 3D shape (samples, timesteps, features) and can not /want not one hot encode them? Thank you in advance.
how would that look like ? And can I not do it with the inference part later only ? Sorry my questions could sound a bit stupid, I try to understand the topics.
Hi Jason,
thank you for sharing your codes. I used this for my own problem and it works, but I still get good prediction results on values that are far away from the ones used in the training. What could my problem be ? I made a regression using mse for loss, do I need a different loss function ?
Hi Jason, great contribution! when I use timeseries data for this model, can I also use not the shfitet case in the target data for y, so: model.fit([input, output], output) , so output=input.reversed() and than would this make sense as well? because I want to use sliding windows for input and output; and than shfiting by one for the output being would not make sense in my eyes.
lets say I trained with shape (1000,20,1) but I want to predict with (20000,20,1) than this would not work, because the sample size is bigger. how do I have to adjust this ?
output=list()
for t in range(2):
output_tokens, h, c = decoder_model.predict([target_seqs] + states_values)
output.append(output_tokens[0,0,:])
states_values = [h,c]
target_seq = output_tokens
it says the following: index 1000 is out of bounds for axis 0 with size 1000,
so the axis of the second one needs to be in the same length. But I will not train with the same length of data that I am predicting. How can this be solved?
still not working Jason, Unfortunately it seems like variable sequence length is not possible ? I trained my model with a part of the whole data and wanted to use in the inference the whole data ?
I correct myself: to I have to padd my data with zeros in the beginning of my training data since I want to use the last state of the encoder as initial state ?
I have 2 questions:
1- This example is using teacher forcing, right? I’m trying to re-implement it without teacher forcing but it fails. When I define the train model as (line 49 of your example): model = Model(encoder_inputs, decoder_outputs), it gives me this error: RuntimeError: Graph disconnected: cannot obtain value for tensor Tensor(“decoder_inputs:0”, shape=(?, n_units, n_output_features), dtype=float32) at layer “decoder_inputs”. The following previous layers were accessed without issue: [‘encoder_inputs’, ‘encoder_LSTM’]
2- Can you please explain a bit more about how you defined the decoder model? I don’t get what is happening in the part between line 52 to 60 of the code (copied below)? Why do you need to re-define the decoder_outputs? How the model is defined?
HI Jason, I looked at different pages and found that a seq2seq is not possible with variable length without manipulating the data with zeros etc. So in your example, is it right that you can only use in inference data with shape (100000,timesteps,features), so not having variable length? If not how you can change that ? thanks a lot for responding!
nice explanation, a last question: my timesteps woud be the same in all cases,just the sample size woud be different. The keras padding sequences shows only padding for timesteps or am I wrong ? in that case I would need to pad my samples
These are really awesome little tutorials and you do a great job explaining them.
Just as an FYI, to help out other readers, I had to use tensorflow v1.7 to get this to run with Keras 2.2.0. With older versions I got a couple of errors while initializing the models and with the newer v1.8 I got some session errors with TF.
Hello Jason, Your work has always been awesome. I have learned a lot form your tutorials.
I am trying a simple encoder-decoder model following your example but facing some problem.
my issue is vocabulary size where it is around 5600, which makes my one hot encoder really big and puts my pc to freeze. can you give some simple example in which I don’t need to one hot encode my data? I know about sparse_categorical_crossentropy but I am facing trouble implementing it. Maybe my approach is wrong. your guidance can help me a lot.
Hi Jason
Why I got this shape ((100000, 1, 6, 51), (100000, 1, 3, 51), (100000, 1, 3, 51)) when I run your code….Or Do I need to reshape or i did not copy correct
Because it shows you get ((100000,6, 51), (100000,3, 51), (100000,3, 51))
Try removing the bracket in the to_categorical argument, that is, try using
to_categorical(source, num_classes=cardinality) instead of
to_categorical([source], num_classes=cardinality).
+500
A bit annoying that this mishap is not fixed. My guess it is an intentional overlooking intended to enhance training value of the tutorial 🙂
A teaching method of sorts…
good explanations appreciate your sharings! I wanted to ask if in the line for the inference prediction
for t in range(n_steps):
you also could go with not the n_steps but also with one more ? Or why are you looping with n_steps? you also would get a result with for t in range(1), right= I hope you understood what I try to find out.
so in your code here below, you are predicting in a for loop with n_steps, what needs n_steps to be ? Can you also go with 1? or do you need that n_steps from the data shape (batch,n_steps,features) as timesteps? Because when you infdec.predict isnt the model is taking the whole target_seq for prediction at once why you need n_steps?
for t in range(n_steps):
# predict next char
yhat, h, c = infdec.predict([target_seq] + state)
# store prediction
output.append(yhat[0,0,:])
# update state
state = [h, c]
# update target sequence
target_seq = yhat
return array(output)
How do we use Normalized Discounted Cumulative Rate (NDCR) for evaluating the model?
Is it necessary to use NDCR or we can live with accuracy as a performance metric?
Hi,
I added the embediing matrix to your code and received an error related to matrix dimentions same as what Luke mentioned in the previous comments. do you have any post for adding embedding matrix to encoder-decoder?
Hi Jason, I was using your code to solve a regression problem. I have the data defined exactly like you have but instead of casting them to one-hot-vectors I wish to leave them integers or floats.
I modified the code as follows:
def define_models(n_input, n_output, n_units):
# define training encoder
encoder_inputs = Input(shape=(None, n_input))
encoder = LSTM(n_units, return_state=True)
encoder_outputs, state_h, state_c = encoder(encoder_inputs)
encoder_states = [state_h, state_c]
# define training decoder
decoder_inputs = Input(shape=(None, n_output))
decoder_lstm = LSTM(n_units, return_sequences=True, return_state=True)
decoder_outputs, _, _ = decoder_lstm(decoder_inputs, initial_state=encoder_states)
decoder_dense = Dense(n_output, activation='relu')
decoder_outputs = decoder_dense(decoder_outputs)
model = Model([encoder_inputs, decoder_inputs], decoder_outputs)
# define inference encoder
encoder_model = Model(encoder_inputs, encoder_states)
# define inference decoder
decoder_state_input_h = Input(shape=(n_units,))
decoder_state_input_c = Input(shape=(n_units,))
decoder_states_inputs = [decoder_state_input_h, decoder_state_input_c]
decoder_outputs, state_h, state_c = decoder_lstm(decoder_inputs, initial_state=decoder_states_inputs)
decoder_states = [state_h, state_c]
decoder_outputs = decoder_dense(decoder_outputs)
decoder_model = Model([decoder_inputs] + decoder_states_inputs, [decoder_outputs] + decoder_states)
# return all models
return model, encoder_model, decoder_model
However the model does not learn to predict for more than one future timesteps, gives correct prediction for only one ahead. Could you please suggest some solution. Much thanks!
I make the prediction then as follows:
def predict_sequence(infenc, infdec, source, n_steps):
state = infenc.predict(source)
output = list()
pred=np.array([0]).reshape(1,1,1)
for t in range(n_steps):
yhat, h, c = infdec.predict([pred]+state)
output.append(yhat[0,0,0])
state = [h, c]
pred = yhat
return array(output)
Hi Jason, thanks for great serial about MLs,
In this tutorial, i have a bit complex (I’m a beginner in Python. I just have a little AI and ML theory).
y set (target sequence) is a part of X1. Clearly, y specified by X (reserve and subset). So,
1, In train model, Have you use y in X1 as input sequence ( sequence X1(y) => sequence y )
2, Can i define y separate with X1 (such as not subset, reserve…)?
Thanks you!
hi sir
i want to generate seq from pretrained embedding and in details i have a set of embedding list and its corresponding sentence.and i want to have a model to generate sentence with that embedding data. but i don’t know how to develop that model.
Great work again! I am a big fan of your tutorials!
I am working on a water inflow forecast problem. I have access to weather predictions and I want to predict the water inflow, given the historical values of both weather and inflows.
I have tried a simple LSTM model with overlapping sequences (time series to supervised), taking weather predictions and past inflows as input, and outputting future inflows. This works pretty well.
Seeing all this Seq2Seq time series forecast trend, I have also tried it, by encoding the weather forecast and decoding them to water inflow (with past inflows as decoder inputs), expecting even better results.
But this Seq2Seq model is performing very poorly. Do you have an idea why? Should I give up this kind of models for my problem?
I have read couple of your blogs about seq2seq and lstm. Wondering how should I combine this encoder-decoder model with attention? My scenario is kind of translation.
hey Jason, I have 2 questions :
question 1 – how do you estimate a “confidence” for a whole sequence prediction in a neural translation model. i guess you could multiply the individual probabilities for each time-step. somehow i’m not sure that is a proper way to do it. another approach is to feed the output sequence probabilities into a binary classifier (confident/not-confident) and take its value as the confidence score.
question 2 – how do ensure that the whole sequence prediction in a neural translation model is the optimal sequence. if you have a greedy approach where you take the max at each time-step you end up with a sequence which itself is probably not the most likely one. i’ve heard of beam search and other approaches. do you have an idea of the state-of-the-art ?
You can do a greedy search through the predicted probabilities to get the most likely word at each step, but it does not mean that it is the best sequence.
I am dealing with the same scenario of sequences of integers.
Before you input the sequence, you need to reshape the sequences to 3D and best to train the model in mini batches as it will reset the states after every iteration which works really well for LSTM based model.
However, the inference encoder/decoder models (infenc and infdec) seem to still un-trained.
I don’t understand how, where, or when the information (weights, states, etc.) from the “train model” is transfer to the inference models.
At prediction time, you said that:
“During prediction, the inference_encoder model is used to encode the input sequence once which returns states that are used to initialize the inference_decoder model. From that point, the inference_decoder model is used to generate predictions step by step.”
But aren’t the inference_encoder and inference_decoder un-trained?
I just wonder why you specified the “epochs” to 1. Is it just because the accuracy already reach 100%?
If it were not the accuracy of 100% with the “epochs” equal to 1, should I switch to any other epoch number to get increased accuracy?
Hi Jason,
nice post as always, I enjoy reading your blog. I got on question here. I might missed something, but why do we need the shifted target sequence as input for the decoder? and one more question: why do we need to shift it? Would be nice if you can clearify that for me. Thanks in advance 🙂
Hi Jason,
Thank you very much for your blog and its excellent content. Regarding this post, it seems that the encoder_outputs is not used. Why don’t we use this out-put? Can we put an auto-decoder on top of it to reproduce the input1? Would this help the network in predicting the sequences?
Bests
Mostafa
Hi Jason, Thanks for the tutorial! I want to add BatchNormalization and Dropout layer after the decoder LSTM layer. Do you have any idea how I can do it?
Thank you so much for your exciting blog. It’s great and I have a question.
What if we have more than one input series that are related to each other and want to predict the result?
For example, predicting the weather which we have more than one features and series?
I need to ask one question that you may think is very silly question.
I have a sequence of integers indicating the locations visited by some user xyz having user type “category1”. I have many users belonging to one of the category and each user has visited some locations.
Given a sequence of some user, I want to predict on which location that user will go next. Also, I want to predict it by taking into consideration the user type/category.
The question is, how can we use the above post for the stated problem since in the post, the values are predicted in reverse order only.
@Jason, while giving free tips, mind that code should be working in the real world for large datasets. To_categorical is the worst thing to use and not keeping the memory footprint optimized. Hence, I would recommend re-edit of this post and using “sparse_softmax_cross_entropy_with_logits” as a proxy for “categorical_cross_entropy”. Seq2seq models are generally trained on large vocab datasets and your examples sadly don’t work. One has to go to other places for a solution. BTW, your posts are intuitive.
which is also introucing to the Encoder-Decoder LSTMs for
sequence-to-sequence prediction with example Python code which is very simple
model = Sequential()
model.add(LSTM(…, input_shape=(…)))
model.add(RepeatVector(…))
model.add(LSTM(…, return_sequences=True))
model.add(TimeDistributed(Dense(…)))
Can you please let me know the exact difference between both of these ? is the later one with simple 5 lines of code the implementation of this sophistcated in a better way using LSTM’s? or which is better?
I generally teach an approach to the encoder-decoder that uses an autoencoder architecture as it often gives the same or better results as the more advanced encoder-decoder.
I have chunks (each chunk has different length, from 700 rows to 2000 rows) of data that include multivariate Inputs (3 time series) and dependent series. For example my first chunk of data has 700 rows of 3 input time series and dependent (one output) time series. I want to use the 3 inputs and predict (generate) the dependent series.
How should I do it?
wouldn’t it be possible to input a sequence and output also a sequence instead of having to loop the inference decoder over the predicted outputs to obtain the whole predicted sequence?
any thoughts on what would be better?
my particular case is in predicting video frames using the approach of this post
Alejandro Oñate LatorreSeptember 9, 2019 at 2:49 am#
Hi!
I am trying to train my model with several gigabytes of data. My machine runs out of memory.
How can I do to train the batch model? I want to invoke the fit method with packages of 10,000 examples, but I don’t know how to do it.
I’m sure I’ll have questions come up here and there, but let me just say how amazed I am with the sheer number of topics you cover in your posts. This one in particular is so incredibly helpful. Thank you for all your work!
first of all, I want to thank you for your awesome website. It has helped me a great deal with writing my thesis so far!
I am currently trying to implement an autoencoder with teacher forcing. As my data is purely continous, I have been trying to avoid one-hot encoding. However, I got stuck on the question, how I should mark the beginning of my target sequence. I have tried using a number which is inside or outside the range of the numbers used in the source/target sequences, but the results are poor. My network seems to repeat the same output (with only small alterations) no matter what I feed as an input sequence. I may have made another mistake in my implementation, but maybe you have a asuggestion for me regarding the start of sequence “character”, when no one-hot encoding is used?
My output length is fixed. My question was rather regarding the type of data used. Let me try to rephrase it: Is their a standard way to mark the beginning and/or end of a sequence, if the sequence consists of continous (data type: double or float) data and I do NOT want to bin and one-hot encode it? An example of such a seuqnce could be a time series of sensor data.
I have a sequence problem. Each sample is one trajectory having 200 points in chronological order. Each point exists in a 2D grid, where each grid cell is represented by a unique integer id. e,g a trajectory of 10 points passes through following grid cells –> [23, 32, 38, 18, 58, 41, 28, 28, 30, 48]. How to model this problem?
I have 8000 samples, and each sample has a sequence of 200 points, and their is only one feature (that is grid cell number). What should be the shape of X, if this is (8000,200,1), then their are 200 timesteps and each time step has only one entry. then the problem would be to generate shifted sequence in get_dataset.
or other way is to use single timestep for all samples like (8000,1,200). is this logical to solve sequence to sequence problem with single timestep?
Hello, Jason, I would like to ask how to extract the status returned by each time part of LSTM, for example, I want to extract the output of the first and second time steps.
Using return_sequences=True, the function I want to achieve is to splicing the two outputs close to each other, followed by a Dense(1), how to realize this function, expect to get your answer, thank you
Hi and thanks a lot for writing this tutorial!
I’m going to have a stab at modifying this to predict/fill in the middle 1/3 of a long sentence.
Do you think that is possible and would you be able to give any pointers?
Hey Jason I wanted to know. Can this work with a dataframe where the label is one number and the target is a sequence.
example
dataframe
label | Prediction
9000 | [5000,8000,9000]
Like a one to many but i would want the model to give me a sequence based off of its label
is that possible with encoder-decoder? if not can you direct me to a better setup.
And sorry to bother you again.
You have used the keras layers to build seq2seq models many times in other blogs, such as:
model = Sequential()
model.add(LSTM(…, input_shape=(…)))
model.add(RepeatVector(…))
model.add(LSTM(…, return_sequences=True))
model.add(TimeDistributed(Dense(…)))
I am confused about what is the difference of this keras seq2seq from the above dynamic one in this blog?
Thank you!
Thanks for your reply. My english is not that good, so I did not understand your answer, could you elaborate it a bit please?
In the meanwhile using the following code proved me that (since keras 2.0) the Dense layer can handle 3 dimensional inputs:
from keras.layers import Dense, TimeDistributed
from keras.models import Sequential
from numpy import arange
batch = 3
steps = 10
features = 16
# model using TimeDistributed
model = Sequential()
model.add(TimeDistributed(Dense(8), input_shape=(steps, features)))
model.compile(loss=’mean_squared_error’, optimizer=’adam’, metrics=[‘accuracy’])
# model without TimeDistributed
model2 = Sequential()
model2.add(Dense(8, input_shape=(steps, features)))
model2.compile(loss=’mean_squared_error’, optimizer=’adam’, metrics=[‘accuracy’])
X = arange(batch * steps * features).reshape(batch, steps, features)
y = model.predict(X)
y2 = model.predict(X)
# both outputs are of the same shape
print(y.shape, y2.shape)
Can you please point out the reason why you don’t agree. I have got also the same understanding with the link you provided.
Following the code again to show what I mean. What is wrong with that (using keras 2.3.1)?
from keras.layers import Dense, TimeDistributed
from keras.models import Sequential
from numpy import arange
n_samples = 3
n_steps = 10
n_features = 16
# model using TimeDistributed
model = Sequential()
model.add(TimeDistributed(Dense(8), batch_input_shape=(n_samples, n_steps, n_features)))
model.compile(loss=’mean_squared_error’, optimizer=’adam’, metrics=[‘accuracy’])
# model without TimeDistributed
model2 = Sequential()
model2.add(Dense(8, batch_input_shape=(n_samples, n_steps, n_features)))
model2.compile(loss=’mean_squared_error’, optimizer=’adam’, metrics=[‘accuracy’])
X = arange(n_samples * n_steps * n_features).reshape(n_samples, n_steps, n_features)
y = model.predict(X)
y2 = model2.predict(X)
# both outputs are of the same shape: (3, 10, 8)
print(y.shape, y2.shape)
from keras.layers import Dense, TimeDistributed
from keras.models import Sequential
from numpy import arange
batch = 3
steps = 10
features = 16
# model using TimeDistributed
model = Sequential()
model.add(TimeDistributed(Dense(8), input_shape=(steps, features)))
model.compile(loss=’mean_squared_error’, optimizer=’adam’, metrics=[‘accuracy’])
# model without TimeDistributed
model2 = Sequential()
model2.add(Dense(8, input_shape=(steps, features)))
model2.compile(loss=’mean_squared_error’, optimizer=’adam’, metrics=[‘accuracy’])
X = arange(batch * steps * features).reshape(batch, steps, features)
y = model.predict(X)
y2 = model2.predict(X)
# both outputs are of the same shape: (3, 10, 8)
print(y.shape, y2.shape)
After training what variables are required for prediction
Error when checking model input: the list of Numpy arrays that you are passing to your model is not the size the model expected. Expected to see 2 array(s), but instead got the following list of 1 array:
Can we also use encoder decoder model for univariate data and give infinite output length also? For example giving input as 50 data points and output as 1000 data point? and will this work and give good results? If not, what will be the best way to train encoder and decoder model for seq to seq univariate prediction with arbitrary input and output length?
can you give me any example where you have trained the model with infinite output length of data points. My data is basically a univariate data of temperature program
Thank you for your reply!
But why the encoder-decoder in your link doesn’t use the decoder_inputs or inference model like in this post, instead of using the repeatvector() directly?
From what I understood here we train the model to predict only one step into the future, then using recursion we predict multiple steps, meanwhile the the lesson that I’ve linked you too, it trains the model to predict as many times as RepeatVector(n)
They are both encoder-decoder models but the linked model uses a simpler auto-encoder based architecture, whereas the example in this post is more complex but matches the original paper.
Thank you for sharing. This is pretty comprehensive. I wonder how you write so many blogs on so many topics being a single person. Really helpful to understand the models!
Thanks Jason for this presentation, please kindly help out, im not sure i know how to give new input sequence to the model without having to retrain it.
I modified the example for my application, it is fixing an input series of events each with a start and end point in seconds. The output sequence is a list of ‘fixes’ needed to repair the input sequence. The features/categorical values were high (upto 3000) so I converted/condensed the data into different formats first to experiment example shape below.
It works ok, but I think the output sequence is so long that there is often a few mistakes in there which has a big outcome on the results, as they all go out of sync.
Is there a way to skip the one_hot_encoding and feed the integer values straight in? I tinkered but it seems to be always expecting 3 dimensions in.
Then I can try the raw data. At the moment the arrays would take up too much ram at higher categorical levels.
Yes, you can use a sparse cross entropy loss and use target integers directly instead of one hot. For input, you can use an embedding and pas integers directly in.
Thanks Jason. Can you use the raw integers for output (y) also? Or do they always need to be one hot encoded? I updated the model and it fits ok, but having issues with the predict function.
I had to make the decoder dense layer = n_units (128) rather than features which is now 1, so within the predict function it goes wrong because I now have 1 feature and it is expecting more. I.e the decoder is.
“expected input_67 to have shape (82, 1) but got array with shape (82, 128)”
When saving the model for future use, I understand the train will need to be saved. But infenc and infdec need to be saved to make predictions as well right?
I am trying to add a masking layer to this example, as my sequences are all variable length padded with zeros at the end. It still works with no masking, but would like to see what difference masking makes to the output. Do you have any good tutuorials covering masking?
I tried the below code, however it makes no difference to the output, but increases training time by about x4.
one thing to add is, I usually want to output some sequences with different length, (eg: a simple conversation model), so what I am usually doing is, add an feature on target data. so, n_features will be:
n_features = 50 + 2
0 is in target data,
1~50 are real features
51 will be
target_in = [0] + target[:-1]
will be
target_in = [0] + target
target will be:
target = target + [51]
not sure if this is the right idea though.
plus, attention layer is implemented in keras. I am having hard time in implementing it on this seq2seq method…
my problem is to predict pen trajectory from a handwritting character image.
i have a feature vector extracted from the image which its size is (1,4096),(as my input vector).
i have a x and y coordinate vector which is the pen trajectory for the image,that its size is (1,20),(as my output vector).
the elements of these two vectors, have different values.I mean the elements of the output vectors are integers but the input vectors are real numbers or decimal.
i have 2000 train input vectors.
I am looking for an algorithm that after training it,for a specific input feature vector (1,4096),it could predict the output vector(1,20),pen trajectory coordinates.
can i use your “Encoder-Decoder Model for Sequence-to-Sequence Prediction”?!
it dose not matter that my input and output values are not in a same type?!
I recommend first checking the literature for similar projects, then test a suite of models in order to discover what works well/best for your specific dataset.
The purpose of the X_shifted input seems to be just to let the model where to start in the seq e.g. the first value. Why then do we feed in an exact shifted copy of X, and not just some sort of mask e.g. 0,1,1,1,1,1,1, etc?
Is there any other purpose to the X shifted input as the model works on through the seq past the first value? In my input sequences there are setions with a lot of repetative values, so not sure if this will cause issues.
Hi Jason, I’m working on an autoencoder for anomaly detection. I’ve tried your other tutorial on lstm autoencoders but it doesn’t fit the data (I get only the mean value as reconstructed signal). However if use only the “train” model of this tutorial as autoencoder (so [X,X] as input encoder and input decoder respectively) the model works perfectly as an autoencoder, recostructing a simplified signal. But if I run the inference model it doesn’t reconstruc the signal. Why does this happen? Can I use only the “train” model as an autoencoder?
Hi Jason! Thank you so much for your blog posts! I trained seq2seq network on one batch with 638 each with dimensions: 26*30 and predicts a sequence of 7 numbers using ‘mse’ as the loss function. However, when I calculate the mse loss and compare it to the one returned by history[‘loss’] they differ by ~0.2. Do you know how ‘mse’ is calculated for this input/output shape?
Hi Jason, thank you for you great posts.
I am not sure if I am getting something wrong here, but I run the complete code of this example and got an error.
The shape of the dataset returned by method get_dataset is (n_samples, 1, 3, 51) instead of (n_samples, 3, 51), which I think is the expected one to the model.
Then I get the error “expected input_9 to have 3 dimensions, but got array with shape (2, 1, 6, 51)”. I just copy and paste your code. What am I missing?
I ask you to guide me for a code that it can predict an output sequence from an input sequence.
for example, for every sample we have:
X(input)={1 ,2, 3, …,10} , Y(output) ={ 80,10,64,79,60}
that the output sequence type is completely different from the input sequence (X).
our input sequence is the feature vector extracted from an image in a specified class.
and the output sequence for every input sample is the place of a spesific object in an image from a specified class.
also i have a little database which it contains just 4000 sample.
can i use one-shot learning algorithm for training the Lstm network.
would you please guide me a code to implement one shot for sequence to sequence Lstm?
I think there’s an isssue with the dimensions of the generated data.
The example code doesn’t run (for me anyway), because the data is four dimensional rather than three dimensional. I fixed it by taking the first element of src, tar and tar2 encoded. Alternatively, call to_categorical with ‘source’ instead of ‘[source]’
There are other instances of the same issue in the comments section, even fairly recent: see Mairon, August 5 2020.
[quote]Then I get the error “expected input_9 to have 3 dimensions, but got array with shape (2, 1, 6, 51)”. I just copy and paste your code. What am I missing?[quote]
Upshot:
The example code (in the call to ‘to_categorical’) wraps/may wrap an addittional array/list around the generated training examples where this is not expected by the model, and the code doesn’t run as a result.
I don’t know why or if it’s a platform issue. I think we can agree it’s not desirable behaviour for example code though.
Dear Jason,
I have a problem and don’t know how to use LSTM for that.
The problem is arranging a set of actions, such as {B,D,F,A}, to the proper arrangement, i.e. (A,B,C,F). I have a database that includes the true arrangemetn of actions. Which architecture of the LSTM can I use?
when a turn the code i have this error:
ValueError: Input 0 of layer lstm_2 is incompatible with the layer: expected ndim=3, found ndim=4. Full shape received: [32, 1, 6, 51]
Hi Jason.
I’ve been struggling with the sek2sek problem for a while.
I have multi feature input of timeseries, about 10 features(less after PCA, but it is not in main focus of the question) and I need to predict sequence of (0, 1) values as output.
Let’s say my data look like this:
A, B y
0.3 0.3 0
0.4 0.1 0
0.2 0.2 0
0.7 0.5 1
. . 1
. . .
For sake of simplicity I want to predict sequence of 2 outputs based on 3 inputs.
From the example above one training example has shape of :
(3, 2), 3=input_size, 2=num_of_features and it should predict 2 values ex. [1, 0]
I know how to make windows, reshape inputs, build encoder and decoder, train model, test model…
The main problem is what should I do with discrete output?
Maybe I can try to observe it as single number [0, 1] (binary) = 2
Maybe I can try to make some embedding of my output.
Maybe I can just convert output to float.
It sounds like your problem is a binary classification, ensure you have a sigmoid activation function in the output layer and use binary cross entropy loss
Hello, I have a problem that I thought could be solved by an autocoder-decoder, the problem is that I don’t know if it is possible to start with a set of carctarisricas(18) and the latent space between autoencoder-decoder can be a matrix of dimension nxm, then use the decoder to rebuild the features
Could you tell me your opinion about it? it’s possible?
Not sure I follow, but my general advice is to try it and see – e.g. develop a small prototype and use it to learn more about how to frame the problem and what might work.
Hi Jason,
thank you for your posts and books. how would you modify the encoder-decoder if my input sequences consist of multiple features? For example, I have time series of temperature, pressure, humidity as input?
Thanks,
Jason,
another question if you don’t mind. I noticed you used teacher-forcing by shifting the target sequence by one time step. How would you modify the code to either removing teacher-forcing and using teacher forcing only, say 50% of the training steps?
Thank you
Hello, I see all the helpful answers you are providing in relation to seq2seq models… There is one question I have that nobody seems to be able to show a practical way to do… In the Keras examples https://keras.io/examples/nlp/lstm_seq2seq/ (pretty similar to yours), it has a function decode_sequence that decodes 1 sequence at a time (like your example)… I want to be able to ‘batch’ predict the seq2seq as 1 by one is ‘very’ slow’, whereas the model can quickly be built and evaluate in batch very quickly. The goal would be to provide a list of the training examples that are not correct predicted, again in a batch rather than 1 by 1. Is it even possible to do this? If so, what would the changes in the decode_sequence routine look like to handle batches? Thanks in advance.
when i run the code, in my notebook, i often get warning message, about retracing :
WARNING:tensorflow:11 out of the last 11 calls to <function Model.make_predict_function..predict_function at 0x000001B88FDEA268> triggered tf.function retracing
Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has experimental_relax_shapes=True option that relaxes argument shapes that can avoid unnecessary retracing.
Yes i can ignore but is make slow, any help to avoid this 😀
Intuitively what is the benefit of this encoder-decoder model, I mean if compare using normal
LSTM/RNN design when predicting sequence?
Is it more accurate? sequence prediction using this architecture?
Thanks for this great article Jason! Very informative.
When running this code without making any changes I get the following error when trying to train the model: “ValueError: Input 0 is incompatible with layer model: expected shape=(None, None, 51), found shape=(32, 1, 6, 51)”
It seems the “to_categorical” function adds an empty dimension to the generated array, resulting in a shape of: (100000, 1, 6, 51). I managed to remove this dimension and successfully train the model with the following code added after line 29 to the “get_dataset” function:
Dear Jason, do you know the reasoning behind choosing a ‘non informative’ start of sequence character for the decoder like 0, instead of using the last previous known value as a starting point?
Lets assume I’m trying to predict the path of a rolling ball, wouldn’t it make sense to provide the last vector of the ball in addition to the encoded state instead of a generic start index?
LSTM(n_units)
TensorFlow website mentioned that n_units refer dimensionality of the output vector space ( i.e. the number of feature for the hidden state ) and it does not refers to the number of LSTM unit created.
By default the no. of LSTM cell units is equal to the length of input Sequence
Hi, thanks for you tutorial. I have a question: if I train the model with a seq length of, let’s say, 600 and then use it for variable lengths sequences (e.g., 300, 1200) how my model is doing inference?
Also, how should I choose the training seq length and what a Bidirectional LSTM is learning from these sequences??
What if the my input sequence is a set of coordinates say [(3,0), (1,2), (4,5),(9,10),…] and my target sequence is a set of binary array say [0,1,1,0,…].
In this case, each time-step consists of 2 integers; (3, 0). In this case, how can i one-hot encode my input sequence?
Another question. I have variable sequence length for both input and output. My output is a binary array of 0s and1s.
The target has to be one time step ahead of the decoder input so i added a zero in front of the binary array. I also padded the binary array with zeros in order to create a fixed length length to the network.
Since my output is a binary arrays of 0s and1s, will the added zeros (starting value and padding values) confuse the network? Any suggestions?
Hi!
Thank you for this tutorial. It was highly informative.
I have a question on the “predict_sequence” function:
Why do you use a target_seq which is all zeroes? I would have expected an initial target sequence of [1,0, 0…, n_features], which should represent a 0 in the decoded sequence. Am I missing something?
Thank you for your answer. I’m still a little confused.
You write:
“We will use the value of 0 as the padding or start of sequence character, therefore it is reserved and we cannot use it in our source sequences. To achieve this, we will add 1 to our configured cardinality to ensure the one-hot encoding is large enough (e.g. a value of 1 maps to a ‘1’ value in index 1).”
So if “0” is the , shouldn’t it be one-hot encoded too?
“0” should be [1, 0, 0, …, 0].
This is confusing because in the inference decoder you use an initial input character which is all zeroes [0, 0, 0, …, 0] instead of [1, 0, 0, …, 0]. Shouldn’t we feed the symbol to the decoder to start the inference?
Is the decoder in your code being implemented as a Greedy Search decoder? If we want to use a beam search decoder, which part of the code should we change? Or is this question not relevant to this example? Thank you so much.
I used an encoder-decoder model for generating summarization news, but the predicted sequence is like this:
actual: [[‘startseq as of thursday facebook allows users to edit comments rather than retype them each comment will show its editing history in a dropdown menu to give users context editing will be rolled out to users gradually over the next few days endseq’]]
predicted: [‘startseq the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the’]
As you can see it generated a lot of “the”, have you ever encountered such a problem?
do you have any suggestion?
That happens when your model is not well-trained, or when the model is too simple for this job so it cannot hold the correct state to produce the sentence.
Is this model suited for sequence regression too? For example the shampoo sales problem
You could try, but generally LSTMs do not perform well on autoregression problems:
https://machinelearningmastery.com/suitability-long-short-term-memory-networks-time-series-forecasting/
Hello, can this example be applied to the prediction of floating point numbers?For example [0.123,0.234,0.345], the target is [0.234,0.123],
Yes, see an example here:
https://machinelearningmastery.com/how-to-develop-lstm-models-for-time-series-forecasting/
Hi, thank you for your post. I am new to LSTM. It looks like the target should always be a subset of the source, could we use LSTM to predict the target which is not a subset of the source? For example, the source is [0.123,0.234,0.345], and the target is [0.564, 0.923, 0.667]? Thanks in advance.
Yes, you can.
Hi. is it possible to have multi layers of LSTM in encoder and decoder in this code? thank you for your great blog
Yes, but I don’t have an example. For this specific case it would require some careful re-design.
Hi, maybe this time you got any idea of multi-layer of LSTM autoencoder?
Perhaps this will help as a start:
https://machinelearningmastery.com/lstm-autoencoders/
@Teimour @Dk @jason Brownlee Here is a great example of a multilayer encoder-decoder using the Keras functional API.
Could you give some more detail as to how it would need to be modified to have multiple LSTM layers in the decoder? I am working on something similar and looking to add layers to the decoder.
How can I extract the bottleneck layer to extract the important features with sequence data?
You could access the returned states to get the context vector, but it does not help you understand which input features are relevant/important.
Thank you Jason!
You’re welcome.
Thanks for the wonderful tutorial, Jason!
I am facing an issue, though: I tried to execute your code as is (copy-pasted it), but it throws an error:
Using TensorFlow backend.
Traceback (most recent call last):
File “C:\Users\User\Documents\pystuff\keras_auto.py”, line 91, in
train, infenc, infdec = define_models(n_features, n_features, 128)
File “C:\Users\User\Documents\pystuff\keras_auto.py”, line 40, in define_models
encoder = LSTM(n_units, return_state=True)
File “C:\Users\User\Anaconda3\envs\py35\lib\site-packages\keras\legacy\interfaces.py”, line 88, in wrapper
return func(*args, **kwargs)
File “C:\Users\User\Anaconda3\envs\py35\lib\site-packages\keras\layers\recurrent.py”, line 949, in __init__
super(LSTM, self).__init__(**kwargs)
File C:\Users\User\Anaconda3\envs\py35\lib\site-packages\keras\layers\recurrent.py”, line 191, in __init__
super(Recurrent, self).__init__(**kwargs)
File “C:\Users\User\Anaconda3\envs\py35\lib\site-packages\keras\engine\topology.py”, line 281, in __init__
raise TypeError(‘Keyword argument not understood:’, kwarg)
TypeError: (‘Keyword argument not understood:’, ‘return_state’)
I am using an anaconda environment (python 3.5.3). What could have possibly gone wrong?
Perhaps confirm that you have the most recent version of Keras and TensorFlow installed.
I had the same problem, and updated Keras (to version 2.1.2) and TensorFlow (to version 1.4.0). The problem above was solved. However, I now see that the shapes of X1, X2, and y are ((100000, 1, 6, 51), (100000, 1, 3, 51), (100000, 1, 3, 51)) instead of ((100000, 6, 51), (100000, 3, 51), (100000, 3, 51)). Why could this be?
I’m not sure, perhaps related to recent API changes in Keras?
Here’s how I fixed the problem.
At the top of the code, include this line (before any ‘from numpy import’ statements:
import numpy as np
Change the get_dataset() function to the following:
Notice instead of returning array(X1), array(X2), array(y), we now return arrays that have been squeezed – one axis has been removed. We remove axis 1 because it’s the wrong shape for what we need.
The output is now as it should be (although I’m getting 98% accuracy instead of 100%).
Thanks for sharing.
Perhaps confirm that you have updated Keras to 2.1.2, it fixes bugs with to_categorical()?
yes, we have to reshape the model and then everything works fine
what is(n_in, cardinality)?
I am facing difficulty in using it with a user-defined variable.for random what should be the input and input shape for the arguments
See this:
https://machinelearningmastery.com/faq/single-faq/what-is-the-difference-between-samples-timesteps-and-features-for-lstm-input
I removed the brackets [ ] in the parameters to to_categorical instead. I think because parameters like target etc are already arrays the brackets are not necessary.
Fair enough.
As I was facing the same issue I think the simpler solution is just use:
to_categorical(source, num_classes=cardinality)instead of
to_categorical([source], num_classes=cardinality).shapefor the 3 lists.
I also had to do that to get the data in the right format. There’s also a function tensorflow.one_hot which I prefer over to_categorical. They do the same thing.
Hi Jason!
Are the encoder-decoder networks suitable for time series classification?
In my experience LSTMs have not proven effective at autoregression compared to MLPs.
See this post for more details:
https://machinelearningmastery.com/suitability-long-short-term-memory-networks-time-series-forecasting/
for people later, you don’ t need to use squeeze,
Let ‘s try:
from
src_encoded = to_categorical([source], num_classes=cardinality)
tar_encoded = to_categorical([target], num_classes=cardinality)
tar2_encoded = to_categorical([target_in], num_classes=cardinality)
to:
src_encoded = to_categorical(source, num_classes=cardinality)
tar_encoded = to_categorical(target, num_classes=cardinality)
tar2_encoded = to_categorical(target_in, num_classes=cardinality)
Thanks.
Thanks Jason, for writing blogs for machinelearningmastery.com. I have seen no. of blogs.
I have one query – –
In my dataset —-
no. of columns are 5 (inputs),
No. of outputs – 3 (feature , which I want to predict) and
number of rows – 34079.
Then how to put these parameters in your code –
n_features = 34079
n_steps_in = 5
n_steps_out = 3
# generate training dataset
X1, X2, y = get_dataset(n_steps_in, n_steps_out, n_features, 1)
print(X1.shape,X2.shape,y.shape)
I am getting error like ——–>>> Your session crashed after using all available RAM. View runtime logs. I am using 14Gb RAM. please suggest me how to arrange my parameters as per your code.. thanks in advance.
Sounds like you might need to reduce your dataset size or use a machine with more RAM?
Thanks Jason for for reply,
but I think, I may not be keeping parameters properly in the variables.
In my dataset —-
no. of columns are 5 (inputs),
No. of outputs – 3 (feature , which I want to predict) and
number of rows – 34079.
then how to put in your variables —
n_features = ???
n_steps_in = 5
n_steps_out = 3
sample = ???
thanks
Ah I see, this will help you map your problem onto the terminology of samples, time steps, features:
https://machinelearningmastery.com/faq/single-faq/what-is-the-difference-between-samples-timesteps-and-features-for-lstm-input
Does that help?
Hi Jason,
running the get_dataset the function returns one additional row in the Arrays X1, X2, y:
(1,1,6,51) (1,1,3,51)(1,1,3,51).
This results form numpy.array(), before the X1, X2, y are lists with the correct sizes:
(1,6,51) (1,3,51)(1,3,51).
It seems the comand array() adds an additional dimension. Could you help on solving this problem?
how to train the keras ,it has to identify capital letter and small letter has to same
Please suggest any tactics for it.
Start by clearly defining your problem:
http://machinelearningmastery.com/how-to-define-your-machine-learning-problem/
Could you please give me a tutorial for a case where we are input to the seq2seq model is word embeddings and outputs is also word embeddings. I find it frustrating to see a Dense layer at the end. this is what is stopping a fully seq2seq model with input as well as output word embeddings.
Why would we have a word embedding at the output layer?
If embeddings are coming in, we’d want to have embeddings going out (auto-encoder). Imagine input = category (cat, dog, frog, wale, human). These animals are quite different, so we represent w/ embedding. Rather than having a dense output of 5 OHE, if an embedding is used for output, the assumption is that, especially if weights are shared between inputs + outputs, we could train the net with and give it more detail about what exactly each class is… rather than use something like cross entropy.
Ok.
Is there such a tutorial yet? Sounds interesting.
I’ve not written one, I still don’t get/see benefit in the approach. Happy to be proven wrong.
Hi Jason,
I am trying to put embedding layer at encoder and decoder input with dense layer as it as you mentioned in the above code.
Later in the prediction function call, when I give 3D input to target_seq, it throws dimensional error: Error when checking input: expected Decoder_input to have 2 dimensions, but got array with shape (1, 1, 341), here 341 is my original feature dimension which is compressed to 32 by embedding layer.
Could you please advice, what’s going wrong.
I cannot debug your changes, sorry. Perhaps post your code and error to stackoverflow?
Thanks Jason. Just wanted to get an idea in scenarios when decoder_input and decoder_output have different dimensions, what happens to your prediction function (target_seq) shape?
Could you please guide.
Not sure off the cuff, I think you will need to experiment.
Hi ! When adding dropout and recurrent_dropout as LSTM arguments on line 40 of the last complete code example with everything else being the same, the code went wrong. So how can I add dropout in this case? Thanks!
I give a worked example of dropout with LSTMs here:
https://machinelearningmastery.com/use-dropout-lstm-networks-time-series-forecasting/
Hi Jason! Thanks for your great effort to put encoder decoder implementations here. As Dinter mentioned, when dropout is added, the code runs well for training phase but gives following error during prediction.
InvalidArgumentError (see above for traceback): You must feed a value for placeholder tensor ‘lstm_1/keras_learning_phase’ with dtype bool
[[Node: lstm_1/keras_learning_phase = Placeholder[dtype=DT_BOOL, shape=, _device=”/job:localhost/replica:0/task:0/cpu:0″]()]]
How to fix the problem in this particular implementation?
[Note: Your worked example of dropout however worked for me, but the difference is you are adding layer by layer in sequential model there which is different than this example of encoder decoder]
Sorry to hear that, perhaps it’s a bug? See if you can reproduce the fault on a small standalone network?
When I tried with exactly the same network in the example you presented and added dropout=0.0 in line 10 and line 15 of define_models function, the program runs but for other values of dropout it gives error. Also changing the size of network, for example, number of units to 5, 10, 20 does give the same error.
Any idea to add dropout?
line 5: encoder = LSTM(n_units, return_state=True,dropout=0.0)
line 10: decoder_lstm = LSTM(n_units, return_sequences=True, return_state=True,dropout=0.0)
See this tutorial:
https://machinelearningmastery.com/use-dropout-lstm-networks-time-series-forecasting/
Hi Jason,
what is the difference between specifying the model input:
Model( [decoder_inputs] + decoder_states_inputs,….)
and this
Model([decoder_inputs,decoder_states_inputs],…)
Does the 1st version add the elements of decoder_states_inputs array to corresponding elements of decoder_inputs
Hi Jason, Thanks for sharing this tutorial. I am only confused when you are defining the model. This is the line:
train, infenc, infdec = define_models(n_features, n_features, 128)
It is a silly question but why n_features in this case is used for the n_input and for the n_output instead of n_input equal to 6 and n_output equal to 3 ?
I look forward to hearing from you soon.
Thanks
Good question, because the model only does one time step per call, so we walk the input/output time steps manually.
Hi Jason, I got the same doubt as above. Can you please explain once again. Sorry, I didn’t understand your reply
I would like to see the hidden states vector. Because there are 96 training samples, there would be 96 of these (each as a vector of length 4).
I added the “return_sequences=True” in the LSTM
model = Sequential()
model.add( LSTM(4, input_shape=(1, look_back), return_sequences=True ) )
model.add(Dense(1))
model.compile(loss=’mean_squared_error’, optimizer=’adam’)
model.fit(trainX, trainY, epochs=20, batch_size=20, verbose=2)
But, I get the error
Traceback (most recent call last):
File “”, line 1, in
File “E:\ProgramData\Anaconda3\lib\site-packages\keras\models.py”, line 965, in fit
validation_steps=validation_steps)
File “E:\ProgramData\Anaconda3\lib\site-packages\keras\engine\training.py”, line 1593, in fit
batch_size=batch_size)
File “E:\ProgramData\Anaconda3\lib\site-packages\keras\engine\training.py”, line 1430, in _standardize_user_data
exception_prefix=’target’)
File “E:\ProgramData\Anaconda3\lib\site-packages\keras\engine\training.py”, line 110, in _standardize_input_data
‘with shape ‘ + str(data_shape))
ValueError: Error when checking target: expected dense_24 to have 3 dimensions, but got array with shape (94, 1)
How can I make this model work, and also how can I view the hidden states for each of the input samples (should be 96 hidden states).
Thank you.
Return sequences does not return the hidden state, but instead the outcome from each time step.
This post might clear things up for you regarding outputs and hidden states:
https://machinelearningmastery.com/return-sequences-and-return-states-for-lstms-in-keras/
Hi Jason,
I like your blog posts. I have some code based on this post, but I get this error message all the time. There’s something wrong with my dense layer. Can you point it out? Here units is 300 and tokens_per_sentence is 25.
an error message:
ValueError: Error when checking target: expected dense_layer_b to have 2 dimensions, but got array with shape (1, 25, 300)
this is some code:
Perhaps the data does not match the model, you could change one or the other.
I’m eager to help, but I cannot debug the code for you sorry.
hi. so I think I needed to set ‘return_sequences’ to True for both lstm_a and lstm_b.
Dear Jason,
Do you think that this algorithm works for weather prediction? For example, by having the input integer variables as dew point, humidity, and temperature, to predict rainfall as output
Only for demonstration purposes.
In practice, weather forecasts are performed using simulations of physics models and are more accurate than small machine learning models.
Hi Jason.
I would like tou ask you, how could I use this model with float numbers? Yours training data seems like this:
[[
[0,0,0,0,1,0,0]
[0,0,1,0,0,1,0]
[0,1,0,0,0,0,0]]
.
.
.
]]
I would need something like this:
[[
[0.12354,0.9854,5875, 0.0659]
[0.12354,0.9854,5875, 0.0659]
[0.12354,0.9854,5875, 0.0659]
[0.12354,0.9854,5875, 0.0659]
]]
Whan i run your model with float numbers, the network doesn’t learn. Should I use some different LOSS function?
Thank you
The loss function is related to the output, if you have a real-valued output, consider mse or mae loss functions.
How to add bidirectional layer in encoder decoder architecture?
Use it directly on the encoder or decoder.
Here’s how to in Keras:
https://machinelearningmastery.com/develop-bidirectional-lstm-sequence-classification-python-keras/
Hi.
I would like to use your model with word embedding. I was inspired by https://blog.keras.io/a-ten-minute-introduction-to-sequence-to-sequence-learning-in-keras.html ->features -> word-level model
I decoded words in sentences as integer numbers. My input is list of sentences with 15 words. [[1,5,7,5,6,4,5, 10,15,12,11,10,8,1,2], […], [….], …]
My model seems:
encoder_inputs = Input(shape=(None,))
x = Embedding(num_encoder_tokens, latent_dim)(encoder_inputs)
x, state_h, state_c = LSTM(latent_dim, return_state=True)(x)
encoder_states = [state_h, state_c]
# Set up the decoder, using
encoder_statesas initial state.decoder_inputs = Input(shape=(None,))
x = Embedding(num_decoder_tokens, latent_dim)(decoder_inputs)
x = LSTM(latent_dim, return_sequences=True)(x, initial_state=encoder_states)
decoder_outputs = Dense(num_decoder_tokens, activation=’softmax’)(x)
# Define the model that will turn
#
encoder_input_data&decoder_input_dataintodecoder_target_datamodel = Model([encoder_inputs, decoder_inputs], decoder_outputs)
Whan i try to train the model, i get this error: expected dense_1 to have 3 dimensions, but got array with shape (10, 15). Could you help me with that please?
Thank you
Hello,
I also have the same issue. could you solve your problem?
Hi ,
I am trying to do seq2seq problem using Keras – LSTM. Predicted output words matches with most frequent words of the vocabulary built using the dataset. Not sure what could be the reason. After training is completed while trying to predict the output for the given input sequence model is predicting same output irrespective of the input seq. Also using separate embedding layer for both encoder and decoder.
Can you help me what could be the reason ?
Question elaborated here:
https://stackoverflow.com/questions/49638685/keras-seq2seq-model-predicting-same-output-for-all-test-inputs
Thanks.
It suggests the model has not learned the problem.
Here are a list of ideas to try:
http://machinelearningmastery.com/improve-deep-learning-performance/
Hi Jason,
In your current setup, how would you add a pre-trained embedding matrix, like glove?
Here are some examples of loading a word embedding:
https://machinelearningmastery.com/use-word-embedding-layers-deep-learning-keras/
Hi,
Could you help me with my problem? I think that a lot of required logic is implemented in your code but I am very beginner in python. I want to predict numbers according to input test sequence (seq2seq) so output of my decoder should by sequence of 6 numbers (1-7). U can imagine it as lottery prediction. I have very long input vector of numbers 1-7 (contains sequenses of 6 numbers) so I don’t need to generate test data. I just need to predict next 6 numbers which should be generated. 1,1,2,2,3 -> 3,4,4,5,5,6
Thank you
Perhaps here would be a good place for you to get stared with LSTMs:
https://machinelearningmastery.com/start-here/#lstm
Thank you Jason, it was very helpful for me. And can you give me advice or link how to correctly initiate and train network with multiple input sequences?
They can be side by side:
https://machinelearningmastery.com/multivariate-time-series-forecasting-lstms-keras/
Or separate inputs entirely:
https://machinelearningmastery.com/keras-functional-api-deep-learning/
Thank you Jason for this tutorial it gets me started. I tried to use larger sequence where input is 400 series of numbers and output is 40 numbers. I have problem with categorical because of index error and i don’t know how to set or get the the value for cardinality/n_features. Can you give me an idea on this?
Im also not clear if this is a classification type of model. Can you please confirm. Thanks
You can integer encode or one hot encode categorial input features. Here is a tutorial on the topic:
https://machinelearningmastery.com/how-to-one-hot-encode-sequence-data-in-python/
This post will make the distinction between classification and regression clear:
https://machinelearningmastery.com/classification-versus-regression-in-machine-learning/
Hi,
thank you for this totu, please i receive this error when i run your example :
ValueError: Error when checking input: expected input_1 to have 3 dimensions, but got array with shape (100000, 1, 6, 51)
Hi! I have the same problem.. Did you solve it ? Thanks!
change this:
src_encoded = to_categorical([source], num_classes=cardinality)[0]
tar_encoded = to_categorical([target], num_classes=cardinality)[0]
tar2_encoded = to_categorical([target_in], num_classes=cardinality)[0]
Hi Jason, thank you very much for the tutorial. Is it possible to decode many sequences simultaneously instead of decoding a single sequence one character at a time? The inference for my project takes too long and I thought that doing it in larger batches may help.
You could use copies of the model to make prediction in parallel for different inputs.
Hi im just wondering why do we need to use to_categorical if the sequence is already numbers. On my case i have a series of input features(numbers) and another series of output features(number). Should i still use to_categorical method?
Good question, it will one hot encode the numbers:
https://keras.io/utils/#to_categorical
Hi Jason,
I am working on word boundary detection problem where dataset containing .wav files in which a sentence is spoken are given, and corresponding to each .wav file a .wrd file is also given which contains the words spoken in a sentence and also its boundaries (starting and end boundaries).
Our task is to identify word boundaries in test .wav file (words spoken will also be given).
I want to do this with sequential models .
What I have tried is:
I have read .wav files using librosa module in numpy array (made it equal to max size using padding)
Its output is like 3333302222213333022221333302222133333 (for i/p ex: I am hero)
where (0:start of word, 1:end of word, 2:middle, 3:space)
means I want to solve this as supervised learning problem, can I train such model with RNN?
Sounds like a great project.
I don’t have examples of working with audio data sorry, I cannot give you good off the cuff advice.
Perhaps find some code bases on related modeling problems and use them for inspiration?
Hello.
I’ve tried this example for word-level chatbot. Everything works great, on a small data (5000 sentences)
When I use dataset of 50 000 sentences something is wrong. Model accuracy is 95% but when i try to chat with this chatbot, responses are generated randomly. Chatbot is capable of learning sentences from dataset, but it use them randomly to respond to users questions.
How it is possible, when accuracy is so hight?
Thanks
Perhaps it memorized the training data? E.g. overfitting?
Sir, how to create confusion matrix, evaluated and the accuracy printed for this model :
# Define an input sequence and process it.
encoder_inputs = Input(shape=(None, num_encoder_tokens))
encoder = LSTM(latent_dim, return_state=True)
encoder_outputs, state_h, state_c = encoder(encoder_inputs)
# We discard
encoder_outputsand only keep the states.encoder_states = [state_h, state_c]
# Set up the decoder, using
encoder_statesas initial state.decoder_inputs = Input(shape=(None, num_decoder_tokens))
# We set up our decoder to return full output sequences,
# and to return internal states as well. We don’t use the
# return states in the training model, but we will use them in inference.
decoder_lstm = LSTM(latent_dim, return_sequences=True, return_state=True)
decoder_outputs, _, _ = decoder_lstm(decoder_inputs,
initial_state=encoder_states)
decoder_dense = Dense(num_decoder_tokens, activation=’softmax’)
decoder_outputs = decoder_dense(decoder_outputs)
# Define the model that will turn
#
encoder_input_data&decoder_input_dataintodecoder_target_datamodel = Model([encoder_inputs, decoder_inputs], decoder_outputs)
model.compile(optimizer=’rmsprop’, loss=’categorical_crossentropy’, metrics=[‘accuracy’])
model.fit([encoder_input_data, decoder_input_data], decoder_target_data,
batch_size=batch_size,
epochs=epochs,
validation_split=0.2)
model.summary()
Here is information on how to calculate a confusion matrix:
https://machinelearningmastery.com/confusion-matrix-machine-learning/
Hi Jason,
Thank you for this awesome tutorial, so useful. I have one simple question. Is there any specific
reason why use 50+1 as n_features?
Please advise
The +1 is to leave room for the “0” value, for “no data”.
Hi Jason,
Thanks for all the wonderful tutorial ..great work.
i have question,
in time series prediction does multivariate give better result then uni-variate.
eg.- for “Beijing PM2.5 Data Set” we have multivariate data will the multivariate give better results, or by taking the single pollution data for uni-variate will give better result.
2 – what is better encoder-decoder or normal RNN for time series prediction.
For both questions, it depends on the specific problem.
Hi Jason, here it looks like one time step in the model. What do I have to change to add here more time steps in the model ?
# returns train, inference_encoder and inference_decoder models
def define_models(n_input, n_output, n_units):
# define training encoder
encoder_inputs = Input(shape=(None, n_input))
encoder = LSTM(n_units, return_state=True)
encoder_outputs, state_h, state_c = encoder(encoder_inputs)
encoder_states = [state_h, state_c]
# define training decoder
decoder_inputs = Input(shape=(None, n_output))
decoder_lstm = LSTM(n_units, return_sequences=True, return_state=True)
decoder_outputs, _, _ = decoder_lstm(decoder_inputs, initial_state=encoder_states)
decoder_dense = Dense(n_output, activation=’softmax’)
decoder_outputs = decoder_dense(decoder_outputs)
model = Model([encoder_inputs, decoder_inputs], decoder_outputs)
# define inference encoder
encoder_model = Model(encoder_inputs, encoder_states)
# define inference decoder
decoder_state_input_h = Input(shape=(n_units,))
decoder_state_input_c = Input(shape=(n_units,))
decoder_states_inputs = [decoder_state_input_h, decoder_state_input_c]
decoder_outputs, state_h, state_c = decoder_lstm(decoder_inputs, initial_state=decoder_states_inputs)
decoder_states = [state_h, state_c]
decoder_outputs = decoder_dense(decoder_outputs)
decoder_model = Model([decoder_inputs] + decoder_states_inputs, [decoder_outputs] + decoder_states)
# return all models
return model, encoder_model, decoder_model
Hi Jason,
Thank you very much! I would like to ask a question which seems silly…When training the model, we store the weights in training model. Are the inference encoder and inference decoder empty? At predict stage, the training model is not used, so how are the training model weights used to predict?
Looking forward to your reply. Thank you!
No silly questions here!
The state of the model is reset at the end of each batch.
Get it. Thank you a lot!
Glad to hear it.
Can you kindly explain this a bit more. I don’t seem to understand how model.fit relates to inference_encoder/decoder. Thank you!
(great post, btw) I could also use a bit more. Here is my misunderstanding, 3 models were instantiated (train, infenc, infdec). One was trained (train) and developed weights that (hopefully) would generate accurate predictions.
Then the other two models are used to test the predictive power, but I do not understand where the weights from
trainwere parsed and transferred to infenc and infdec, respectively. (and, I suspect I fundamentally am missing something about the keras infrastructure which informs this)Same question here, was wondering how the weights from train are used in infenc
Good question.
I recommend reviewing the define_models() function, you can see that model weights are shared between the models – but each model provides a different use case.
Can this model described in this blog post be used when we have variable length input? How.
And also variable length output.
Yes, it processes time steps one at a time, therefore supports variable length by default.
Hi Jason how to deal and implement this model if you have time series data with 3D shape (samples, timesteps, features) and can not /want not one hot encode them? Thank you in advance.
You can integer encode the inputs and use an embedding layer on the input.
how would that look like ? And can I not do it with the inference part later only ? Sorry my questions could sound a bit stupid, I try to understand the topics.
I provide a ton more help on preparing data for LSTMs here:
https://machinelearningmastery.com/faq/single-faq/how-do-i-prepare-my-data-for-an-lstm
Hi Jason,
thank you for sharing your codes. I used this for my own problem and it works, but I still get good prediction results on values that are far away from the ones used in the training. What could my problem be ? I made a regression using mse for loss, do I need a different loss function ?
I have some suggestions for improving model skill here that may give you some ideas:
http://machinelearningmastery.com/improve-deep-learning-performance/
Hi Jason, great contribution! when I use timeseries data for this model, can I also use not the shfitet case in the target data for y, so: model.fit([input, output], output) , so output=input.reversed() and than would this make sense as well? because I want to use sliding windows for input and output; and than shfiting by one for the output being would not make sense in my eyes.
Not sure I follow sorry.
Perhaps this post will make things clearer:
https://machinelearningmastery.com/convert-time-series-supervised-learning-problem-python/
lets say I trained with shape (1000,20,1) but I want to predict with (20000,20,1) than this would not work, because the sample size is bigger. how do I have to adjust this ?
output=list()
for t in range(2):
output_tokens, h, c = decoder_model.predict([target_seqs] + states_values)
output.append(output_tokens[0,0,:])
states_values = [h,c]
target_seq = output_tokens
Why would it not work?
it says the following: index 1000 is out of bounds for axis 0 with size 1000,
so the axis of the second one needs to be in the same length. But I will not train with the same length of data that I am predicting. How can this be solved?
Perhaps double check your data.
still not working Jason, Unfortunately it seems like variable sequence length is not possible ? I trained my model with a part of the whole data and wanted to use in the inference the whole data ?
I correct myself: to I have to padd my data with zeros in the beginning of my training data since I want to use the last state of the encoder as initial state ?
I have 2 questions:
1- This example is using teacher forcing, right? I’m trying to re-implement it without teacher forcing but it fails. When I define the train model as (line 49 of your example): model = Model(encoder_inputs, decoder_outputs), it gives me this error: RuntimeError: Graph disconnected: cannot obtain value for tensor Tensor(“decoder_inputs:0”, shape=(?, n_units, n_output_features), dtype=float32) at layer “decoder_inputs”. The following previous layers were accessed without issue: [‘encoder_inputs’, ‘encoder_LSTM’]
2- Can you please explain a bit more about how you defined the decoder model? I don’t get what is happening in the part between line 52 to 60 of the code (copied below)? Why do you need to re-define the decoder_outputs? How the model is defined?
# define inference decoder
decoder_state_input_h = Input(shape=(n_units,))
decoder_state_input_c = Input(shape=(n_units,))
decoder_states_inputs = [decoder_state_input_h, decoder_state_input_c]
decoder_outputs, state_h, state_c = decoder_lstm(decoder_inputs, initial_state=decoder_states_inputs)
decoder_states = [state_h, state_c]
decoder_outputs = decoder_dense(decoder_outputs)
decoder_model = Model([decoder_inputs] + decoder_states_inputs, [decoder_outputs] + decoder_states)
# return all models
Correct. If performance is poor without teacher forcing, then don’t train without it. I’m not sure why you would want to remove it?!?
The decoder is a new model that uses parts of the encoder. Does that help?
HI Jason, I looked at different pages and found that a seq2seq is not possible with variable length without manipulating the data with zeros etc. So in your example, is it right that you can only use in inference data with shape (100000,timesteps,features), so not having variable length? If not how you can change that ? thanks a lot for responding!
Generally, variable length inputs can be truncated or padded and a masking layer can be used to ignore the padding.
Alternately, the above model can be used time-step wise, allowing truely multivariate inputs.
nice explanation, a last question: my timesteps woud be the same in all cases,just the sample size woud be different. The keras padding sequences shows only padding for timesteps or am I wrong ? in that case I would need to pad my samples
Good question. Only the time steps and feature dimensions are fixed, the number of samples can vary.
Jason,
These are really awesome little tutorials and you do a great job explaining them.
Just as an FYI, to help out other readers, I had to use tensorflow v1.7 to get this to run with Keras 2.2.0. With older versions I got a couple of errors while initializing the models and with the newer v1.8 I got some session errors with TF.
Thanks for the tip.
Hello Jason, Your work has always been awesome. I have learned a lot form your tutorials.
I am trying a simple encoder-decoder model following your example but facing some problem.
my issue is vocabulary size where it is around 5600, which makes my one hot encoder really big and puts my pc to freeze. can you give some simple example in which I don’t need to one hot encode my data? I know about sparse_categorical_crossentropy but I am facing trouble implementing it. Maybe my approach is wrong. your guidance can help me a lot.
Thanks once again for such great tutorials…..
Perhaps try a word embedding instead?
Or, perhaps try training on an EC2 instance?
Hi Jason
Why I got this shape ((100000, 1, 6, 51), (100000, 1, 3, 51), (100000, 1, 3, 51)) when I run your code….Or Do I need to reshape or i did not copy correct
Because it shows you get ((100000,6, 51), (100000,3, 51), (100000,3, 51))
Is your version of Keras up to date?
Did you copy all of the code exactly?
Hi Jason, the version is different i put this
X1 = np.squeeze(array(X1), axis=1)
X2 = np.squeeze(array(X2), axis=1)
y = np.squeeze(array(y), axis=1)
Its Ok now, What are you doing is called many to one encoding? and in decoding case is it called one to many or?
another question I want to remove those one hot encode, I want to encode the exactly number and predict the exactly number
Also to remove this option src_encoded = to_categorical([source], num_classes=cardinality)
but I got a lot of error
I have advice on changing between regression/classification in keras:
https://machinelearningmastery.com/faq/single-faq/how-can-i-change-a-neural-network-from-regression-to-classification
Try removing the bracket in the to_categorical argument, that is, try using
to_categorical(source, num_classes=cardinality) instead of
to_categorical([source], num_classes=cardinality).
+500
A bit annoying that this mishap is not fixed. My guess it is an intentional overlooking intended to enhance training value of the tutorial 🙂
A teaching method of sorts…
I think the API changed. I need to fix it…
Hi Jason,
good explanations appreciate your sharings! I wanted to ask if in the line for the inference prediction
for t in range(n_steps):
you also could go with not the n_steps but also with one more ? Or why are you looping with n_steps? you also would get a result with for t in range(1), right= I hope you understood what I try to find out.
Sorry, i don’t follow. Perhaps you can provide more details?
so in your code here below, you are predicting in a for loop with n_steps, what needs n_steps to be ? Can you also go with 1? or do you need that n_steps from the data shape (batch,n_steps,features) as timesteps? Because when you infdec.predict isnt the model is taking the whole target_seq for prediction at once why you need n_steps?
for t in range(n_steps):
# predict next char
yhat, h, c = infdec.predict([target_seq] + state)
# store prediction
output.append(yhat[0,0,:])
# update state
state = [h, c]
# update target sequence
target_seq = yhat
return array(output)
Sure, you can set it to 1.
and what is the benefit of using 1 or a higher iteration number ?
for multi-step forecasts.
In the “def define_models()”, there are three models: model, encoder_model, decoder_model,
what is the function of encoder_model and decoder_model? Can I use only the “model” for
prediction? Looking forward to your reply
You can learn more about the architecture here:
https://machinelearningmastery.com/encoder-decoder-long-short-term-memory-networks/
How do we use Normalized Discounted Cumulative Rate (NDCR) for evaluating the model?
Is it necessary to use NDCR or we can live with accuracy as a performance metric?
What is NDCR exactly? I’ve never heard of it.
Hi, thank you for your great description. why you didn’t use “rmsprop” optimizer?
I find I get great results from Adam, an extension of RMSProp:
https://machinelearningmastery.com/adam-optimization-algorithm-for-deep-learning/
Hi,
I added the embediing matrix to your code and received an error related to matrix dimentions same as what Luke mentioned in the previous comments. do you have any post for adding embedding matrix to encoder-decoder?
I have some suggestions here:
https://machinelearningmastery.com/faq/single-faq/why-does-the-code-in-the-tutorial-not-work-for-me
Hi Jason,
I have a low-level question. why did you train the model in only “one” epoch?wasn’t better to choose the higher number?
Because we have a very large number of random samples.
Perhaps re-read the tutorial?
Thank you, Jason. How can we save the results of our model to use them later on?
See this tutorial:
https://machinelearningmastery.com/save-load-keras-deep-learning-models/
In your code, I suppose the 3 models should be saved (i.e., the 3 returned by defined_models):
train, infenc, infdec = define_models(n_features, n_features, 128)
Yes, perhaps try using the save() function to save each.
Hi Jason, I was using your code to solve a regression problem. I have the data defined exactly like you have but instead of casting them to one-hot-vectors I wish to leave them integers or floats.
I modified the code as follows:
def define_models(n_input, n_output, n_units):
# define training encoder
encoder_inputs = Input(shape=(None, n_input))
encoder = LSTM(n_units, return_state=True)
encoder_outputs, state_h, state_c = encoder(encoder_inputs)
encoder_states = [state_h, state_c]
# define training decoder
decoder_inputs = Input(shape=(None, n_output))
decoder_lstm = LSTM(n_units, return_sequences=True, return_state=True)
decoder_outputs, _, _ = decoder_lstm(decoder_inputs, initial_state=encoder_states)
decoder_dense = Dense(n_output, activation='relu')
decoder_outputs = decoder_dense(decoder_outputs)
model = Model([encoder_inputs, decoder_inputs], decoder_outputs)
# define inference encoder
encoder_model = Model(encoder_inputs, encoder_states)
# define inference decoder
decoder_state_input_h = Input(shape=(n_units,))
decoder_state_input_c = Input(shape=(n_units,))
decoder_states_inputs = [decoder_state_input_h, decoder_state_input_c]
decoder_outputs, state_h, state_c = decoder_lstm(decoder_inputs, initial_state=decoder_states_inputs)
decoder_states = [state_h, state_c]
decoder_outputs = decoder_dense(decoder_outputs)
decoder_model = Model([decoder_inputs] + decoder_states_inputs, [decoder_outputs] + decoder_states)
# return all models
return model, encoder_model, decoder_model
However the model does not learn to predict for more than one future timesteps, gives correct prediction for only one ahead. Could you please suggest some solution. Much thanks!
I make the prediction then as follows:
def predict_sequence(infenc, infdec, source, n_steps):
state = infenc.predict(source)
output = list()
pred=np.array([0]).reshape(1,1,1)
for t in range(n_steps):
yhat, h, c = infdec.predict([pred]+state)
output.append(yhat[0,0,0])
state = [h, c]
pred = yhat
return array(output)
I have some ideas here:
http://machinelearningmastery.com/improve-deep-learning-performance/
Hello Khan, I have a similar proble the network not predicting more than one step ahead. did you find a solution?
Hi Jason, thanks for great serial about MLs,
In this tutorial, i have a bit complex (I’m a beginner in Python. I just have a little AI and ML theory).
y set (target sequence) is a part of X1. Clearly, y specified by X (reserve and subset). So,
1, In train model, Have you use y in X1 as input sequence ( sequence X1(y) => sequence y )
2, Can i define y separate with X1 (such as not subset, reserve…)?
Thanks you!
Not sure I follow. Perhaps this will help you define your problem:
http://machinelearningmastery.com/how-to-define-your-machine-learning-problem/
hi sir
i want to generate seq from pretrained embedding and in details i have a set of embedding list and its corresponding sentence.and i want to have a model to generate sentence with that embedding data. but i don’t know how to develop that model.
You can use a model like an LSTM to generate text, but not an embedding alone.
Hi Jason,
Great work again! I am a big fan of your tutorials!
I am working on a water inflow forecast problem. I have access to weather predictions and I want to predict the water inflow, given the historical values of both weather and inflows.
I have tried a simple LSTM model with overlapping sequences (time series to supervised), taking weather predictions and past inflows as input, and outputting future inflows. This works pretty well.
Seeing all this Seq2Seq time series forecast trend, I have also tried it, by encoding the weather forecast and decoding them to water inflow (with past inflows as decoder inputs), expecting even better results.
But this Seq2Seq model is performing very poorly. Do you have an idea why? Should I give up this kind of models for my problem?
Perhaps try improving the performance of the model:
http://machinelearningmastery.com/improve-deep-learning-performance/
Hi Jason,
I have read couple of your blogs about seq2seq and lstm. Wondering how should I combine this encoder-decoder model with attention? My scenario is kind of translation.
Sure, attention often improves the performance of an encoder-decoder model.
hey Jason, I have 2 questions :
question 1 – how do you estimate a “confidence” for a whole sequence prediction in a neural translation model. i guess you could multiply the individual probabilities for each time-step. somehow i’m not sure that is a proper way to do it. another approach is to feed the output sequence probabilities into a binary classifier (confident/not-confident) and take its value as the confidence score.
question 2 – how do ensure that the whole sequence prediction in a neural translation model is the optimal sequence. if you have a greedy approach where you take the max at each time-step you end up with a sequence which itself is probably not the most likely one. i’ve heard of beam search and other approaches. do you have an idea of the state-of-the-art ?
You can do a greedy search through the predicted probabilities to get the most likely word at each step, but it does not mean that it is the best sequence.
Perhaps look into a beam search.
Hi Luke,
I am dealing with the same scenario of sequences of integers.
Before you input the sequence, you need to reshape the sequences to 3D and best to train the model in mini batches as it will reset the states after every iteration which works really well for LSTM based model.
Hope that helps.
Why not apply TimeDistributed to the Decoder as in https://machinelearningmastery.com/develop-neural-machine-translation-system-keras/ ?
In this case we have a dynamic 1-step model – e.g. it’s not needed.
Hi Jason !
Can this model be used to summarize the sentence ? Am working on abstractive summarizer and trying to build one using encoder decoder with attention.
Can you help me out.
I have a number of posts on summarization:
https://machinelearningmastery.com/?s=text+summarization&post_type=post&submit=Search
Thank you for the great tutorial!! There is one thing I don’t understand, hopefully you can clarify:
We train a model as:
train, infenc, infdec = define_models(n_features, n_features, 128)
train.compile(optimizer=’adam’, loss=’categorical_crossentropy’, metrics=[‘acc’])
train.fit([X1, X2], y, epochs=1)
However, the inference encoder/decoder models (infenc and infdec) seem to still un-trained.
I don’t understand how, where, or when the information (weights, states, etc.) from the “train model” is transfer to the inference models.
At prediction time, you said that:
“During prediction, the inference_encoder model is used to encode the input sequence once which returns states that are used to initialize the inference_decoder model. From that point, the inference_decoder model is used to generate predictions step by step.”
But aren’t the inference_encoder and inference_decoder un-trained?
The weights are trained, it is just we have two references to the same weights so we can use them different ways (training/inference).
Hi Jason,
Is it possible to apply Batchnormalization with the above code?
Sure.
Here’s some examples of using batchnorm that you can adapt:
https://machinelearningmastery.com/how-to-accelerate-learning-of-deep-neural-networks-with-batch-normalization/
Hi Jason,
Since the above code doesn’t use Keras Sequential model, so it doesn’t allow to add Batchnormalization layer directly to the model.
Could you please help if we want to apply Bn in the code above?
You can add it to the model using the functional API:
https://machinelearningmastery.com/keras-functional-api-deep-learning/
Thanks Jason. Your posts are really helpful !
Thanks Jason!
I’m glad it helped.
Hi Jason,
I just wonder why you specified the “epochs” to 1. Is it just because the accuracy already reach 100%?
If it were not the accuracy of 100% with the “epochs” equal to 1, should I switch to any other epoch number to get increased accuracy?
Thank you in advance!
Kyu
Not quite, it is because we defined a very large number of random examples that acted like a proxy for epochs.
You could use fewer examples and more epochs to achieve the same effect.
Hi Jason,
nice post as always, I enjoy reading your blog. I got on question here. I might missed something, but why do we need the shifted target sequence as input for the decoder? and one more question: why do we need to shift it? Would be nice if you can clearify that for me. Thanks in advance 🙂
Cheers,
Tobs
To transform it into a supervised learning problem, for example, see this:
https://machinelearningmastery.com/convert-time-series-supervised-learning-problem-python/
Hi Jason,
Could you please help with gru based inference model for autoencoder.
/Ashima
You can use the LSTM autoencoder in this tutorial and change the layers to GRU:
https://machinelearningmastery.com/lstm-autoencoders/
Thanks Jason
You’re welcome.
Hi Jason,
Thank you very much for your blog and its excellent content. Regarding this post, it seems that the encoder_outputs is not used. Why don’t we use this out-put? Can we put an auto-decoder on top of it to reproduce the input1? Would this help the network in predicting the sequences?
Bests
Mostafa
It is used – the encoder output is connected to the decoder.
Hi Jason, I see the encoder_outputs is not used at all. Any purpose capturing it in a variable? I see only the states being propagated to the decoder.
Not really.
Hi Jason, Thanks for the tutorial! I want to add BatchNormalization and Dropout layer after the decoder LSTM layer. Do you have any idea how I can do it?
Regards,
Gunay
Be careful with dropout on LSTMs, use LSTM specific dropout:
https://machinelearningmastery.com/how-to-reduce-overfitting-with-dropout-regularization-in-keras/
Also batch norm and dropout can interact, be careful not to use them side by side – always test.
Hi Jason,
Thank you so much for your exciting blog. It’s great and I have a question.
What if we have more than one input series that are related to each other and want to predict the result?
For example, predicting the weather which we have more than one features and series?
You can have parallel input features or have a multi-input model.
I show how to do both here:
https://machinelearningmastery.com/how-to-develop-lstm-models-for-time-series-forecasting/
Great, thanks a lot
Hi Jason,
Thanks for the great post.
I need to ask one question that you may think is very silly question.
I have a sequence of integers indicating the locations visited by some user xyz having user type “category1”. I have many users belonging to one of the category and each user has visited some locations.
Given a sequence of some user, I want to predict on which location that user will go next. Also, I want to predict it by taking into consideration the user type/category.
The question is, how can we use the above post for the stated problem since in the post, the values are predicted in reverse order only.
Perhaps there are multiple ways to frame the problem. I’d encourage you to brainstorm and then test a few to see what works.
It sounds like a time series classification problem. I think some of the tutorials here will give you ideas:
https://machinelearningmastery.com/start-here/#deep_learning_time_series
@Jason, while giving free tips, mind that code should be working in the real world for large datasets. To_categorical is the worst thing to use and not keeping the memory footprint optimized. Hence, I would recommend re-edit of this post and using “sparse_softmax_cross_entropy_with_logits” as a proxy for “categorical_cross_entropy”. Seq2seq models are generally trained on large vocab datasets and your examples sadly don’t work. One has to go to other places for a solution. BTW, your posts are intuitive.
Thanks for the suggestion.
Hi Jason, I am trying with machine translation and going through all your articles.
This post is an implementation of “Encoder-Decoder Model for Sequence-to-Sequence Prediction in Keras” with some sophisticated code in place.
I have seen one more post of your’s at
https://machinelearningmastery.com/develop-neural-machine-translation-system-keras/
and
https://machinelearningmastery.com/encoder-decoder-long-short-term-memory-networks/
which is also introucing to the Encoder-Decoder LSTMs for
sequence-to-sequence prediction with example Python code which is very simple
model = Sequential()
model.add(LSTM(…, input_shape=(…)))
model.add(RepeatVector(…))
model.add(LSTM(…, return_sequences=True))
model.add(TimeDistributed(Dense(…)))
Can you please let me know the exact difference between both of these ? is the later one with simple 5 lines of code the implementation of this sophistcated in a better way using LSTM’s? or which is better?
I generally teach an approach to the encoder-decoder that uses an autoencoder architecture as it often gives the same or better results as the more advanced encoder-decoder.
More here:
https://machinelearningmastery.com/lstm-autoencoders/
So the one in this post isn’t autoencoder but have teacher forcing in place, can we have teacher forcing in place for auto-encoder approaches even?
Correct.
Hi Jason, thank you for this tutorial!
I have a question about teacher forcing.
if I understand your example correctly, you are not using here any validation set (is it right?).
What if I add validation split during fitting, would the model use teacher forcing during validation phase as well?
Would this choice be correct, or should the model use greedy or beam search during the validation to simulate a more realistic performance?
Thank you!
Not quite. I use walk forward validation.
You can learn more about teacher forcing here:
https://machinelearningmastery.com/teacher-forcing-for-recurrent-neural-networks/
Hi Jason,
I have chunks (each chunk has different length, from 700 rows to 2000 rows) of data that include multivariate Inputs (3 time series) and dependent series. For example my first chunk of data has 700 rows of 3 input time series and dependent (one output) time series. I want to use the 3 inputs and predict (generate) the dependent series.
How should I do it?
Thank you in advance!
Perhaps this post will help or give you ideas:
https://machinelearningmastery.com/make-predictions-long-short-term-memory-models-keras/
And this:
https://machinelearningmastery.com/how-to-make-classification-and-regression-predictions-for-deep-learning-models-in-keras/
Hi,
which would be the difference between this encoder-decoder vs. the one proposed here:
https://machinelearningmastery.com/how-to-develop-lstm-models-for-multi-step-time-series-forecasting-of-household-power-consumption/
the codification is done by the states of the LSTM in this case and just by the conv filters in the link?
Besides complexity, there is any case in which this architecture wouldn’t be a better pick than the other one?
The example in this post meets the definition of encoder-decoder provided in the paper and is an example of a dynamic RNN.
The example in the other post is a simpler encoder-decoder model based on the idea of an autoencoder.
I generally recommend the latter approach because it is a lot simpler to train and use.
Jason,
wouldn’t it be possible to input a sequence and output also a sequence instead of having to loop the inference decoder over the predicted outputs to obtain the whole predicted sequence?
any thoughts on what would be better?
my particular case is in predicting video frames using the approach of this post
Yes, you could achieve this with a vector output or with a decoder model based on an LSTM autoencoder.
The encoder architecture needs to be the same as the decoder or I could have more LSTM layers in one?
No, they can vary.
Hi!
I am trying to train my model with several gigabytes of data. My machine runs out of memory.
How can I do to train the batch model? I want to invoke the fit method with packages of 10,000 examples, but I don’t know how to do it.
You can help?
You can use a data generator and progressively load your data into memory for the model.
I give a few examples on the blog for loading large image and text datasets, for example:
https://machinelearningmastery.com/develop-a-deep-learning-caption-generation-model-in-python/
Hey Jason,
I’m sure I’ll have questions come up here and there, but let me just say how amazed I am with the sheer number of topics you cover in your posts. This one in particular is so incredibly helpful. Thank you for all your work!
Eli
Thanks Eli!
Great post, thanks
How should I think about when to use teacher-forcing models (which is what I think is described in this post), versus a simple vanilla LSTM like this:
https://machinelearningmastery.com/encoder-decoder-long-short-term-memory-networks/
Thank you
Try a few framings of the problem and see what works/makes sense for your specific dataset.
Hi Jason,
first of all, I want to thank you for your awesome website. It has helped me a great deal with writing my thesis so far!
I am currently trying to implement an autoencoder with teacher forcing. As my data is purely continous, I have been trying to avoid one-hot encoding. However, I got stuck on the question, how I should mark the beginning of my target sequence. I have tried using a number which is inside or outside the range of the numbers used in the source/target sequences, but the results are poor. My network seems to repeat the same output (with only small alterations) no matter what I feed as an input sequence. I may have made another mistake in my implementation, but maybe you have a asuggestion for me regarding the start of sequence “character”, when no one-hot encoding is used?
Thank you very much in advance.
Thanks.
I use a token to mark the beginning and end of the sequence on problems with variable length output. An example is caption generation for photos:
https://machinelearningmastery.com/develop-a-deep-learning-caption-generation-model-in-python/
Hi Jason,
thanks for the quick reply.
My output length is fixed. My question was rather regarding the type of data used. Let me try to rephrase it: Is their a standard way to mark the beginning and/or end of a sequence, if the sequence consists of continous (data type: double or float) data and I do NOT want to bin and one-hot encode it? An example of such a seuqnce could be a time series of sensor data.
Thank you for your help.
Yes, use a value out of the scope of normal values, like -1 or -999, etc.
I have a sequence problem. Each sample is one trajectory having 200 points in chronological order. Each point exists in a 2D grid, where each grid cell is represented by a unique integer id. e,g a trajectory of 10 points passes through following grid cells –> [23, 32, 38, 18, 58, 41, 28, 28, 30, 48]. How to model this problem?
I have 8000 samples, and each sample has a sequence of 200 points, and their is only one feature (that is grid cell number). What should be the shape of X, if this is (8000,200,1), then their are 200 timesteps and each time step has only one entry. then the problem would be to generate shifted sequence in get_dataset.
or other way is to use single timestep for all samples like (8000,1,200). is this logical to solve sequence to sequence problem with single timestep?
Perhaps this will help you to determine the shape:
https://machinelearningmastery.com/faq/single-faq/what-is-the-difference-between-samples-timesteps-and-features-for-lstm-input
Perhaps try a few different models and framings of the problem in order to see what works best.
Hello, Jason, I would like to ask how to extract the status returned by each time part of LSTM, for example, I want to extract the output of the first and second time steps.
Perhaps use return_sequences=True on the layer of interest and use that layer as an output layer?
Using return_sequences=True, the function I want to achieve is to splicing the two outputs close to each other, followed by a Dense(1), how to realize this function, expect to get your answer, thank you
Sorry, I don’t understand.
Perhaps try posting your question and code to stackoverflow?
hello Jason,
I tried to run the above code but got the following error:
ValueError Traceback (most recent call last)
in ()
—-> 1 train.fit([X1, X2], y, epochs=1)
2 frames
/usr/local/lib/python3.6/dist-packages/keras/engine/training_utils.py in standardize_input_data(data, names, shapes, check_batch_axis, exception_prefix)
129 ‘: expected ‘ + names[i] + ‘ to have ‘ +
130 str(len(shape)) + ‘ dimensions, but got array ‘
–> 131 ‘with shape ‘ + str(data_shape))
132 if not check_batch_axis:
133 data_shape = data_shape[1:]
ValueError: Error when checking input: expected input_9 to have 3 dimensions, but got array with shape (100000, 1, 6, 51)
can you please help me to solve it ?
Sorry to hear that, I have some suggestions here:
https://machinelearningmastery.com/faq/single-faq/why-does-the-code-in-the-tutorial-not-work-for-me
Hi and thanks a lot for writing this tutorial!
I’m going to have a stab at modifying this to predict/fill in the middle 1/3 of a long sentence.
Do you think that is possible and would you be able to give any pointers?
Sounds fun!
Yes, the tutorials on language modeling here will help:
https://machinelearningmastery.com/start-here/#nlp
Hey Jason I wanted to know. Can this work with a dataframe where the label is one number and the target is a sequence.
example
dataframe
label | Prediction
9000 | [5000,8000,9000]
Like a one to many but i would want the model to give me a sequence based off of its label
is that possible with encoder-decoder? if not can you direct me to a better setup.
You can model that problem, but one number does not look like enough information to make a sequence prediction.
It seems that encoding a large number hits a memory error. a list of numbers higher than 100000
is there a way to fix this issue
in get_dataset(n_in, n_out, cardinality, n_samples)
15 target_in.append(in_target)
16 # encode
—> 17 src_encoded = to_categorical(source)
18 tar_encoded = to_categorical(target)
19 tar2_encoded = to_categorical(target_in)
~/anaconda3/envs/amazonei_tensorflow_p36/lib/python3.6/site-packages/tensorflow/python/keras/utils/np_utils.py in to_categorical(y, num_classes, dtype)
46 num_classes = np.max(y) + 1
47 n = y.shape[0]
—> 48 categorical = np.zeros((n, num_classes), dtype=dtype)
49 categorical[np.arange(n), y] = 1
50 output_shape = input_shape + (num_classes,)
MemoryError:
Some ideas:
– Use fewer categories.
– Use a machine with more RAM
– Use a label encoding instead of one hot encoding.
More ideas:
https://machinelearningmastery.com/faq/single-faq/how-do-i-handle-a-large-number-of-categories
How to add attention to this dynamic encoder-decoder model?
Thank you very much for your help.
Perhaps try using the TensorFlow attention layers?
And sorry to bother you again.
You have used the keras layers to build seq2seq models many times in other blogs, such as:
model = Sequential()
model.add(LSTM(…, input_shape=(…)))
model.add(RepeatVector(…))
model.add(LSTM(…, return_sequences=True))
model.add(TimeDistributed(Dense(…)))
I am confused about what is the difference of this keras seq2seq from the above dynamic one in this blog?
Thank you!
The approach I typically use is based on an LSTM autoencoder and is much easier to implement in Keras:
https://machinelearningmastery.com/lstm-autoencoders/
The dynamic lstm above is a closer fit to the original paper.
Performance appears to be much the same for both models on a range of problems.
Thanks a lot!
Hi
Looking at the folowing lines of code by the define_models function:
decoder_outputs, _, _ = decoder_lstm(decoder_inputs, initial_state=encoder_states)
decoder_dense = Dense(n_output, activation=’softmax’)
Why there’s no need for a TimeDistributed wrapper?
That’s I would expect to see the following:
decoder_dense = TimeDistributed(Dense(n_output, activation=’softmax’))
As because we apply the Dense layer to each given timestep given by decoder_outputs (because of return_sequences=True)
Thanks
It is a dynamic rnn that makes a single step prediction per call.
Thanks, but that code snippet belongs to the training and not inference phase… So we’re not in the predication step yet.
Hi Jason
Would really appreciate if you could shed some light on this.
Thanks
Ah the puzzle solved:
https://stackoverflow.com/questions/47305618/what-is-the-role-of-timedistributed-layer-in-keras/47309453#47309453
Thanks
Creates the output for the decoder by the look of things off the cuff.
Thanks for your reply. My english is not that good, so I did not understand your answer, could you elaborate it a bit please?
In the meanwhile using the following code proved me that (since keras 2.0) the Dense layer can handle 3 dimensional inputs:
from keras.layers import Dense, TimeDistributed
from keras.models import Sequential
from numpy import arange
batch = 3
steps = 10
features = 16
# model using TimeDistributed
model = Sequential()
model.add(TimeDistributed(Dense(8), input_shape=(steps, features)))
model.compile(loss=’mean_squared_error’, optimizer=’adam’, metrics=[‘accuracy’])
# model without TimeDistributed
model2 = Sequential()
model2.add(Dense(8, input_shape=(steps, features)))
model2.compile(loss=’mean_squared_error’, optimizer=’adam’, metrics=[‘accuracy’])
X = arange(batch * steps * features).reshape(batch, steps, features)
y = model.predict(X)
y2 = model.predict(X)
# both outputs are of the same shape
print(y.shape, y2.shape)
Does this make sense?
I don’t think so.
I recommend reading this to understand the difference between samples, time steps and features:
https://machinelearningmastery.com/faq/single-faq/what-is-the-difference-between-samples-timesteps-and-features-for-lstm-input
Can you please point out the reason why you don’t agree. I have got also the same understanding with the link you provided.
Following the code again to show what I mean. What is wrong with that (using keras 2.3.1)?
from keras.layers import Dense, TimeDistributed
from keras.models import Sequential
from numpy import arange
n_samples = 3
n_steps = 10
n_features = 16
# model using TimeDistributed
model = Sequential()
model.add(TimeDistributed(Dense(8), batch_input_shape=(n_samples, n_steps, n_features)))
model.compile(loss=’mean_squared_error’, optimizer=’adam’, metrics=[‘accuracy’])
# model without TimeDistributed
model2 = Sequential()
model2.add(Dense(8, batch_input_shape=(n_samples, n_steps, n_features)))
model2.compile(loss=’mean_squared_error’, optimizer=’adam’, metrics=[‘accuracy’])
X = arange(n_samples * n_steps * n_features).reshape(n_samples, n_steps, n_features)
y = model.predict(X)
y2 = model2.predict(X)
# both outputs are of the same shape: (3, 10, 8)
print(y.shape, y2.shape)
model.summary()
model2.summary()
Which outputs:
(3, 10, 8) (3, 10, 8)
Model: “sequential_1”
_________________________________________________________________
Layer (type) Output Shape Param #
=================================================================
time_distributed_1 (TimeDist (3, 10, 8) 136
=================================================================
Total params: 136
Trainable params: 136
Non-trainable params: 0
_________________________________________________________________
Model: “sequential_2”
_________________________________________________________________
Layer (type) Output Shape Param #
=================================================================
dense_2 (Dense) (3, 10, 8) 136
=================================================================
Total params: 136
Trainable params: 136
Non-trainable params: 0
_________________________________________________________________
Sorry, I don’t have the capacity to review/debug this code.
Sorry for the typo above, the line:
y2 = model.predict(X)
Should be replaced with:
y2 = model2.predict(X)
Following the complete code again:
from keras.layers import Dense, TimeDistributed
from keras.models import Sequential
from numpy import arange
batch = 3
steps = 10
features = 16
# model using TimeDistributed
model = Sequential()
model.add(TimeDistributed(Dense(8), input_shape=(steps, features)))
model.compile(loss=’mean_squared_error’, optimizer=’adam’, metrics=[‘accuracy’])
# model without TimeDistributed
model2 = Sequential()
model2.add(Dense(8, input_shape=(steps, features)))
model2.compile(loss=’mean_squared_error’, optimizer=’adam’, metrics=[‘accuracy’])
X = arange(batch * steps * features).reshape(batch, steps, features)
y = model.predict(X)
y2 = model2.predict(X)
# both outputs are of the same shape: (3, 10, 8)
print(y.shape, y2.shape)
Hi! So, if my 2nd Dimension for Input is not defined like so:
encoder_inputs = Input(shape=(None, None))
encoder = LSTM(32, return_state=True)
encoder_outputs, state_h, state_c = encoder(encoder_inputs)
encoder_states = [state_h, state_c]
I get an error:
TypeError: unsupported operand type(s) for +: ‘NoneType’ and ‘int’
Any solutions?
After training what variables are required for prediction
Error when checking model input: the list of Numpy arrays that you are passing to your model is not the size the model expected. Expected to see 2 array(s), but instead got the following list of 1 array:
Sounds like you need to provide 2 arrays to your model.
thanks. I figured that out.
This model is guessing the last three elements of the sequence i.e it is just copying the last three elements
Hi how can i save and load the model for inference in later?
See this tutorial:
https://machinelearningmastery.com/save-load-keras-deep-learning-models/
Hi
Is there anyway you can add attention mechanism in this seq2seq model?
Yes. You can add an attention layer. Sorry, I don’t have a modern example.
if i want predict the next sequence of six numbers. what should i do?
call model.predict()
Perhaps this will help:
https://machinelearningmastery.com/make-predictions-long-short-term-memory-models-keras/
How does seq2seq do multivariate prediction，like weather prediction
It can be used for that purpose. See examples here:
https://machinelearningmastery.com/how-to-develop-lstm-models-for-time-series-forecasting/
Hi Jason,
Can we also use encoder decoder model for univariate data and give infinite output length also? For example giving input as 50 data points and output as 1000 data point? and will this work and give good results? If not, what will be the best way to train encoder and decoder model for seq to seq univariate prediction with arbitrary input and output length?
Thank you.
Yes.
Good results depend on the specifics of the data and the model.
can you give me any example where you have trained the model with infinite output length of data points. My data is basically a univariate data of temperature program
I don’t have an example, but the above model can achieve this.
But isn’t it that the above model is used for categorical or classification task?
It is a sequence prediction task.
But I am not able to understand what is the categorical here for and cardinality?? and why you did one hot encoding instead of scaling the data
This is a contrived problem of modeling sequences of numerical characters.
and can this model also be used for regression seq-seq task ? if yes, how can I use it?
Perhaps try it and see?
Hi Jason!
Can I use seq2seq model for multi-step time series forecasting?
Sure, see the examples here:
https://machinelearningmastery.com/how-to-develop-lstm-models-for-multi-step-time-series-forecasting-of-household-power-consumption/
Thank you for your reply!
But why the encoder-decoder in your link doesn’t use the decoder_inputs or inference model like in this post, instead of using the repeatvector() directly?
There are two main approaches to the model, one reuses the internal state, the the other uses an auto-encoder structure.
I prefer the latter as its much simpler and generally as effective.
Hi Jason,
Greetings,
Currently i am a java developer with 4 years of experience. I would like to move A&I.
But i am getting little bit confused to start or not.
Could you please guid me how can i proceed.
please send mail : [email protected]
Start here:
https://machinelearningmastery.com/start-here/#getstarted
What is the difference between the approach you took here, and the approach in this tutorial: https://machinelearningmastery.com/how-to-develop-lstm-models-for-multi-step-time-series-forecasting-of-household-power-consumption/
From what I understood here we train the model to predict only one step into the future, then using recursion we predict multiple steps, meanwhile the the lesson that I’ve linked you too, it trains the model to predict as many times as RepeatVector(n)
Is my understanding correct ?
They are both encoder-decoder models but the linked model uses a simpler auto-encoder based architecture, whereas the example in this post is more complex but matches the original paper.
Thank you for sharing. This is pretty comprehensive. I wonder how you write so many blogs on so many topics being a single person. Really helpful to understand the models!
Thanks!
This is a common question that I answer here:
https://machinelearningmastery.com/faq/single-faq/how-do-you-write-so-much
Thanks Jason for this presentation, please kindly help out, im not sure i know how to give new input sequence to the model without having to retrain it.
This tutorial will show you how to make predictions generally:
https://machinelearningmastery.com/how-to-make-classification-and-regression-predictions-for-deep-learning-models-in-keras/
This tutorial will show you how to make predictions with LSTMs:
https://machinelearningmastery.com/make-predictions-long-short-term-memory-models-keras/
Hi Jason. Great tutorial!
I modified the example for my application, it is fixing an input series of events each with a start and end point in seconds. The output sequence is a list of ‘fixes’ needed to repair the input sequence. The features/categorical values were high (upto 3000) so I converted/condensed the data into different formats first to experiment example shape below.
Test train split (198500, 164) (500, 164) (198500, 82) (500, 82) (198500, 82) (500, 82)
to_categorical (198500, 164, 121) (500, 164, 121) (198500, 82, 52) (500, 82, 52) (198500, 82, 52) (500, 82, 52)
It works ok, but I think the output sequence is so long that there is often a few mistakes in there which has a big outcome on the results, as they all go out of sync.
Is there a way to skip the one_hot_encoding and feed the integer values straight in? I tinkered but it seems to be always expecting 3 dimensions in.
Then I can try the raw data. At the moment the arrays would take up too much ram at higher categorical levels.
Thanks
Well done.
Yes, you can use a sparse cross entropy loss and use target integers directly instead of one hot. For input, you can use an embedding and pas integers directly in.
Thanks Jason. Can you use the raw integers for output (y) also? Or do they always need to be one hot encoded? I updated the model and it fits ok, but having issues with the predict function.
I had to make the decoder dense layer = n_units (128) rather than features which is now 1, so within the predict function it goes wrong because I now have 1 feature and it is expecting more. I.e the decoder is.
“expected input_67 to have shape (82, 1) but got array with shape (82, 128)”
One hot encoded allows the model to perform better. Use argmax to convert to integers:
https://machinelearningmastery.com/argmax-in-machine-learning/
When saving the model for future use, I understand the train will need to be saved. But infenc and infdec need to be saved to make predictions as well right?
Hi Jason.
I am trying to add a masking layer to this example, as my sequences are all variable length padded with zeros at the end. It still works with no masking, but would like to see what difference masking makes to the output. Do you have any good tutuorials covering masking?
I tried the below code, however it makes no difference to the output, but increases training time by about x4.
def define_models_mask(n_in, n_out, n_units):
# define encoder
enc_inputs = Input(shape=(None, n_in))
encoder_inputs = Masking(mask_value=0)(enc_inputs) #****** TEST *****
encoder = LSTM(n_units, return_state=True)
encoder_outputs, state_h, state_c = encoder(encoder_inputs)
encoder_states = [state_h, state_c]
# define decoder
dec_inputs = Input(shape=(None, n_out))
decoder_inputs = Masking(mask_value=0)(dec_inputs) #****** TEST *****
decoder_lstm = LSTM(n_units, return_sequences=True, return_state=True)
decoder_outputs, _, _ = decoder_lstm(decoder_inputs, initial_state=encoder_states)
decoder_dense = Dense(n_out, activation=’softmax’)
decoder_outputs = decoder_dense(decoder_outputs)
model = Model([enc_inputs, dec_inputs], decoder_outputs)
# define inference encoder
encoder_model = Model(enc_inputs, encoder_states)
# define inference decoder
decoder_state_input_h = Input(shape=(n_units,))
decoder_state_input_c = Input(shape=(n_units,))
decoder_states_inputs = [decoder_state_input_h, decoder_state_input_c]
decoder_outputs, state_h, state_c = decoder_lstm(decoder_inputs, initial_state=decoder_states_inputs)
decoder_states = [state_h, state_c]
decoder_outputs = decoder_dense(decoder_outputs)
decoder_model = Model([dec_inputs] + decoder_states_inputs, [decoder_outputs] + decoder_states)
# return all models
return model, encoder_model, decoder_model
This may help:
https://machinelearningmastery.com/handle-missing-timesteps-sequence-prediction-problems-python/
(100000, 1, 6, 51) (100000, 1, 3, 51) (100000, 1, 3, 51)
—————————————————————————
ValueError Traceback (most recent call last)
in ()
95 print(X1.shape,X2.shape,y.shape)
96 # train model
—> 97 train.fit([X1, X2], y, epochs=1)
98 # evaluate LSTM
99 total, correct = 100, 0
2 frames
/usr/local/lib/python3.6/dist-packages/keras/engine/training_utils.py in standardize_input_data(data, names, shapes, check_batch_axis, exception_prefix)
133 ‘: expected ‘ + names[i] + ‘ to have ‘ +
134 str(len(shape)) + ‘ dimensions, but got array ‘
–> 135 ‘with shape ‘ + str(data_shape))
136 if not check_batch_axis:
137 data_shape = data_shape[1:]
ValueError: Error when checking input: expected input_1 to have 3 dimensions, but got array with shape (100000, 1, 6, 51)
This is showing when I run this code
I’m sorry to hear that, this may help:
https://machinelearningmastery.com/faq/single-faq/why-does-the-code-in-the-tutorial-not-work-for-me
As always, great post !
one thing to add is, I usually want to output some sequences with different length, (eg: a simple conversation model), so what I am usually doing is, add an feature on target data. so, n_features will be:
n_features = 50 + 2
0 is in target data,
1~50 are real features
51 will be
target_in = [0] + target[:-1]
will be
target_in = [0] + target
target will be:
target = target + [51]
not sure if this is the right idea though.
plus, attention layer is implemented in keras. I am having hard time in implementing it on this seq2seq method…
Hello Mr Jason
thank you for your great posts.
my problem is to predict pen trajectory from a handwritting character image.
i have a feature vector extracted from the image which its size is (1,4096),(as my input vector).
i have a x and y coordinate vector which is the pen trajectory for the image,that its size is (1,20),(as my output vector).
the elements of these two vectors, have different values.I mean the elements of the output vectors are integers but the input vectors are real numbers or decimal.
i have 2000 train input vectors.
I am looking for an algorithm that after training it,for a specific input feature vector (1,4096),it could predict the output vector(1,20),pen trajectory coordinates.
can i use your “Encoder-Decoder Model for Sequence-to-Sequence Prediction”?!
it dose not matter that my input and output values are not in a same type?!
That sounds like a fun project!
I recommend first checking the literature for similar projects, then test a suite of models in order to discover what works well/best for your specific dataset.
Hi Jason,
Thank you for sharing this, I have two questions
1- can we use seq2seq for human activity recognition?
2- have you used attention with seq2seq ?
Thank you
Yes.
No.
Hi Jason.
The purpose of the X_shifted input seems to be just to let the model where to start in the seq e.g. the first value. Why then do we feed in an exact shifted copy of X, and not just some sort of mask e.g. 0,1,1,1,1,1,1, etc?
Is there any other purpose to the X shifted input as the model works on through the seq past the first value? In my input sequences there are setions with a lot of repetative values, so not sure if this will cause issues.
Thanks
Phil
Perhaps this will help in understanding how we represent sequence prediction as a supervised learning problem:
https://machinelearningmastery.com/time-series-forecasting-supervised-learning/
Thanks Jason, ill have a proper read of that tomorrow.
Phil
Hi Jason, I’m working on an autoencoder for anomaly detection. I’ve tried your other tutorial on lstm autoencoders but it doesn’t fit the data (I get only the mean value as reconstructed signal). However if use only the “train” model of this tutorial as autoencoder (so [X,X] as input encoder and input decoder respectively) the model works perfectly as an autoencoder, recostructing a simplified signal. But if I run the inference model it doesn’t reconstruc the signal. Why does this happen? Can I use only the “train” model as an autoencoder?
We train an autoencoder and the decoder part of the model after training can be used to encode data.
Hi Jason! Thank you so much for your blog posts! I trained seq2seq network on one batch with 638 each with dimensions: 26*30 and predicts a sequence of 7 numbers using ‘mse’ as the loss function. However, when I calculate the mse loss and compare it to the one returned by history[‘loss’] they differ by ~0.2. Do you know how ‘mse’ is calculated for this input/output shape?
Yes, the loss reported during training is an average across batches in an epoch. I would recommend trusting your own loss calculations.
Hi Jason, thank you for you great posts.
I am not sure if I am getting something wrong here, but I run the complete code of this example and got an error.
The shape of the dataset returned by method get_dataset is (n_samples, 1, 3, 51) instead of (n_samples, 3, 51), which I think is the expected one to the model.
Then I get the error “expected input_9 to have 3 dimensions, but got array with shape (2, 1, 6, 51)”. I just copy and paste your code. What am I missing?
Perhaps confirm that your tensorlfow and keras are up to date?
Hello Mr jason
I ask you to guide me for a code that it can predict an output sequence from an input sequence.
for example, for every sample we have:
X(input)={1 ,2, 3, …,10} , Y(output) ={ 80,10,64,79,60}
that the output sequence type is completely different from the input sequence (X).
our input sequence is the feature vector extracted from an image in a specified class.
and the output sequence for every input sample is the place of a spesific object in an image from a specified class.
also i have a little database which it contains just 4000 sample.
can i use one-shot learning algorithm for training the Lstm network.
would you please guide me a code to implement one shot for sequence to sequence Lstm?
I really thank you for your help.
Perhaps start with the simple models here and adapt them for your project:
https://machinelearningmastery.com/how-to-develop-lstm-models-for-time-series-forecasting/
Hi,
Thanks for all this material !
In few words what is the difference/advantages between the implementation above (dealing with state) and the simple one you propose as well here with RepaetVector layer to make the connection possible with seq of differente sizes:https://machinelearningmastery.com/encoder-decoder-long-short-term-memory-networks/ ?
BR.
This example is simple and efficient and is based on an LSTM autoencoder.
The other example is a lot more complex and is based on a dynamic rnn and a is a closer match to the original paper.
Both appear to have similar performance in practice in my experience.
I think there’s an isssue with the dimensions of the generated data.
The example code doesn’t run (for me anyway), because the data is four dimensional rather than three dimensional. I fixed it by taking the first element of src, tar and tar2 encoded. Alternatively, call to_categorical with ‘source’ instead of ‘[source]’
Took me a while to figure out 😉
Interesting, are your libs up to date?
Not sure about my libs. Keras version is 2.4.3, Tensorflow is 2.3.0
This issue is not new though. I had a look through the comments, it’s been reported as far back as Nov. 30 2017 (comment by ‘Python’).
‘Kadirou’ reports the same problem, April 30, 2018.
Gary (April 30 2018) offers exactly what I suggested:
[quote]change this:
src_encoded = to_categorical([source], num_classes=cardinality)[0]
tar_encoded = to_categorical([target], num_classes=cardinality)[0]
tar2_encoded = to_categorical([target_in], num_classes=cardinality)[0][/quote]
There are other instances of the same issue in the comments section, even fairly recent: see Mairon, August 5 2020.
[quote]Then I get the error “expected input_9 to have 3 dimensions, but got array with shape (2, 1, 6, 51)”. I just copy and paste your code. What am I missing?[quote]
Upshot:
The example code (in the call to ‘to_categorical’) wraps/may wrap an addittional array/list around the generated training examples where this is not expected by the model, and the code doesn’t run as a result.
I don’t know why or if it’s a platform issue. I think we can agree it’s not desirable behaviour for example code though.
Thanks Dan. Perhaps the API changed since the code was written and has not been updated to reflect the change.
Dear Jason,
I have just finished your book “”Long Short Term Memory Networks With Python” and I have published a review here: http://questioneurope.blogspot.com/2020/08/long-short-term-memory-networks-with.html
Thanks for your very valuable knowledge that you share in your book.
Kind regards,
Dominique
Well done on your progress, very impressive Dominique!
Dear Jason,
I have a problem and don’t know how to use LSTM for that.
The problem is arranging a set of actions, such as {B,D,F,A}, to the proper arrangement, i.e. (A,B,C,F). I have a database that includes the true arrangemetn of actions. Which architecture of the LSTM can I use?
Perhaps you can use a seq2seq model with an encoder-decoder architecture. Try it and see if it is effective.
I used a seq2seq model as you described here:
https://machinelearningmastery.com/develop-encoder-decoder-model-sequence-sequence-prediction-keras/
But the accuracy is so low (around 50%). I used multiple layers and also increased epoches, but didn’t work out. Is there any other model that can be effective?
Perhaps try some of the techniques here to improve model performance:
https://machinelearningmastery.com/start-here/#better
when a turn the code i have this error:
ValueError: Input 0 of layer lstm_2 is incompatible with the layer: expected ndim=3, found ndim=4. Full shape received: [32, 1, 6, 51]
Sorry to hear that, this may help:
https://machinelearningmastery.com/faq/single-faq/why-does-the-code-in-the-tutorial-not-work-for-me
Hello Jason, I want to know what is the significance of using X2 in this model. I didnt get this clear in the blog.
See the end of section “Encoder-Decoder Model in Keras” where we explain how data is prepared and provided to the model.
Hi Jason.
I’ve been struggling with the sek2sek problem for a while.
I have multi feature input of timeseries, about 10 features(less after PCA, but it is not in main focus of the question) and I need to predict sequence of (0, 1) values as output.
Let’s say my data look like this:
A, B y
0.3 0.3 0
0.4 0.1 0
0.2 0.2 0
0.7 0.5 1
. . 1
. . .
For sake of simplicity I want to predict sequence of 2 outputs based on 3 inputs.
From the example above one training example has shape of :
(3, 2), 3=input_size, 2=num_of_features and it should predict 2 values ex. [1, 0]
I know how to make windows, reshape inputs, build encoder and decoder, train model, test model…
The main problem is what should I do with discrete output?
Maybe I can try to observe it as single number [0, 1] (binary) = 2
Maybe I can try to make some embedding of my output.
Maybe I can just convert output to float.
Perhaps test a suite of different algorithms and algorithm configurations in order to discover what works well or best. This may help with examples to start with:
https://machinelearningmastery.com/how-to-develop-lstm-models-for-time-series-forecasting/
It sounds like your problem is a binary classification, ensure you have a sigmoid activation function in the output layer and use binary cross entropy loss
Hello, I have a problem that I thought could be solved by an autocoder-decoder, the problem is that I don’t know if it is possible to start with a set of carctarisricas(18) and the latent space between autoencoder-decoder can be a matrix of dimension nxm, then use the decoder to rebuild the features
Could you tell me your opinion about it? it’s possible?
Not sure I follow, but my general advice is to try it and see – e.g. develop a small prototype and use it to learn more about how to frame the problem and what might work.
Hi Jason,
How can I improve the runtime of the network? In your example there are 2 for loops that take too much time.
Good question, here are some ideas:
https://machinelearningmastery.com/faq/single-faq/how-do-i-speed-up-the-training-of-my-model
Hi Jason,
thank you for your posts and books. how would you modify the encoder-decoder if my input sequences consist of multiple features? For example, I have time series of temperature, pressure, humidity as input?
Thanks,
You’re welcome.
The model supports multiple features directly, perhaps this will help:
https://machinelearningmastery.com/faq/single-faq/what-is-the-difference-between-samples-timesteps-and-features-for-lstm-input
Jason,
another question if you don’t mind. I noticed you used teacher-forcing by shifting the target sequence by one time step. How would you modify the code to either removing teacher-forcing and using teacher forcing only, say 50% of the training steps?
Thank you
You can remove teacher forcing by feeding predictions in as inputs on subsequent samples/time steps instead of true values.
Perhaps this will help:
https://machinelearningmastery.com/teacher-forcing-for-recurrent-neural-networks/
Hello, I see all the helpful answers you are providing in relation to seq2seq models… There is one question I have that nobody seems to be able to show a practical way to do… In the Keras examples https://keras.io/examples/nlp/lstm_seq2seq/ (pretty similar to yours), it has a function decode_sequence that decodes 1 sequence at a time (like your example)… I want to be able to ‘batch’ predict the seq2seq as 1 by one is ‘very’ slow’, whereas the model can quickly be built and evaluate in batch very quickly. The goal would be to provide a list of the training examples that are not correct predicted, again in a batch rather than 1 by 1. Is it even possible to do this? If so, what would the changes in the decode_sequence routine look like to handle batches? Thanks in advance.
I don’t believe that model can operate in the way you want.
You must simplify the model to an autoencoder-based encoder-decoder and then you can operate in batches. I have tens of examples of this on the blog – you can use the search box to find them, perhaps start here:
https://machinelearningmastery.com/how-to-develop-lstm-models-for-time-series-forecasting/
Hi Jason
when i run the code, in my notebook, i often get warning message, about retracing :
WARNING:tensorflow:11 out of the last 11 calls to <function Model.make_predict_function..predict_function at 0x000001B88FDEA268> triggered tf.function retracing
Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has experimental_relax_shapes=True option that relaxes argument shapes that can avoid unnecessary retracing.
Yes i can ignore but is make slow, any help to avoid this 😀
Thanks
Mike
I believe you safely can ignore that warning for now.
Hi Jason.
Your rock 😀
Intuitively what is the benefit of this encoder-decoder model, I mean if compare using normal
LSTM/RNN design when predicting sequence?
Is it more accurate? sequence prediction using this architecture?
Thanks
Mike
Thank you!
The architecture lets you handle problems where the output sequence has a different length from the input sequence.
Thanks for this great article Jason! Very informative.
When running this code without making any changes I get the following error when trying to train the model: “ValueError: Input 0 is incompatible with layer model: expected shape=(None, None, 51), found shape=(32, 1, 6, 51)”
It seems the “to_categorical” function adds an empty dimension to the generated array, resulting in a shape of: (100000, 1, 6, 51). I managed to remove this dimension and successfully train the model with the following code added after line 29 to the “get_dataset” function:
# reshape
src_encoded = np.reshape(src_encoded,(n_in, cardinality))
tar_encoded = np.reshape(tar_encoded,(n_out, cardinality))
tar2_encoded = np.reshape(tar2_encoded,(n_out, cardinality))
There might be a way to do this more efficiently. I’m no Python hero 😉
You’re welcome.
Thanks for sharing!
Dear Jason, do you know the reasoning behind choosing a ‘non informative’ start of sequence character for the decoder like 0, instead of using the last previous known value as a starting point?
Lets assume I’m trying to predict the path of a rolling ball, wouldn’t it make sense to provide the last vector of the ball in addition to the encoded state instead of a generic start index?
Yes, it may not make sense in your case.
Thanks for your reply!
You’re welcome.
Can I use it as the next basket product prediction? Suppose
order 1 contains items[3, 4, 6]
order 2 contains items [4, 5, 1]
order 3 contains items [10, 29, 3, 1]
Now Want to find out the next 4th no order items[??????]. is it the right approach?
Perhaps each order can be modelled as one sample with a sequence of items.
LSTM(n_units)
TensorFlow website mentioned that n_units refer dimensionality of the output vector space ( i.e. the number of feature for the hidden state ) and it does not refers to the number of LSTM unit created.
By default the no. of LSTM cell units is equal to the length of input Sequence
Okay.
Hi, thanks for you tutorial. I have a question: if I train the model with a seq length of, let’s say, 600 and then use it for variable lengths sequences (e.g., 300, 1200) how my model is doing inference?
Also, how should I choose the training seq length and what a Bidirectional LSTM is learning from these sequences??
Perhaps experiment and discover what works well or best for your dataset.
Hi Jason,
What if the my input sequence is a set of coordinates say [(3,0), (1,2), (4,5),(9,10),…] and my target sequence is a set of binary array say [0,1,1,0,…].
In this case, each time-step consists of 2 integers; (3, 0). In this case, how can i one-hot encode my input sequence?
Thanks
Each integer would be encoded and the resulting vectors would be concatenated as input to the model.
Thanks Jason!
Another question. I have variable sequence length for both input and output. My output is a binary array of 0s and1s.
The target has to be one time step ahead of the decoder input so i added a zero in front of the binary array. I also padded the binary array with zeros in order to create a fixed length length to the network.
Since my output is a binary arrays of 0s and1s, will the added zeros (starting value and padding values) confuse the network? Any suggestions?
Thank you very much.
Perhaps compare results with the current approach to alternatives, such as using a different token to mark the start or end of the sequence.
Hi!
Thank you for this tutorial. It was highly informative.
I have a question on the “predict_sequence” function:
Why do you use a target_seq which is all zeroes? I would have expected an initial target sequence of [1,0, 0…, n_features], which should represent a 0 in the decoded sequence. Am I missing something?
Thank you for everything, this site is amazing.
You’re welcome.
From memory, I think we feed in zeros at the start and then feed in the last outputs as inputs to prime the prediction of the next step.
I believe zero is reserved for unknown/special, or we can teach the model to prime the process with anything we want – that would be my guess.
Thank you for your answer. I’m still a little confused.
You write:
“We will use the value of 0 as the padding or start of sequence character, therefore it is reserved and we cannot use it in our source sequences. To achieve this, we will add 1 to our configured cardinality to ensure the one-hot encoding is large enough (e.g. a value of 1 maps to a ‘1’ value in index 1).”
So if “0” is the , shouldn’t it be one-hot encoded too?
“0” should be [1, 0, 0, …, 0].
This is confusing because in the inference decoder you use an initial input character which is all zeroes [0, 0, 0, …, 0] instead of [1, 0, 0, …, 0]. Shouldn’t we feed the symbol to the decoder to start the inference?
We could, but in this case, we chose to feed in a zero to start inference.
Perhaps experiment with other reserved characters and see if it makes a difference.
Ok thank you. I will experiment
You’re welcome.
Hi Jason,
Is the decoder in your code being implemented as a Greedy Search decoder? If we want to use a beam search decoder, which part of the code should we change? Or is this question not relevant to this example? Thank you so much.
If you’re interested in beam search decoder, this may help: https://machinelearningmastery.com/beam-search-decoder-natural-language-processing/
Hi Jason,
I used an encoder-decoder model for generating summarization news, but the predicted sequence is like this:
actual: [[‘startseq as of thursday facebook allows users to edit comments rather than retype them each comment will show its editing history in a dropdown menu to give users context editing will be rolled out to users gradually over the next few days endseq’]]
predicted: [‘startseq the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the the’]
As you can see it generated a lot of “the”, have you ever encountered such a problem?
do you have any suggestion?
That happens when your model is not well-trained, or when the model is too simple for this job so it cannot hold the correct state to produce the sentence.