I am trying to build a CNN model on Keras. The data has a dimension of 921 rows × 10000 columns.

Here is the code:

import numpy as np
import keras
from keras.models import Sequential
from keras.layers import Dense, Dropout, Flatten, Activation
from keras.optimizers import SGD

from sklearn.model_selection import train_test_split
X_train, X_test, y_train, y_test = train_test_split(merge.iloc[:,166:10166], merge[['Result_cat','Result_cat1']].values, test_size=0.2)

model = Sequential()

model.add(Dense(50, input_shape=(10000,))) 
model.add(Dense(50, activation='softmax')) 
model.add(Dense(1, activation='linear')) 


model.fit(X_train, y_train, batch_size=100, epochs=10)
score = model.evaluate(X_test, y_test, batch_size=32)

Then I encountered error

ValueError: Error when checking target: expected dense_3 to have shape (1,) but got array with shape (2,)

I am new to Keras and CNN. Can someone please explain to me what this means and how I can fix this? Thanks.


Problem is in the output layer and you are using categorical_crossentropy for a loss function. Quoting Keras documentation:

Note: when using the categorical_crossentropy loss, your targets should be in categorical format (e.g. if you have 10 classes, the target for each sample should be a 10-dimensional vector that is all-zeros except for a 1 at the index corresponding to the class of the sample). In order to convert integer targets into categorical targets, you can use the Keras utility to_categorical:

I would check if the target values are defined consistently. They seem to be defined for sparse_categorical_crossentropy, which requires a dense layer where number of neurons = number of classes of the problem. If they are defined as integers - as required for sparse_categorical_crossentropy, you can convert them to categorical formatting using to_categorical function, also defined in the documentation page linked above; or you can keep them as integers, and change the number of neurons in the final layer to 2, and loss function to sparse_categorical_crossentropy.

  • $\begingroup$ thank you! The data has a temperature time series data in each row for each observation, and classification labelling Y/N in the last two columns. It worked after changing the number of neurones in the final layer to 2. However, after making the change to batch_size=1000, epochs=1000, I experienced a repeated loss/ accuracy level for each Epoch:736/736 [==============================] - 0s 563us/step - loss: 1.9146 - acc: 0.5584. Is there a way I can fix this? $\endgroup$ Nov 18 '19 at 12:31
  • $\begingroup$ That seems to be unrelated to this question. It would be better if you create a new question for that issue. $\endgroup$
    – serali
    Nov 18 '19 at 12:36
  • $\begingroup$ Sure. I will check some reference before asking the new question. Thank you! $\endgroup$ Nov 18 '19 at 13:10

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