Floating point exception when creating a TensorFlow TimeDistributed layer - tensorflow

I have so far been unable to resolve this bug. I am running my code and getting floating point exception with no stack trace. I tried to debug and step through my code and it dies after going through the call function twice. Here is the full code:
import os
import sys
from typing import Counter
import tensorflow as tf
import numpy as np
from tensorflow.keras import models, layers, callbacks
from tensorflow.keras.utils import to_categorical
from tensorflow.keras.optimizers import Adam
from tensorflow.keras.datasets import mnist
from matplotlib import pyplot as plt
# Change this to the location of the database directories
DB_DIR = os.path.dirname(os.path.realpath(__file__))
# Import databases
sys.path.insert(1, DB_DIR)
from db_utils import get_imdb_dataset, get_speech_dataset, get_single_digit_dataset
def Secure_Voice_Channel(func):
"""Define Secure_Voice_Channel decorator."""
def execute_func(*args, **kwargs):
print('Established Secure Connection.')
returned_value = func(*args, **kwargs)
print("Ended Secure Connection.")
return returned_value
return execute_func
#Secure_Voice_Channel
class generic_vns_function(tf.keras.Model):
def __init__(self, input_shape, layers, layer_units):
super().__init__()
self.convolutions = []
# Dynamically create Convolutional layers and MaxPools
for layer in range(len(layers)):
self.convolutions.append(tf.keras.layers.Conv2D(layer, 3, padding="same", input_shape=input_shape, activation="relu"))
# Add MaxPooling layer
self.convolutions.append(tf.keras.layers.MaxPooling2D((2,2)))
# Flatten
self.flatten = tf.keras.layers.Flatten()
# Dense layer
self.dense1 = tf.keras.layers.Dense(1024, activation="relu")
def call(self, input):
x = input
for layer in self.convolutions:
x = layer(x)
x = self.flatten(x)
x = self.dense1(x)
return x
def train_model(model, epochs, batch_size, X_train, y_train, X_test, y_test):
"""Generic Deep Learning Model training function."""
cb = [callbacks.EarlyStopping(monitor='val_loss', patience=3)]
model.fit(X_train, y_train, validation_data=(X_test, y_test), epochs=epochs,
batch_size=batch_size, verbose=1, callbacks=cb)
scores = model.evaluate(X_test, y_test, verbose=2)
print("Baseline Error: %.2f%%" % (100-scores[1]*100))
return model
def choose_dataset(dataset_type):
"""Select dataset based on string variable."""
if dataset_type == "nlp":
return get_imdb_dataset(dir=DB_DIR)
elif dataset_type == "computer_vision":
(X_train, y_train), (X_test, y_test) = mnist.load_data()
elif dataset_type == "speech_recognition":
# (X_train, y_train), (X_test, y_test), (_, _) = get_speech_dataset()
(X_train, y_train), (X_test, y_test), (_, _) = get_single_digit_dataset(0)
else:
raise ValueError("Couldn't find dataset.")
(X_train, X_test) = normalize_dataset(dataset_type, X_train, X_test)
(X_train, y_train), (X_test, y_test) = reshape_dataset(X_train, y_train, X_test, y_test)
return (X_train, y_train), (X_test, y_test)
def normalize_dataset(string, X_train, X_test):
"""Normalize speech recognition and computer vision datasets."""
if string == "computer vision":
X_train = X_train / 255
X_test = X_test / 255
else:
mean = np.mean(X_train)
std = np.std(X_train)
X_train = (X_train-std)/mean
X_test = (X_test-std)/mean
return (X_train, X_test)
def reshape_dataset(X_train, y_train, X_test, y_test):
"""Reshape Computer Vision and Speech datasets."""
y_train = to_categorical(y_train)
y_test = to_categorical(y_test)
return (X_train, y_train), (X_test, y_test)
def create_LSTM(cnn_model, input_shape, num_classes):
input_layer = layers.Input(shape=input_shape)
distributed_cnn = tf.keras.layers.TimeDistributed(cnn_model)(input_layer)
x, state_a, state_b = layers.LSTM(distributed_cnn)
output = layers.Dense(num_classes, activation="softmax")(x)
model = models.Model(inputs=input_layer, outputs=output)
opt = Adam()
model.compile(loss='categorical_crossentropy', optimizer=opt, metrics=['accuracy'])
return model
def main():
# Hyperparameters
layers = [64, 32]
layer_units = 1000
epochs = 10
batch_size = 200
lr = 0.001
filter = 64
kernal_size = 3
window = 3
dataset = "speech_recognition"
# Import Datasets
(X_train, y_train), (X_test, y_test) = choose_dataset(dataset)
num_classes = y_train.shape[1]
# Reshape both the train and test dataset
X_train = X_train.reshape(X_train.shape[0], window, int(X_train.shape[1]/window), X_train.shape[2], 1)
X_test = X_test.reshape(X_test.shape[0], window, int(X_test.shape[1]/window), X_test.shape[2], 1)
# Generate CNN model
cnn_model = generic_vns_function(X_train.shape[1:], layers, layer_units)
print("Created generic CNN model")
# Create the LSTM CNN with time distributed layer
model = create_LSTM(cnn_model, X_train.shape[1:], num_classes)
print("Created LST model")
trained_model = train_model(model, epochs, batch_size, X_train, y_train, X_test, y_test)
save_format="tf"
# # Save model to h5 file
trained_model.save(save_format, 'models/model_%s_a3.h5' % dataset)
return None
The error occurs after looping through the call function twice while creating the distributed_cnn = tf.keras.layers.TimeDistributed(cnn_model)(input_layer). Any ideas as to why? This is baffling to me.
To run the code, you also need to create the database via this file: https://gist.github.com/logankilpatrick/e621cf31f620524591a24cd9d4cf30f3

Related

Tensorflow keras, no gradients error when use MSE

I am trying the code from tensorflow "Writing a training loop from scratch" with some changes by myself. I changed the loss function from SparseCategoricalCrossentropy to MeanSquaredError. I also changed the architecture of the model by adding a new Lambda layer for loss calculation. However, I have the Value error that no gradients provided for variable. Is there any way that I can make the code to run with MSE?
import numpy as np
import tensorflow as tf
from tensorflow import keras
from tensorflow.keras import layers
inputs = keras.Input(shape=(784,), name="digits")
x1 = layers.Dense(64, activation="relu")(inputs)
x2 = layers.Dense(64, activation="relu")(x1)
outputs = layers.Dense(10, name="predictions")(x2)
final_outputs = layers.Lambda(lambda x: tf.math.argmax(x, axis = -1))(outputs)
model = keras.Model(inputs=inputs, outputs=final_outputs)
# Instantiate an optimizer.
optimizer = keras.optimizers.SGD(learning_rate=1e-3)
# Instantiate a loss function.
loss_fn = keras.losses.MeanSquaredError()
# Prepare the training dataset.
batch_size = 64
(x_train, y_train), (x_test, y_test) = keras.datasets.mnist.load_data()
x_train = np.reshape(x_train, (-1, 784))
x_test = np.reshape(x_test, (-1, 784))
# Reserve 10,000 samples for validation.
x_val = x_train[-10000:]
y_val = y_train[-10000:]
x_train = x_train[:-10000]
y_train = y_train[:-10000]
# Prepare the training dataset.
train_dataset = tf.data.Dataset.from_tensor_slices((x_train, y_train))
train_dataset = train_dataset.shuffle(buffer_size=1024).batch(batch_size)
# Prepare the validation dataset.
val_dataset = tf.data.Dataset.from_tensor_slices((x_val, y_val))
val_dataset = val_dataset.batch(batch_size)
epochs = 2
for epoch in range(epochs):
print("\nStart of epoch %d" % (epoch,))
for step, (x_batch_train, y_batch_train) in enumerate(train_dataset):
with tf.GradientTape() as tape:
logits = model(x_batch_train, training=True)
loss_value = loss_fn(y_batch_train, logits)
grads = tape.gradient(loss_value, model.trainable_weights)
optimizer.apply_gradients(zip(grads, model.trainable_weights))
argmax ops is not differentiable. To use an integer label and MSE loss, you want to convert your labels y_train and y_val to integers.
y_train = np.argmax(y_train, axis=-1)
y_val = np.argmax(y_val, axis=-1)
And adjust the output layer to output integer labels
outputs = layers.Dense(1, name="predictions")(x2)

Why does it complain 'images' variable not available?

I am running the TF2 tutorial, and copied exactly the code into a .py file and run it in PyCharm, but got this error message:
Testing started at 12:50 AM ...
/home/martin/nlp/my-env/tf/bin/python /home/martin/.local/share/JetBrains/Toolbox/apps/PyCharm-C/ch-0/193.5233.109/plugins/python-ce/helpers/pycharm/_jb_pytest_runner.py --path /home/martin/tf2-tutorial/cnn_mnist.py
Launching pytest with arguments /home/martin/tf2-tutorial/cnn_mnist.py in /home/martin/tf2-tutorial
============================= test session starts ==============================
platform linux -- Python 3.7.1, pytest-5.3.1, py-1.8.0, pluggy-0.13.1 -- /home/martin/nlp/my-env/tf/bin/python
cachedir: .pytest_cache
rootdir: /home/martin/tf2-tutorial
collecting ... collected 1 item
cnn_mnist.py::test2_step ERROR [100%]
test setup failed
file /home/martin/tf2-tutorial/cnn_mnist.py, line 60
#tf.function
def test_step(images, labels):
E fixture 'images' not found
> available fixtures: cache, capfd, capfdbinary, caplog, capsys, capsysbinary, doctest_namespace, monkeypatch, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
Why does it think it's a pytest program? And why does it issue this error message? The tutorial should work "as is".
The copied code from the tutorial is below (exact copy):
from __future__ import absolute_import, division, print_function, unicode_literals
import tensorflow as tf
from tensorflow.keras.layers import Dense, Flatten, Conv2D
from tensorflow.keras import Model
mnist = tf.keras.datasets.mnist
(x_train, y_train), (x_test, y_test) = mnist.load_data()
x_train, x_test = x_train / 255.0, x_test / 255.0
# Add a channels dimension
x_train = x_train[..., tf.newaxis]
x_test = x_test[..., tf.newaxis]
train_ds = tf.data.Dataset.from_tensor_slices(
(x_train, y_train)).shuffle(10000).batch(32)
test_ds = tf.data.Dataset.from_tensor_slices((x_test, y_test)).batch(32)
class MyModel(Model):
def __init__(self):
super(MyModel, self).__init__()
self.conv1 = Conv2D(32, 3, activation='relu')
self.flatten = Flatten()
self.d1 = Dense(128, activation='relu')
self.d2 = Dense(10, activation='softmax')
def call(self, x):
x = self.conv1(x)
x = self.flatten(x)
x = self.d1(x)
return self.d2(x)
# Create an instance of the model
model = MyModel()
loss_object = tf.keras.losses.SparseCategoricalCrossentropy()
optimizer = tf.keras.optimizers.Adam()
train_loss = tf.keras.metrics.Mean(name='train_loss')
train_accuracy = tf.keras.metrics.SparseCategoricalAccuracy(name='train_accuracy')
test_loss = tf.keras.metrics.Mean(name='test_loss')
test_accuracy = tf.keras.metrics.SparseCategoricalAccuracy(name='test_accuracy')
#tf.function
def train_step(images, labels):
with tf.GradientTape() as tape:
predictions = model(images)
loss = loss_object(labels, predictions)
gradients = tape.gradient(loss, model.trainable_variables)
optimizer.apply_gradients(zip(gradients, model.trainable_variables))
train_loss(loss)
train_accuracy(labels, predictions)
#tf.function
def test_step(images, labels):
predictions = model(images)
t_loss = loss_object(labels, predictions)
test_loss(t_loss)
test_accuracy(labels, predictions)
EPOCHS = 5
for epoch in range(EPOCHS):
for images, labels in train_ds:
train_step(images, labels)
for test_images, test_labels in test_ds:
test_step(test_images, test_labels)
template = 'Epoch {}, Loss: {}, Accuracy: {}, Test Loss: {}, Test Accuracy: {}'
print(template.format(epoch+1,
train_loss.result(),
train_accuracy.result()*100,
test_loss.result(),
test_accuracy.result()*100))
# Reset the metrics for the next epoch
train_loss.reset_states()
train_accuracy.reset_states()
test_loss.reset_states()
test_accuracy.reset_states()
Could this be due to the PyCharm environment issue? But it has been working all fine?

How to modify weights of Keras layers?

I am trying to freeze some of the weights of a layer by setting them to a specific value in Keras. How can I achieve this without moving weights to CPU ?
I checked similar questions such as modify layer weights in keras and modify layer parameters in keras
Answers suggest usage of get_weights() and 'set_weights()', however those functions moves weights between CPU and GPU.
I created a custom lambda layer and modified model.trainable_weights inside of that layer, however weights are not updated.
I used tf advanced tutorial, and just added a custom lambda layer that multiplies weights with zero.
Colab notebook with same code
from __future__ import absolute_import, division, print_function, unicode_literals
import tensorflow as tf
from tensorflow.keras.layers import Dense, Flatten, Conv2D, Lambda
from tensorflow.keras import Model
mnist = tf.keras.datasets.mnist
(x_train, y_train), (x_test, y_test) = mnist.load_data()
x_train, x_test = x_train / 255.0, x_test / 255.0
# Add a channels dimension
x_train = x_train[..., tf.newaxis]
x_test = x_test[..., tf.newaxis]
def antirectifier(x):
for i,w in enumerate(model.trainable_weights):
model.trainable_weights[i] = tf.multiply(w,0)
return x
class MyModel(Model):
def __init__(self):
super(MyModel, self).__init__()
self.conv1 = Conv2D(32, 3, activation='relu')
self.flatten = Flatten()
self.d1 = Dense(128, activation='relu')
self.d2 = Dense(10, activation='softmax')
self.mask = Lambda(antirectifier)
def call(self, x):
x = self.conv1(x)
x = self.flatten(x)
x = self.d1(x)
x = self.mask(x)
return self.d2(x)
# Create an instance of the model
model = MyModel()
loss_object = tf.keras.losses.SparseCategoricalCrossentropy()
optimizer = tf.keras.optimizers.Adam()
train_loss = tf.keras.metrics.Mean(name='train_loss')
train_accuracy = tf.keras.metrics.SparseCategoricalAccuracy(name='train_accuracy')
test_loss = tf.keras.metrics.Mean(name='test_loss')
test_accuracy = tf.keras.metrics.SparseCategoricalAccuracy(name='test_accuracy')
#tf.function
def train_step(images, labels):
with tf.GradientTape() as tape:
predictions = model(images)
loss = loss_object(labels, predictions)
gradients = tape.gradient(loss, model.trainable_variables)
optimizer.apply_gradients(zip(gradients, model.trainable_variables))
train_loss(loss)
train_accuracy(labels, predictions)
#tf.function
def test_step(images, labels):
predictions = model(images)
t_loss = loss_object(labels, predictions)
test_loss(t_loss)
test_accuracy(labels, predictions)
EPOCHS = 5
for epoch in range(EPOCHS):
for images, labels in train_ds:
train_step(images, labels)
for test_images, test_labels in test_ds:
test_step(test_images, test_labels)
template = 'Epoch {}, Loss: {}, Accuracy: {}, Test Loss: {}, Test Accuracy: {}'
print(template.format(epoch+1,
train_loss.result(),
train_accuracy.result()*100,
test_loss.result(),
test_accuracy.result()*100))
# Reset the metrics for the next epoch
train_loss.reset_states()
train_accuracy.reset_states()
test_loss.reset_states()
test_accuracy.reset_states()
Since weights are zero, accuracy should be low. However weights are not changed.

How to freeze weights in certain layer with Keras?

I am trying to freeze the weights of certain layer in a prediction model with Keras and mnist dataset, but it does not work. The code is like:
from keras.layers import Dense, Flatten
from keras.utils import to_categorical
from keras.models import Sequential, load_model
from keras.datasets import mnist
from keras.losses import categorical_crossentropy
import numpy as np
def load_data():
(x_train, y_train), (x_test, y_test) = mnist.load_data()
x_train = x_train.astype('float32')
x_test = x_test.astype('float32')
x_train /= 255
x_test /= 255
y_train = to_categorical(y_train, num_classes=10)
y_test = to_categorical(y_test, num_classes=10)
return x_train, y_train, x_test, y_test
def run():
x_train, y_train, x_test, y_test = load_data()
model = Sequential([Flatten(input_shape=(28, 28)),
Dense(300, name='dense1', activation='relu'),
Dense(100, name='dense2', activation='relu'),
Dense(10, name='dense3', activation='softmax')])
model.trainable = True
model.compile(optimizer='Adam',
metrics=['accuracy'],
loss=categorical_crossentropy)
print(model.summary())
model.fit(x_train, y_train, epochs=5, verbose=2)
print(model.evaluate(x_test, y_test))
return model
def freeze(model):
x_train, y_train, x_test, y_test = load_data()
name = 'dense1'
weightsAndBias = model.get_layer(name=name).get_weights()
# freeze the weights of this layer
model.get_layer(name=name).trainable = False
# record the weights before retrain
weights_before = weightsAndBias[0]
# retrain
model.fit(x_train, y_train, verbose=2, epochs=1)
weights_after = model.get_layer(name=name).get_weights()[0]
if (weights_before == weights_after).all():
print('the weights did not change!!!')
else:
print('the weights changed!!!!')
if __name__ == '__main__':
model = run()
freeze(model)
The program outputs 'the weights changed!!!!'.
I do not understand why the weights of the layer named 'dense1' changes after setting model.get_layer(name=name).trainable = False.
You can do it by using:
model=Sequential()
layer=Dense(64,init='glorot_uniform',input_shape=(784,))
layer.trainable=False
model.add(layer)
layer2=Dense(784, activation='sigmoid',init='glorot_uniform')
layer2.trainable=True
model.add(layer2)
model.compile(loss='relu', optimizer=sgd,metrics = ['mae'])
You need to compile the graph after setting 'trainable'.
more info here
let me keep my layers freezed upto 5th layer, rest i will keep trainable
Here is more simple & more efficient code
for layer in model.layers[:5]:
layer.trainable=False
for layer in model.layers[5:]:
layer.trainable=True

Keras model failed to learn anything after changing to use tf.data api

I was trying to convert a simple Keras model to use tf.data api for data loading, but somehow the accuracy remains about 10% during the whole 10 epochs.
In comparison, the original code without using tf.data api can easily achieve about 98% accuracy. Did I do anything wrong?
The version using tf.data api
import math
import tensorflow as tf
import numpy as np
batch_size = 32
def load_data():
mnist = tf.keras.datasets.mnist
(train_data, train_label), (validation_data, validation_label) = mnist.load_data()
train_data, validation_data = train_data / 255.0, validation_data / 255.0
train_label = train_label.astype(np.float32)
return train_data, train_label
def build_model():
class MyModel(tf.keras.Model):
def __init__(self):
super(MyModel, self).__init__(name='my_model')
self.flatten = tf.keras.layers.Flatten()
self.dense_1 = tf.keras.layers.Dense(512, activation=tf.nn.relu)
self.dropout = tf.keras.layers.Dropout(0.2)
self.dense_2 = tf.keras.layers.Dense(10, activation=tf.nn.softmax)
def call(self, inputs):
x = self.flatten(inputs)
x = self.dense_1(x)
x = self.dropout(x)
y = self.dense_2(x)
return y
model = MyModel()
model.compile(optimizer=tf.train.AdamOptimizer(),
loss='sparse_categorical_crossentropy',
metrics=['accuracy'])
return model
train_data, train_label = load_data()
train_sample_count = len(train_data)
train_dataset = tf.data.Dataset.from_tensor_slices((train_data, train_label))
train_dataset = train_dataset.batch(batch_size)
train_dataset = train_dataset.repeat()
model = build_model()
model.fit(
train_dataset,
epochs=10,
steps_per_epoch=math.ceil(train_sample_count/batch_size)
)
The version without using tf.data api
# load_data and build_model are exactly same as those in the tf.data api version
train_data, train_label = load_data()
model = build_model()
model.fit(
train_data,
train_label,
epochs=10
)