If I insert the function, e.g., tf.fft(input, name=None), into a neural network, how does TensorFlow calculate the gradients in backpropagation?
I didn't find any documentation about this.
I am using TensorFlow 1.0.
If you're just inserting the tf.fft(...) function in the middle of a model I'm not certain tensorflow will even be able to handle a forward pass. If you read the docs on tf.signal.fft (https://www.tensorflow.org/api_docs/python/tf/signal/fft) or even just read the tf.fft function header, they both require inputs with dtype=tf.complex64 or dtype=tf.complex128. Perhaps tensorflow will cast float32 inputs to complex and then back again, allowing you to complete a forward pass, I'm not sure, but from what I can gather from reading tensorflow gradient documents casting values causes a disconnect between error gradient and Model parameters, meaning a backward pass won't work. You could try implementing a custom fft function which doesn't cast values and see if that works? It's not so easy though.
I have a setup like this:
model = keras.Model(input,[output1,output2])
My loss function is only a function of output1. How do I tell Keras to ignore output2 for the purposes of computing loss? The best I have come up with is to generate a bogus loss function which always returns 0.0:
model.compile(optimizer=..., loss=[realLossFunction, zeroLossFunction])
I can live with this, but I have to see the statistics and progress of this loss function all over the place and would like to know if there is a more elegant way.
You could just avoid putting this output in the model, and then reusing the weights (or sharing them with the functional API) to add the additional output to the full model.
But using a zero loss is also fine.
This is my third attempt to get a deep learning project off the ground. I'm working with protein sequences. First I tried TFLearn, then raw TensorFlow, and now I'm trying Keras.
The previous two attempts taught me a lot, and gave me some code and concepts that I can re-use. However there has always been an obstacle, and I've asked questions that the developers can't answer (in the case of TFLearn), or I've simply gotten bogged down (TensorFlow object introspection is tedious).
I have written this TensorFlow loss function, and I know it works:
def l2_angle_distance(pred, tgt):
with tf.name_scope("L2AngleDistance"):
# Scaling factor
count = tgt[...,0,0]
scale = tf.to_float(tf.count_nonzero(tf.is_finite(count)))
# Mask NaN in tgt
tgt = tf.where(tf.is_nan(tgt), pred, tgt)
# Calculate L1 losses
losses = tf.losses.cosine_distance(pred, tgt, -1, reduction=tf.losses.Reduction.NONE)
# Square the losses, then sum, to get L2 scalar loss.
# Divide the loss result by the scaling factor.
return tf.reduce_sum(losses * losses) / scale
My target values (tgt) can include NaN, because my protein sequences are passed in a 4D Tensor, despite the fact that the individual sequences differ in length. Before you ask, the data can't be resampled like an image. So I use NaN in the tgt Tensor to indicate "no prediction needed here." Before I calculate the L2 cosine loss, I replace every NaN with the matching values in the prediction (pred) so the loss for every NaN is always zero.
Now, how can I re-use this function in Keras? It appears that the Keras Lambda core layer is not a good choice, because a Lambda only takes a single argument, and a loss function needs two arguments.
Alternately, can I rewrite this function in Keras? I shouldn't ever need to use the Theano or CNTK backend, so it isn't necessary for me to rewrite my function in Keras. I'll use whatever works.
I just looked at the Keras losses.py file to get some clues. I imported keras.backend and had a look around. I also found https://keras.io/backend/. I don't seem to find wrappers for ANY of the TensorFlow function calls I happen to use: to_float(), count_nonzero(), is_finite(), where(), is_nan(), cosine_distance(), or reduce_sum().
Thanks for your suggestions!
I answered my own question. I'm posting the solution for anyone who may come across this same problem.
I tried using my TF loss function directly in Keras, as was independently suggested by Matias Valdenegro. I did not provoke any errors from Keras by doing so, however, the loss value went immediately to NaN.
Eventually I identified the problem. The calling convention for a Keras loss function is first y_true (which I called tgt), then y_pred (my pred). But the calling convention for a TensorFlow loss function is pred first, then tgt. So if you want to keep a Tensorflow-native version of the loss function around, this fix works:
def keras_l2_angle_distance(tgt, pred):
return l2_angle_distance(pred, tgt)
<snip>
model.compile(loss = keras_l2_angle_distance, optimizer = "something")
Maybe Theano or CNTK uses the same parameter order as Keras, I don't know. But I'm back in business.
You don't need to use keras.backend, as your loss is directly written in TensorFlow, then you can use it directly in Keras. The backend functions are an abstraction layer so you can code a loss/layer that will work with the multiple available backends in Keras.
You just have to put your loss in the model.compile call:
model.compile(loss = l2_angle_distance, optimizer = "something")
I have an external function which takes y and y_prediction (in matrix format), and computes a metric which depicts how good or bad the prediction actually is.
Unfortunately the metric is no simple y - ypred or confusion matrix, but still very useful and important. How can I use this number computed for the loss or as an argument for optimizer.minimize?
If i understood correctly i think there is two way to do this:
Either the loss you want to compute can be writen as tensorflow ops which gradient is defined (for exemple SVD has no gradient defined in tensorflow library saddly) then the optimisation is direct.
Or you can always write your loss function with numpy operators and use tf.py_func() https://www.tensorflow.org/api_docs/python/tf/py_func and then you have to explicit the gradient by hand as said in here : How to make a custom activation function with only Python in Tensorflow?
But you have to know an explicit formula of your gradient ...
I have been using tensorflow to train deep NN acoustic models for speech recognition for a while. The loss function I use is Cross Entropy and the NN models performe very well. Now I want to change the loss function to a more complex one named MMI (Maximum Mutual Information) which is also a classical criterion used in speech recognition domain. I put one paper here which describes this loss function in case that you have interests.
When using this special loss function, the derivatives of the loss function w.r.t. the activations of output layer can be computed by some special algorithms defined in Hidden Markov Model scenario. It means that I can compute the derivatives of the loss function w.r.t. the activations of output layer by myself rather than just write out the loss function and leave Tensorflow to calculate the derivatives automatically.
But based on my poor experiences, I don't know how to backprob the derivatives which I calculate by myself. Is there any way to do this without touching Tensorflow C++ source code?
Probably yes if all the computation involved use existing tensorflow functions.
You just have to set up the chain of operations that compute the gradients from the current variables.
Then you just use tf.assign_add() to the variables with your gradients multiplied by minus the learning rate.
You are thus mimicking what happens in the background in TF usually.
EDIT: If calculations are made in numpy for instance for the gradients you can use.
#perform numpy calculations
a=f(output_npy,variables_npy)
grad_from_user=tf.placeholder(tf.float32, a.shape)
grad_update=tf.assign_add(variables_tf,-lr*grad_from_user)
#and then
sess.run(grad_update,feed_dict={grad_from_user:a,...})