The main objective of this article is to introduce you to the basics of Keras framework and use with other known libraries to make a quick experiment and take the first conclusions.
Introduction
Supervised Deep Learning is widely used for machine learning, i.e., computer vision systems. In this article, we will see some key notes for using supervised deep learning using the Keras framework.
Keras is a high level framework for machine learning that we can code in Python and it can be run in the most known machine learning frameworks like TensorFlow, CNTK, or Theano. It was developed in order to make the experimentation process easy and quick.
Background
This article doesn't give you an introduction to deep learning. You are supposed to know the basics of deep learning and a little of Python coding. The main objective of this article is to introduce you to the basics of Keras framework and use with other known libraries to make a quick experiment and take the first conclusions.
Using the Code
In this first article, we will train a simple neural net and, for the next articles, we will see some known deep learning architectures and make some comparisons.
All the experiments are done for educational purposes and the train process will be very quick and the results won't be perfect.
First Step: Load Libraries
First, we will load the libraries we need: numpy, TensorFlow (in this experiment, we will run Keras with this framework), Keras, Scikit Learn, Pandas... and more.
import numpy as np
from scipy import misc
from PIL import Image
import glob
import matplotlib.pyplot as plt
import scipy.misc
from matplotlib.pyplot import imshow
%matplotlib inline
from IPython.display import SVG
import cv2
import seaborn as sn
import pandas as pd
import pickle
from keras import layers
from keras.layers import Flatten, Input, Add, Dense, Activation,
ZeroPadding2D, BatchNormalization, Flatten,
Conv2D, AveragePooling2D,
MaxPooling2D, GlobalMaxPooling2D, Dropout
from keras.models import Sequential, Model, load_model
from keras.preprocessing import image
from keras.preprocessing.image import load_img
from keras.preprocessing.image import img_to_array
from keras.applications.imagenet_utils import decode_predictions
from keras.utils import layer_utils, np_utils
from keras.utils.data_utils import get_file
from keras.applications.imagenet_utils import preprocess_input
from keras.utils.vis_utils import model_to_dot
from keras.utils import plot_model
from keras.initializers import glorot_uniform
from keras import losses
import keras.backend as K
from keras.callbacks import ModelCheckpoint
from sklearn.metrics import confusion_matrix, classification_report
import tensorflow as tf
Set Up Datasets
For this exercise, we will use the CIFAR-100 dataset. This dataset has been used for a long time. It has 600 images per class with a total of 100 classes. It has 500 images for training and 100 images for validation per each class. Every one of the 100 classes are grouped in 20 superclasses. Each image has one "fine" label (the main class) and a "coarse" label (it superclass).
Keras framework has the module for direct download:
from keras.datasets import cifar100
(x_train_original, y_train_original),
(x_test_original, y_test_original) = cifar100.load_data(label_mode='fine')
Actually, we have downloaded the train and test datasets. x_train_original and x_test_original have the train and test images respectively, whereas y_train_original and y_test_original have the labels.
Let's see the y_train_original:
array([[19], [29], [ 0], ..., [ 3], [ 7], [73]])
As you can see, it is an array where each number corresponds to a label. Then, the first thing we have to do is convert these arrays to the one-hot-encoding version (see Wikipedia).
y_train = np_utils.to_categorical(y_train_original, 100)
y_test = np_utils.to_categorical(y_test_original, 100)
OK, now, let's see the train dataset (x_train_original):
array([[[255, 255, 255],
[255, 255, 255],
[255, 255, 255],
...,
[195, 205, 193],
[212, 224, 204],
[182, 194, 167]],
[[255, 255, 255],
[254, 254, 254],
[254, 254, 254],
...,
[170, 176, 150],
[161, 168, 130],
[146, 154, 113]],
[[255, 255, 255],
[254, 254, 254],
[255, 255, 255],
...,
[189, 199, 169],
[166, 178, 130],
[121, 133, 87]],
...,
[[148, 185, 79],
[142, 182, 57],
[140, 179, 60],
...,
[ 30, 17, 1],
[ 65, 62, 15],
[ 76, 77, 20]],
[[122, 157, 66],
[120, 155, 58],
[126, 160, 71],
...,
[ 22, 16, 3],
[ 97, 112, 56],
[141, 161, 87]],
...and more...
], dtype=uint8)
This dataset represents the 3 channels of 256 RGB pixels. Want to see it?
imgplot = plt.imshow(x_train_original[3])
plt.show()
Next, we have to normalize the images. That is, divide each element of the dataset by the total pixel number: 255. Once this is done, the array will have values between 0 and 1.
x_train = x_train_original/255
x_test = x_test_original/255
Setting Up the Training Environment
Before training, we have to set two parameters in Keras environment. First, we have to tell Keras where in the array are the channels. In an image array, channels can be in the last index or in the first. This is known channels first or channels last. In our exercise, we will set to channel last.
K.set_image_data_format('channels_last')
And the second thing is to tell Keras which phase it is. In our case, learning phase.
K.set_learning_phase(1)
Training a Simple Neural Net
We will train a simple neural net, so we have to code the method to return a simple neural net model.
def create_simple_nn():
model = Sequential()
model.add(Flatten(input_shape=(32, 32, 3), name="Input_layer"))
model.add(Dense(1000, activation='relu', name="Hidden_layer_1"))
model.add(Dense(500, activation='relu', name="Hidden_layer_2"))
model.add(Dense(100, activation='softmax', name="Output_layer"))
return model
Some keynotes from the code. The Flatten instruction converts the inputs (image matrix) in a one dimension array. Next, Dense instruction, adds a hidden layer to the model. The first hidden layer will have 1000 nodes, the second 500 and the third (output layer) 100. In the hidden layers, we will use the ReLu activation function and, for the output layer, the SoftMax function.
Once the model is defined, we compile it specifying optimization function, the loss function and the metrics we want to use. In all articles of this series, we will use exactly the same functions. We will use the Stochastic Gradient Descent optimization function, the Categorical Cross Entropy loss function and the accuracy and mse (Average of Cuadratic Errors) metrics. All of them are precoded in Keras.
snn_model = create_simple_nn()
snn_model.compile(loss='categorical_crossentropy', optimizer='sgd', metrics=['acc', 'mse'])
Once done, let's see the model summary.
snn_model.summary()
_________________________________________________________________
Layer (type) Output Shape Param
=================================================================
Input_layer (Flatten) (None, 3072) 0
_________________________________________________________________
Hidden_layer_1 (Dense) (None, 1000) 3073000
_________________________________________________________________
Hidden_layer_2 (Dense) (None, 500) 500500
_________________________________________________________________
Output_layer (Dense) (None, 100) 50100
=================================================================
Total params: 3,623,600
Trainable params: 3,623,600
Non-trainable params: 0
_________________________________________________________________
As we can see, despite being a simple neural network model, it has to train more than 3 million parameters. This will be the main reason for the existence of the Deep learning because if you want to train very complex networks, it would be necessary to train large amounts of parameters in this way.
Now, we just have to train. Do the following:
snn = snn_model.fit(x=x_train, y=y_train, batch_size=32,
epochs=10, verbose=1, validation_data=(x_test, y_test), shuffle=True)
We tell Keras we want to use for training the train normalized image dataset and the one-hot-encoding train labelled array. We will use batches of 32 blocks (for reducing the use of memory) and we will take 10 epochs. For validation, we will use x_test and y_test. The training results will be assigned to the snn variable. From that, we will extract the training history for making comparisons between models.
Train on 50000 samples, validate on 10000 samples
Epoch 1/10
50000/50000 [==============================] - 16s 318us/step - loss: 4.1750 -
acc: 0.0740 - mean_squared_error: 0.0097 - val_loss: 3.9633 - val_acc: 0.1051 -
val_mean_squared_error: 0.0096
Epoch 2/10
50000/50000 [==============================] - 15s 301us/step - loss: 3.7919 -
acc: 0.1298 - mean_squared_error: 0.0095 - val_loss: 3.7409 - val_acc: 0.1427 -
val_mean_squared_error: 0.0094
Epoch 3/10
50000/50000 [==============================] - 15s 294us/step - loss: 3.6357 -
acc: 0.1579 - mean_squared_error: 0.0093 - val_loss: 3.6429 - val_acc: 0.1525 -
val_mean_squared_error: 0.0093
Epoch 4/10
50000/50000 [==============================] - 15s 301us/step - loss: 3.5300 -
acc: 0.1758 - mean_squared_error: 0.0092 - val_loss: 3.6055 - val_acc: 0.1626 -
val_mean_squared_error: 0.0093
Epoch 5/10
50000/50000 [==============================] - 15s 300us/step - loss: 3.4461 -
acc: 0.1904 - mean_squared_error: 0.0091 - val_loss: 3.5030 - val_acc: 0.1812 -
val_mean_squared_error: 0.0092
Epoch 6/10
50000/50000 [==============================] - 15s 301us/step - loss: 3.3714 -
acc: 0.2039 - mean_squared_error: 0.0090 - val_loss: 3.4600 - val_acc: 0.1912 -
val_mean_squared_error: 0.0091
Epoch 7/10
50000/50000 [==============================] - 15s 301us/step - loss: 3.3050 -
acc: 0.2153 - mean_squared_error: 0.0089 - val_loss: 3.4329 - val_acc: 0.1938 -
val_mean_squared_error: 0.0091
Epoch 8/10
50000/50000 [==============================] - 15s 300us/step - loss: 3.2464 -
acc: 0.2275 - mean_squared_error: 0.0089 - val_loss: 3.3965 - val_acc: 0.2013 -
val_mean_squared_error: 0.0090
Epoch 9/10
50000/50000 [==============================] - 15s 301us/step - loss: 3.1902 -
acc: 0.2361 - mean_squared_error: 0.0088 - val_loss: 3.3371 - val_acc: 0.2133 -
val_mean_squared_error: 0.0089
Epoch 10/10
50000/50000 [==============================] - 15s 299us/step - loss: 3.1354 -
acc: 0.2484 - mean_squared_error: 0.0087 - val_loss: 3.3233 - val_acc: 0.2154 -
val_mean_squared_error: 0.0089
Despite the fact that we have been evaluating the training during the training, we should use a new test dataset. I expose how to do it in Keras.
evaluation = snn_model.evaluate(x=x_test, y=y_test, batch_size=32, verbose=1)
evaluation
10000/10000 [==============================] - 1s 127us/step
[3.323309226989746, 0.2154, 0.008915210169553756]
Let's see the results metrics graphically (we will use the matplotlib library).
plt.figure(0)
plt.plot(snn.history['acc'],'r')
plt.plot(snn.history['val_acc'],'g')
plt.xticks(np.arange(0, 11, 2.0))
plt.rcParams['figure.figsize'] = (8, 6)
plt.xlabel("Num of Epochs")
plt.ylabel("Accuracy")
plt.title("Training Accuracy vs Validation Accuracy")
plt.legend(['train','validation'])
plt.figure(1)
plt.plot(snn.history['loss'],'r')
plt.plot(snn.history['val_loss'],'g')
plt.xticks(np.arange(0, 11, 2.0))
plt.rcParams['figure.figsize'] = (8, 6)
plt.xlabel("Num of Epochs")
plt.ylabel("Loss")
plt.title("Training Loss vs Validation Loss")
plt.legend(['train','validation'])
plt.show()
Well, at first, the model doesn't generalize well, If you see, there is an accuracy difference of 4%.
Confusion Matrix using SciKit Learn
Once we have trained our model, we want to see another metrics before taking any conclusion of the usability of the model we have been created. For this, we will create the confusion matrix and, from that, we well see the precision, recall y F1-score metrics (see wikipedia).
To create the confusion matrix, we need to make the predictions over the test set and then, we can create the confusion matrix and show that metrics. Each higher value of the array of predictions will be the real prediction. Really, the usual way is to take a bias value to discriminate if a prediction value can be positive.
snn_pred = snn_model.predict(x_test, batch_size=32, verbose=1)
snn_predicted = np.argmax(snn_pred, axis=1)
The Scikit Learn library has the methods to make the confusion matrix.
snn_cm = confusion_matrix(np.argmax(y_test, axis=1), snn_predicted)
snn_df_cm = pd.DataFrame(snn_cm, range(100), range(100))
plt.figure(figsize = (20,14))
sn.set(font_scale=1.4)
sn.heatmap(snn_df_cm, annot=True, annot_kws={"size": 12})
plt.show()
At last, show metrics:
snn_report = classification_report(np.argmax(y_test, axis=1), snn_predicted)
print(snn_report)
precision recall f1-score support
0 0.47 0.32 0.38 100
1 0.29 0.34 0.31 100
2 0.24 0.12 0.16 100
3 0.14 0.10 0.12 100
4 0.06 0.02 0.03 100
5 0.14 0.17 0.16 100
6 0.19 0.13 0.15 100
7 0.14 0.26 0.19 100
8 0.22 0.18 0.20 100
9 0.23 0.39 0.29 100
10 0.29 0.02 0.04 100
11 0.27 0.09 0.14 100
12 0.34 0.23 0.28 100
13 0.26 0.16 0.20 100
14 0.19 0.13 0.15 100
15 0.16 0.14 0.15 100
16 0.28 0.19 0.23 100
17 0.32 0.25 0.28 100
18 0.18 0.26 0.21 100
19 0.42 0.08 0.13 100
20 0.35 0.45 0.40 100
21 0.27 0.43 0.33 100
22 0.27 0.18 0.22 100
23 0.30 0.46 0.37 100
24 0.49 0.31 0.38 100
25 0.14 0.10 0.11 100
26 0.17 0.11 0.13 100
27 0.06 0.29 0.09 100
28 0.32 0.37 0.34 100
29 0.12 0.21 0.15 100
30 0.50 0.13 0.21 100
31 0.24 0.04 0.07 100
32 0.29 0.19 0.23 100
33 0.18 0.28 0.22 100
34 0.17 0.03 0.05 100
35 0.17 0.07 0.10 100
36 0.21 0.19 0.20 100
37 0.24 0.06 0.10 100
38 0.17 0.06 0.09 100
39 0.12 0.07 0.09 100
40 0.26 0.23 0.24 100
41 0.62 0.45 0.52 100
42 0.10 0.05 0.07 100
43 0.09 0.44 0.16 100
44 0.10 0.12 0.11 100
45 0.20 0.03 0.05 100
46 0.22 0.19 0.20 100
47 0.37 0.19 0.25 100
48 0.14 0.48 0.22 100
49 0.38 0.11 0.17 100
50 0.14 0.05 0.07 100
51 0.16 0.15 0.16 100
52 0.43 0.60 0.50 100
53 0.27 0.61 0.37 100
54 0.48 0.26 0.34 100
55 0.07 0.01 0.02 100
56 0.45 0.13 0.20 100
57 0.10 0.42 0.16 100
58 0.35 0.17 0.23 100
59 0.13 0.36 0.19 100
60 0.40 0.65 0.50 100
61 0.42 0.34 0.38 100
62 0.25 0.49 0.33 100
63 0.31 0.21 0.25 100
64 0.14 0.03 0.05 100
65 0.13 0.02 0.03 100
66 0.00 0.00 0.00 100
67 0.20 0.35 0.25 100
68 0.24 0.66 0.35 100
69 0.26 0.30 0.28 100
70 0.37 0.22 0.28 100
71 0.37 0.46 0.41 100
72 0.11 0.01 0.02 100
73 0.22 0.22 0.22 100
74 0.09 0.06 0.07 100
75 0.27 0.28 0.27 100
76 0.29 0.38 0.33 100
77 0.20 0.01 0.02 100
78 0.19 0.03 0.05 100
79 0.25 0.02 0.04 100
80 0.14 0.02 0.04 100
81 0.13 0.02 0.03 100
82 0.59 0.50 0.54 100
83 0.14 0.15 0.14 100
84 0.18 0.06 0.09 100
85 0.20 0.52 0.28 100
86 0.31 0.23 0.26 100
87 0.21 0.27 0.23 100
88 0.07 0.02 0.03 100
89 0.16 0.44 0.24 100
90 0.20 0.03 0.05 100
91 0.30 0.34 0.32 100
92 0.20 0.10 0.13 100
93 0.18 0.17 0.17 100
94 0.46 0.25 0.32 100
95 0.23 0.41 0.29 100
96 0.24 0.17 0.20 100
97 0.10 0.16 0.12 100
98 0.09 0.13 0.11 100
99 0.39 0.15 0.22 100
avg / total 0.24 0.22 0.20 10000
ROC Curve
The ROC curve is used by binary classifiers because it is a good tool to see the true positives rate versus false positives.
We will code the ROC curve for a multiclass classification. This code is from DloLogy, but you can go to the Scikit Learn documentation page.
from sklearn.datasets import make_classification
from sklearn.preprocessing import label_binarize
from scipy import interp
from itertools import cycle
n_classes = 100
from sklearn.metrics import roc_curve, auc
lw = 2
fpr = dict()
tpr = dict()
roc_auc = dict()
for i in range(n_classes):
fpr[i], tpr[i], _ = roc_curve(y_test[:, i], snn_pred[:, i])
roc_auc[i] = auc(fpr[i], tpr[i])
fpr["micro"], tpr["micro"], _ = roc_curve(y_test.ravel(), snn_pred.ravel())
roc_auc["micro"] = auc(fpr["micro"], tpr["micro"])
all_fpr = np.unique(np.concatenate([fpr[i] for i in range(n_classes)]))
mean_tpr = np.zeros_like(all_fpr)
for i in range(n_classes):
mean_tpr += interp(all_fpr, fpr[i], tpr[i])
mean_tpr /= n_classes
fpr["macro"] = all_fpr
tpr["macro"] = mean_tpr
roc_auc["macro"] = auc(fpr["macro"], tpr["macro"])
plt.figure(1)
plt.plot(fpr["micro"], tpr["micro"],
label='micro-average ROC curve (area = {0:0.2f})'
''.format(roc_auc["micro"]),
color='deeppink', linestyle=':', linewidth=4)
plt.plot(fpr["macro"], tpr["macro"],
label='macro-average ROC curve (area = {0:0.2f})'
''.format(roc_auc["macro"]),
color='navy', linestyle=':', linewidth=4)
colors = cycle(['aqua', 'darkorange', 'cornflowerblue'])
for i, color in zip(range(n_classes-97), colors):
plt.plot(fpr[i], tpr[i], color=color, lw=lw,
label='ROC curve of class {0} (area = {1:0.2f})'
''.format(i, roc_auc[i]))
plt.plot([0, 1], [0, 1], 'k--', lw=lw)
plt.xlim([0.0, 1.0])
plt.ylim([0.0, 1.05])
plt.xlabel('False Positive Rate')
plt.ylabel('True Positive Rate')
plt.title('Some extension of Receiver operating characteristic to multi-class')
plt.legend(loc="lower right")
plt.show()
plt.figure(2)
plt.xlim(0, 0.2)
plt.ylim(0.8, 1)
plt.plot(fpr["micro"], tpr["micro"],
label='micro-average ROC curve (area = {0:0.2f})'
''.format(roc_auc["micro"]),
color='deeppink', linestyle=':', linewidth=4)
plt.plot(fpr["macro"], tpr["macro"],
label='macro-average ROC curve (area = {0:0.2f})'
''.format(roc_auc["macro"]),
color='navy', linestyle=':', linewidth=4)
colors = cycle(['aqua', 'darkorange', 'cornflowerblue'])
for i, color in zip(range(3), colors):
plt.plot(fpr[i], tpr[i], color=color, lw=lw,
label='ROC curve of class {0} (area = {1:0.2f})'
''.format(i, roc_auc[i]))
plt.plot([0, 1], [0, 1], 'k--', lw=lw)
plt.xlabel('False Positive Rate')
plt.ylabel('True Positive Rate')
plt.title('Some extension of Receiver operating characteristic to multi-class')
plt.legend(loc="lower right")
plt.show()
Finally, we will save the train history data.
with open(path_base + '/simplenn_history.txt', 'wb') as file_pi:
pickle.dump(snn.history, file_pi)
Points of Interest
Despite training 10 epochs with this model is good enough, we see in the graphics of accuracy and loss that the model will not improve much better by taking more epochs. The ROC curve has a good true positive rate versus the false positive rate (means that when predict one class label, it have a low rate to be a false positive). Anyway, the rate is so much low for the accuracy, recall and precision.
In the next chapter, we will train the same dataset with a very simple convolutional neural network also using the same metrics, and loss and optimization functions. See you soon!
History
- 20th May, 2018: Initial version
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