Keras Autoencoder: Tying Weights from Encoder To Decoder not working

6
votes

Im creating an Autoencoder as part of my full model for a Kaggle competition. Im trying to tie the weighs of the Encoder, transposed to the Decoder. Before the first Epoch the weights are correctly sync, after that, the Decoder weights just freeze, and dont keep up with the Encoder weights that are being updated by the Gradient Descent.

I look for 12 hours in almost every post about this problem i reach on google, no one seems to have the answer for my case. The closest one is this Tying Autoencoder Weights in a Dense Keras Layer but the problem was solved by not using a variable tensor as kernel, but im already not using that type of tensor as my Decoder kernel, so was no usefull.

Im using a DenseTied Keras custom Layer class defined in this article https://towardsdatascience.com/build-the-right-autoencoder-tune-and-optimize-using-pca-principles-part-ii-24b9cca69bd6, is exactly the same, just change the way i reference the Keras backed for suit my imports style.

import tensorflow as tf
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import os

This is the custom layer definition

class DenseTied(tf.keras.layers.Layer):

    def __init__(self, units,
                 activation=None,
                 use_bias=True,
                 kernel_initializer='glorot_uniform',
                 bias_initializer='zeros',
                 kernel_regularizer=None,
                 bias_regularizer=None,
                 activity_regularizer=None,
                 kernel_constraint=None,
                 bias_constraint=None,
                 tied_to=None,
                 **kwargs):
        self.tied_to = tied_to
        if 'input_shape' not in kwargs and 'input_dim' in kwargs:
            kwargs['input_shape'] = (kwargs.pop('input_dim'),)
        super().__init__(**kwargs)
        self.units = units
        self.activation = tf.keras.activations.get(activation)
        self.use_bias = use_bias
        self.kernel_initializer = tf.keras.initializers.get(kernel_initializer)
        self.bias_initializer = tf.keras.initializers.get(bias_initializer)
        self.kernel_regularizer = tf.keras.regularizers.get(kernel_regularizer)
        self.bias_regularizer = tf.keras.regularizers.get(bias_regularizer)
        self.activity_regularizer = tf.keras.regularizers.get(activity_regularizer)
        self.kernel_constraint = tf.keras.constraints.get(kernel_constraint)
        self.bias_constraint = tf.keras.constraints.get(bias_constraint)
        self.input_spec = tf.keras.layers.InputSpec(min_ndim=2)
        self.supports_masking = True

    def build(self, input_shape):
        assert len(input_shape) >= 2
        input_dim = input_shape[-1]

        if self.tied_to is not None:
            self.kernel = tf.keras.backend.transpose(self.tied_to.kernel)
            self.non_trainable_weights.append(self.kernel)
        else:
            self.kernel = self.add_weight(shape=(input_dim, self.units),
                                          initializer=self.kernel_initializer,
                                          name='kernel',
                                          regularizer=self.kernel_regularizer,
                                          constraint=self.kernel_constraint)
        if self.use_bias:
            self.bias = self.add_weight(shape=(self.units,),
                                        initializer=self.bias_initializer,
                                        name='bias',
                                        regularizer=self.bias_regularizer,
                                        constraint=self.bias_constraint)
        else:
            self.bias = None
        self.input_spec = tf.keras.layers.InputSpec(min_ndim=2, axes={-1: input_dim})
        self.built = True

    def compute_output_shape(self, input_shape):
        assert input_shape and len(input_shape) >= 2
        output_shape = list(input_shape)
        output_shape[-1] = self.units
        return tuple(output_shape)

    def call(self, inputs):
        output = tf.keras.backend.dot(inputs, self.kernel)
        if self.use_bias:
            output = tf.keras.backend.bias_add(output, self.bias, data_format='channels_last')
        if self.activation is not None:
            output = self.activation(output)
        return output

And this the model training and testing with a dummy data set

rand_samples = np.random.rand(16, 51)
dummy_ds = tf.data.Dataset.from_tensor_slices((rand_samples, rand_samples)).shuffle(16).batch(16)

encoder = tf.keras.layers.Dense(1, activation="linear", input_shape=(51,), use_bias=True)
decoder = DenseTied(51, activation="linear", tied_to=encoder, use_bias=True)

autoencoder = tf.keras.Sequential()
autoencoder.add(encoder)
autoencoder.add(decoder)

autoencoder.compile(metrics=['accuracy'],
                    loss='mean_squared_error',
                    optimizer='sgd')

autoencoder.summary()

print("Encoder Kernel Before 1 Epoch", encoder.kernel[0])
print("Decoder Kernel Before 1 Epoch", decoder.kernel[0][0])

autoencoder.fit(dummy_ds, epochs=1)

print("Encoder Kernel After 1 Epoch", encoder.kernel[0])
print("Decoder Kernel After 1 Epoch", decoder.kernel[0][0])

The Expected output is have the two kernels exactly the same in the first element (Print just one weight for simplicity)

The current output shows that Decoder Kernel is not updated as the same as the Transposed Encoder Kernel

2019-09-06 14:55:42.070003: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library nvcuda.dll
2019-09-06 14:55:42.984580: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1640] Found device 0 with properties:
name: GeForce GTX 1060 major: 6 minor: 1 memoryClockRate(GHz): 1.733
pciBusID: 0000:01:00.0
2019-09-06 14:55:43.088109: I tensorflow/stream_executor/platform/default/dlopen_checker_stub.cc:25] GPU libraries are statically linked, skip dlopen check.        
2019-09-06 14:55:43.166145: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1763] Adding visible gpu devices: 0
2019-09-06 14:55:43.203865: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2
2019-09-06 14:55:43.277988: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1640] Found device 0 with properties:
name: GeForce GTX 1060 major: 6 minor: 1 memoryClockRate(GHz): 1.733
pciBusID: 0000:01:00.0
2019-09-06 14:55:43.300888: I tensorflow/stream_executor/platform/default/dlopen_checker_stub.cc:25] GPU libraries are statically linked, skip dlopen check.        
2019-09-06 14:55:43.309040: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1763] Adding visible gpu devices: 0
2019-09-06 14:55:44.077814: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1181] Device interconnect StreamExecutor with strength 1 edge matrix:
2019-09-06 14:55:44.094542: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1187]      0
2019-09-06 14:55:44.099411: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1200] 0:   N
2019-09-06 14:55:44.103424: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1326] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 4712 MB memory) -> physical GPU (device: 0, name: GeForce GTX 1060, pci bus id: 0000:01:00.0, compute capability: 6.1)
Model: "sequential"
_________________________________________________________________
Layer (type)                 Output Shape              Param #
=================================================================
dense (Dense)                (None, 1)                 52
_________________________________________________________________
dense_tied (DenseTied)       (None, 51)                103
=================================================================
Total params: 103
Trainable params: 103
Non-trainable params: 0
_________________________________________________________________
Encoder Kernel Before 1 Epoch tf.Tensor([0.20486075], shape=(1,), dtype=float32)
Decoder Kernel Before 1 Epoch tf.Tensor(0.20486075, shape=(), dtype=float32)
1/1 [==============================] - 1s 657ms/step - loss: 0.3396 - accuracy: 0.0000e+00
Encoder Kernel After 1 Epoch tf.Tensor([0.20530733], shape=(1,), dtype=float32)
Decoder Kernel After 1 Epoch tf.Tensor(0.20486075, shape=(), dtype=float32)
PS C:\Users\whitm\Desktop\CodeProjects\ForestClassifier-DEC>

i dont see what im doing wrong.

2
pythontensorflowdeep-learningautoencodertf.keras
Did you try running the code on the TDS article line-by-line? I tried running the code in article, train it one epoch at a time, and check the equality of the weights on encoder and decoder. They are matching. I suggest trying encoder with a size greater than 1 for a sanity test. – inferno
i already test the encoder with varied sizes, i put 1 for simplicity – ElPapi42
also in the reproduction sample i put the model to train only one epoch – ElPapi42
This is a minimal reproduction example, my full autoencoder is a bit more complex – ElPapi42

2 Answers

1
votes

To tie the weights, I would suggest using the Keras functional API which enables to share layers. That said, here is an alternative implementation that ties the weights between the encoder and decoder:

class TransposableDense(tf.keras.layers.Dense):

    def __init__(self, units, **kwargs):
        super().__init__(units, **kwargs)

    def build(self, input_shape):
        assert len(input_shape) >= 2
        input_dim = input_shape[-1]
        self.t_output_dim = input_dim

        self.kernel = self.add_weight(shape=(int(input_dim), self.units),
                                      initializer=self.kernel_initializer,
                                      name='kernel',
                                      regularizer=self.kernel_regularizer,
                                      constraint=self.kernel_constraint)
        if self.use_bias:
            self.bias = self.add_weight(shape=(self.units,),
                                        initializer=self.bias_initializer,
                                        name='bias',
                                        regularizer=self.bias_regularizer,
                                        constraint=self.bias_constraint)
            self.bias_t = self.add_weight(shape=(input_dim,),
                                          initializer=self.bias_initializer,
                                          name='bias_t',
                                          regularizer=self.bias_regularizer,
                                          constraint=self.bias_constraint)
        else:
            self.bias = None
            self.bias_t = None
        # self.input_spec = tf.keras.layers.InputSpec(min_ndim=2, axes={-1: input_dim})
        self.built = True

    def call(self, inputs, transpose=False):
        bs, input_dim = inputs.get_shape()

        kernel = self.kernel
        bias = self.bias
        if transpose:
            assert input_dim == self.units
            kernel = tf.keras.backend.transpose(kernel)
            bias = self.bias_t

        output = tf.keras.backend.dot(inputs, kernel)
        if self.use_bias:
            output = tf.keras.backend.bias_add(output, bias, data_format='channels_last')
        if self.activation is not None:
            output = self.activation(output)
        return output

    def compute_output_shape(self, input_shape):
        bs, input_dim = input_shape
        output_dim = self.units
        if input_dim == self.units:
            output_dim = self.t_output_dim
        return bs, output_dim

The kernel of this dense layer can be transposed by calling the layer with transpose=True. Note that this might break some basic Keras principles (e.g. the layer has multiple output shapes), but it should work for your case.

Here is an example showing how you can use it to define your model:

a = tf.keras.layers.Input((51,))
dense = TransposableDense(1, activation='linear', use_bias=True)
encoder_out = dense(a)
decoder_out = dense(encoder_out, transpose=True)
encoder = tf.keras.Model(a, encoder_out)
autoencoder = tf.keras.Model(a, decoder_out)
0
votes

The weights are not tied. You are just initializing the weights of the tied layer with the transposed weights of the first layer and then never train them. transpose returns a new tensor/different object and add_weight creates a new variable, thus any relation between the two layers is lost after build. I think it would be better do so something like this:

def call(self, inputs):
    output = tf.keras.backend.dot(inputs, tf.keras.backend.transpose(self.tied_to.kernel))
    if self.use_bias:
        output = tf.keras.backend.bias_add(output, self.tied_to.bias, data_format='channels_last')
    if self.activation is not None:
        output = self.activation(output)
    return output

Here, the tied layer always uses the first layer's weights explicitly and would not have any weights itself (i.e. remove the add_weight parts from build).