Custom Data Generator for Keras LSTM with TimeSeriesGenerator - python

So I'm trying to use Keras' fit_generator with a custom data generator to feed into an LSTM network.
What works
To illustrate the problem, I have created a toy example trying to predict the next number in a simple ascending sequence, and I use the Keras TimeseriesGenerator to create a Sequence instance:
WINDOW_LENGTH = 4
data = np.arange(0,100).reshape(-1,1)
data_gen = TimeseriesGenerator(data, data, length=WINDOW_LENGTH,
sampling_rate=1, batch_size=1)
I use a simple LSTM network:
data_dim = 1
input1 = Input(shape=(WINDOW_LENGTH, data_dim))
lstm1 = LSTM(100)(input1)
hidden = Dense(20, activation='relu')(lstm1)
output = Dense(data_dim, activation='linear')(hidden)
model = Model(inputs=input1, outputs=output)
model.compile(loss='mse', optimizer='rmsprop', metrics=['accuracy'])
and train it using the fit_generator function:
model.fit_generator(generator=data_gen,
steps_per_epoch=32,
epochs=10)
And this trains perfectly, and the model makes predictions as expected.
The problem
Now the problem is, in my non-toy situation I want to process the data coming out from the TimeseriesGenerator before feeding the data into the fit_generator. As a step towards this, I create a generator function which just wraps the TimeseriesGenerator used previously.
def get_generator(data, targets, window_length = 5, batch_size = 32):
while True:
data_gen = TimeseriesGenerator(data, targets, length=window_length,
sampling_rate=1, batch_size=batch_size)
for i in range(len(data_gen)):
x, y = data_gen[i]
yield x, y
data_gen_custom = get_generator(data, data,
window_length=WINDOW_LENGTH, batch_size=1)
But now the strange thing is that when I train the model as before, but using this generator as the input,
model.fit_generator(generator=data_gen_custom,
steps_per_epoch=32,
epochs=10)
There is no error but the training error is all over the place (jumping up and down instead of consistently going down like it did with the other approach), and the model doesn't learn to make good predictions.
Any ideas what I'm doing wrong with my custom generator approach?

It could be because the object type is changed from Sequence which is what a TimeseriesGenerator is to a generic generator. The fit_generator function treats these differently. A cleaner solution would be to inherit the class and override the processing bit:
class CustomGen(TimeseriesGenerator):
def __getitem__(self, idx):
x, y = super()[idx]
# do processing here
return x, y
And use this class like before as the rest of internal logic will remain the same.

I personally had a problem with the code by nuric. For some reason I had the error saying super not being subscriptable. Here is my possible fix. Let me known if this could possibly work?
class CustomGen(TimeseriesGenerator):
def __getitem__(self, idx):
x,y = super().__getitem__(idx)
return x, y

Related

Implement a custom loss function in Tensorflow BoostedTreesEstimator

I'm trying to implement a boosting model using Tensorflow "BoostedTreesRegressor".
For that, I need to implement a custom loss function where during training, the loss will be calculated according to the logic defined in my custom function rather than using the usual mean_squared_error.
I read in articles that this can be implemented using the interface, "BoostedTreesEstimator" by specifying a head. So, I tried to implement my model as follows:
#define custom loss function to calculate smape
def custom_loss_fn(labels, logits):
return (np.abs(logits - labels) / (np.abs(logits) + np.abs(labels))) * 2
#create input functions
def make_input_fn(X, y, n_epochs=None, shuffle=True):
def input_fn():
dataset = tf.data.Dataset.from_tensor_slices((dict(X), y))
if shuffle:
dataset = dataset.shuffle(NUM_EXAMPLES)
dataset = dataset.repeat(n_epochs)
dataset = dataset.batch(NUM_EXAMPLES)
return dataset
return input_fn
train_input_fn = make_input_fn(dftrain, y_train)
eval_input_fn = make_input_fn(dfeval, y_eval, n_epochs=1, shuffle=False)
my_head = tf.estimator.RegressionHead(loss_fn=custom_loss_fn)
#Training a boosted trees model
est = tf.estimator.BoostedTreesEstimator(feature_columns,
head=my_head,
n_batches_per_layer=1,
n_trees=90,
max_depth=2)
est.train(train_input_fn, max_steps=100)
predictions = list(est.predict(eval_input_fn))
This code provided an error as follows:
'Subclasses of Head must implement create_estimator_spec() or 'NotImplementedError: Subclasses of Head must implement create_estimator_spec() or _create_tpu_estimator_spec().
As I read in articles, create_estimator_spec() is used when we define a model_fn() when creating a new Estimator. Here, I do not want to create any new models or Estimators, I only want to use a custom loss function (instead of default mean squared error) when training where the training model should be equal to BoostedTreesRegressor/BoostingTreesEstimator.
It is a great help if anybody can give me some hint to implement this model.
Make sure you aren't using numpy functions in your loss function--you cannot convert tensors to numpy arrays. Try replacing np.abs with tf.abs. You might be getting the NotImplementedError because your loss function is breaking.

Custom Neural Network Implementation on MNIST using Tensorflow 2.0?

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 around 85 respectively. But If I build the using Keras I was getting very low training loss and accuracy above 95% with just 8-10 epochs.
I believe that maybe I'm not updating my weights or something? So do I need to assign my new weights which I compute in backprop function backs to their respective weights/bias variables?
I really appreciate if someone could help me out with this and these few more questions that I've mentioned below.
Few more Questions:
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)
2) How can I use callbacks in this code? i.e (making use of EarlyStopping and ModelCheckpoint callbacks)
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.)
4) I would also require to extract the final weights that I obtain for plotting and checking their distributions. To investigate issues like gradient vanishing or exploding. (Eg: Maybe Tensorboard)
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.
Here's my full code for easy reproducibility :
Note: I know I can use high-level API like Keras to build the model much easier but that is not my goal here. Please understand.
import numpy as np
import os
import logging
logging.getLogger('tensorflow').setLevel(logging.ERROR)
import tensorflow as tf
import tensorflow_datasets as tfds
(x_train, y_train), (x_test, y_test) = tfds.load('mnist', split=['train', 'test'],
batch_size=-1, as_supervised=True)
# reshaping
x_train = tf.reshape(x_train, shape=(x_train.shape[0], 784))
x_test = tf.reshape(x_test, shape=(x_test.shape[0], 784))
ds_train = tf.data.Dataset.from_tensor_slices((x_train, y_train))
# rescaling
ds_train = ds_train.map(lambda x, y: (tf.cast(x, tf.float32)/255.0, y))
class Model(object):
def __init__(self, hidden1_size, hidden2_size, device=None):
# layer sizes along with input and output
self.input_size, self.output_size, self.device = 784, 10, device
self.hidden1_size, self.hidden2_size = hidden1_size, hidden2_size
self.lr_rate = 1e-03
# weights initializationg
self.glorot_init = tf.initializers.glorot_uniform(seed=42)
# weights b/w input to hidden1 --> 1
self.w_h1 = tf.Variable(self.glorot_init((self.input_size, self.hidden1_size)))
# weights b/w hidden1 to hidden2 ---> 2
self.w_h2 = tf.Variable(self.glorot_init((self.hidden1_size, self.hidden2_size)))
# weights b/w hidden2 to output ---> 3
self.w_out = tf.Variable(self.glorot_init((self.hidden2_size, self.output_size)))
# bias initialization
self.b1 = tf.Variable(self.glorot_init((self.hidden1_size,)))
self.b2 = tf.Variable(self.glorot_init((self.hidden2_size,)))
self.b_out = tf.Variable(self.glorot_init((self.output_size,)))
self.variables = [self.w_h1, self.b1, self.w_h2, self.b2, self.w_out, self.b_out]
def feed_forward(self, x):
if self.device is not None:
with tf.device('gpu:0' if self.device=='gpu' else 'cpu'):
# layer1
self.layer1 = tf.nn.sigmoid(tf.add(tf.matmul(x, self.w_h1), self.b1))
# layer2
self.layer2 = tf.nn.sigmoid(tf.add(tf.matmul(self.layer1,
self.w_h2), self.b2))
# output layer
self.output = tf.nn.softmax(tf.add(tf.matmul(self.layer2,
self.w_out), self.b_out))
return self.output
def loss_fn(self, y_pred, y_true):
self.loss = tf.nn.sparse_softmax_cross_entropy_with_logits(labels=y_true,
logits=y_pred)
return tf.reduce_mean(self.loss)
def acc_fn(self, y_pred, y_true):
y_pred = tf.cast(tf.argmax(y_pred, axis=1), tf.int32)
y_true = tf.cast(y_true, tf.int32)
predictions = tf.cast(tf.equal(y_true, y_pred), tf.float32)
return tf.reduce_mean(predictions)
def backward_prop(self, batch_xs, batch_ys):
optimizer = tf.keras.optimizers.Adam(learning_rate=self.lr_rate)
with tf.GradientTape() as tape:
predicted = self.feed_forward(batch_xs)
step_loss = self.loss_fn(predicted, batch_ys)
grads = tape.gradient(step_loss, self.variables)
optimizer.apply_gradients(zip(grads, self.variables))
n_shape = x_train.shape[0]
epochs = 20
batch_size = 128
ds_train = ds_train.repeat().shuffle(n_shape).batch(batch_size).prefetch(batch_size)
neural_net = Model(512, 256, 'gpu')
for epoch in range(epochs):
no_steps = n_shape//batch_size
avg_loss = 0.
avg_acc = 0.
for (batch_xs, batch_ys) in ds_train.take(no_steps):
preds = neural_net.feed_forward(batch_xs)
avg_loss += float(neural_net.loss_fn(preds, batch_ys)/no_steps)
avg_acc += float(neural_net.acc_fn(preds, batch_ys) /no_steps)
neural_net.backward_prop(batch_xs, batch_ys)
print(f'Epoch: {epoch}, Training Loss: {avg_loss}, Training ACC: {avg_acc}')
# output for 10 epochs:
Epoch: 0, Training Loss: 1.7005115111824125, Training ACC: 0.7603832868262543
Epoch: 1, Training Loss: 1.6052448933478445, Training ACC: 0.8524806404020637
Epoch: 2, Training Loss: 1.5905528008006513, Training ACC: 0.8664196092868224
Epoch: 3, Training Loss: 1.584107405738905, Training ACC: 0.8727630912326276
Epoch: 4, Training Loss: 1.5792385798413306, Training ACC: 0.8773203844903037
Epoch: 5, Training Loss: 1.5759121985174716, Training ACC: 0.8804754322627559
Epoch: 6, Training Loss: 1.5739163148682564, Training ACC: 0.8826455712551251
Epoch: 7, Training Loss: 1.5722616605926305, Training ACC: 0.8840812018606812
Epoch: 8, Training Loss: 1.569699136307463, Training ACC: 0.8867688354803249
Epoch: 9, Training Loss: 1.5679460542742163, Training ACC: 0.8885049475356936
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:
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:
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
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:
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
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.
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).
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)
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?
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
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.
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.
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.
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.
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).
---
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.

Calling "fit_generator()" multiple times in Keras

I have a generator function which generates tuples of (inputs, targets) on which my model is trained using the fit_generator() method in Keras.
My dataset is divided into 9 equal parts. I wish to perform a leave-one-out cross validation on the dataset using the fit_generator() method and keep the learned parameters of the previous training intact.
My question is that will calling fit_generator() multiple times on the model make it re-learn its learned parameters on the previous train and validation sets from scratch or will it keep those learned parameters intact leading to improvement of accuracy?
After a little digging I found that the fit() method in Keras retains the learned parameters as over here Calling "fit" multiple times in Keras but I'm not sure if the same happens for fit_generator() and if it does can it be used for cross-validation of data.
The pseudo-code I'm thinking of implementing to achieve the cross-validation is as follows:
class DatasetGenerator(Sequence):
def __init__(validation_id, mode):
#Some code
def __getitem__():
#The generator function
#Some code
return (inputs, targets)
for id in range(9):
train_set = DatasetGenerator(id, 'train')
#train_set contains all 8 parts leaving the id part out for validation.
validation_set = DatasetGenerator(id, 'val')
#val_set contains the id part.
history = model.fit_generator(train_set, epochs = 10, steps_per_epoch = 24000, validation_data = val_set, validation_steps = 3000)
print('History Dict:', history.history)
results = model.evaluate_generator(test_set, steps=steps)
print('Test loss, acc:', results)
Will the model keep the learned parameters intact and improve upon them for each iteration of the for loop?
fit and fit_generator behave the same in that regard, calling them again will resume training from the previously trained weights.
Also note that what you are trying to do is not cross-validation, as to do real cross-validation, you train one model for each fold, and the models are completely independent, not continued from training of the previous fold.
As far as I know it will keep the previous trained params. Also, I think what you are trying to do can be done by modifying the on_epoch_end() method of Sequence. Could be something like this:
class DatasetGenerator(Sequence):
def __init__(self, id, mode):
self.id = id
self.mode = mode
self.current_epoch=0
#some code
def __getitem__(self, idx):
id = self.id
#Some code
return (inputs, targets)
def on_epoch_end():
self.current_epoch += 1
if self.current_epoch % 10 == 0:
self.id += 1

keras model.evaluate() does not show loss

I've created a neural network of the following form in keras:
from keras.layers import Dense, Activation, Input
from keras import Model
input_dim_v = 3
hidden_dims=[100, 100, 100]
inputs = Input(shape=(input_dim_v,))
net = inputs
for h_dim in hidden_dims:
net = Dense(h_dim)(net)
net = Activation("elu")(net)
outputs = Dense(self.output_dim_v)(net)
model_v = Model(inputs=inputs, outputs=outputs)
model_v.compile(optimizer='adam', loss='mean_squared_error', metrics=['mse'])
Later, I train it on single examples using model_v.train_on_batch(X[i],y[i]).
To test, whether the neural network is becoming a better function approximator, I wanted to evaluate the model on the accumulated X and y (in my case, X and y grow over time) periodically. However, when I call model_v.evaluate(X, y), only the characteristic progress bars appear in the console, but neither the loss value nor the mse-metric (which are the same in this case) are printed.
How can I change that?
The loss and metric values are not shown in the progress bar of evaluate() method. Instead, they are returned as the output of the evaluate() method and therefore you can print them:
for i in n_iter:
# ... get the i-th batch or sample
# ... train the model using the `train_on_batch` method
# evaluate the model on whole or part of test data
loss_metric = model.evaluate(test_data, test_labels)
print(loss_metric)
According to the documentation, if your model has multiple outputs and/or metrics, you can use model.metric_names attribute to find out what the values in loss_metric correspond to.

How to access shape of new features selected in sklearn custom transformer for different hyperparamters

I am using custom defined transformer for important features selection via following code
class fs(TransformerMixin, BaseEstimator):
def __init__(self, n_estimators=10):
self.ss=None
self.n_estimators = n_estimators
self.x_new = None
def fit(self, X, y):
m = ExtraTreesClassifier(10)
m.fit(X,y)
self.ss = SelectFromModel(m, prefit=True)
return self
def transform(self, X):
self.x_new=self.ss.transform(X)
return self.x_new`
Here x_new are the new features selected by my custom transformer fs.
Then I am defining my Neural Network as a classifier in my pipeline as follows.
def create_model(dropout_rate=0.1):
my_model=fs()
x_new=my_model.x_new
n_x_new=x_new.shape[1]
np.random.seed(6000)
model_new = Sequential()
model_new.add(Dense(n_x_new,input_dim=n_x_new ,kernel_initializer='glorot_uniform', activation='sigmoid'))
...............................rest of the code................................
Using sklearn Pipeline with the following code.
clf=KerasClassifier(build_fn=create_model, epochs=10, batch_size=1000, verbose=0)
model = Pipeline([('fs', fs()),('clf', clf)])
grid = GridSearchCV(estimator=model,param_grid={"clf__dropout_rate": [0.1, 0.2]},scoring='roc_auc', n_jobs=1)
grid_result = grid.fit(train_cv_x, train_cv_y)
I am getting the following error. How will my Keras model know about the shape of x_new selected for every hyperparamter.
'NoneType' object has no attribute 'shape'
So I solved the problem without making a custom estimate wrapper for my keras model with a very simple trick. When I looked at the error I was getting, It was something like this.
I just hard coded the input_dim value to check if those selected important features are passed to my keras model or not.
model_new.add(Dense(n_x_new,input_dim=200 ,kernel_initializer='glorot_uniform', activation='sigmoid'))
expected dense_22_input to have shape (None, 200) but got array with shape (10328, 428)
The error says that my keras model is actually getting the selecting important features from fs() but as I have defined the input_dim=200and this is not matching with the feature seize it gets from fs().
The only issue was to somehow know about the number of features selected for every hyperparameter and then give that number to input_dim of the keras model.
I declared a global variable and saved the self.x_new value in my fs() in that global variable.
That global variable is accessible in keras model.
There might be some other more robust solutions like, making custom wrapper for keras classifier.

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