Custom Neural Network Implementation on MNIST using Tensorflow 2.0?

Question

I tried to write a custom implementation of basic neural network with two hidden layers on MNIST dataset using *TensorFlow 2.0 beta* but I\'m not sure what went wrong here but m

Answer 1

I tried to write a custom implementation of basic neural network with two hidden layers on MNIST dataset using tensorflow 2.0 beta but I'm not sure what went wrong here but my training loss and accuracy seems to stuck at 1.5 and around85's respectively.

Where is the training part? Training of TF 2.0 models either Keras' syntax or Eager execution with tf.GradientTape(). Can you paste the code with conv and dense layers, and how you trained it?

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Other questions:

1) How to add a Dropout layer in this custom implementation? i.e (making it work for both train and test time)

You can add a Dropout() layer with:

from tensorflow.keras.layers import Dropout

And then you insert it into a Sequential() model just with:

Dropout(dprob)     # where dprob = dropout probability

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2) How to add Batch Normalization in this code?

Same as before, with:

from tensorflow.keras.layers import BatchNormalization

The choise of where to put batchnorm in the model, well, that's up to you. There is no rule of thumb, I suggest you to make experiments. With ML it's always a trial and error process.

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3) How can I use callbacks in this code? i.e (making use of EarlyStopping and ModelCheckpoint callbacks)

If you are training using Keras' syntax, you can simply use that. Please check this very thorough tutorial on how to use it. It just takes few lines of code. If you are running a model in Eager execution, you have to implement these techniques yourself, with your own code. It's more complex, but it also gives you more freedom in the implementation.

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4) Is there anything else in the code that I can optimize further in this code? i.e (making use of tensorflow 2.x @tf.function decorator etc.)

It depends. If you are using Keras syntax, I don't think you need to add more to it. In case you are training the model in Eager execution, then I'd suggest you to use the @tf.function decorator on some function to speed up a bit. You can see a practical TF 2.0 example on how to use the decorator in this Notebook.

Other than this, I suggest you to play with regularization techniques such as weights initializations, L1-L2 loss, etc.

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5) Also I need a way to extract all my final weights for all layers after training so I can plot them and check their distributions. To check issues like gradient vanishing or exploding.

Once the model is trained, you can extract its weights with:

weights = model.get_weights()

or:

weights = model.trainable_weights

If you want to keep only trainable ones.

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6) I also want help in writing this code in a more generalized way so I can easily implement other networks like convolutional network (i.e Conv, MaxPool etc.) based on this code easily.

You can pack all your code into a function, then . At the end of this Notebook I did something like this (it's for a feed-forward NN, which is much more simple, but that's a start and you can change the code according to your needs).

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UPDATE:

Please check my TensorFlow 2.0 implementaion of a CNN classifier. This might be a useful hint: it is trained on the Fashion MNIST dataset, which makes it very similar to your task.

Answer 2

Also If there's something I could improve in the code do let me know as well.

Embrace the high-level API for something like this. You can do it in just a few lines of code and it's much easier to debug, read and reason about:

(x_train, y_train), (x_test, y_test) = tfds.load('mnist', split=['train', 'test'], 
                                                  batch_size=-1, as_supervised=True)

x_train = tf.cast(tf.reshape(x_train, shape=(x_train.shape[0], 784)), tf.float32)
x_test  = tf.cast(tf.reshape(x_test, shape=(x_test.shape[0], 784)), tf.float32)

model = tf.keras.models.Sequential([
  tf.keras.layers.Dense(512, activation='sigmoid'),
  tf.keras.layers.Dense(256, activation='sigmoid'),
  tf.keras.layers.Dense(10, activation='softmax')
])
model.fit(x_train, y_train, epochs=5)
model.evaluate(x_test, y_test)

Answer 3

I wondered where to start with your multiquestion, and I decided to do so with a statement:

Your code definitely should not look like that and is nowhere near current Tensorflow best practices.

Sorry, but debugging it step by step is waste of everyone's time and would not benefit either of us.

Now, moving to the third point:

3. Is there anything else in my code below that I can optimize further in this code like maybe making use of tensorflow 2.x @tf.function decorator etc.)

Yes, you can use tensorflow2.0 functionalities and it seems like you are running away from those (tf.function decorator is of no use here actually, leave it for the time being).

Following new guidelines would alleviate your problems with your 5th point as well, namely:

5. I also want help in writing this code in a more generalized way so I can easily implement other networks like ConvNets (i.e Conv, MaxPool etc.) based on this code easily.

as it's designed specifically for that. After a little introduction I will try to introduce you to those concepts in a few steps:

1. Divide your program into logical parts

Tensorflow did much harm when it comes to code readability; everything in tf1.x was usually crunched in one place, globals followed by function definition followed by another globals or maybe data loading, all in all mess. It's not really developers fault as the system's design encouraged those actions.

Now, in tf2.0 programmer is encouraged to divide his work similarly to the structure one can see in pytorch, chainer and other more user-friendly frameworks.

1.1 Data loading

You were on good path with Tensorflow Datasets but you turned away for no apparent reason.

Here is your code with commentary what's going on:

# You already have tf.data.Dataset objects after load
(x_train, y_train), (x_test, y_test) = tfds.load('mnist', split=['train', 'test'], 
                                                  batch_size=-1, as_supervised=True)

# But you are reshaping them in a strange manner...
x_train = tf.reshape(x_train, shape=(x_train.shape[0], 784))
x_test  = tf.reshape(x_test, shape=(x_test.shape[0], 784))

# And building from slices...
ds_train = tf.data.Dataset.from_tensor_slices((x_train, y_train))
# Unreadable rescaling (there are built-ins for that)

You can easily generalize this idea for any dataset, place this in separate module, say datasets.py:

import tensorflow as tf
import tensorflow_datasets as tfds


class ImageDatasetCreator:
    @classmethod
    # More portable and readable than dividing by 255
    def _convert_image_dtype(cls, dataset):
        return dataset.map(
            lambda image, label: (
                tf.image.convert_image_dtype(image, tf.float32),
                label,
            )
        )

    def __init__(self, name: str, batch: int, cache: bool = True, split=None):
        # Load dataset, every dataset has default train, test split
        dataset = tfds.load(name, as_supervised=True, split=split)
        # Convert to float range
        try:
            self.train = ImageDatasetCreator._convert_image_dtype(dataset["train"])
            self.test = ImageDatasetCreator._convert_image_dtype(dataset["test"])
        except KeyError as exception:
            raise ValueError(
                f"Dataset {name} does not have train and test, write your own custom dataset handler."
            ) from exception

        if cache:
            self.train = self.train.cache()  # speed things up considerably
            self.test = self.test.cache()

        self.batch: int = batch

    def get_train(self):
        return self.train.shuffle().batch(self.batch).repeat()

    def get_test(self):
        return self.test.batch(self.batch).repeat()

So now you can load more than mnist using simple command:

from datasets import ImageDatasetCreator

if __name__ == "__main__":
    dataloader = ImageDatasetCreator("mnist", batch=64, cache = True)
    train, test = dataloader.get_train(), dataloader.get_test()

And you could use any name other than mnist you want to load datasets from now on.

Please, stop making everything deep learning related one hand-off scripts, you are a programmer as well.

1.2 Model creation

Since tf2.0 there are two advised ways one can proceed depending on models complexity:

• tensorflow.keras.models.Sequential - this way was shown by @Stewart_R, no need to reiterate his points. Used for the simplest models (you should use this one with your feedforward).
• Inheriting tensorflow.keras.Model and writing custom model. This one should be used when you have some kind of logic inside your module or it's more complicated (things like ResNets, multipath networks etc.). All in all more readable and customizable.

Your Model class tried to resemble something like that but it went south again; backprop definitely is not part of the model itself, neither is loss or accuracy, separate them into another module or function, defo not a member!

That said, let's code the network using the second approach (you should place this code in model.py for brevity). Before that, I will code YourDense feedforward layer from scratch by inheriting from tf.keras.Layers (this one might go into layers.py module):

import tensorflow as tf

class YourDense(tf.keras.layers.Layer):
    def __init__(self, units):
        # It's Python 3, you don't have to specify super parents explicitly
        super().__init__()
        self.units = units

    # Use build to create variables, as shape can be inferred from previous layers
    # If you were to create layers in __init__, one would have to provide input_shape
    # (same as it occurs in PyTorch for example)
    def build(self, input_shape):
        # You could use different initializers here as well
        self.kernel = self.add_weight(
            shape=(input_shape[-1], self.units),
            initializer="random_normal",
            trainable=True,
        )
        # You could define bias in __init__ as well as it's not input dependent
        self.bias = self.add_weight(shape=(self.units,), initializer="random_normal")
        # Oh, trainable=True is default

    def call(self, inputs):
        # Use overloaded operators instead of tf.add, better readability
        return tf.matmul(inputs, self.kernel) + self.bias

Regarding your

1. How to add a Dropout and Batch Normalization layer in this custom implementation? (i.e making it work for both train and test time)

I suppose you would like to create a custom implementation of those layers. If not, you can just import from tensorflow.keras.layers import Dropout and use it anywhere you want as @Leevo pointed out. Inverted dropout with different behaviour during train and test below:

class CustomDropout(layers.Layer):
    def __init__(self, rate, **kwargs):
        super().__init__(**kwargs)
        self.rate = rate

    def call(self, inputs, training=None):
        if training:
            # You could simply create binary mask and multiply here
            return tf.nn.dropout(inputs, rate=self.rate)
        # You would need to multiply by dropout rate if you were to do that
        return inputs

Layers taken from here and modified to better fit showcasing purpose.

Now you can create your model finally (simple double feedforward):

import tensorflow as tf

from layers import YourDense


class Model(tf.keras.Model):
    def __init__(self):
        super().__init__()
        # Use Sequential here for readability
        self.network = tf.keras.Sequential(
            [YourDense(100), tf.keras.layers.ReLU(), YourDense(10)]
        )

    def call(self, inputs):
        # You can use non-parametric layers inside call as well
        flattened = tf.keras.layers.Flatten()(inputs)
        return self.network(flattened)

Ofc, you should use built-ins as much as possible in general implementations.

This structure is pretty extensible, so generalization to convolutional nets, resnets, senets, whatever should be done via this module. You can read more about it here.

I think it fulfills your 5th point:

5. I also want help in writing this code in a more generalized way so I can easily implement other networks like ConvNets (i.e Conv, MaxPool etc.) based on this code easily.

Last thing, you may have to use model.build(shape) in order to build your model's graph.

model.build((None, 28, 28, 1))

This would be for MNIST's 28x28x1 input shape, where None stands for batch.

1.3 Training

Once again, training could be done in two separate ways:

• standard Keras model.fit(dataset) - useful in simple tasks like classification
• tf.GradientTape - more complicated training schemes, most prominent example would be Generative Adversarial Networks, where two models optimize orthogonal goals playing minmax game

As pointed out by @Leevo once again, if you are to use the second way, you won't be able to simply use callbacks provided by Keras, hence I'd advise to stick with the first option whenever possible.

In theory you could call callback's functions manually like on_batch_begin() and others where needed, but it would be cumbersome and I'm not sure how would this work.

When it comes to the first option, you can use tf.data.Dataset objects directly with fit. Here is it presented inside another module (preferably train.py):

def train(
    model: tf.keras.Model,
    path: str,
    train: tf.data.Dataset,
    epochs: int,
    steps_per_epoch: int,
    validation: tf.data.Dataset,
    steps_per_validation: int,
    stopping_epochs: int,
    optimizer=tf.optimizers.Adam(),
):
    model.compile(
        optimizer=optimizer,
        # I used logits as output from the last layer, hence this
        loss=tf.losses.SparseCategoricalCrossentropy(from_logits=True),
        metrics=[tf.metrics.SparseCategoricalAccuracy()],
    )

    model.fit(
        train,
        epochs=epochs,
        steps_per_epoch=steps_per_epoch,
        validation_data=validation,
        validation_steps=steps_per_validation,
        callbacks=[
            # Tensorboard logging
            tf.keras.callbacks.TensorBoard(
                pathlib.Path("logs")
                / pathlib.Path(datetime.datetime.now().strftime("%Y%m%d-%H%M%S")),
                histogram_freq=1,
            ),
            # Early stopping with best weights preserving
            tf.keras.callbacks.EarlyStopping(
                monitor="val_sparse_categorical_accuracy",
                patience=stopping_epochs,
                restore_best_weights=True,
            ),
        ],
    )
    model.save(path)

More complicated approach is very similar (almost copy and paste) to PyTorch training loops, so if you are familiar with those, they should not pose much of a problem.

You can find examples throughout tf2.0 docs, e.g. here or here.

2. Other things

2.1 Unanswered questions

4. Is there anything else in the code that I can optimize further in this code? i.e (making use of tensorflow 2.x @tf.function decorator etc.)

Above already transforms the Model into graphs, hence I don't think you would benefit from calling it in this case. And premature optimization is the root of all evil, remember to measure your code before doing this.

You would gain much more with proper caching of data (as described at the beginning of #1.1) and good pipeline rather than those.

5. Also I need a way to extract all my final weights for all layers after training so I can plot them and check their distributions. To check issues like gradient vanishing or exploding.

As pointed out by @Leevo above,

weights = model.get_weights()

Would get you the weights. You may transform them into np.array and plot using seaborn, matplotlib, analyze, check or whatever else you want.

2.2 Putting it altogether

All in all, your main.py (or entrypoint or something similar) would consist of this (more or less):

from dataset import ImageDatasetCreator
from model import Model
from train import train

# You could use argparse for things like batch, epochs etc.
if __name__ == "__main__":
    dataloader = ImageDatasetCreator("mnist", batch=64, cache=True)
    train, test = dataloader.get_train(), dataloader.get_test()
    model = Model()
    model.build((None, 28, 28, 1))
    train(
        model, train, path epochs, test, len(train) // batch, len(test) // batch, ...
    )  # provide necessary arguments appropriately
    # Do whatever you want with those
    weights = model.get_weights()

Oh, remember that above functions are not for copy pasting and should be treated more like a guideline. Hit me up if you have any questions.

3. Questions from comments

3.1 How to initialize custom and built-in layers

3.1.1 TLDR what you are about to read

• Custom Poisson initalization function, but it takes three arguments
• tf.keras.initalization API needs two arguments (see last point in their docs), hence one is specified via Python's lambda inside custom layer we have written before
• Optional bias for the layer is added, which can be turned off with boolean

Why is it so uselessly complicated? To show that in tf2.0 you can finally use Python's functionality, no more graph hassle, if instead of tf.cond etc.

3.1.2 From TLDR to implementation

Keras initializers can be found here and Tensorflow's flavor here.

Please note API inconsistencies (capital letters like classes, small letters with underscore like functions), especially in tf2.0, but that's beside the point.

You can use them by passing a string (as it's done in YourDense above) or during object creation.

To allow for custom initialization in your custom layers, you can simply add additional argument to the constructor (tf.keras.Model class is still Python class and it's __init__ should be used same as Python's).

Before that, I will show you how to create custom initialization:

# Poisson custom initialization because why not.
def my_dumb_init(shape, lam, dtype=None):
    return tf.squeeze(tf.random.poisson(shape, lam, dtype=dtype))

Notice, it's signature takes three arguments, while it should take (shape, dtype) only. Still, one can "fix" this easily while creating his own layer, like the one below (extended YourLinear):

import typing

import tensorflow as tf


class YourDense(tf.keras.layers.Layer):
    # It's still Python, use it as Python, that's the point of tf.2.0
    @classmethod
    def register_initialization(cls, initializer):
        # Set defaults if init not provided by user
        if initializer is None:
            # let's make the signature proper for init in tf.keras
            return lambda shape, dtype: my_dumb_init(shape, 1, dtype)
        return initializer

    def __init__(
        self,
        units: int,
        bias: bool = True,
        # can be string or callable, some typing info added as well...
        kernel_initializer: typing.Union[str, typing.Callable] = None,
        bias_initializer: typing.Union[str, typing.Callable] = None,
    ):
        super().__init__()
        self.units: int = units
        self.kernel_initializer = YourDense.register_initialization(kernel_initializer)
        if bias:
            self.bias_initializer = YourDense.register_initialization(bias_initializer)
        else:
            self.bias_initializer = None

    def build(self, input_shape):
        # Simply pass your init here
        self.kernel = self.add_weight(
            shape=(input_shape[-1], self.units),
            initializer=self.kernel_initializer,
            trainable=True,
        )
        if self.bias_initializer is not None:
            self.bias = self.add_weight(
                shape=(self.units,), initializer=self.bias_initializer
            )
        else:
            self.bias = None

    def call(self, inputs):
        weights = tf.matmul(inputs, self.kernel)
        if self.bias is not None:
            return weights + self.bias

I have added my_dumb_initialization as the default (if user does not provide one) and made the bias optional with bias argument. Note you can use if freely as long as it's not data dependent. If it is (or is dependent on tf.Tensor somehow), one has to use @tf.function decorator which changes Python's flow to it's tensorflow counterpart (e.g. if to tf.cond).

See here for more on autograph, it's very easy to follow.

If you want to incorporate above initializer changes into your model, you have to create appropriate object and that's it.

... # Previous of code Model here
self.network = tf.keras.Sequential(
    [
        YourDense(100, bias=False, kernel_initializer="lecun_uniform"),
        tf.keras.layers.ReLU(),
        YourDense(10, bias_initializer=tf.initializers.Ones()),
    ]
)
... # and the same afterwards

With built-in tf.keras.layers.Dense layers, one can do the same (arguments names differ, but idea holds).

3.2 Automatic Differentiation using tf.GradientTape

3.2.1 Intro

Point of tf.GradientTape is to allow users normal Python control flow and gradient calculation of variables with respect to another variable.

Example taken from here but broken into separate pieces:

def f(x, y):
  output = 1.0
  for i in range(y):
    if i > 1 and i < 5:
      output = tf.multiply(output, x)
  return output

Regular python function with for and if flow control statements

def grad(x, y):
  with tf.GradientTape() as t:
    t.watch(x)
    out = f(x, y)
  return t.gradient(out, x)

Using gradient tape you can record all operations on Tensors (and their intermediate states as well) and "play" it backwards (perform automatic backward differentiation using chaing rule).

Every Tensor within tf.GradientTape() context manager is recorded automatically. If some Tensor is out of scope, use watch() method as one can see above.

Finally, gradient of output with respect to x (input is returned).

3.2.2 Connection with deep learning

What was described above is backpropagation algorithm. Gradients w.r.t (with respect to) outputs are calculated for each node in the network (or rather for every layer). Those gradients are then used by various optimizers to make corrections and so it repeats.

Let's continue and assume you have your tf.keras.Model, optimizer instance, tf.data.Dataset and loss function already set up.

One can define a Trainer class which will perform training for us. Please read comments in the code if in doubt:

class Trainer:
    def __init__(self, model, optimizer, loss_function):
        self.model = model
        self.loss_function = loss_function
        self.optimizer = optimizer
        # You could pass custom metrics in constructor
        # and adjust train_step and test_step accordingly
        self.train_loss = tf.keras.metrics.Mean(name="train_loss")
        self.test_loss = tf.keras.metrics.Mean(name="train_loss")

    def train_step(self, x, y):
        # Setup tape
        with tf.GradientTape() as tape:
            # Get current predictions of network
            y_pred = self.model(x)
            # Calculate loss generated by predictions
            loss = self.loss_function(y, y_pred)
        # Get gradients of loss w.r.t. EVERY trainable variable (iterable returned)
        gradients = tape.gradient(loss, self.model.trainable_variables)
        # Change trainable variable values according to gradient by applying optimizer policy
        self.optimizer.apply_gradients(zip(gradients, self.model.trainable_variables))
        # Record loss of current step
        self.train_loss(loss)

    def train(self, dataset):
        # For N epochs iterate over dataset and perform train steps each time
        for x, y in dataset:
            self.train_step(x, y)

    def test_step(self, x, y):
        # Record test loss separately
        self.test_loss(self.loss_function(y, self.model(x)))

    def test(self, dataset):
        # Iterate over whole dataset
        for x, y in dataset:
            self.test_step(x, y)

    def __str__(self):
        # You need Python 3.7 with f-string support
        # Just return metrics
        return f"Loss: {self.train_loss.result()}, Test Loss: {self.test_loss.result()}"

Now, you could use this class in your code really simply like this:

EPOCHS = 5

# model, optimizer, loss defined beforehand
trainer = Trainer(model, optimizer, loss)
for _ in range(EPOCHS):
    trainer.train(train_dataset) # Same for training and test datasets
    trainer.test(test_dataset)
    print(f"Epoch {epoch}: {trainer})")

Print would tell you training and test loss for each epoch. You can mix training and testing any way you want (e.g. 5 epochs for training and 1 testing), you could add different metrics etc.

See here if you want non-OOP oriented approach (IMO less readable, but to each it's own).