Tensorflow error : Dimensions must be equal - python-3.x

Question

I have a dataset of 25000 colored pictures 100*100(*3) and I am trying to build a simple neural network with one convolutional layer. Its pictures of cells that are infected or not by Malaria, so my output is 2.
But it seems like I have a dimension mismatch, and I don't know where my error comes from.
My neural network :
def simple_nn(X_training, Y_training, X_test, Y_test):
input = 100*100*3
batch_size = 25
X = tf.placeholder(tf.float32, [batch_size, 100, 100, 3])
#Was:
# W = tf.Variable(tf.zeros([input, 2]))
# b = tf.Variable(tf.zeros([2]))
#Now:
W = tf.Variable(tf.truncated_normal([4, 4, 3, 3], stddev=0.1))
B = tf.Variable(tf.ones([3])/10) # What should I put here ??
init = tf.global_variables_initializer()
# model
#Was:
# Y = tf.nn.softmax(tf.matmul(tf.reshape(X, [-1, input]), W) + b)
#Now:
stride = 1 # output is still 28x28
Ycnv = tf.nn.conv2d(X, W, strides=[1, stride, stride, 1], padding='SAME')
Y = tf.nn.relu(Ycnv + B)
# placeholder for correct labels
Y_ = tf.placeholder(tf.float32, [None, 2])
# loss function
cross_entropy = -tf.reduce_sum(Y_ * tf.log(Y))
# % of correct answers found in batch
is_correct = tf.equal(tf.argmax(Y,1), tf.argmax(Y_,1))
accuracy = tf.reduce_mean(tf.cast(is_correct, tf.float32))
learning_rate = 0.00001
optimizer = tf.train.GradientDescentOptimizer(learning_rate)
train_step = optimizer.minimize(cross_entropy)
sess = tf.Session()
sess.run(init)
#Training here...
My error :
Traceback (most recent call last):
File "neural_net.py", line 135, in <module>
simple_nn(X_training, Y_training, X_test, Y_test)
File "neural_net.py", line 69, in simple_nn
cross_entropy = -tf.reduce_sum(Y_ * tf.log(Y))
...
ValueError: Dimensions must be equal, but are 2 and 3 for 'mul' (op: 'Mul') with input shapes: [?,2], [25,100,100,3].
I used a simple layer before, and it was working. I changed my weight and bias, and honestly, I don't know why my bias are setup like this, I followed a tutorial (https://codelabs.developers.google.com/codelabs/cloud-tensorflow-mnist/#11) but it is not explained.
I also replaced my Y to a conv2D.
And I don't know what my ouput should be if I want to get a vector of size 2*1 as a result.

Answer 1

You have correctly defined your labels as
Y_ = tf.placeholder(tf.float32, [None, 2])
So the last dimension is 2. However, the output from the convolution step is not directly suitable for comparing it to the labels. What I mean is the following: if you do
Ycnv = tf.nn.conv2d(X, W, strides=[1, stride, stride, 1], padding='SAME')
Y = tf.nn.relu(Ycnv + B)
The dimensions of this are going to be four as the error says:
ValueError: Dimensions must be equal, but are 2 and 3 for 'mul' (op: 'Mul') with input shapes: [?,2], [25,100,100,3].
So it is impossible to multiply directly (or operate) the output from convolution with the labels. What I recommend is to flatten (reshape it to only one dimension) the output of convolution and pass it to a fully connected layer of 2 units (as much as classes you have). Like this:
Y = tf.reshape(Y, [1,-1])
logits = tf.layers.dense(Y, units= 2)
and you can pass this to the loss.
Also I recommend you to change the loss to a more approprite version. For example, tf.losses.sigmoid_cross_entropy.
Also, the way you use convolutions is strange. Why do you put handmade filters in the convolution? besides you should have to initialize and before it putting them in a collection. In conclusion I recommend you to delete all the following code:
W = tf.Variable(tf.truncated_normal([4, 4, 3, 3], stddev=0.1))
B = tf.Variable(tf.ones([3])/10) # What should I put here ??
init = tf.global_variables_initializer()
# model
#Was:
# Y = tf.nn.softmax(tf.matmul(tf.reshape(X, [-1, input]), W) + b)
#Now:
stride = 1 # output is still 28x28
Ycnv = tf.nn.conv2d(X, W, strides=[1, stride, stride, 1], padding='SAME')
Y = tf.nn.relu(Ycnv + B)
and substitute it by:
conv1 = tf.layers.conv2d(X, filters=64, kernel_size=3,
strides=1, padding='SAME',
activation=tf.nn.relu, name="conv1")
Also the init = tf.global_variable_initializer() should be at the end of the graph construction becuase, if not, there will be variables it won't catch.
My final working code is:
def simple_nn():
inp = 100*100*3
batch_size = 2
X = tf.placeholder(tf.float32, [batch_size, 100, 100, 3])
Y_ = tf.placeholder(tf.float32, [None, 2])
#Was:
# W = tf.Variable(tf.zeros([input, 2]))
# b = tf.Variable(tf.zeros([2]))
#Now:
# model
#Was:
# Y = tf.nn.softmax(tf.matmul(tf.reshape(X, [-1, input]), W) + b)
#Now:
stride = 1 # output is still 28x28
conv1 = tf.layers.conv2d(X, filters=64, kernel_size=3,
strides=1, padding='SAME',
activation=tf.nn.relu, name="conv1")
Y = tf.reshape(conv1, [1,-1])
logits = tf.layers.dense(Y, units=2, activation=tf.nn.relu)
# placeholder for correct labels
# loss function
cross_entropy = tf.nn.softmax_cross_entropy_with_logits_v2(labels=Y_, logits=logits)
loss = tf.reduce_mean(cross_entropy)
# % of correct answers found in batch
is_correct = tf.equal(tf.argmax(Y,1), tf.argmax(Y_,1))
accuracy = tf.reduce_mean(tf.cast(is_correct, tf.float32))
learning_rate = 0.00001
optimizer = tf.train.GradientDescentOptimizer(learning_rate)
train_step = optimizer.minimize(cross_entropy)
init = tf.global_variables_initializer()
with tf.Session() as sess:
sess.run(init)
...