How to format input and output shapes for convolutional (1D) keras neural network? (Python)

Question

I am new to deep learning, the keras API, and convolutional networks so apologies before-hand if these mistakes are naive. I am trying to build a simple convolutional neural network for classification. The input data X has 286 samples each with 500 timepoints of 4 dimensions. The dimensions are one-hot-encodings of categorical variables. I wasn't sure what to do for Y so I just did some clustering of the samples and the one-hot-encoded them to have data to experiment with for the modeling. The Y target data has 286 samples with one-hot-encodings for 6 categories. My ultimate goal is just to get it to run so I can figure out how to change it for actually useful learning problems and use the hidden layers for feature extraction.

My problem is that I can't get the shapes to match up in the final layer.

The model I made does the following:

(1) Inputs the data

(2) Convolutional layer

(3) Maxpooling layer

(4) Dropout regularization

(5) Large fully connected layer

(6) Output layer

import tensorflow as tf
import numpy as np
# Data Description
print(X[0,:])
# [[0 0 1 0]
#  [0 0 1 0]
#  [0 1 0 0]
#  ..., 
#  [0 0 1 0]
#  [0 0 1 0]
#  [0 0 1 0]]
print(Y[0,:])
# [0 0 0 0 0 1]
X.shape, Y.shape
# ((286, 500, 4), (286, 6))

# Tensorboard callback
tensorboard= tf.keras.callbacks.TensorBoard()

# Build the model
# Input Layer taking in 500 time points with 4 dimensions
input_layer = tf.keras.layers.Input(shape=(500,4), name="sequence")
# 1 Dimensional Convolutional layer with 320 filters and a kernel size of 26 
conv_layer = tf.keras.layers.Conv1D(320, 26, strides=1, activation="relu", )(input_layer)
# Maxpooling layer 
maxpool_layer = tf.keras.layers.MaxPooling1D(pool_size=13, strides=13)(conv_layer)
# Dropout regularization
drop_layer = tf.keras.layers.Dropout(0.3)(maxpool_layer)
# Fully connected layer
dense_layer = tf.keras.layers.Dense(512, activation='relu')(drop_layer)
# Softmax activation to get probabilities for output layer
activation_layer = tf.keras.layers.Activation("softmax")(dense_layer)
# Output layer with probabilities
output = tf.keras.layers.Dense(num_classes)(activation_layer)
# Build model
model = tf.keras.models.Model(inputs=input_layer, outputs=output, name="conv_model")
model.compile(loss="categorical_crossentropy", optimizer="adam", callbacks=[tensorboard])
model.summary()
# _________________________________________________________________
# Layer (type)                 Output Shape              Param #   
# =================================================================
# sequence (InputLayer)        (None, 500, 4)            0         
# _________________________________________________________________
# conv1d_9 (Conv1D)            (None, 475, 320)          33600     
# _________________________________________________________________
# max_pooling1d_9 (MaxPooling1 (None, 36, 320)           0         
# _________________________________________________________________
# dropout_9 (Dropout)          (None, 36, 320)           0         
# _________________________________________________________________
# dense_16 (Dense)             (None, 36, 512)           164352    
# _________________________________________________________________
# activation_7 (Activation)    (None, 36, 512)           0         
# _________________________________________________________________
# dense_17 (Dense)             (None, 36, 6)             3078      
# =================================================================
# Total params: 201,030
# Trainable params: 201,030
# Non-trainable params: 0
model.fit(X,Y, batch_size=128, epochs=100)
# ValueError: Error when checking target: expected dense_17 to have shape (None, 36, 6) but got array with shape (286, 6, 1)

ldavid ldavid · Accepted Answer · 2017-11-23T01:21:00

Conv1D's output's shape is a 3-rank tensor (batch, observations, kernels):

> x = Input(shape=(500, 4))
> y = Conv1D(320, 26, strides=1, activation="relu")(x)
> y = MaxPooling1D(pool_size=13, strides=13)(y)
> print(K.int_shape(y))
(None, 36, 320)

However, Dense layers expects a 2-rank tensor (batch, features). A Flatten, GlobalAveragePooling1D or GlobalMaxPooling1D separating the convolutions from the denses is sufficient to fix this:

Flatten will reshape a (batch, observations, kernels) tensor into a (batch, observations * kernels) one:

....
y = Conv1D(320, 26, strides=1, activation="relu")(x)
y = MaxPooling1D(pool_size=13, strides=13)(y)
y = Flatten()(y)
y = Dropout(0.3)(y)
y = Dense(512, activation='relu')(y)
....

GlobalAveragePooling1D will average all observations in (batch, observations, kernels) tensor, resulting in a (batch, kernels) one:

....
y = Conv1D(320, 26, strides=1, activation="relu")(x)
y = GlobalAveragePooling1D(pool_size=13, strides=13)(y)
y = Flatten()(y)
y = Dropout(0.3)(y)
y = Dense(512, activation='relu')(y)
....

There seems to be a problem with your tensorboard callback initialization also. This one is easy to fix.

For temporal data processing, take a look at the TimeDistributed wrapper.

How to format input and output shapes for convolutional (1D) keras neural network? (Python)

1 Answers