It can be hard to prepare data when you’re just getting started with deep learning.

Long Short-Term Memory, or LSTM, recurrent neural networks expect three-dimensional input in the Keras Python deep learning library.

If you have a long sequence of thousands of observations in your time series data, you must split your time series into samples and then reshape it for your LSTM model.

In this tutorial, you will discover exactly how to prepare your univariate time series data for an LSTM model in Python with Keras.

Let’s get started.

## How to Prepare Time Series Data

Perhaps the most common question I get is how to prepare time series data for supervised learning.

I have written a few posts on the topic, such as:

- How to Convert a Time Series to a Supervised Learning Problem in Python
- Time Series Forecasting as Supervised Learning

But, these posts don’t help everyone.

I recently got this email:

I have two columns in my data file with 5000 rows, column 1 is time (with 1 hour interval) and column 2 is bits/sec and I am trying to forecast bits/sec. In that case can you please help me to set sample, time step and feature [for LSTMs]?

There are few problems here:

- LSTMs expect 3D input, and it can be challenging to get your head around this the first time.
- LSTMs don’t like sequences of more than 200-400 time steps, so the data will need to be split into samples.

In this tutorial, we will use this question as the basis for showing one way to specifically prepare data for the LSTM network in Keras.

## 1. Load the Data

I assume you know how to load the data as a Pandas Series or DataFrame.

If not, see these posts:

Here, we will mock loading by defining a new dataset in memory with 5,000 time steps.

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from numpy import array # load... data = list() n = 5000 for i in range(n): data.append([i+1, (i+1)*10]) data = array(data) print(data[:5, :]) print(data.shape) |

Running this piece both prints the first 5 rows of data and the shape of the loaded data.

We can see we have 5,000 rows and 2 columns: a standard univariate time series dataset.

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[[ 1 10] [ 2 20] [ 3 30] [ 4 40] [ 5 50]] (5000, 2) |

## 2. Drop Time

If your time series data is uniform over time and there is no missing values, we can drop the time column.

If not, you may want to look at imputing the missing values, resampling the data to a new time scale, or developing a model that can handle missing values. See posts like:

- How to Handle Missing Timesteps in Sequence Prediction Problems with Python
- How to Handle Missing Data with Python
- How To Resample and Interpolate Your Time Series Data With Python

Here, we just drop the first column:

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# drop time data = data[:, 1] print(data.shape) |

Now we have an array of 5,000 values.

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(5000,) |

## 3. Split Into Samples

LSTMs need to process samples where each sample is a single time series.

In this case, 5,000 time steps is too long; LSTMs work better with 200-to-400 time steps based on some papers I’ve read. Therefore, we need to split the 5,000 time steps into multiple shorter sub-sequences.

I write more about splitting up long sequences here:

- How to Handle Very Long Sequences with Long Short-Term Memory Recurrent Neural Networks
- How to Prepare Sequence Prediction for Truncated Backpropagation Through Time in Keras

There are many ways to do this, and you may want to explore some depending on your problem.

For example, perhaps you need overlapping sequences, perhaps non-overlapping is good but your model needs state across the sub-sequences and so on.

Here, we will split the 5,000 time steps into 25 sub-sequences of 200 time steps each. Rather than using NumPy or Python tricks, we will do this the old fashioned way so you can see what is going on.

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# split into samples (e.g. 5000/200 = 25) samples = list() length = 200 # step over the 5,000 in jumps of 200 for i in range(0,n,length): # grab from i to i + 200 sample = data[i:i+length] samples.append(sample) print(len(samples)) |

We now have 25 sub sequences of 200 time steps each.

1 |
25 |

If you’d prefer to do this in a one liner, go for it. I’d love to see what you can come up with.

Post your approach in the comments below.

## 4. Reshape Subsequences

The LSTM needs data with the format of [samples, time steps and features].

Here, we have 25 samples, 200 time steps per sample, and 1 feature.

First, we need to convert our list of arrays into a 2D NumPy array of 25 x 200.

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# convert list of arrays into 2d array data = array(samples) print(data.shape) |

Running this piece, you should see:

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(25, 200) |

Next, we can use the *reshape()* function to add one additional dimension for our single feature.

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# reshape into [samples, timesteps, features] # expect [25, 200, 1] data = data.reshape((len(samples), length, 1)) print(data.shape) |

And that is it.

The data can now be used as an input (X) to an LSTM model.

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(25, 200, 1) |

## Further Reading

This section provides more resources on the topic if you are looking to go deeper.

### Related Posts

- How to Convert a Time Series to a Supervised Learning Problem in Python
- Time Series Forecasting as Supervised Learning
- How to Load and Explore Time Series Data in Python
- How To Load Machine Learning Data in Python
- How to Handle Missing Timesteps in Sequence Prediction Problems with Python
- How to Handle Missing Data with Python
- How To Resample and Interpolate Your Time Series Data With Python
- How to Handle Very Long Sequences with Long Short-Term Memory Recurrent Neural Networks
- How to Prepare Sequence Prediction for Truncated Backpropagation Through Time in Keras

### API

## Summary

In this tutorial, you discovered how to convert your long univariate time series data into a form that you can use to train an LSTM model in Python.

Did this post help? Do you have any questions?

Let me know in the comments below.

Great article! I wish I had this a couple months ago when I was struggling with doing the same thing for Tensorflow. Glad to see the solution I had mostly aligns with yours.

You mention some papers that discuss optimal sample size. Would you be able to share a link to those? I’m interested to see how the authors arrive at that number.

Thanks.

Perhaps check this post:

https://machinelearningmastery.com/much-training-data-required-machine-learning/

Hi Jason, thx for sharing.

let say I have a timeseries dataset [1,2,3,4,5,6,7,8] and need to split it with time steps of 4, in your article, the result will be [1,2,3,4], [5,6,7,8]. But in some other articles I’ve read, the result sometime will be is this way: [1,2,3,4], [2,3,4,5],[3,4,5,6],[4,5,6,7],[5,6,7,8].

so what will be the best way to split the samples? thx.

All 3 approaches you have listed are valid, try each and see what works best for your problem.

Is there litterature on the subject? The 3 solutions seem to have a very distinct training time for large datasets. I assume that for the second solution we should keep the memory for the cell, but not for the third, right?

Also, is there a risk that the training overexposed certain timesteps(timestep 5 in the example) in early learning, giving a bigger weight to this data.

BTW great blog and your book on LSTM is the best I found on the subject. thx.

Not really.

I would suggest framing the problem each of the 3 ways and compare them to see what works best for your specific data.

Perhaps this post will help you with reframing the problem:

https://machinelearningmastery.com/reshape-input-data-long-short-term-memory-networks-keras/

Nice article. One thing I live about Python is list comprehension. One possible one-liner could be

samples = [data[i:i+length] for i in range(0,n, length)]

Nice, thanks.

Went, what you want is called “sliding window”, you could get it in the next code:

from itertools import islice

def window(seq, n=2):

“Returns a sliding window (of width n) over data from the iterable”

” s -> (s0,s1,…s[n-1]), (s1,s2,…,sn), … ”

it = iter(seq)

result = tuple(islice(it, n))

if len(result) == n:

yield result

for elem in it:

result = result[1:] + (elem,)

yield result

Hi Jason! First, I have to say that I really like your posts, they are very helpful.

I’m facing a time series classification problem (two classes) where I have series of around 120-200 time steps and 7 variables each. The problem is that I have only 3000 samples to train. What do you think, Is it feasible a priori to feed a LSTM network or I need more samples?

You mention that LSTM doesn’t work well with more than 200-400 timesteps. What about the number of features? Would you do dimensionality reduction?

Thank you very much in advance!

LSTMs can support multiple features.

It does not sound like enough data.

You could try splitting the sequence up into multiple subsequences to see if that helps?

Hi Jason,

Thank you for this excellent summary, your work is really impressive…I’m especially impressed by how many blog posts you have taken the time to write.

I was wondering why an LSTM network prefers a sequence of 200 – 400 samples, is this due to a memory allocation issue? Or can a longer sequence affect accuracy (I wouldn’t guess this but perhaps it’s possible)?

What role does the batch size play here? Couldn’t this restriction in sequence length be mitigated by selecting a correct batch size?

BR

Staffan

It seems to be a limitation on the training algorithm. I have seen this issue discussed in the literature, but have not pushed hard to better understand it myself.

I’d encourage you to test different configurations on your problem.

Hi jason,

Nice post! a little confused about the “time-steps” parameter. The “time-steps” means the steps span of input data? For example, for univariate problem,and one-step forecasting, i constructed the data with “sliding window”. For each sample,the structure is “t-6,t-5,t-4,t-3,t-2,t-1,t for input(train_x),and t+1 for output(train_y) ” .Using 7 data to forecast to the 8th. i reshaped the input(train_x) as [samples, 7,1]. Is that right?

Learn more about time steps in this post:

https://machinelearningmastery.com/gentle-introduction-backpropagation-time/

Hello Jason, sorry for my english. I’m new to neural nework and i am trying to develop a neural network to generate music.

I have many .txt file with a sequence of notes like these

[int(note number), int(time), int(length)]

68 2357 159,

64 2357 260,

…

…

What kind of neural network I have to choose for this purpose?

How can i preprocess this kind of data?

Congratulations for this website and thank you.

For sequence prediction, perhaps RNNs like the LSTM would be a good place to start.

hi

I want to classify classes each class consists of 8_time steps in each time steps 16 features. is this reshape correct

reshape(124,8,1)

I think it would be (?, 6, 16) where “?” is the number of samples, perhaps 124 if I understand your case.

Hello, Jason, thanks for the great work.

I’ve read your articles about organizing the data for LSTM in 3D, but I can not do this with my data, it always presents an error like this:

“Error when checking target: expected dense_363 to have 2 dimensions, but got array with shape (3455, 1, 1)”

My data is organized as follows:

Appetizer:

11,000 lines with 48 columns, each row represents one day and each column represents 0.5h,

The output Y (0, 1) is binary, it represents the occurrence of an event 1 = yes, 0 = no.

So I have X = [0.1, 0.2, 0.3, …, 0.48] Y = [0] or Y = [1]

for more details see my code:

# load data

dataframe = pd.read_csv(‘Parque_A_Classificado_V2.csv’, header=None)

dataset = dataframe.values

# split data to variables train and test

train_size = int(len(dataset) * 0.7)

test_size = len(dataset) – train_size

trainX, trainY = dataset[0:train_size,:48], dataset[train_size:len(dataset),48]

testX, testY = dataset[0:test_size, :48], dataset[test_size:len(dataset), 48]

# reshape input to be [samples, time steps, features]

trainX = trainX.reshape(trainX.shape[0],trainX.shape[1], 1)

testX = testX.reshape(testX.shape[0], testX.shape[1], 1)

trainY = trainY.reshape(trainY.shape[0], 1, 1)

testY = testY.reshape(testY.shape[0], 1, 1)

#criando modelo

model = Sequential()

model.add(LSTM(100, input_shape=(48, 1)))

model.add(Dense(1, activation=’sigmoid’))

# Compile model

model.compile(loss=’binary_crossentropy’, optimizer=’adam’, metrics=[‘acc’])

model.fit(trainX, trainY, validation_data(testX, testY), epochs=1, batch_size=1)

I can not find the error, can you help me?

Maybe this post will make it clearer:

https://machinelearningmastery.com/reshape-input-data-long-short-term-memory-networks-keras/

Many thanks, Jason, your attitude is commendable.

This time I had to run my model.

Glad to hear you worked out your problem.

Hi Jason,

I’m struggling with a problem similar to those described here with a slight difference.

I’m solving a disaggregation problem and so my the dimensions of my output are higher than my input. in order to simplify lets say my original data looks something like this:

X.shape == [1000,1]

Y.shape == [1000,10]

I do some of the input to make things work:

X = X.reshape(1,X.shape[0[,X.shape[1]) #leaving this parameter dependent in case I want to

later use more features

My net looks like this:

model.sequential()

model.add(LSTM(50,batch_input_shape = X.shape, stateful = True)

model.add(Dense(Y.shape[1],activation = ‘relu’) #my output values aren’t between +/-1 so I

chose relu

went with a stateful model because I will most likely have to do batch seperation when running my actual training as I have close to a 10^6 samples

and then I’ve tried both doing the same thing to the Y vector and not touching it, either way I get error (when I reshaped Y I then changed Y.shape[1] to Y.shape[2])

Any thoughts?

Output will be 2D not 3D.