Classification by a neural network using Keras

Overview

Questions

• How do I compose a neural network using Keras?
• How do I train this network on a dataset?
• How do I get insight into learning process?
• How do I measure the performance of the network?

Objectives

• Use the deep learning workflow to structure the notebook
• Explore the dataset using pandas and seaborn
• Identify the inputs and outputs of a deep neural network.
• Use one-hot encoding to prepare data for classification in Keras
• Describe a fully connected layer
• Implement a fully connected layer with Keras
• Use Keras to train a small fully connected network on prepared data
• Interpret the loss curve of the training process
• Use a confusion matrix to measure the trained networks’ performance on a test set

Introduction

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In this episode we will learn how to create and train a neural network using Keras to solve a simple classification task.

The goal of this episode is to quickly get your hands dirty in actually defining and training a neural network, without going into depth of how neural networks work on a technical or mathematical level. We want you to go through the full deep learning workflow once before going into more details.

In fact, this is also what we would recommend you to do when working on real-world problems: First quickly build a working pipeline, while taking shortcuts. Then, slowly make the pipeline more advanced while you keep on evaluating the approach.

In episode 3 we will expand on the concepts that are lightly introduced in this episode. Some of these concepts include: how to monitor the training progress and how optimization works.

As a reminder below are the steps of the deep learning workflow:

1. Formulate / Outline the problem
2. Identify inputs and outputs
3. Prepare data
4. Choose a pretrained model or start building architecture from scratch
5. Choose a loss function and optimizer
6. Train the model
7. Perform a Prediction/Classification
8. Measure performance
9. Refine the model
10. Save model

In this episode we will focus on a minimal example for each of these steps, later episodes will build on this knowledge to go into greater depth for some or all of these steps.

GPU usage

For this lesson having a GPU (graphics processing unit) available is not needed. We specifically use very small toy problems so that you do not need one. However, Keras will use your GPU automatically when it is available. Using a GPU becomes necessary when tackling larger datasets or complex problems which require a more complex neural network.

1. Formulate/outline the problem: penguin classification

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In this episode we will be using the penguin dataset. This is a dataset that was published in 2020 by Allison Horst and contains data on three different species of the penguins.

We will use the penguin dataset to train a neural network which can classify which species a penguin belongs to, based on their physical characteristics.

Goal

The goal is to predict a penguins’ species using the attributes available in this dataset.

The palmerpenguins data contains size measurements for three penguin species observed on three islands in the Palmer Archipelago, Antarctica. The physical attributes measured are flipper length, beak length, beak width, body mass, and sex.

Artwork by @allison_horst

Artwork by @allison_horst

These data were collected from 2007 - 2009 by Dr. Kristen Gorman with the Palmer Station Long Term Ecological Research Program, part of the US Long Term Ecological Research Network. The data were imported directly from the Environmental Data Initiative (EDI) Data Portal, and are available for use by CC0 license (“No Rights Reserved”) in accordance with the Palmer Station Data Policy.

2. Identify inputs and outputs

---

To identify the inputs and outputs that we will use to design the neural network we need to familiarize ourselves with the dataset. This step is sometimes also called data exploration.

We will start by importing the Seaborn library that will help us get the dataset and visualize it. Seaborn is a powerful library with many visualizations. Keep in mind it requires the data to be in a pandas dataframe, luckily the datasets available in seaborn are already in a pandas dataframe.

PYTHON

import seaborn as sns

We can load the penguin dataset using

PYTHON

penguins = sns.load_dataset('penguins')

This will give you a pandas dataframe which contains the penguin data.

Inspecting the data

Using the pandas head function gives us a quick look at the data:

PYTHON

penguins.head()

	species	island	bill_length_mm	bill_depth_mm	flipper_length_mm	body_mass_g	sex
0	Adelie	Torgersen	39.1	18.7	181.0	3750.0	Male
1	Adelie	Torgersen	39.5	17.4	186.0	3800.0	Female
2	Adelie	Torgersen	40.3	18.0	195.0	3250.0	Female
3	Adelie	Torgersen	NaN	NaN	NaN	NaN	NaN
4	Adelie	Torgersen	36.7	19.3	193.0	3450.0	Female

We can use all columns as features to predict the species of the penguin, except for the species column itself.

Let’s look at the shape of the dataset:

PYTHON

penguins.shape

There are 344 samples and 7 columns (plus the index column), so 6 features.

Visualization

Looking at numbers like this usually does not give a very good intuition about the data we are working with, so let us create a visualization.

Pair Plot

One nice visualization for datasets with relatively few attributes is the Pair Plot. This can be created using sns.pairplot(...). It shows a scatterplot of each attribute plotted against each of the other attributes. By using the hue='species' setting for the pairplot the graphs on the diagonal are layered kernel density estimate plots for the different values of the species column.

PYTHON

sns.pairplot(penguins, hue="species")

Pairplot

Take a look at the pairplot we created. Consider the following questions:

• Is there any class that is easily distinguishable from the others?
• Which combination of attributes shows the best separation for all 3 class labels at once?
• (optional) Create a similar pairplot, but with hue="sex". Explain the patterns you see. Which combination of features distinguishes the two sexes best?

Show me the solution

• The plots show that the green class, Gentoo is somewhat more easily distinguishable from the other two.
• The other two seem to be separable by a combination of bill length and bill depth (other combinations are also possible such as bill length and flipper length).

Answer to optional question:

PYTHON

sns.pairplot(penguins, hue='sex')

You see that for each species females have smaller bills and flippers, as well as a smaller body mass. You would need a combination of the species and the numerical features to successfully distinguish males from females. The combination of bill_depth_mm and body_mass_g gives the best separation.

Input and Output Selection

Now that we have familiarized ourselves with the dataset we can select the data attributes to use as input for the neural network and the target that we want to predict.

In the rest of this episode we will use the bill_length_mm, bill_depth_mm, flipper_length_mm, body_mass_g attributes. The target for the classification task will be the species.

Data Exploration

Exploring the data is an important step to familiarize yourself with the problem and to help you determine the relevant inputs and outputs.

3. Prepare data

---

The input data and target data are not yet in a format that is suitable to use for training a neural network.

For now we will only use the numerical features bill_length_mm, bill_depth_mm, flipper_length_mm, body_mass_g only, so let’s drop the categorical columns:

PYTHON

# Drop categorical columns
penguins_filtered = penguins.drop(columns=['island', 'sex'])

Clean missing values

During the exploration phase you may have noticed that some rows in the dataset have missing (NaN) values, leaving such values in the input data will ruin the training, so we need to deal with them. There are many ways to deal with missing values, but for now we will just remove the offending rows by adding a call to dropna():

PYTHON

# Drop the rows that have NaN values in them
penguins_filtered = penguins_filtered.dropna()

Finally, we select only the features

PYTHON

# Extract columns corresponding to features
features = penguins_filtered.drop(columns=['species'])

Prepare target data for training

Second, the target data is also in a format that cannot be used in training. A neural network can only take numerical inputs and outputs, and learns by calculating how “far away” the species predicted by the neural network is from the true species.

When the target is a string category column as we have here, we need to transform this column into a numerical format first. Again, there are many ways to do this. We will be using the one-hot encoding. This encoding creates multiple columns, as many as there are unique values, and puts a 1 in the column with the corresponding correct class, and 0’s in the other columns. For instance, for a penguin of the Adelie species the one-hot encoding would be 1 0 0.

Fortunately, Pandas is able to generate this encoding for us.

PYTHON

import pandas as pd

target = pd.get_dummies(penguins_filtered['species'])
target.head() # print out the top 5 to see what it looks like.

One-hot encoding

How many output neurons will our network have now that we one-hot encoded the target class?

• A: 1
• B: 2
• C: 3

Show me the solution

C: 3, one for each output variable class

Split data into training and test set

Finally, we will split the dataset into a training set and a test set. As the names imply we will use the training set to train the neural network, while the test set is kept separate. We will use the test set to assess the performance of the trained neural network on unseen samples. In many cases a validation set is also kept separate from the training and test sets (i.e. the dataset is split into 3 parts). This validation set is then used to select the values of the parameters of the neural network and the training methods. For this episode we will keep it at just a training and test set however.

To split the cleaned dataset into a training and test set we will use a very convenient function from sklearn called train_test_split.

This function takes a number of parameters which are extensively explained in the scikit-learn documentation : - The first two parameters are the dataset (in our case features) and the corresponding targets (i.e. defined as target). - Next is the named parameter test_size this is the fraction of the dataset that is used for testing, in this case 0.2 means 20% of the data will be used for testing. - random_state controls the shuffling of the dataset, setting this value will reproduce the same results (assuming you give the same integer) every time it is called. - shuffle which can be either True or False, it controls whether the order of the rows of the dataset is shuffled before splitting. It defaults to True. - stratify is a more advanced parameter that controls how the split is done. By setting it to target the train and test sets the function will return will have roughly the same proportions (with regards to the number of penguins of a certain species) as the dataset.

PYTHON

from sklearn.model_selection import train_test_split

X_train, X_test, y_train, y_test = train_test_split(features, target, test_size=0.2, random_state=0, shuffle=True, stratify=target)

4. Build an architecture from scratch or choose a pretrained model

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Keras for neural networks

Keras is a machine learning framework with ease of use as one of its main features. It is part of the tensorflow python package and can be imported using from tensorflow import keras.

Keras includes functions, classes and definitions to define deep learning models, cost functions and optimizers (optimizers are used to train a model).

Before we move on to the next section of the workflow we need to make sure we have Keras imported. We do this as follows:

PYTHON

from tensorflow import keras

For this episode it is useful if everyone gets the same results from their training. Keras uses a random number generator at certain points during its execution. Therefore we will need to set two random seeds, one for numpy and one for tensorflow:

PYTHON

from numpy.random import seed
seed(1)
keras.utils.set_random_seed(2)

Build a neural network from scratch

Now we will build a neural network from scratch, which is surprisingly straightforward using Keras.

With Keras you compose a neural network by creating layers and linking them together. For now we will only use one type of layer called a fully connected or Dense layer. In Keras this is defined by the keras.layers.Dense class.

A dense layer has a number of neurons, which is a parameter you can choose when you create the layer. When connecting the layer to its input and output layers every neuron in the dense layer gets an edge (i.e. connection) to all of the input neurons and all of the output neurons. The hidden layer in the image in the introduction of this episode is a Dense layer.

The input in Keras also gets special treatment, Keras automatically calculates the number of inputs and outputs a layer needs and therefore how many edges need to be created. This means we need to inform Keras how big our input is going to be. We do this by instantiating a keras.Input class and tell it how big our input is, thus the number of columns it contains.

PYTHON

inputs = keras.Input(shape=(X_train.shape[1],))

We store a reference to this input class in a variable so we can pass it to the creation of our hidden layer. Creating the hidden layer can then be done as follows:

PYTHON

hidden_layer = keras.layers.Dense(10, activation="relu")(inputs)

The instantiation here has 2 parameters and a seemingly strange combination of parentheses, so let us take a closer look. The first parameter 10 is the number of neurons we want in this layer, this is one of the hyperparameters of our system and needs to be chosen carefully. We will get back to this in the section on refining the model.

The second parameter is the activation function to use. We choose relu which returns 0 for inputs that are 0 and below and the identity function (returning the same value) for inputs above 0. This is a commonly used activation function in deep neural networks that is proven to work well.

Next we see an extra set of parenthenses with inputs in them. This means that after creating an instance of the Dense layer we call it as if it was a function. This tells the Dense layer to connect the layer passed as a parameter, in this case the inputs.

Finally we store a reference in the hidden_layer variable so we can pass it to the output layer in a minute.

Now we create another layer that will be our output layer. Again we use a Dense layer and so the call is very similar to the previous one.

PYTHON

output_layer = keras.layers.Dense(3, activation="softmax")(hidden_layer)

Because we chose the one-hot encoding, we use three neurons for the output layer.

The softmax activation ensures that the three output neurons produce values in the range (0, 1) and they sum to 1. We can interpret this as a kind of ‘probability’ that the sample belongs to a certain species.

Now that we have defined the layers of our neural network we can combine them into a Keras model which facilitates training the network.

PYTHON

model = keras.Model(inputs=inputs, outputs=output_layer)
model.summary()

The model summary here can show you some information about the neural network we have defined.

Trainable and non-trainable parameters

Keras distinguishes between two types of weights, namely:

• trainable parameters: these are weights of the neurons that are modified when we train the model in order to minimize our loss function (we will learn about loss functions shortly!).

• non-trainable parameters: these are weights of the neurons that are not changed when we train the model. These could be for many reasons - using a pre-trained model, choice of a particular filter for a convolutional neural network, and statistical weights for batch normalization are some examples.

If these reasons are not clear right away, don’t worry! In later episodes of this course, we will touch upon a couple of these concepts.

Create the neural network

With the code snippets above, we defined a Keras model with 1 hidden layer with 10 neurons and an output layer with 3 neurons.

1. How many parameters does the resulting model have?
2. What happens to the number of parameters if we increase or decrease the number of neurons in the hidden layer?

(optional) Keras Sequential vs Functional API

So far we have used the Functional API of Keras. You can also implement neural networks using the Sequential model. As you can read in the documentation, the Sequential model is appropriate for a plain stack of layers where each layer has exactly one input tensor and one output tensor.

3. (optional) Use the Sequential model to implement the same network

Show me the solution

Have a look at the output of model.summary():

PYTHON

model.summary()

OUTPUT

Model: "model_1"
_________________________________________________________________
Layer (type)                 Output Shape              Param #
=================================================================
input_1 (InputLayer)         [(None, 4)]               0
_________________________________________________________________
dense (Dense)                (None, 10)                50
_________________________________________________________________
dense_1 (Dense)              (None, 3)                 33
=================================================================
Total params: 83
Trainable params: 83
Non-trainable params: 0
_________________________________________________________________

The model has 83 trainable parameters. Each of the 10 neurons in the in the dense hidden layer is connected to each of the 4 inputs in the input layer resulting in 40 weights that can be trained. The 10 neurons in the hidden layer are also connected to each of the 3 outputs in the dense_1 output layer, resulting in a further 30 weights that can be trained. By default Dense layers in Keras also contain 1 bias term for each neuron, resulting in a further 10 bias values for the hidden layer and 3 bias terms for the output layer. 40+30+10+3=83 trainable parameters.

If you increase the number of neurons in the hidden layer the number of trainable parameters in both the hidden and output layer increases or decreases in accordance with the number of neurons added. Each extra neuron has 4 weights connected to the input layer, 1 bias term, and 3 weights connected to the output layer. So in total 8 extra parameters.

The name in quotes within the string Model: "model_1" may be different in your view; this detail is not important.

(optional) Keras Sequential vs Functional API

3. This implements the same model using the Sequential API:

PYTHON

model = keras.Sequential(
    [
        keras.Input(shape=(X_train.shape[1],)),
        keras.layers.Dense(10, activation="relu"),
        keras.layers.Dense(3, activation="softmax"),
    ]
)

We will use the Functional API for the remainder of this course, since it is more flexible and more explicit.

How to choose an architecture?

Even for this small neural network, we had to make a choice on the number of hidden neurons. Other choices to be made are the number of layers and type of layers (as we will see later). You might wonder how you should make these architectural choices. Unfortunately, there are no clear rules to follow here, and it often boils down to a lot of trial and error. However, it is recommended to look what others have done with similar datasets and problems. Another best practice is to start with a relatively simple architecture. Once running start to add layers and tweak the network to see if performance increases.

Choose a pretrained model

If your data and problem is very similar to what others have done, you can often use a pretrained network. Even if your problem is different, but the data type is common (for example images), you can use a pretrained network and finetune it for your problem. A large number of openly available pretrained networks can be found on Hugging Face (especially LLMs), MONAI (medical imaging), the Model Zoo, pytorch hub or tensorflow hub.

5. Choose a loss function and optimizer

---

We have now designed a neural network that in theory we should be able to train to classify Penguins. However, we first need to select an appropriate loss function that we will use during training. This loss function tells the training algorithm how wrong, or how ‘far away’ from the true value the predicted value is.

For the one-hot encoding that we selected earlier a suitable loss function is the Categorical Crossentropy loss. In Keras this is implemented in the keras.losses.CategoricalCrossentropy class. This loss function works well in combination with the softmax activation function we chose earlier. The Categorical Crossentropy works by comparing the probabilities that the neural network predicts with ‘true’ probabilities that we generated using the one-hot encoding. This is a measure for how close the distribution of the three neural network outputs corresponds to the distribution of the three values in the one-hot encoding. It is lower if the distributions are more similar.

For more information on the available loss functions in Keras you can check the documentation.

Next we need to choose which optimizer to use and, if this optimizer has parameters, what values to use for those. Furthermore, we need to specify how many times to show the training samples to the optimizer.

Once more, Keras gives us plenty of choices all of which have their own pros and cons, but for now let us go with the widely used Adam optimizer. Adam has a number of parameters, but the default values work well for most problems. So we will use it with its default parameters.

Combining this with the loss function we decided on earlier we can now compile the model using model.compile. Compiling the model prepares it to start the training.

PYTHON

model.compile(optimizer='adam', loss=keras.losses.CategoricalCrossentropy())

6. Train model

---

We are now ready to train the model.

Training the model is done using the fit method, it takes the input data and target data as inputs and it has several other parameters for certain options of the training. Here we only set a different number of epochs. One training epoch means that every sample in the training data has been shown to the neural network and used to update its parameters.

PYTHON

history = model.fit(X_train, y_train, epochs=100)

The fit method returns a history object that has a history attribute with the training loss and potentially other metrics per training epoch. It can be very insightful to plot the training loss to see how the training progresses. Using seaborn we can do this as follow:

PYTHON

sns.lineplot(x=history.epoch, y=history.history['loss'])

This plot can be used to identify whether the training is well configured or whether there are problems that need to be addressed.

The Training Curve

Looking at the training curve we have just made.

1. How does the training progress?
   • Does the training loss increase or decrease?
   • Does it change quickly or slowly?
   • Does the graph look very jittery?
2. Do you think the resulting trained network will work well on the test set?

When the training process does not go well:

3. (optional) Something went wrong here during training. What could be the problem, and how do you see that in the training curve? Also compare the range on the y-axis with the previous training curve.

Show me the solution

1. The training loss decreases quickly. It drops in a smooth line with little jitter. This is ideal for a training curve.
2. The results of the training give very little information on its performance on a test set. You should be careful not to use it as an indication of a well trained network.
3. (optional) The loss does not go down at all, or only very slightly. This means that the model is not learning anything. It could be that something went wrong in the data preparation (for example the labels are not attached to the right features). In addition, the graph is very jittery. This means that for every update step, the weights in the network are updated in such a way that the loss sometimes increases a lot and sometimes decreases a lot. This could indicate that the weights are updated too much at every learning step and you need a smaller learning rate (we will go into more details on this in the next episode). Or there is a high variation in the data, leading the optimizer to change the weights in different directions at every learning step. This could be addressed by presenting more data at every learning step (or in other words increasing the batch size). In this case the graph was created by training on nonsense data, so this a training curve for a problem where nothing can be learned really.

We will take a closer look at training curves in the next episode. Some of the concepts touched upon here will also be further explained there.

7. Perform a prediction/classification

---

Now that we have a trained neural network, we can use it to predict new samples of penguin using the predict function.

We will use the neural network to predict the species of the test set using the predict function. We will be using this prediction in the next step to measure the performance of our trained network. This will return a numpy matrix, which we convert to a pandas dataframe to easily see the labels.

PYTHON

y_pred = model.predict(X_test)
prediction = pd.DataFrame(y_pred, columns=target.columns)
prediction

0	0.304484	0.192893	0.502623
1	0.527107	0.095888	0.377005
2	0.373989	0.195604	0.430406
3	0.493643	0.154104	0.352253
4	0.309051	0.308646	0.382303
…	…	…	…
64	0.406074	0.191430	0.402496
65	0.645621	0.077174	0.277204
66	0.356284	0.185958	0.457758
67	0.393868	0.159575	0.446557
68	0.509837	0.144219	0.345943

Remember that the output of the network uses the softmax activation function and has three outputs, one for each species. This dataframe shows this nicely.

We now need to transform this output to one penguin species per sample. We can do this by looking for the index of highest valued output and converting that to the corresponding species. Pandas dataframes have the idxmax function, which will do exactly that.

PYTHON

predicted_species = prediction.idxmax(axis="columns")
predicted_species

OUTPUT

0     Gentoo
1     Adelie
2     Gentoo
3     Adelie
4     Gentoo
      ...
64    Adelie
65    Adelie
66    Gentoo
67    Gentoo
68    Adelie
Length: 69, dtype: object

8. Measuring performance

---

Now that we have a trained neural network it is important to assess how well it performs. We want to know how well it will perform in a realistic prediction scenario, measuring performance will also come back when refining the model.

We have created a test set (i.e. y_test) during the data preparation stage which we will use now to create a confusion matrix.

Confusion matrix

With the predicted species we can now create a confusion matrix and display it using seaborn. To create a confusion matrix we will use another convenient function from sklearn called confusion_matrix. This function takes as a first parameter the true labels of the test set. We can get these by using the idxmax method on the y_test dataframe. The second parameter is the predicted labels which we did above.

PYTHON

from sklearn.metrics import confusion_matrix

true_species = y_test.idxmax(axis="columns")

matrix = confusion_matrix(true_species, predicted_species)
print(matrix)

OUTPUT

[[22  0  8]
 [ 5  0  9]
 [ 6  0 19]]

Unfortunately, this matrix is not immediately understandable. Its not clear which column and which row corresponds to which species. So let’s convert it to a pandas dataframe with its index and columns set to the species as follows:

PYTHON

# Convert to a pandas dataframe
confusion_df = pd.DataFrame(matrix, index=y_test.columns.values, columns=y_test.columns.values)

# Set the names of the x and y axis, this helps with the readability of the heatmap.
confusion_df.index.name = 'True Label'
confusion_df.columns.name = 'Predicted Label'
confusion_df.head()

We can then use the heatmap function from seaborn to create a nice visualization of the confusion matrix. The annot=True parameter here will put the numbers from the confusion matrix in the heatmap.

PYTHON

sns.heatmap(confusion_df, annot=True)

Confusion Matrix

Measure the performance of the neural network you trained and visualize a confusion matrix.

• Did the neural network perform well on the test set?
• Did you expect this from the training loss you saw?
• What could we do to improve the performance?

Show me the solution

The confusion matrix shows that the predictions for Adelie and Gentoo are decent, but could be improved. However, Chinstrap is not predicted ever. The training loss was very low, so from that perspective this may be surprising. But this illustrates very well why a test set is important when training neural networks. We can try many things to improve the performance from here. One of the first things we can try is to balance the dataset better. Other options include: changing the network architecture or changing the training parameters

Note that the outcome you have might be slightly different from what is shown in this tutorial.

9. Refine the model

---

As we discussed before the design and training of a neural network comes with many hyperparameter and model architecture choices. We will go into more depth of these choices in later episodes. For now it is important to realize that the parameters we chose were somewhat arbitrary and more careful consideration needs to be taken to pick hyperparameter values.

10. Share model

---

It is very useful to be able to use the trained neural network at a later stage without having to retrain it. This can be done by using the save method of the model. It takes a string as a parameter which is the path of a directory where the model is stored.

PYTHON

model.save('my_first_model')

This saved model can be loaded again by using the load_model method as follows:

PYTHON

pretrained_model = keras.models.load_model('my_first_model')

This loaded model can be used as before to predict.

PYTHON

# use the pretrained model here
y_pretrained_pred = pretrained_model.predict(X_test)
pretrained_prediction = pd.DataFrame(y_pretrained_pred, columns=target.columns.values)

# idxmax will select the column for each row with the highest value
pretrained_predicted_species = pretrained_prediction.idxmax(axis="columns")
print(pretrained_predicted_species)

OUTPUT

0     Adelie
1     Gentoo
2     Adelie
3     Gentoo
4     Gentoo
      ...
64    Gentoo
65    Gentoo
66    Adelie
67    Adelie
68    Gentoo
Length: 69, dtype: object

Key Points

• The deep learning workflow is a useful tool to structure your approach, it helps to make sure you do not forget any important steps.
• Exploring the data is an important step to familiarize yourself with the problem and to help you determine the relavent inputs and outputs.
• One-hot encoding is a preprocessing step to prepare labels for classification in Keras.
• A fully connected layer is a layer which has connections to all neurons in the previous and subsequent layers.
• keras.layers.Dense is an implementation of a fully connected layer, you can set the number of neurons in the layer and the activation function used.
• To train a neural network with Keras we need to first define the network using layers and the Model class. Then we can train it using the model.fit function.
• Plotting the loss curve can be used to identify and troubleshoot the training process.
• The loss curve on the training set does not provide any information on how well a network performs in a real setting.
• Creating a confusion matrix with results from a test set gives better insight into the network’s performance.