I have this LSTM model

model = Sequential()
model.add(Masking(mask_value=0, input_shape=(timesteps, features)))
model.add(LSTM(100, dropout=0.2, recurrent_dropout=0.2, return_sequences=False))
model.add(Dense(features, activation='softmax'))
model.compile(loss='categorical_crossentropy', optimizer='adam', metrics=['accuracy'])

and shapes X_train (21, 11, 5), y_train (21, 5).

Each timestep is represented by 5 features and return_sequences is set to False because I want to predict one 5D array (the next timestep) for each input sequence of 11 timesteps.

I get the error

ValueError: y_true and y_pred have different number of output (5!=1)

If I reshape the data as X_train (21, 11, 5), y_train (21, 1, 5) instead I get the error

ValueError: Invalid shape for y: (14, 1, 5)

Note: the value 14 is due to the fact that I'm using cross validation.

What should I do?


I changed the model to

model = Sequential()
model.add(Masking(mask_value=0, input_shape=(timesteps, features)))
model.add(LSTM(100, dropout=0.2, recurrent_dropout=0.2))
model.add(Dense(features, activation='sigmoid')) 
model.compile(loss='binary_crossentropy', optimizer='adam', metrics=['accuracy'])

and used the same shapes as before. Here model.summary() gives

Layer (type)                 Output Shape              Param #   
masking_1 (Masking)          (None, 11, 5)             0         
lstm_1 (LSTM)                (None, 100)               42400     
dense_1 (Dense)              (None, 5)                 505       

The idea is to produce a multilabel classification. After training the model, I evaluate it on the test data and this is what I get:

X[0] = [[0 0 0 0 0],[1 0 0 1 0], ...,[0 0 1 0 0],[0 0 1 0 0]]

y_true[0] = [0 0 1 0 0]

y_pred[0] = 2

which is not what I want. How can I get an output of the same shape as y_true, so as to transform it into a multilabel classification?


2 Answers 2


What are your features like? Given that you have a Dense layer outputting a softmax of size 5, this implies that all you want to predict is 1 feature, a categorical feature with 5 options.

If this is not true, more information about the features is needed to help here.

Your Y-variable for each feature should be of size (num_samples, time_step_len, num_categories_of_feature). You need to one-hot-encode each categorical feature separately, which gives the last dimension size, num_categories_of_feature. As you have it currently, the Y_train size is (num_samples, features). So, as you have the problem framed, the network has no way to learn the sequence patterns, as you only give it the end result. You should create your Y_train data to be the true value for the next time-step, for every time-step. Hence, (num_samples, time_step_len, num_categories_of_feature). Side note: I've only worked with LSTMs/RNN's on one problem, and this is how I did it. I cared about learning the sequences in it's entirety, because my inputs at prediction time are variable. If you always have 11 time-steps and always just want the next time-step prediction, this might not apply. I really don't know to be honest.

This is where I'm not totally sure if this is the only way to do this, but the way I think of this problem for wanting to predict 5 categorical variables, you need a way to output softmaxs for each variable. A softmax activation of size "features", like you have it here, is estimating a probability distribution of size 5, which implies your Y variable is only 1 categorical feature that has 5 potential values. So, you will need to set up your network to have 5 outputs with independent softmax outputs the size equal to the number of categories for each variable. A single softmax should only be used to estimate a distribution over a single class variable. 10 options for feat1? Softmax of size 10. etc.

losses = {"feat1_output": "categorical_crossentropy", "feat2_output": "categorical_crossentropy", "feat3_output": "categorical_crossentropy", "feat4_output": "categorical_crossentropy", "feat5_output": "categorical_crossentropy"}
lossWeights = {"feat1_output": 1.0, "feat2_output": 1.0, ... , ...}# if everything is equal, dont worry about specifying loss weights.
metrics = {"feat1_output": "categorical_accuracy", "feat2_output": "categorical_accuracy", "feat3_output": "categorical_accuracy", "feat4_output": "categorical_accuracy", "feat5_output": "categorical_accuracy"}
opt = Adam(lr=init_lr,decay=init_lr / num_epochs)
model.compile(loss = losses, loss_weights = lossWeights, optimizer=opt, metrics=metrics)

Now, you will be optimizing 5 loss functions at the same time, one for each categorical prediction. You must now have 5 Y-variable datasets, each of size (num_samples, time_step_len, num_categories_of_feature). You will then give 5 y datasets for the outputs in the fit function, as a list. However, to properly name the output layers, you will need to specify the names for the output layers in the model definition.

  • $\begingroup$ My data is shaped in the way I explained in this other question: datascience.stackexchange.com/questions/45867/…, but with size 5 instead of 3. The idea was to predict the one-hot encoded categorical vectors of size 5 for the next timestep at the same time, given the list of all the encodings for the previous timesteps (11 timesteps in the example). $\endgroup$ Commented Feb 25, 2019 at 20:57
  • 1
    $\begingroup$ So, each of the 5 features can only take a value of 0 or 1, right? They only have a single dimension, so this seems like what you have. If these variables were "one-hot-encoded", you would have a timestep that looks like this: [(1,0),(0,1),(0,1)] instead of [0,1,0]. One-Hot-Encoding means that each feature is represented as however many classes the feature can take. If a feature can take 6 values, it takes 5 0's and a single 1 (in the "column" representing that class) to represent which class it is. $\endgroup$
    – kylec123
    Commented Feb 25, 2019 at 21:17
  • $\begingroup$ If you reshape your y-data to be like I mention above, you can then have 5 separate softmax activations, once for each categorical variable. $\endgroup$
    – kylec123
    Commented Feb 25, 2019 at 21:18
  • $\begingroup$ Actually it is slightly different. I concatenated different encodings into the same 5D array because otherwise I would have a 4 dimensional input, but I don't know if it's a reasonable thing to do. $\endgroup$ Commented Feb 25, 2019 at 21:48
  • 1
    $\begingroup$ If you are trying to use a Softmax activation, you will only ever get a probability distribution the size of the "features". I believe you need to reevaluate how you represent your Y-data. $\endgroup$
    – kylec123
    Commented Feb 25, 2019 at 21:53


I found the solution to my problem here: https://github.com/keras-team/keras/issues/9331 I just had to override KerasClassifier wrapper and make it work for multilabel sequence prediction.


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