Keras Model fit throws shape mismatch error

Issue

I am building a Siamese network using Keras(TensorFlow) where the target is a binary column, i.e., match or mismatch(1 or 0). But the model fit method throws an error saying that the y_pred is not compatible with the y_true shape. I am using the binary_crossentropy loss function.

Here is the error I see:

enter image description here

Here is the code I am using:

model.compile(loss='binary_crossentropy', optimizer=optimizer, metrics=[tf.keras.metrics.Recall()])
history = model.fit([X_train_entity_1.todense(),X_train_entity_2.todense()],np.array(y_train),
                    epochs=2, 
                    batch_size=32,
                    verbose=2,
                    shuffle=True)

My Input data shapes are as follows:

Inputs:
X_train_entity_1.shape is (700,2822)
X_train_entity_2.shape is (700,2822)

Target:
y_train.shape is (700,1)

In the error it throws, y_pred is the variable which was created internally. What is y_pred dimension is 2822 when I am having a binary target. And 2822 dimension actually matches the input size, but how do I understand this?

Here is the model I created:

in_layers = []
out_layers = []
for i in range(2):
  input_layer = Input(shape=(1,))
  embedding_layer = Embedding(embed_input_size+1, embed_output_size)(input_layer)
  lstm_layer_1 = Bidirectional(LSTM(1024, return_sequences=True,recurrent_dropout=0.2, dropout=0.2))(embedding_layer)
  lstm_layer_2 = Bidirectional(LSTM(512, return_sequences=True,recurrent_dropout=0.2, dropout=0.2))(lstm_layer_1)

  in_layers.append(input_layer)
  out_layers.append(lstm_layer_2)

merge = concatenate(out_layers)
dense1 = Dense(256, activation='relu', kernel_initializer='he_normal', name='data_embed')(merge)
drp1 = Dropout(0.4)(dense1)
btch_norm1 = BatchNormalization()(drp1)
dense2 = Dense(32, activation='relu', kernel_initializer='he_normal')(btch_norm1)
drp2 = Dropout(0.4)(dense2)
btch_norm2 = BatchNormalization()(drp2)
output = Dense(1, activation='sigmoid')(btch_norm2)
model = Model(inputs=in_layers, outputs=output)
model.summary()

Since my data is very sparse, I used todense. And there the type is as follows:

type(X_train_entity_1) is scipy.sparse.csr.csr_matrix
type(X_train_entity_1.todense()) is numpy.matrix
type(X_train_entity_2) is scipy.sparse.csr.csr_matrix
type(X_train_entity_2.todense()) is numpy.matrix

Summary of last few layers as follows:
enter image description here

Solution

Mismatched shape in the Input layer. The input shape needs to match the shape of a single element passed as x, or dataset.shape[1:]. So since your dataset size is (700,2822), that is 700 samples of size 2822. So your input shape should be 2822.

Change:

input_layer = Input(shape=(1,))

To:

input_layer = Input(shape=(2822,))

Answered By – Djinn

This Answer collected from stackoverflow, is licensed under cc by-sa 2.5 , cc by-sa 3.0 and cc by-sa 4.0

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