Python - Keras: LSTM data structure ValueError

Question

I'm trying to train an LSTM model using return_sequence to return the hidden state output for each input time step, solving a regression problem.

My Data shape is: (31, 2720, 16) i.e 31 batches of 2720 samples with 16 features.
My target shape is: (31, 2720, 1) i.e 31 batches of 2720 rows containing 1 value.

I've built the following model:

model = Sequential()
opt = Adam(learning_rate=0.0001, clipnorm=1)

num_samples = train_x.shape[1]
num_features = train_x.shape[2]

model.add(Masking(mask_value=-10., input_shape=(num_samples, num_features)))


model.add(LSTM(32, return_sequences=True, stateful=False, activation='tanh'))
model.add(Dropout(0.3))

#this is the last LSTM layer, use return_sequences=False
model.add(LSTM(16, return_sequences=False, stateful=False,  activation='tanh'))
model.add(Dropout(0.3))
model.add(Dense(16, activation='tanh'))
model.add(Dense(8, activation='tanh'))
model.add(Dense(1, activation='sigmoid'))

model.compile(loss='mse', optimizer='adam' ,metrics=[metrics.mean_absolute_error, metrics.mean_squared_error])

logdir = os.path.join(logs_base_dir, datetime.datetime.now().strftime("%Y%m%d-%H%M%S"))
tensorboard_callback = TensorBoard(log_dir=logdir, update_freq=1)
model.summary()

summary:

Model: "sequential_33"

_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
masking_24 (Masking)         (None, 2720, 16)          0         
_________________________________________________________________
lstm_61 (LSTM)               (None, 2720, 32)          6272      
_________________________________________________________________
dropout_51 (Dropout)         (None, 2720, 32)          0         
_________________________________________________________________
lstm_62 (LSTM)               (None, 16)                3136      
_________________________________________________________________
dropout_52 (Dropout)         (None, 16)                0         
_________________________________________________________________
dense_67 (Dense)             (None, 16)                272       
_________________________________________________________________
dense_68 (Dense)             (None, 8)                 136       
_________________________________________________________________
dense_69 (Dense)             (None, 1)                 9         
=================================================================
Total params: 9,825
Trainable params: 9,825
Non-trainable params: 0
_________________________________________________________________

When trying to fit the model, I get the following error:

ValueError                                Traceback (most recent call last)
<ipython-input-354-afdba8dea179> in <module>()
----> 1 model.fit(train_x, train_y, epochs=1000, batch_size=128,validation_split = 0.2, callbacks=[tensorboard_callback,checkpoint])

5 frames
/usr/local/lib/python3.6/dist-packages/tensorflow_core/python/keras/engine/training_utils.py in check_loss_and_target_compatibility(targets, loss_fns, output_shapes)
    808           raise ValueError('A target array with shape ' + str(y.shape) +
    809                            ' was passed for an output of shape ' + str(shape) +
--> 810                            ' while using as loss `' + loss_name + '`. '
    811                            'This loss expects targets to have the same shape '
    812                            'as the output.')

I'm trying to grasp the right way to structure the data, what am I missing?

score 1 · Answer 1 · answered Apr 26 '20 at 15:26

Your desired target shape is inconsistent with the model output.

Change this line

model.add(LSTM(16, return_sequences=False, stateful=False, activation='tanh'))

to

model.add(LSTM(16, return_sequences=True, stateful=False, activation='tanh'))

So that the temporal dimension is there.

from tensorflow.keras.layers import *
from tensorflow.keras.models import Model, Sequential
from tensorflow.keras.optimizers import Adam
import tensorflow as tf
import numpy as np

from tensorflow.keras.models import Sequential
from tensorflow.keras.layers import Dense

from tensorflow.keras import metrics
import tensorflow as tf
import numpy as np 

model = Sequential()
opt = Adam(learning_rate=0.0001, clipnorm=1)

num_samples = 2720
num_features = 16

model.add(Masking(mask_value=-10., input_shape=(num_samples, num_features)))


model.add(LSTM(32, return_sequences=True, stateful=False, activation='tanh'))
model.add(Dropout(0.3))

#this is the last LSTM layer, use return_sequences=False
model.add(LSTM(16, return_sequences=True, stateful=False,  activation='tanh'))
model.add(Dropout(0.3))
model.add(Dense(16, activation='tanh'))
model.add(Dense(8, activation='tanh'))
model.add(Dense(1, activation='sigmoid'))

model.compile(loss='mse', optimizer='adam' ,metrics=[metrics.mean_absolute_error, metrics.mean_squared_error])

model.summary()

Model: "sequential_3"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
masking_1 (Masking)          (None, 2720, 16)          0         
_________________________________________________________________
lstm_2 (LSTM)                (None, 2720, 32)          6272      
_________________________________________________________________
dropout_2 (Dropout)          (None, 2720, 32)          0         
_________________________________________________________________
lstm_3 (LSTM)                (None, 2720, 16)          3136      
_________________________________________________________________
dropout_3 (Dropout)          (None, 2720, 16)          0         
_________________________________________________________________
dense_3 (Dense)              (None, 2720, 16)          272       
_________________________________________________________________
dense_4 (Dense)              (None, 2720, 8)           136       
_________________________________________________________________
dense_5 (Dense)              (None, 2720, 1)           9         
=================================================================
Total params: 9,825
Trainable params: 9,825
Non-trainable params: 0

thank you so much, can you please have a look here https://stackoverflow.com/questions/61459436/computing-the-loss-across-all-lstm-timesteps-then-predicting-on-partial-data ? — Shlomi Schwartz, Apr 27 '20 at 20:23

score 1 · Accepted Answer · answered Apr 26 '20 at 15:32

Your target is of shape (31, 2720, 1) and the output of your current model will be of shape (31, 1). The error in this case is self explainatory.

You can solve this in one of two ways:

Looking at your model, I'm guessing you only want the loss with respect to the last sequence. In this case, you can call model.fit as follows:
```
model.fit(train_x, train_y[:, -1, :], ...) 
```
If you want to compute the loss across all timesteps, add return_sequences=True to the second LSTM layer:
```
model.add(LSTM(16, return_sequences=True, stateful=False,  activation='tanh'))
```

Thanks, my mistake was that I forgot to set return_sequences=True — Shlomi Schwartz, Apr 26 '20 at 15:38

Python - Keras: LSTM data structure ValueError

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