Keras CNN Error: expected Sequence to have 3 dimensions, but got array with shape (500, 400)

Question

I'm getting this error:

ValueError: Error when checking input: expected Sequence to have 3 dimensions, but got array with shape (500, 400)

These are the below codes that I'm using.

print(X1_Train.shape)
print(X2_Train.shape)
print(y_train.shape)

Output (here I've 500 rows in each):

(500, 400)
(500, 1500)
(500,)

400 => timesteps (below)
1500 => n (below)

Code:

timesteps = 50 * 8
n = 50 * 30

def createClassifier():
    sequence = Input(shape=(timesteps, 1), name='Sequence')
    features = Input(shape=(n,), name='Features')

    conv = Sequential()
    conv.add(Conv1D(10, 5, activation='relu', input_shape=(timesteps, 1)))
    conv.add(Conv1D(10, 5, activation='relu'))
    conv.add(MaxPool1D(2))
    conv.add(Dropout(0.5))

    conv.add(Conv1D(5, 6, activation='relu'))
    conv.add(Conv1D(5, 6, activation='relu'))
    conv.add(MaxPool1D(2))
    conv.add(Dropout(0.5))
    conv.add(Flatten())
    part1 = conv(sequence)

    merged = concatenate([part1, features])

    final = Dense(512, activation='relu')(merged)
    final = Dropout(0.5)(final)
    final = Dense(num_class, activation='softmax')(final)

    model = Model(inputs=[sequence, features], outputs=[final])
    model.compile(loss='binary_crossentropy', optimizer='adam', metrics=['accuracy'])
    return model

model = createClassifier()
# print(model.summary())
history = model.fit([X1_Train, X2_Train], y_train, epochs =5)

Any insights?

Dinari · Accepted Answer · 2018-11-25 09:22:21Z

4

Two things -

Conv1D layer expects input to be in the shape (batch_size, x, filters), in your case (500,400,1).
You need to reshape your input layer, add another axis, of size 1. (this does not change anything in your data).

You are trying to use multiple inputs, Sequential API is not the best choice for that. I would recommend using the Functional API

Edit: Regarding your comment, not sure what you did wrong, but this is a working version of your code (with fake data), with a reshape:

import keras

import numpy as np



X1_Train = np.ones((500,400))
X2_Train = np.ones((500,1500))
y_train = np.ones((500))
print(X1_Train.shape)
print(X2_Train.shape)
print(y_train.shape)

num_class = 1


timesteps = 50 * 8
n = 50 * 30

def createClassifier():
    sequence = keras.layers.Input(shape=(timesteps, 1), name='Sequence')
    features = keras.layers.Input(shape=(n,), name='Features')

    conv = keras.Sequential()
    conv.add(keras.layers.Conv1D(10, 5, activation='relu', input_shape=(timesteps, 1)))
    conv.add(keras.layers.Conv1D(10, 5, activation='relu'))
    conv.add(keras.layers.MaxPool1D(2))
    conv.add(keras.layers.Dropout(0.5))

    conv.add(keras.layers.Conv1D(5, 6, activation='relu'))
    conv.add(keras.layers.Conv1D(5, 6, activation='relu'))
    conv.add(keras.layers.MaxPool1D(2))
    conv.add(keras.layers.Dropout(0.5))
    conv.add(keras.layers.Flatten())
    part1 = conv(sequence)

    merged = keras.layers.concatenate([part1, features])

    final = keras.layers.Dense(512, activation='relu')(merged)
    final = keras.layers.Dropout(0.5)(final)
    final = keras.layers.Dense(num_class, activation='softmax')(final)

    model = keras.Model(inputs=[sequence, features], outputs=[final])
    model.compile(loss='binary_crossentropy', optimizer='adam', metrics=['accuracy'])
    return model

model = createClassifier()
# print(model.summary())
X1_Train = X1_Train.reshape((500,400,1))
history = model.fit([X1_Train, X2_Train], y_train, epochs =5)

With output:

Using TensorFlow backend.
(500, 400)
(500, 1500)
(500,)
Epoch 1/5
500/500 [==============================] - 1s 3ms/step - loss: 1.1921e-07 - acc: 1.0000
Epoch 2/5
500/500 [==============================] - 0s 160us/step - loss: 1.1921e-07 - acc: 1.0000
Epoch 3/5
500/500 [==============================] - 0s 166us/step - loss: 1.1921e-07 - acc: 1.0000
Epoch 4/5
500/500 [==============================] - 0s 154us/step - loss: 1.1921e-07 - acc: 1.0000
Epoch 5/5
500/500 [==============================] - 0s 157us/step - loss: 1.1921e-07 - acc: 1.0000

edited Nov 25, 2018 at 9:22

answered Nov 25, 2018 at 7:27

Dinari

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2 Comments

SHM Over a year ago

changed accordingly to (500, 400, 1). But it didn't work. I'm still getting an error. I changed the CNN layer as per functional API. But, I'm getting the below error. tensorflow.python.framework.errors_impl.InvalidArgumentError: indices[22,330] = -1 is not in [0, 400)

Dinari Over a year ago

Not sure what you did wrong with the reshape, edited and added a working version of your code, with fake data, note that I only added the reshape line.

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