Same model produces consistently different accuracies in Keras and Tensorflow - python

I'm trying to implement the same model in Keras, and in Tensorflow using Keras layers, using custom data. The two models produce consistently different accuracies over many times of training (keras ~71%, tensorflow ~65%). I want tensorflow to do as well as keras so I can go into the tensorflow iterations to tweak some lower level algorithms.
Here's my original Keras code:
from keras.layers import Dense, Dropout, Input
from keras.models import Model, Sequential
from keras import backend as K
input_size = 2000
num_classes = 4
num_industries = 22
num_aux_inputs = 3
main_input = Input(shape=(input_size,),name='text_vectors')
x = Dense(units=64, activation='relu', name = 'dense1')(main_input)
drop1 = Dropout(0.2,name='dropout1')(x)
auxiliary_input = Input(shape=(num_aux_inputs,), name='aux_input')
x = keras.layers.concatenate([drop1,auxiliary_input])
x = Dense(units=64, activation='relu',name='dense2')(x)
drop2 = Dropout(0.1,name='dropout2')(x)
x = Dense(units=32, activation='relu',name='dense3')(drop2)
main_output = Dense(units=num_classes,
activation='softmax',name='main_output')(x)
model = Model(inputs=[main_input, auxiliary_input],
outputs=main_output)
model.compile(loss=keras.losses.categorical_crossentropy, metrics= ['accuracy'],optimizer=keras.optimizers.Adadelta())
history = model.fit([train_x,train_x_auxiliary], train_y, batch_size=128, epochs=20, verbose=1, validation_data=([val_x,val_x_auxiliary], val_y))
loss, accuracy = model.evaluate([val_x,val_x_auxiliary], val_y, verbose=0)
Here's I moved the keras layers to tensorflow following this article:
import tensorflow as tf
from keras import backend as K
import keras
from keras.layers import Dense, Dropout, Input # Dense layers are "fully connected" layers
from keras.metrics import categorical_accuracy as accuracy
from keras.objectives import categorical_crossentropy
tf.reset_default_graph()
sess = tf.Session()
K.set_session(sess)
input_size = 2000
num_classes = 4
num_industries = 22
num_aux_inputs = 3
x = tf.placeholder(tf.float32, shape=[None, input_size], name='X')
x_aux = tf.placeholder(tf.float32, shape=[None, num_aux_inputs], name='X_aux')
y = tf.placeholder(tf.float32, shape=[None, num_classes], name='Y')
# build graph
layer = Dense(units=64, activation='relu', name = 'dense1')(x)
drop1 = Dropout(0.2,name='dropout1')(layer)
layer = keras.layers.concatenate([drop1,x_aux])
layer = Dense(units=64, activation='relu',name='dense2')(layer)
drop2 = Dropout(0.1,name='dropout2')(layer)
layer = Dense(units=32, activation='relu',name='dense3')(drop2)
output_logits = Dense(units=num_classes, activation='softmax',name='main_output')(layer)
loss = tf.reduce_mean(categorical_crossentropy(y, output_logits))
acc_value = tf.reduce_mean(accuracy(y, output_logits))
correct_prediction = tf.equal(tf.argmax(output_logits, 1), tf.argmax(y, 1), name='correct_pred')
optimizer = tf.train.AdadeltaOptimizer(learning_rate=1.0, rho=0.95,epsilon=tf.keras.backend.epsilon()).minimize(loss)
init = tf.global_variables_initializer()
sess.run(init)
epochs = 20 # Total number of training epochs
batch_size = 128 # Training batch size
display_freq = 300 # Frequency of displaying the training results
num_tr_iter = int(len(y_train) / batch_size)
with sess.as_default():
for epoch in range(epochs):
print('Training epoch: {}'.format(epoch + 1))
# Randomly shuffle the training data at the beginning of each epoch
x_train, x_train_aux, y_train = randomize(x_train, x_train_auxiliary, y_train)
for iteration in range(num_tr_iter):
start = iteration * batch_size
end = (iteration + 1) * batch_size
x_batch, x_aux_batch, y_batch = get_next_batch(x_train, x_train_aux, y_train, start, end)
# Run optimization op (backprop)
feed_dict_batch = {x: x_batch, x_aux:x_aux_batch, y: y_batch,K.learning_phase(): 1}
optimizer.run(feed_dict=feed_dict_batch)
I also implemented the whole model from scratch in tensorflow, but it also is a ~65% accuracy, so I decided to try this Keras-layers-within-TF set up to identify problems.
I've looked up posts on similar problems with Keras and Tensorflow, and have tried the following which didn't help in my case:
Keras's dropout layer is only active in the training phase, so I did the same in my tf code by setting keras.backend.learning_phase().
Keras and Tensorflow have different variable initializations. I've tried initializing my weights in tensorflow these following 3 ways, which is supposed to be the same as Keras's weight initialization, but they also didn't affect the accuracies:
initer = tf.glorot_uniform_initializer()
initer = tf.contrib.layers.xavier_initializer()
initer = tf.random_normal(shape) * (np.sqrt(2.0/(shape[0] + shape[1])))
The optimizer in the two versions are set to be exactly the same! Though it doesn't look like the accuracy depends on the optimizer - I tried using different optimizers in both keras and tf and the accuracies each converge to the same.
Help!

It seems to me that this is most probably the weight initialization problem. What I would suggest you to do is to initialize keras layers and before training get the layer weights and initialize tf layers with those values.
I have ran into that kind of problems and it solved problems for me but it was a long time ago and I don't know if they made those initializers the same. At that time tf and keras initializations were not the same obviously.

I checked with initializers,seed, parameters and hyperparameters but accuracy is different.
I checked the code for Keras and they randomly shuffle the batch of images and then fed into the network, so this shuffling is different across different engines. So we need to figure out a way in which we can fed the same set of batch images to the network in order to get same accuracy

Related

Neural network written with keras outputs only 0

my neural network written in keras, for the problem of binary image classification, after selecting hyperparameters using the keras tuner, produces only zeros.
import keras_tuner
from kerastuner import BayesianOptimization
from keras_tuner import Objective
from tensorflow.keras.models import Model
from tensorflow.keras.applications import Xception
from tensorflow.keras.layers import Dense
from tensorflow.keras.layers import Dropout
from tensorflow.keras.layers import Flatten
from torch.nn.modules import activation
def build_model(hp):
# create the base pre-trained model
base_model = Xception(include_top=False, input_shape=(224, 224, 3))
base_model.trainable = False
x = base_model.output
x = Flatten()(x)
hp_units = hp.Int('units', min_value=32, max_value=4096, step=32)
x = Dense(units = hp_units, activation="relu")(x)
hp_rate = hp.Float('rate', min_value = 0.01, max_value=0.9, step=0.01)
x = Dropout(rate = hp_rate)(x)
predictions = Dense(1, activation='sigmoid')(x)
# this is the model we will train
model = Model(inputs=base_model.input, outputs=predictions)
hp_learning_rate = hp.Float('learning_rate', max_value = 1e-2, min_value = 1e-7, step = 0.0005)
optimizer = hp.Choice('optimizer', ['adam', 'sgd', 'adagrad', 'rmsprop'])
model.compile(optimizer,
loss=tf.keras.losses.BinaryCrossentropy(),
metrics=['accuracy'])
return model
stop_early = keras.callbacks.EarlyStopping(monitor='val_loss', patience=5, min_delta= 0.0001)
tuner = BayesianOptimization(
hypermodel = build_model,
objective = Objective(name="val_accuracy",direction="max"),
max_trials = 10,
directory='/content/best_model_s',
overwrite=False
)
tuner.search(train_batches,
validation_data = valid_batches,
epochs = 100,
callbacks=[stop_early]
)
best_hps=tuner.get_best_hyperparameters(num_trials=1)[0]
model = tuner.hypermodel.build(best_hps)
history = model.fit(train_batches, validation_data = valid_batches ,epochs=50)
val_acc_per_epoch = history.history['val_accuracy']
best_epoch = val_acc_per_epoch.index(max(val_acc_per_epoch)) + 1
print('Best epoch: %d' % (best_epoch,))
best_model = tuner.hypermodel.build(best_hps)
# Retrain the model
best_model.fit(train_batches, validation_data = valid_batches , epochs=best_epoch)
test_generator.reset()
predict = best_model.predict_generator(test_generator, steps = len(test_generator.filenames))
I'm guessing that maybe the problem is that the ImageDataGenerator is fed to train with 2 batches of 16 images each, and to test the ImageDataGenerator with 2 batches of 4 images (each batch has an equal number of class representatives).I also noticed that with a small number of epochs, the neural network produces values ​​from 0 to 1, but the more epochs, the closer the response of the neural network is to zero. For a solution, I tried to stop training as soon as the next 5 iterations do not decrease the loss on validation. Again, it seems to me that the matter is in the validation sample, it is very small.
Any advice?

How to fit basic custom built model in tensorflow

I am used to working in PyTorch but now have to learn Tensorflow for my job. I am trying to get up to speed by creating a simple dense network and training it on the MNIST dataset, but I cannot get it to train. My super simple code:
import tensorflow as tf
from tensorflow.keras import Input
from tensorflow.keras.layers import Dense, Flatten
from tensorflow.keras.models import Model
from tensorflow.keras.optimizers import SGD
from tensorflow.keras.utils import to_categorical
# Load mnist data from keras
(train_data, train_label), (test_data, test_label) = tf.keras.datasets.mnist.load_data(path="mnist.npz")
train_label, test_label = to_categorical(train_label), to_categorical(test_label)
train_data, train_label, test_data, test_label = Flatten()(train_data), Flatten()(train_label), Flatten()(test_data), Flatten()(test_label)
# Create generic SGD optimizer (no learning schedule)
optimizer = SGD(learning_rate = 0.01)
# Define function to build and compile model
def build_mnist_model(input_shape, batch_size = 30):
input_img = Input(shape = input_shape, batch_size = batch_size)
# Pass through dense layer
x = Dense(200, activation = 'relu', use_bias = True)(input_img)
x = Dense(400, activation = 'relu', use_bias = True)(x)
scores = Dense(10, activation = 'softmax', use_bias = True)(x)
# Create and compile tf model
mnist_model = Model(input_img, scores)
mnist_model.compile(optimizer = optimizer, loss = 'categorical_crossentropy')
return mnist_model
# Build the model
mnist_model = build_mnist_model(train_data[0].shape)
# Train the model
mnist_model.fit(
x = train_data,
y = train_label,
batch_size = 30,
epochs = 20,
verbose = 2,
shuffle = True,
# steps_per_epoch = 200
)
When I run this I get
ValueError: When using data tensors as input to a model, you should specify the `steps_per_epoch` argument.
This does not really make sense to me because my train_data and train_label are just regular tensors and per the Tensorflow documentation in this case it should default to the number of samples in the dataset divided by the batch size (which would be 200 in my case).
At any rate, I tried specifying steps_per_epoch = 200 when I call mnist_model.fit() but then I get a different error:
InvalidArgumentError: Incompatible shapes: [60000,10] vs. [30,1]
[[{{node training_4/SGD/gradients/gradients/loss_5/dense_17_loss/softmax_cross_entropy_with_logits_grad/mul}}]]
I can't seem to discern where a size mismatch would come from. In PyTorch, I am used to manually creating batches (by subindexing my data and label tensors) but in Tensorflow this seems to happen automatically. As such, this leaves me quite confused about what batch has the wrong size, how it got the wrong size, etc. I hope this simple model is way easier than I am making it and I just do not know the Tensorflow tricks yet.
Thanks for the help.

Use tensorflow learning-rate decay in a Keras-to-TPU model

I'm following the "How to train Keras model x20 times faster with TPU for free" guide (click here) to run a keras model on google's colab TPU. It works perfectly. But...I like to use cosine restart learning rate decay when I fit my models. I've coded up my own as a keras callback, but it won't work within this framework because the tensorflow TFOptimizer class doesn't have a learning-rate variable that can be reset. I see that tensorflow itself has a bunch of decay function in tf.train, like tf.train.cosine_decay but I can't figure out how to embed it within my model.
Here's the basic code from that blog post. Anyone have a fix?
import tensorflow as tf
import os
from tensorflow.python.keras.layers import Input, LSTM, Bidirectional, Dense, Embedding
def make_model(batch_size=None):
source = Input(shape=(maxlen,), batch_size=batch_size,
dtype=tf.int32, name='Input')
embedding = Embedding(input_dim=max_features,
output_dim=128, name='Embedding')(source)
lstm = LSTM(32, name='LSTM')(embedding)
predicted_var = Dense(1, activation='sigmoid', name='Output')(lstm)
model = tf.keras.Model(inputs=[source], outputs=[predicted_var])
model.compile(
optimizer=tf.train.RMSPropOptimizer(learning_rate=0.01),
loss='binary_crossentropy',
metrics=['acc'])
return model
training_model = make_model(batch_size=128)
# This address identifies the TPU we'll use when configuring TensorFlow.
TPU_WORKER = 'grpc://' + os.environ['COLAB_TPU_ADDR']
tf.logging.set_verbosity(tf.logging.INFO)
tpu_model = tf.contrib.tpu.keras_to_tpu_model(
training_model,
strategy=tf.contrib.tpu.TPUDistributionStrategy(
tf.contrib.cluster_resolver.TPUClusterResolver(TPU_WORKER)))
history = tpu_model.fit(x_train, y_train,
epochs=20,
batch_size=128 * 8,
validation_split=0.2)
One option is to manually set the learning rates - there is a Keras+TPU example with a callback here: https://github.com/tensorflow/tpu/blob/master/models/experimental/resnet50_keras/resnet50.py#L197-L201
The following seems to work, where lr is the initial learning rate you choose and M is the number of initial steps over which you want to the cosine decay to work.
def make_model(batch_size=None,lr=1.e-3,n_steps=2000):
source = Input(shape=(maxlen,), batch_size=batch_size,
dtype=tf.int32, name='Input')
embedding = Embedding(input_dim=max_features,
output_dim=128, name='Embedding')(source)
lstm = LSTM(32, name='LSTM')(embedding)
predicted_var = Dense(1, activation='sigmoid', name='Output')(lstm)
model = tf.keras.Model(inputs=[source], outputs=[predicted_var])
# implement cosine decay or other learning rate decay here
global_step = tf.Variable(0)
global_step=1
learning_rate = tf.train.cosine_decay_restarts(
learning_rate=lr,
global_step=global_step,
first_decay_steps=n_steps,
t_mul= 1.5,
m_mul= 1.,
alpha=0.1
)
# now feed this into the optimizer as shown below
model.compile(
optimizer=tf.train.RMSPropOptimizer(learning_rate=learning_rate),
loss='binary_crossentropy',
metrics=['acc'])
return model

Keras: unsupervised pre-training kills performance

I'm trying to train a deep classifier in Keras both with and without pretraining of the hidden layers via stacked autoencoders. My problem is that the pretraining seems to drastically degrade performance (i.e. if pretrain is set to False in the code below the training error of the final classification layer converges much faster). This seems completely outrageous to me given that pretraining should only initialize the weights of the hidden layers and I don't see how that could completely kill the models performance even if that initialization does not work very well. I can not include the specific dataset I used but the effect should occur for any appropriate dataset (e.g. minist). What is going on here and how can I fix it?
EDIT: code is now reproducible with the MNIST data, final line prints change in loss function, which is significantly lower with pre-training.
I have also slightly modified the code and added sample learning curves below:
from functools import partial
import matplotlib.pyplot as plt
from keras.datasets import mnist
from keras.layers import Dense
from keras.models import Sequential
from keras.optimizers import SGD
from keras.regularizers import l2
from keras.utils import to_categorical
(inputs_train, targets_train), _ = mnist.load_data()
inputs_train = inputs_train[:1000].reshape(1000, 784)
targets_train = to_categorical(targets_train[:1000])
hidden_nodes = [256] * 4
learning_rate = 0.01
regularization = 1e-6
epochs = 30
def train_model(pretrain):
model = Sequential()
layer = partial(Dense,
activation='sigmoid',
kernel_initializer='random_normal',
kernel_regularizer=l2(regularization))
for i, hn in enumerate(hidden_nodes):
kwargs = dict(units=hn, name='hidden_{}'.format(i + 1))
if i == 0:
kwargs['input_dim'] = inputs_train.shape[1]
model.add(layer(**kwargs))
if pretrain:
# train autoencoders
inputs_train_ = inputs_train.copy()
for i, hn in enumerate(hidden_nodes):
autoencoder = Sequential()
autoencoder.add(layer(units=hn,
input_dim=inputs_train_.shape[1],
name='hidden'))
autoencoder.add(layer(units=inputs_train_.shape[1],
name='decode'))
autoencoder.compile(optimizer=SGD(lr=learning_rate, momentum=0.9),
loss='binary_crossentropy')
autoencoder.fit(
inputs_train_,
inputs_train_,
batch_size=32,
epochs=epochs,
verbose=0)
autoencoder.pop()
model.layers[i].set_weights(autoencoder.layers[0].get_weights())
inputs_train_ = autoencoder.predict(inputs_train_)
num_classes = targets_train.shape[1]
model.add(Dense(units=num_classes,
activation='softmax',
name='classify'))
model.compile(optimizer=SGD(lr=learning_rate, momentum=0.9),
loss='categorical_crossentropy')
h = model.fit(
inputs_train,
targets_train,
batch_size=32,
epochs=epochs,
verbose=0)
return h.history['loss']
plt.plot(train_model(pretrain=False), label="Without Pre-Training")
plt.plot(train_model(pretrain=True), label="With Pre-Training")
plt.xlabel("Epoch")
plt.ylabel("Cross-Entropy")
plt.legend()
plt.show()

TensorFlow Dense and ReLU layers causing Segmentation fault error

I'm creating a neural network using TensorFlow.
I have some helper functions in the help.py file:
import tensorflow as tf
import numpy as np
from tensorflow.examples.tutorials.mnist import input_data
def read_mnist(folder_path="MNIST_data/"):
return input_data.read_data_sets(folder_path, one_hot=True)
def build_training(y_labels, y_output, learning_rate=0.5):
# Define loss function
loss = tf.reduce_mean(tf.nn.softmax_cross_entropy_with_logits(labels=y_labels, logits=y_output))
#train_step = tf.train.GradientDescentOptimizer(learning_rate).minimize(loss)
train_step = tf.train.AdamOptimizer(1e-4).minimize(loss)
# Calculate accuracy
correct_prediction = tf.equal(tf.argmax(y_output,1), tf.argmax(y_labels,1))
accuracy = tf.reduce_mean(tf.cast(correct_prediction, tf.float32))
return train_step, accuracy
def train_test_model(mnist, x_input, y_labels, accuracy, train_step, steps=1000, batch=100):
sess = tf.InteractiveSession()
sess.run(tf.global_variables_initializer())
for i in range(steps):
input_batch, labels_batch = mnist.train.next_batch(batch)
feed_dict = {x_input: input_batch, y_labels: labels_batch}
if i%100 == 0:
train_accuracy = accuracy.eval(feed_dict=feed_dict)
print("Step %d, training batch accuracy %g"%(i, train_accuracy))
train_step.run(feed_dict=feed_dict)
print("The end of training!")
print("Test accuracy: %g"%accuracy.eval(feed_dict={x_input: mnist.test.images, y_labels: mnist.test.labels}))
Then I try to use it when training the network.
First I use very simple 1 output layer:
import help
import tensorflow as tf
import numpy as np
# Read mnist data
mnist = help.read_mnist()
image_size = 28
labels_size = 10
# Input layer - flattened images
x_input = tf.placeholder(tf.float32, [None, image_size*image_size])
y_labels = tf.placeholder(tf.float32, [None, labels_size])
# Layers:
# - Input
# - Output (Dense)
# Output dense layer
y_output = tf.layers.dense(inputs=x_input, units=labels_size)
# Define training
train_step, accuracy = help.build_training(y_labels, y_output)
# Run the training & test
help.train_test_model(mnist, x_input, y_labels, accuracy, train_step)
Then I add another ReLU layer:
# Hidden Layer
hidden = tf.layers.dense(inputs=x_input, units=hidden_size, activation=tf.nn.relu)
# Output dense layer
y_output = tf.layers.dense(inputs=hidden, units=labels_size)
I get Segmentation fault error both times.
I tried few things that I found online like reordering numpy and tensorflow import clauses, putting the help.py code in the same file as the network architecture and training process or increasing the memory for the docker image. Nothing worked.
Can someone help?
I upgraded to the next version of TensorFlow, version 1.2. It fixed all the issues.

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