Inference with TimeDistributed(Dense(1, activation="sigmoid")) in Keras 3 is a lot slower than in Keras 2 (tf.keras) Profiling shows TimeDistributed is the bottleneck.
Model: Conv1D → LSTM → Conv1DTranspose → TimeDistributed(Dense(1)).
input shape (none,none,1)
Tried: run_eagerly=False, tf.function, TensorFlow/JAX/PyTorch backends—no significant improvement.
Question
Is there a solution to fix the TimeDistributed slowdown in Keras 3 without changing the model architecture? Currently using tf_keras as a workaround.
Details
Keras Version: 3.9.0
While this does not explain or address the issue directly, there is actually no need to use TimeDistributed on Dense layers. The Dense implementation is such that it will always be applied on the last axis only.
So you can just use Dense on the Conv1D outputs and it will work the same way (assuming you are using channels_last format for convolutions). Unfortunately, this does imply "changing the model architecture" as you say.