I am trying a simple model ensemble with 2 different input datasets and 1 output. I want to get predictions for one dataset and hope model will extract some useful features from the second one. I get an error:

ValueError: Data cardinality is ambiguous: x sizes: 502, 1002 y sizes: 502 Make sure all arrays contain the same number of samples.

But I want it to fit for smaller dataset.

Architecture is like this:

enter image description here


import pandas as pd
from keras.models import Model
from keras.layers import Input, Dense, Flatten
from keras.layers.merge import concatenate
from keras.utils import plot_model

train_1d_X = pd.read_csv('train1d_x.csv').values
train_12h_X = pd.read_csv('train12h_x.csv').values
train_1d_y = pd.read_csv('train1d_y.csv').values
train_12h_y = pd.read_csv('train12h_y.csv').values

#model 1d
input_1d = Input(shape=train_1d_X.shape)
dense_1d_1 = Dense(16, activation='relu')(input_1d)

#model 12h
input_12h = Input(shape=train_12h_X.shape)
dense_12h_1 = Dense(16, activation='relu')(input_12h)

merge = concatenate([dense_1d_1, dense_12h_1], axis=1)

hidden1 = Dense(32, activation='relu')(merge)
output = Dense(1, activation='linear')(hidden1)

model = Model(inputs=[input_1d, input_12h], outputs=[output])

model.compile(loss='mse', optimizer='adam')
model.fit([train_1d_X, train_12h_X], train_1d_y, epochs=10, verbose=2)
  • $\begingroup$ You can not feed your network with such an input data shape. You have 2 inputs with shape (502,) and (1002,). Let's consider the batch size is one. So the model takes one sample each time to move it through layers. Now, regarding you have 502 and 1002 samples, the question is which one them should be selected as the input pair?? $\endgroup$
    – Kaveh
    Jul 6, 2021 at 16:29
  • $\begingroup$ Could we get the data to try to fix this problem on our machine if the data is not private? $\endgroup$
    – user119783
    Jul 9, 2021 at 7:34
  • $\begingroup$ Or at least give us the structure of data or an example of the CSV file to reimplement the problem and help us to verify our solutions. You can read this stackoverflow.com/help/minimal-reproducible-example $\endgroup$
    – user119783
    Jul 9, 2021 at 7:47

3 Answers 3


You can not feed your network with two inputs with a different number of samples, and this also does not make sense.

You have 2 inputs with shapes (502,) and (1002,) (You have said you want to extract features also from your second dataset). Let's consider the batch size as 1 for the sake of simplicity. So the model takes one sample each time to move it through layers.

Problem: Now, regarding you have 502 and 1002 samples, the question is, which one of them should be selected as the input pair? For example, the first sample in your first data set associated with which sample in your second dataset?

Reason: Creating input pairs is the reason that model expects to get inputs in the same number of samples, and it will consider the first sample in your first dataset is associated with the first sample in your second dataset.

Solution: So, you should take a subset of your second dataset in a way each sample in your second dataset corresponds to the same ordered sample in your first dataset. Take care of your sample order. If you shuffle the first dataset, you should shuffle the second dataset in the same order.

  • $\begingroup$ I think you should read more to get a better intuition of neural networks structure. NNs try to tune their weights, to have minimum loss, which is the difference between true_label and pred_label. Each label is associated with one input sample. So, If the number of inputs is say N in the shape (N, any_dimension), the number of labels also should be the same as (N, any_dimension). Always, the first dimension of input and output should be equal. $\endgroup$
    – Kaveh
    Jul 7, 2021 at 10:22
  • $\begingroup$ So there is no way to train them together? I need to train separate models and then concatenate their outputs? That would be very unfortunate $\endgroup$
    – Myron
    Jul 7, 2021 at 10:32
  • $\begingroup$ What is your first data and second data? Images? Features? Text? Number? $\endgroup$
    – Kaveh
    Jul 7, 2021 at 10:37
  • $\begingroup$ Both datasets are trading candles datasets. One contains daily candles and one - 12 hours. I want to make price prediction for daily interval but taking into account changes on 12 hours interval. I tried to concatenate predictions, but also did not help $\endgroup$
    – Myron
    Jul 7, 2021 at 10:42
  • $\begingroup$ So, in this case, each sample could be the data for one day. Organize your data in a way, you have in each row information of a one day. Now, if you have information of 100 consecutive days in your first dataset, you should have 12 hours trading candles in the same 100 consecutive days. $\endgroup$
    – Kaveh
    Jul 7, 2021 at 11:12

Some solutions are better worked out when we understand the underlying layer behind it. In the field of NLP which utilizes Recurrent Neural Networks, ideally allows varying input sizes. Even in Convolutional Neural Networks which is commonly used for images allows varying input sizes. Research discussion on dealing with varying inputs

You have two choices to either downsize your input samples to a fixed size or to up sample your input samples so both the input samples match. For up sizing, you can pad the sequences with zeros to ensure both the inputs have fixed size. Data cardinality issue resolved by using pad_sequences

For CNN models where the neural network graph for multiple inputs is as shown below:

neural network graph for multiple inputs (source)

Code sample for multiple inputs example for CNN as mentioned

Do take a look at the below links for better understanding and make your call on best approach to solving your problem.


I haven't used tensorflow much lately (more of a pytorch guy), but my interpretation of that error is that your X tensor has two dimensions and your y tensor only has 1, so it's not clear which dimension of X is supposed to align with y. Try adding an empty dimension to your labels and see if that fixes the issue:

train_1d_y = tf.expand_dims(train_1d_y, 1) 

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