the same model converged in keras but not tensorflow, how is that possible? - tensorflow

I'm trying to work with lstm in tensorflow, but I got to the point I can't make a simple imdb sentiment model to converge.
I took a keras model and tried to duplicate the exact same model in tensorflow, in keras it trains and converge however in tensorflow it is just stuck at some point (0.69 loss).
I tried to make them as equal as possible, the only difference I can tell of is that in keras the padding is before the sequence, while in tensorflow I use 'post' padding due to the conventions in tensorflow.
Any idea whats wrong with my tensorflow model?
from __future__ import print_function
import random
import numpy as np
from tensorflow.contrib.keras.python.keras.preprocessing import sequence
from tensorflow.contrib.keras.python.keras.models import Sequential
from tensorflow.contrib.keras.python.keras.layers import Dense, Dropout, Activation
from tensorflow.contrib.keras.python.keras.layers import Embedding
from tensorflow.contrib.keras.python.keras.layers import LSTM
from tensorflow.contrib.keras.python.keras.layers import Conv1D, MaxPooling1D
from tensorflow.contrib.keras.python.keras.datasets import imdb
import tensorflow as tf
# Embedding
max_features = 30000
maxlen = 2494
embedding_size = 128
# Convolution
kernel_size = 5
filters = 64
pool_size = 4
# LSTM
lstm_output_size = 70
# Training
batch_size = 30
epochs = 2
class TrainData:
def __init__(self, batch_sz=batch_size):
(x_train, y_train), (_, _) = imdb.load_data(num_words=max_features)
y_train = [[int(x == 1), int(x != 1)] for x in y_train]
self._batch_size = batch_sz
self._train_data = sequence.pad_sequences(x_train, padding='pre')
self._train_labels = y_train
def next_batch(self):
if len(self._train_data) < self._batch_size:
self.__init__()
batch_x, batch_y = self._train_data[:self._batch_size], self._train_labels[:self._batch_size]
self._train_data = self._train_data[self._batch_size:]
self._train_labels = self._train_labels[self._batch_size:]
return batch_x, batch_y
def batch_generator(self):
while True:
if len(self._train_data) < self._batch_size:
self.__init__()
batch_x, batch_y = self._train_data[:self._batch_size], self._train_labels[:self._batch_size]
self._train_data = self._train_data[self._batch_size:]
self._train_labels = self._train_labels[self._batch_size:]
yield batch_x, batch_y
def get_num_batches(self):
return int(len(self._train_data) / self._batch_size)
def length(sequence):
used = tf.sign(tf.abs(sequence))
length = tf.reduce_sum(used, reduction_indices=1)
length = tf.cast(length, tf.int32)
return length
def get_model(x, y):
embedding = tf.get_variable("embedding", [max_features, embedding_size], dtype=tf.float32)
embedded_x = tf.nn.embedding_lookup(embedding, x)
print(x)
print(embedded_x)
print(length(x))
cell_1 = tf.contrib.rnn.BasicLSTMCell(lstm_output_size)
output_1, state_1 = tf.nn.dynamic_rnn(cell_1, embedded_x, dtype=tf.float32, scope="rnn_layer1",
sequence_length=length(x))
# Select last output.
last_index = tf.shape(output_1)[1] - 1
# reshaping to [seq_length, batch_size, num_units]
output = tf.transpose(output_1, [1, 0, 2])
last = tf.gather(output, last_index)
# Softmax layer
with tf.name_scope('fc_layer'):
weight = tf.get_variable(name="weights", shape=[lstm_output_size, 2])
bias = tf.get_variable(shape=[2], name="bias")
logits = tf.matmul(last, weight) + bias
loss = tf.losses.softmax_cross_entropy(y, logits=logits)
optimizer = tf.train.AdamOptimizer()
optimize_step = optimizer.minimize(loss=loss)
return loss, optimize_step
def tf_model():
x_holder = tf.placeholder(tf.int32, shape=[None, maxlen])
y_holder = tf.placeholder(tf.int32, shape=[None, 2])
loss, opt_step = get_model(x_holder, y_holder)
with tf.Session() as sess:
sess.run(tf.global_variables_initializer())
step = 0
for epoch in range(10):
cost_epochs = []
train_data = TrainData()
cost_batch = 0
for batch in range(train_data.get_num_batches()):
x_train, y_train = train_data.next_batch()
_, cost_batch = sess.run([opt_step, loss],
feed_dict={x_holder: x_train,
y_holder: y_train})
cost_epochs.append(cost_batch)
step += 1
# if step % 100 == 0:
print("Epoch: " + str(epoch))
print("\tcost: " + str(np.mean(cost_epochs)))
def keras_model():
# print('Loading data...')
(x_train, y_train), (x_test, y_test) = imdb.load_data(num_words=max_features)
y_test = [[int(x == 1), int(x != 1)] for x in y_test]
x_test = sequence.pad_sequences(x_test, maxlen=maxlen, padding='pre')
model = Sequential()
model.add(Embedding(max_features, embedding_size, input_length=maxlen))
model.add(LSTM(lstm_output_size))
model.add(Dense(2))
model.add(Activation('softmax'))
model.compile(loss='categorical_crossentropy',
optimizer='adam',
metrics=['accuracy'])
print('Train...')
data = TrainData()
model.fit_generator(data.batch_generator(), steps_per_epoch=data.get_num_batches(),
epochs=epochs,
validation_data=(x_test, y_test))
if __name__ == '__main__':
# keras_model()
tf_model()
EDIT
When I limit the sequence length to 100 both models converge, so I assume there is something different in the the lstm layer.

Check the initial values of your operations. In my case the adadelta optimizer in keras had initial learning rate of 1.0 and in tf.keras it had 0.001 so in the mnist dataset it converged much slowly.

Related

ValueError: Input 0 of layer “Discriminator” is incompatible with the layer: expected shape=(None, 3), found shape=(100, 2)

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn import preprocessing
from sklearn.preprocessing import StandardScaler
from sklearn.metrics import precision_score, recall_score, f1_score,\
accuracy_score, balanced_accuracy_score,classification_report,\
plot_confusion_matrix, confusion_matrix
from sklearn.model_selection import KFold, GridSearchCV
from sklearn.model_selection import train_test_split
import lightgbm as lgb
from tensorflow.keras.layers import Input, Dense, Reshape, Flatten, Dropout, multiply, Concatenate
from tensorflow.keras.layers import BatchNormalization, Activation, Embedding, ZeroPadding2D, LeakyReLU
from tensorflow.keras.models import Sequential, Model
from tensorflow.keras.optimizers import Adam
from tensorflow.keras.initializers import RandomNormal
import tensorflow.keras.backend as K
from sklearn.utils import shuffle
import pickle
from tqdm import tqdm
import numpy as np
from scipy import stats
import pandas as pd
np.random.seed(1635848)
def get_data_XYZ_one_dimensional(n, a=-2, c=1/2, random_state=None, verbose=True):
"""
Generates pseudo-random data distributed according to the distribution defined in section 2.1 of the document
"Math/Confounders and data generation.pdf".
:param n: Number of data points to generate.
:param a: Mean of X.
:param c: Shape parameter for Weibull distribution.
:param random_state: Used to set the seed of numpy.random before generation of random numbers.
:param verbose: If True will display a progress bar. If False it will not display a progress bar.
:return: Pandas DataFrame with three columns (corresponding to X, Y and Z) and n rows (corresponding to the n
generated pseudo-random samples).
"""
np.random.seed(random_state)
output = []
iterator = tqdm(range(n)) if verbose else range(n)
for _ in iterator:
X = stats.norm.rvs(loc=-2, scale=1)
Y = stats.bernoulli.rvs(p=1/(1+np.exp(-X)))
if Y == 0:
Z = stats.expon.rvs(scale=np.exp(-X)) # note: np.exp(-X) could be cached for more computational efficiency but would render the code less useful
elif Y == 1:
Z = stats.weibull_min.rvs(c=c, scale=np.exp(-X))
else:
assert False
output.append((X, Y, Z))
return pd.DataFrame(output, columns=["Personal information", "Treatment", "Time to event"])
data = get_data_XYZ_one_dimensional(n=100, random_state=0)
print(data)
# The Architecture of CGAN
class cGAN():
"""
Class containing 3 methods (and __init__): generator, discriminator and train.
Generator is trained using random noise and label as inputs. Discriminator is trained
using real/fake samples and labels as inputs.
"""
def __init__(self,latent_dim=100, out_shape=3):
self.latent_dim = latent_dim
self.out_shape = out_shape
self.num_classes = 2
# using Adam as our optimizer
optimizer = Adam(0.0002, 0.5)
# building the discriminator
self.discriminator = self.discriminator()
self.discriminator.compile(loss=['binary_crossentropy'],
optimizer=optimizer,
metrics=['accuracy'])
# building the generator
self.generator = self.generator()
noise = Input(shape=(self.latent_dim,))
label = Input(shape=(1,))
gen_samples = self.generator([noise, label])
# we don't train discriminator when training generator
self.discriminator.trainable = False
valid = self.discriminator([gen_samples, label])
# combining both models
self.combined = Model([noise, label], valid)
self.combined.compile(loss=['binary_crossentropy'],
optimizer=optimizer,
metrics=['accuracy'])
def generator(self):
init = RandomNormal(mean=0.0, stddev=0.02)
model = Sequential()
model.add(Dense(128, input_dim=self.latent_dim))
model.add(Dropout(0.2))
model.add(LeakyReLU(alpha=0.2))
model.add(BatchNormalization(momentum=0.8))
model.add(Dense(256))
model.add(Dropout(0.2))
model.add(LeakyReLU(alpha=0.2))
model.add(BatchNormalization(momentum=0.8))
model.add(Dense(512))
model.add(Dropout(0.2))
model.add(LeakyReLU(alpha=0.2))
model.add(BatchNormalization(momentum=0.8))
model.add(Dense(self.out_shape, activation='tanh'))
noise = Input(shape=(self.latent_dim,))
label = Input(shape=(1,), dtype='int32')
label_embedding = Flatten()(Embedding(self.num_classes, self.latent_dim)(label))
model_input = multiply([noise, label_embedding])
gen_sample = model(model_input)
model.summary()
return Model([noise, label], gen_sample, name="Generator")
def discriminator(self):
init = RandomNormal(mean=0.0, stddev=0.02)
model = Sequential()
model.add(Dense(512, input_dim=self.out_shape, kernel_initializer=init))
model.add(LeakyReLU(alpha=0.2))
model.add(Dense(256, kernel_initializer=init))
model.add(LeakyReLU(alpha=0.2))
model.add(Dropout(0.4))
model.add(Dense(128, kernel_initializer=init))
model.add(LeakyReLU(alpha=0.2))
model.add(Dropout(0.4))
model.add(Dense(1, activation='sigmoid'))
gen_sample = Input(shape=(self.out_shape,))
label = Input(shape=(1,), dtype='int32')
label_embedding = Flatten()(Embedding(self.num_classes, self.out_shape)(label))
model_input = multiply([gen_sample, label_embedding])
validity = model(model_input)
model.summary()
return Model(inputs=[gen_sample, label], outputs=validity, name="Discriminator")
def train(self, X_train, y_train, pos_index, neg_index, epochs, sampling=False, batch_size=32, sample_interval=100, plot=True):
# though not recommended, defining losses as global helps as in analysing our cgan out of the class
global G_losses
global D_losses
G_losses = []
D_losses = []
# Adversarial ground truths
valid = np.ones((batch_size, 1))
fake = np.zeros((batch_size, 1))
for epoch in range(epochs):
# if sampling==True --> train discriminator with 8 sample from positive class and rest with negative class
if sampling:
idx1 = np.random.choice(pos_index, 3)
idx0 = np.random.choice(neg_index, batch_size-3)
idx = np.concatenate((idx1, idx0))
# if sampling!=True --> train discriminator using random instances in batches of 32
else:
idx = np.random.choice(len(y_train), batch_size)
samples, labels = X_train[idx], y_train[idx]
samples, labels = shuffle(samples, labels)
# Sample noise as generator input
noise = np.random.normal(0, 1, (batch_size, self.latent_dim))
gen_samples = self.generator.predict([noise, labels])
# label smoothing
if epoch < epochs//1.5:
valid_smooth = (valid+0.1)-(np.random.random(valid.shape)*0.1)
fake_smooth = (fake-0.1)+(np.random.random(fake.shape)*0.1)
else:
valid_smooth = valid
fake_smooth = fake
# Train the discriminator
self.discriminator.trainable = True
d_loss_real = self.discriminator.train_on_batch([samples, labels], valid_smooth)
d_loss_fake = self.discriminator.train_on_batch([gen_samples, labels], fake_smooth)
d_loss = 0.5 * np.add(d_loss_real, d_loss_fake)
# Train Generator
self.discriminator.trainable = False
sampled_labels = np.random.randint(0, 2, batch_size).reshape(-1, 1)
# Train the generator
g_loss = self.combined.train_on_batch([noise, sampled_labels], valid)
if (epoch+1)%sample_interval==0:
print('[%d/%d]\tLoss_D: %.4f\tLoss_G: %.4f'
% (epoch, epochs, d_loss[0], g_loss[0]))
G_losses.append(g_loss[0])
D_losses.append(d_loss[0])
if plot:
if epoch+1==epochs:
plt.figure(figsize=(10,5))
plt.title("Generator and Discriminator Loss")
plt.plot(G_losses,label="G")
plt.plot(D_losses,label="D")
plt.xlabel("iterations")
plt.ylabel("Loss")
plt.legend()
plt.show()
data.Treatment.value_counts()
scaler = StandardScaler()
X = scaler.fit_transform(data.drop('Treatment', 1))
y = data['Treatment'].values
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2)
lgb_1 = lgb.LGBMClassifier()
lgb_1.fit(X_train, y_train)
y_pred = lgb_1.predict(X_test)
# evaluation
print(classification_report(y_test, y_pred))
plot_confusion_matrix(lgb_1, X_test, y_test)
plt.show()
le = preprocessing.LabelEncoder()
for i in ['Personal information', 'Treatment', 'Time to event']:
data[i] = le.fit_transform(data[i].astype(str))
y_train = y_train.reshape(-1,1)
pos_index = np.where(y_train==1)[0]
neg_index = np.where(y_train==0)[0]
cgan.train(X_train, y_train, pos_index, neg_index, epochs=500)
Here, the training gives an error ValueError: Input 0 of layer "Discriminator" is incompatible with the layer: expected shape=(None, 3), found shape=(100, 2). Well I understand I have to fix the shape by changing the input but where and how to do it.
Also there are 3 columns in data so how to go about making this work?
I think the fix out_shape=2 and not 3 because the generated output has 2 and you stated the number of classes to be 2 as well. Unless there is something else I am missing.
def __init__(self, latent_dim=100, out_shape=2):

Implementing TensorFlow Triplet Loss

I would like to implement the built in TensorFlow addons version of triplet loss with a tutorial here for a siamese network, however I can't seem to get it quite right. No matter how I wrangle the code another error pops up, currently
TypeError: Could not build a TypeSpec for <KerasTensor: shape=(3, None, 256) dtype=float32 (created by layer 'tf.math.l2_normalize_4')> with type KerasTensor.
Note, this is just a token implementation kept simple in order to understand how to implement Triplet Loss. I don't expect the model to actually learn anything.
Code:
!pip install -U tensorflow-addons
import io
import numpy as np
import tensorflow as tf
import tensorflow_addons as tfa
from tensorflow.keras.datasets import fashion_mnist
# Dummy data to pass to the model
(x_train, y_train), (x_test, y_test) = fashion_mnist.load_data()
train_data = [x_train[:20000],x_train[20000:40000],x_train[40000:]]
train_labels = [y_train[:20000],y_train[20000:40000],y_train[40000:]]
train_data = tf.convert_to_tensor(train_data)
train_labels = tf.convert_to_tensor(train_labels)
#train_data = np.asarray(train_data)
#train_labels = np.asarray(train_labels)
def create_model(input_shape):
inp = tf.keras.layers.Input(shape=input_shape)
x = tf.keras.layers.Conv2D(filters=64, kernel_size=2, padding='same', activation='relu', input_shape=(28,28,1))(inp)
x = tf.keras.layers.MaxPooling2D(pool_size=2)(x)
x = tf.keras.layers.Dropout(0.3)(x)
x = tf.keras.layers.Conv2D(filters=32, kernel_size=2, padding='same', activation='relu')(x)
x = tf.keras.layers.MaxPooling2D(pool_size=2)(x)
x = tf.keras.layers.Dropout(0.3)(x)
x = tf.keras.layers.Flatten()(x)
x = tf.keras.layers.Dense(256, activation=None)(x) # No activation on final dense layer
#x = tf.keras.layers.Lambda(lambda y: tf.math.l2_normalize(x, axis=1))(x)
model = tf.keras.Model(inp,x)
return model
def get_siamese_model(input_shape):
"""
Model architecture
"""
# Define the tensors for the triplet of input images
anchor_input = tf.keras.layers.Input(input_shape, name="anchor_input")
positive_input = tf.keras.layers.Input(input_shape, name="positive_input")
negative_input = tf.keras.layers.Input(input_shape, name="negative_input")
# Convolutional Neural Network (same from earlier)
embedding_model = create_model(input_shape)
# Generate the embedding outputs
encoded_anchor = embedding_model(anchor_input)
encoded_positive = embedding_model(positive_input)
encoded_negative = embedding_model(negative_input)
inputs = [anchor_input, positive_input, negative_input]
outputs = [encoded_anchor, encoded_positive, encoded_negative]
#x = tf.keras.layers.Lambda(lambda x: tf.math.l2_normalize(outputs, axis=1))(outputs)
# Connect the inputs with the outputs
siamese_triplet = tf.keras.Model(inputs=inputs,outputs=outputs)
# return the model
return embedding_model, siamese_triplet
emb_mod, model = get_siamese_model([28,28,1])
# Compile the model
model.compile(
optimizer=tf.keras.optimizers.Adam(0.001),
loss=tfa.losses.TripletSemiHardLoss())
# Train the network
#train_dataset = tf.convert_to_tensor(train_dataset)
history = model.fit(
train_data,
epochs=5)
I am not sure what exactly you are trying to do, but you also have to incorporate your labels into your training dataset when using the tfa.losses.TripletSemiHardLoss(). Here is a working example:
import io
import numpy as np
import tensorflow as tf
import tensorflow_addons as tfa
from tensorflow.keras.datasets import fashion_mnist
# Dummy data to pass to the model
(x_train, y_train), (x_test, y_test) = fashion_mnist.load_data()
train_data = tf.data.Dataset.zip((tf.data.Dataset.from_tensor_slices(x_train[:20000]),
tf.data.Dataset.from_tensor_slices(x_train[20000:40000]),
tf.data.Dataset.from_tensor_slices(x_train[40000:])))
train_labels = tf.data.Dataset.zip((tf.data.Dataset.from_tensor_slices(y_train[:20000]),
tf.data.Dataset.from_tensor_slices(y_train[20000:40000]),
tf.data.Dataset.from_tensor_slices(y_train[40000:])))
dataset = tf.data.Dataset.zip((train_data, train_labels)).batch(32)
def create_model(input_shape):
inp = tf.keras.layers.Input(shape=input_shape)
x = tf.keras.layers.Conv2D(filters=64, kernel_size=2, padding='same', activation='relu', input_shape=(28,28,1))(inp)
x = tf.keras.layers.MaxPooling2D(pool_size=2)(x)
x = tf.keras.layers.Dropout(0.3)(x)
x = tf.keras.layers.Conv2D(filters=32, kernel_size=2, padding='same', activation='relu')(x)
x = tf.keras.layers.MaxPooling2D(pool_size=2)(x)
x = tf.keras.layers.Dropout(0.3)(x)
x = tf.keras.layers.Flatten()(x)
x = tf.keras.layers.Dense(256, activation=None)(x) # No activation on final dense layer
#x = tf.keras.layers.Lambda(lambda y: tf.math.l2_normalize(x, axis=1))(x)
model = tf.keras.Model(inp,x)
return model
def get_siamese_model(input_shape):
"""
Model architecture
"""
# Define the tensors for the triplet of input images
anchor_input = tf.keras.layers.Input(input_shape, name="anchor_input")
positive_input = tf.keras.layers.Input(input_shape, name="positive_input")
negative_input = tf.keras.layers.Input(input_shape, name="negative_input")
# Convolutional Neural Network (same from earlier)
embedding_model = create_model(input_shape)
# Generate the embedding outputs
encoded_anchor = embedding_model(anchor_input)
encoded_positive = embedding_model(positive_input)
encoded_negative = embedding_model(negative_input)
inputs = [anchor_input, positive_input, negative_input]
outputs = [encoded_anchor, encoded_positive, encoded_negative]
#x = tf.keras.layers.Lambda(lambda x: tf.math.l2_normalize(outputs, axis=1))(outputs)
# Connect the inputs with the outputs
siamese_triplet = tf.keras.Model(inputs=inputs,outputs=outputs)
# return the model
return embedding_model, siamese_triplet
emb_mod, model = get_siamese_model([28,28,1])
# Compile the model
model.compile(
optimizer=tf.keras.optimizers.Adam(0.001),
loss=tfa.losses.TripletSemiHardLoss())
# Train the network
history = model.fit(
dataset,
epochs=1)
625/625 [==============================] - 76s 120ms/step - loss: 0.1354 - model_79_loss: 0.0572 - model_79_1_loss: 0.0453 - model_79_2_loss: 0.0330

Why pure tensorflow autoencoder cannot converge, when Keras one fits good

I'm newbie at machine learning(and at stackoverflow too). I want to ask for help.
I have two implementations of same two-layer autoencoder for mnist.
First one fits good:
import tensorflow as tf, numpy as np
def in_pics(pics):
return np.array(pics, np.float32)/255.
def out_pics(pics):
npformed = np.array(pics, np.float32)
samples = np.shape(npformed)[0]
return np.reshape(npformed, (samples, 784))/255.
(train_data, test_data) = tf.keras.datasets.mnist.load_data()
train_dataset = tf.data.Dataset.from_tensor_slices((in_pics(train_data[0]), out_pics(train_data[0]))).batch(100)
test_dataset = tf.data.Dataset.from_tensor_slices((in_pics(test_data[0]), out_pics(test_data[0]))).batch(100)
model = tf.keras.Sequential(
[
tf.keras.layers.InputLayer(input_shape=(28,28)),
tf.keras.layers.Reshape(target_shape=(784,)),
tf.keras.layers.Dense(128, activation="sigmoid", kernel_initializer=tf.keras.initializers.truncated_normal(stddev=0.1),
bias_initializer =tf.keras.initializers.truncated_normal(stddev=0.1)),
tf.keras.layers.Dense(784, activation="sigmoid", kernel_initializer=tf.keras.initializers.truncated_normal(stddev=0.1),
bias_initializer =tf.keras.initializers.truncated_normal(stddev=0.1)),
]
)
model.compile(loss=tf.keras.losses.BinaryCrossentropy(from_logits=True), optimizer="adam")
model.fit(x = train_dataset, epochs=20, verbose=1, validation_data=test_dataset)
Keras result
And I have the same model, same learning procedure, but written in terms of pure tensorflow(almost):
import tensorflow as tf, numpy as np
def prep_pics(pics):
npformed = np.array(pics, np.float32)
samples = np.shape(npformed)[0]
return np.reshape(npformed, (samples, 784))/255.
batch_size, num_batches = 100, 12000
(train_data, test_data) = tf.keras.datasets.mnist.load_data()
(train_pics_prepared, test_pics_prepared) = (prep_pics(train_data[0]), prep_pics(test_data[0]))
train_dataset = tf.data.Dataset.from_tensor_slices((train_pics_prepared, train_pics_prepared))
test_dataset = tf.data.Dataset.from_tensor_slices((test_pics_prepared, test_pics_prepared)).batch(batch_size)
encoder_W = tf.Variable(tf.keras.initializers.truncated_normal(stddev=0.1)(shape = [784,128], dtype = tf.float32))
encoder_b = tf.Variable(tf.keras.initializers.truncated_normal(stddev=0.1)(shape = [128],dtype = tf.float32))
decoder_W = tf.Variable(tf.keras.initializers.truncated_normal(stddev=0.1)(shape = [128,784], dtype = tf.float32))
decoder_b = tf.Variable(tf.keras.initializers.truncated_normal(stddev=0.1)(shape = [784],dtype = tf.float32))
optimizer = tf.keras.optimizers.Adam()
bin_cross = tf.keras.losses.BinaryCrossentropy(from_logits=True)
#tf.function
def trainstep(X_pack, Y_pack):
with tf.GradientTape() as tape:
tape.watch([encoder_W, encoder_b, decoder_W, decoder_b])
encoded = tf.nn.sigmoid(tf.matmul(X_pack, encoder_W) + encoder_b)
decoded = tf.nn.sigmoid(tf.matmul(encoded, decoder_W) + decoder_b)
loss = bin_cross(decoded, Y_pack)
gradients = tape.gradient(loss, [encoder_W, encoder_b, decoder_W, decoder_b])
optimizer.apply_gradients(zip(gradients, [encoder_W, encoder_b, decoder_W, decoder_b]))
num_samples = len(train_data[0])
epochs = num_batches//(num_samples//batch_size)
for i in range(epochs):
print(f"Epoch num {i+1}:")
dataset = train_dataset.shuffle(num_samples).batch(batch_size)
for x,y in dataset:
trainstep(x,y)
Loss is never becomes lower than 0.64(First one had 0.07 in the end of education).
Tensorflow result.
What I tried:
1.) Change optimizer to Adagrad and even to SGD.
2.) Use other loss - sigmoid_cross_entropy_with_logits.
3.) Learn more. Especially for SGD.
Cannot find mistake or typo almost for week. Please, help!

A question about simple Keras and Tensorflow code performance

I wrote simple Sin function predictors using Keras and Tensorflow with LSTM, but found the performance of Keras code is much slower which runs about 5 min while Tensorflow code runs the model just in 20 seconds. Moreover, the Keras prediction performance is less precide as Keras one. Could anyone help me find the code difference between the 2 model?
I hacked the code online and intend to train the model with the same hyper parameters. But the performance is not as expected. Tried searching many materials online, but found no reasons.
Keras Code:
import numpy as np
import os
import sys
import time
from tqdm._tqdm_notebook import tqdm_notebook
import pickle
from keras.models import Sequential, load_model
from keras.layers import Dense, Dropout
from keras.layers import LSTM
from keras.callbacks import ModelCheckpoint, EarlyStopping, ReduceLROnPlateau, CSVLogger
from keras import optimizers
from sklearn.preprocessing import MinMaxScaler
from sklearn.model_selection import train_test_split
from sklearn.metrics import mean_squared_error
stime = time.time()
BATCH_SIZE = 20
TIME_STEPS = 10
LN = 410
DIFF = 2
OUTPUT_PATH = '/Users/xiachang/Documents/RNN/test_outputs'
SCALER_COL_IDX = 0
params = {
"batch_size": BATCH_SIZE, # 20<16<10, 25 was a bust
"epochs": 500,
"lr": 0.00010000,
"time_steps": TIME_STEPS
}
TRAINING_EXAMPLES = 10000
TESTING_EXAMPLES = 1000
SAMPLE_GAP = 0.01
HIDDEN_UNITS = 20
# data = np.array([[i * (DIFF)] for i in range(LN)])
#
# min_max_scaler = MinMaxScaler()
# data = min_max_scaler.fit_transform(data)
def generate_data(seq):
X = []
y = []
for i in range(len(seq) - TIME_STEPS):
X.append([[e] for e in seq[i: i + TIME_STEPS]])
y.append([seq[i + TIME_STEPS]])
return np.array(X, dtype=np.float32), np.array(y, dtype=np.float32)
test_start = (TRAINING_EXAMPLES + TIME_STEPS) * SAMPLE_GAP + 1
test_end = test_start + (TESTING_EXAMPLES + TIME_STEPS) * SAMPLE_GAP + 1
train_X, train_y = generate_data(np.sin(np.linspace(
0, test_start, TRAINING_EXAMPLES + TIME_STEPS, dtype=np.float32)))
test_X, test_y = generate_data(np.sin(np.linspace(
test_start, test_end, TESTING_EXAMPLES + TIME_STEPS, dtype=np.float32)))
x_val, x_test = np.split(test_X, 2)
y_val, y_test = np.split(test_y, 2)
def print_time(text, stime):
seconds = (time.time()-stime)
print(text, seconds//60,"minutes : ",np.round(seconds%60),"seconds")
def create_model():
lstm_model = Sequential()
lstm_model.add(LSTM(HIDDEN_UNITS, return_sequences=True))
lstm_model.add(LSTM(HIDDEN_UNITS, return_sequences=True))
lstm_model.add(LSTM(HIDDEN_UNITS))
lstm_model.add(Dense(1, activation=None))
lstm_model.compile(loss='mean_squared_error', optimizer=optimizers.Adagrad(lr=0.1))
return lstm_model
model = create_model()
es = EarlyStopping(monitor='val_loss', mode='min', verbose=1, patience=30, min_delta=0.0001)
mcp = ModelCheckpoint(os.path.join(OUTPUT_PATH,
"best_model.h5"), monitor='val_loss', verbose=1,
save_best_only=True, save_weights_only=False, mode='min', period=1)
# Not used here. But leaving it here as a reminder for future
r_lr_plat = ReduceLROnPlateau(monitor='val_loss', factor=0.1, patience=30,
verbose=0, mode='auto', min_delta=0.0001, cooldown=0, min_lr=0)
csv_logger = CSVLogger(os.path.join(OUTPUT_PATH, 'training_log_' + time.ctime().replace(" ","_") + '.log'), append=True)
history = model.fit(train_X, train_y, epochs=params["epochs"], verbose=2, batch_size=BATCH_SIZE,
shuffle=False, validation_data=(x_val, y_val), callbacks=[es, mcp, csv_logger])
print("saving model...")
pickle.dump(model, open("test_outputs/lstm_model", "wb"))
# Visualize the training data
from matplotlib import pyplot as plt
plt.figure()
plt.plot(history.history['loss'])
plt.plot(history.history['val_loss'])
plt.title('Model loss')
plt.ylabel('Loss')
plt.xlabel('Epoch')
plt.legend(['Train', 'Test'], loc='upper left')
#plt.show()
plt.savefig(os.path.join(OUTPUT_PATH, 'train_vis_BS_'+str(BATCH_SIZE)+"_"+time.ctime()+'.png'))
# load the saved best model from above
saved_model = load_model(os.path.join(OUTPUT_PATH, 'best_model.h5')) # , "lstm_best_7-3-19_12AM",
print(saved_model)
y_pred = saved_model.predict(x_test, batch_size=BATCH_SIZE)
y_pred = y_pred.flatten()
y_test_t = y_test
error = mean_squared_error(y_test_t, y_pred)
print("Error is", error, y_pred.shape, y_test_t.shape)
print(y_pred[0:15])
print(y_test_t[0:15])
y_pred_org = y_pred
y_test_t_org = y_test_t
print(y_pred_org[0:15])
print(y_test_t_org[0:15])
# Visualize the prediction
from matplotlib import pyplot as plt
plt.figure()
plt.plot(y_pred_org)
plt.plot(y_test_t_org)
plt.title('Prediction vs Real Value')
plt.ylabel('Y')
plt.xlabel('X')
plt.legend(['Prediction', 'Real'], loc='upper left')
# plt.show()
plt.savefig(os.path.join(OUTPUT_PATH, 'pred_vs_real_BS'+str(BATCH_SIZE)+"_"+time.ctime()+'.png'))
print_time("program completed ", stime)
Tensorflow code:
import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
NUM_EPOCH = 1000
HIDDEN_SIZE = 30
NUM_LAYERS = 2
TIMESTEPS = 10
TRAINING_STEPS = 10000
BATCH_SIZE = 20
TRAINING_EXAMPLES = 10000
TESTING_EXAMPLES = 1000
SAMPLE_GAP = 0.01
def generate_data(seq):
X = []
y = []
for i in range(len(seq) - TIMESTEPS):
X.append([seq[i: i + TIMESTEPS]])
y.append([seq[i + TIMESTEPS]])
return np.array(X, dtype=np.float32), np.array(y, dtype=np.float32)
def lstm_model(X, y, is_training):
cell = tf.nn.rnn_cell.MultiRNNCell([tf.nn.rnn_cell.LSTMCell(HIDDEN_SIZE) for _ in range(NUM_LAYERS)])
outputs, _ = tf.nn.dynamic_rnn(cell, X, dtype=tf.float32)
output = outputs[:, -1, :]
predictions = tf.contrib.layers.fully_connected(output, 1, activation_fn=None)
if not is_training:
return predictions, None, None
loss = tf.losses.mean_squared_error(labels=y, predictions=predictions)
train_op = tf.contrib.layers.optimize_loss(
loss, tf.train.get_global_step(), optimizer='Adagrad', learning_rate=0.1)
return predictions, loss, train_op
def train(sess, train_X, train_Y):
ds = tf.data.Dataset.from_tensor_slices((train_X, train_Y))
ds = ds.repeat().shuffle(1000).batch(BATCH_SIZE)
X, y = ds.make_one_shot_iterator().get_next()
losses = np.array([])
with tf.variable_scope('model'):
predictions, loss, train_op = lstm_model(X, y, True)
sess.run(tf.global_variables_initializer())
for i in range(TRAINING_STEPS):
_, l = sess.run([train_op, loss])
losses = np.append(losses, l)
if i % NUM_EPOCH == 0:
print('train step: ' + str(i) + ', loss: ' + str(l))
plt.figure()
plt.plot(losses, label='loss')
plt.legend()
# plt.show()
plt.savefig('./test_outputs/loss.png')
def run_eval(sess, test_X, test_y):
ds = tf.data.Dataset.from_tensor_slices((test_X, test_y))
ds = ds.batch(1)
X, y = ds.make_one_shot_iterator().get_next()
with tf.variable_scope('model', reuse=True):
prediction, _, _ = lstm_model(X, [0, 0], False)
predictions = []
labels = []
for i in range(int(TESTING_EXAMPLES / 2)):
p, l = sess.run([prediction, y])
predictions.append(p)
labels.append(l)
predictions = np.array(predictions).squeeze()
labels = np.array(labels).squeeze()
rmse = np.sqrt(((predictions - labels) ** 2).mean(axis=0))
print('Mean Square Error is: %f' % rmse)
plt.figure()
print(predictions[:15])
print(labels[:15])
plt.plot(predictions, label='predictions')
plt.plot(labels, label='real_val')
plt.legend()
# plt.show()
plt.savefig('./test_outputs/test.png')
test_start = (TRAINING_EXAMPLES + TIMESTEPS) * SAMPLE_GAP + 1
test_end = test_start + (TESTING_EXAMPLES + TIMESTEPS) * SAMPLE_GAP + 1
train_X, train_y = generate_data(np.sin(np.linspace(
0, test_start, TRAINING_EXAMPLES + TIMESTEPS, dtype=np.float32)))
test_X, test_y = generate_data(np.sin(np.linspace(
test_start, test_end, TESTING_EXAMPLES + TIMESTEPS, dtype=np.float32)))
x_val, test_X = np.split(test_X, 2)
y_val, test_y = np.split(test_y, 2)
with tf.Session() as sess:
train(sess, train_X, train_y)
run_eval(sess, test_X, test_y)
You maybe should try to use CuDNNLSTM instead of LSTM. They are CUDA accelerated.
Fast LSTM implementation with CuDNN.
See here: https://github.com/keras-team/keras/blob/master/keras/layers/cudnn_recurrent.py#L328
Your model structure is not same, first has 3 layers of LSTM, other has 2.
Tensorflow data API is highly optimized, It preparing the data-set, without wasting any resources.
Note that: You can even more accelerate the training in tensorflow using parallelization in dynamic_rnn cell. check out this.

Compare the example of Pytorch and Keras on Cifar10 data

I use CIFAR10 dataset to learn how to code using Keras and PyTorch.
The environment is Python 3.6.7, Torch 1.0.0, Keras 2.2.4, Tensorflow 1.14.0.
I use the same batch size, number of epochs, learning rate and optimizer.
I use DenseNet121 as the model.
After training, Keras get 69% accuracy in test data.
PyTorch just get 54% in test data.
I know the results are different, but why is the result so bad in PyTorch?
Here is the Keras code:
import os, keras
from keras.datasets import cifar10
from keras.applications.densenet import DenseNet121
batch_size = 32
num_classes = 10
epochs = 20
# The data, split between train and test sets:
(x_train, y_train), (x_test, y_test) = cifar10.load_data()
print('x_train shape:', x_train.shape)
print(x_train.shape[0], 'train samples')
print(x_test.shape[0], 'test samples')
# Convert class vectors to binary class matrices.
y_train = keras.utils.to_categorical(y_train, num_classes)
y_test = keras.utils.to_categorical(y_test, num_classes)
# model
model = DenseNet121(include_top=True, weights=None, input_shape=(32,32,3), classes=10)
# initiate RMSprop optimizer
opt = keras.optimizers.SGD(lr=0.001, momentum=0.9)
model.compile(loss='categorical_crossentropy', optimizer=opt, metrics=['accuracy'])
x_train = x_train.astype('float32')
x_test = x_test.astype('float32')
x_train /= 255
x_test /= 255
model.fit(x_train, y_train,
batch_size=batch_size,
epochs=epochs,
validation_data=(x_test, y_test),
shuffle=True)
# Score trained model.
scores = model.evaluate(x_test, y_test, verbose=1)
print('Test loss:', scores[0])
print('Test accuracy:', scores[1])
Here is the Pytorch code:
import torch
import torchvision
import torchvision.transforms as transforms
from torch import flatten
import torch.optim as optim
from torchvision import transforms, models
from torch.nn import Linear, Softmax, Module, Sequential, CrossEntropyLoss
import numpy as np
from tqdm import tqdm
classes = ('plane', 'car', 'bird', 'cat', 'deer', 'dog', 'frog', 'horse', 'ship', 'truck')
transform = transforms.Compose([transforms.ToTensor()])
trainset = torchvision.datasets.CIFAR10(root='./DataSet', train=True, download=True, transform=transform)
trainloader = torch.utils.data.DataLoader(trainset, batch_size=32, shuffle=True, num_workers=0)
testset = torchvision.datasets.CIFAR10(root='./DataSet', train=False, download=True, transform=transform)
testloader = torch.utils.data.DataLoader(testset, batch_size=4, shuffle=False, num_workers=0)
import torch.nn as nn
import torch.nn.functional as F
class Net(Module):
def __init__(self):
super(Net, self).__init__()
self.funFeatExtra = Sequential(*[i for i in list(models.densenet121().children())[:-1]])
self.funFlatten = flatten
self.funOutputLayer = Linear(1024, 10)
self.funSoftmax = Softmax(dim=1)
def forward(self, x):
x = self.funFeatExtra(x)
x = self.funFlatten(x, 1)
x = self.funOutputLayer(x)
x = self.funSoftmax(x)
return x
net = Net()
criterion = nn.CrossEntropyLoss()
optimizer = optim.SGD(net.parameters(), lr=0.001, momentum=0.9)
for epoch in range(20): # loop over the dataset multiple times
running_loss = 0.0
for i, data in tqdm(enumerate(trainloader, 0)):
# get the inputs; data is a list of [inputs, labels]
inputs, labels = data
# zero the parameter gradients
optimizer.zero_grad()
# forward + backward + optimize
outputs = net.cuda()(inputs.cuda())
loss = criterion(outputs, labels.cuda())
loss.backward()
optimizer.step()
# print statistics
running_loss += loss.item()
# if i % 2000 == 1999: # print every 2000 mini-batches
# print('[%d, %5d] loss: %.3f' % (epoch + 1, i + 1, running_loss / 2000))
# running_loss = 0.0
print('Finished Training')
########################################################################
# The results seem pretty good.
#
# Let us look at how the network performs on the whole dataset.
correct = 0
total = 0
with torch.no_grad():
for data in tqdm(testloader):
images, labels = data
outputs = net.cpu()(images.cpu())
_, predicted = torch.max(outputs.data, 1)
total += labels.size(0)
correct += (predicted == labels).sum().item()
print('Accuracy of the network on the 10000 test images: %d %%' % (100 * correct / total))
You are not supposed to softmax the model output before you pass it to CrossEntropyLoss. Per the documentation:
This criterion combines nn.LogSoftmax() and nn.NLLLoss() in one single class.
...
The input is expected to contain raw, unnormalized scores for each class.
You can softmax them separately (outside of forward()) when calculating accuracy.