expected ndim=3, found ndim=2

Question

I'm new with Keras and I'm trying to implement a Sequence to Sequence LSTM. Particularly, I have a dataset with 9 features and I want to predict 5 continuous values.

I split the training and the test set and their shape are respectively:

X TRAIN (59010, 9)

X TEST (25291, 9)

Y TRAIN (59010, 5)

Y TEST (25291, 5)

The LSTM is extremely simple at the moment:

model = Sequential()
model.add(LSTM(100, input_shape=(9,), return_sequences=True))
model.compile(loss="mean_absolute_error", optimizer="adam", metrics= ['accuracy'])

history = model.fit(X_train,y_train,epochs=100, validation_data=(X_test,y_test))

But I have the following error:

ValueError: Input 0 is incompatible with layer lstm_1: expected ndim=3, found ndim=2

Can anyone help me?

Solution

LSTM layer expects inputs to have shape of (batch_size, timesteps, input_dim). In keras you need to pass (timesteps, input_dim) for input_shape argument. But you are setting input_shape (9,). This shape does not include timesteps dimension. The problem can be solved by adding extra dimension to input_shape for time dimension. E.g adding extra dimension with value 1 could be simple solution. For this you have to reshape input dataset( X Train) and Y shape. But this might be problematic because the time resolution is 1 and you are feeding length one sequence. With length one sequence as input, using LSTM does not seem the right option.

x_train = x_train.reshape(-1, 1, 9)
x_test  = x_test.reshape(-1, 1, 9)
y_train = y_train.reshape(-1, 1, 5)
y_test = y_test.reshape(-1, 1, 5)

model = Sequential()
model.add(LSTM(100, input_shape=(1, 9), return_sequences=True))
model.add(LSTM(5, input_shape=(1, 9), return_sequences=True))
model.compile(loss="mean_absolute_error", optimizer="adam", metrics= ['accuracy'])

history = model.fit(X_train,y_train,epochs=100, validation_data=(X_test,y_test))

Comments

[Avv]

Thank you very much. I did the same exact thing, but I still got the same issue. Any help please?

[Avv]

Why adding this does solve my issue! I had data of shape (804, 291) for both X and y since I want to build an LSTM autoencoder. I just added ` X = tf.convert_to_tensor(scaled_features.to_numpy().reshape(-1, 804, 291), np.float32) y = tf.convert_to_tensor(scaled_features.to_numpy().reshape(-1, 804, 291), np.float32)` and now it works. Could you please tell me why!

[Avv]

I noticed I have loss nan for adam optimizer during training. Any idea why does that happen please?

[Mitiku]

Which loss are you using?

[Avv]

Thank you for replying back. I did solve nan and infinity loss by removing 0s and 1s, but that might affect credibility of my results! I tried regularization, l2, clipnorm and others but I still got loss around 9.06! Any suggestion please?