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Classification by a Neural Network using Keras


Teaching: 30-60 min
Exercises: 40-45 min
  • What is a neural network?

  • 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

  • Use the deep learning workflow to structure the notebook

  • Explore the dataset using pandas and seaborn

  • 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

  • Plot the loss curve of the training process

  • Use a confusion matrix to measure the trained networks’ performance on a test set


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 most commonly used deep learning workflow that was covered in the introduction. 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. Tune hyperparameters
  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 card) 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

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.


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.

Illustration of the three species of penguins found in the Palmer Archipelago, Antarctica: Chinstrap, Gentoo and Adele Artwork by @allison_horst

Illustration of the beak dimensions called culmen length and culmen depth in the dataset 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.

import seaborn as sns

We can load the penguin dataset using

penguins = sns.load_dataset('penguins')

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

Penguin Dataset

Inspect the penguins dataset.

  1. What are the different features called in the dataframe?
  2. Are the target classes of the dataset stored as numbers or strings?
  3. How many samples does this dataset have?


1. Using the pandas head function you can see the names of the features. Using the describe function we can also see some statistics for the numeric columns

  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
  bill_length_mm bill_depth_mm flipper_length_mm body_mass_g
count 342.000000 342.000000 342.000000 342.000000
mean 43.921930 17.151170 200.915205 4201.754386
std 5.459584 1.974793 14.061714 801.954536
min 32.100000 13.100000 172.000000 2700.000000
25% 39.225000 15.600000 190.000000 3550.000000
50% 44.450000 17.300000 197.000000 4050.000000
75% 48.500000 18.700000 213.000000 4750.000000
max 59.600000 21.500000 231.000000 6300.000000

2. We can get the unique values in the species column using the unique function of pandas. It shows the target class is stored as a string and has 3 unique values. This type of column is usually called a ‘categorical’ column.

array(['Adelie', 'Chinstrap', 'Gentoo'], dtype=object)

3. Using describe function on the species column shows there are 344 samples unique species

count        344
unique         3
top       Adelie
freq         152
Name: species, dtype: object


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.

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

Pair plot showing the separability of the three species of penguin


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?


The plots show that the green class, Gentoo is somewhat more easily distinguishable from the other two. The other two seem to be most easily separated by a combination of bill length and bill depth.

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.

Change types if needed

First, the species column is our categorical target, however pandas still sees it as the generic type Object. We can convert this to the pandas categorical type:

penguins['species'] = penguins['species'].astype('category')

This will make later interaction with this column a little easier.

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():

# Drop two columns and the rows that have NaN values in them
penguins_filtered = penguins.drop(columns=['island', 'sex']).dropna()

# Extract columns corresponding to features
penguins_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 it is very difficult to determine this “distance” or error. Therefore we will transform this column into a more suitable format. Again there are many ways to do this, however 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.

import pandas as pd

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

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:

from sklearn.model_selection import train_test_split

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

Training and Test sets

Take a look at the training and test set we created.

  • How many samples do the training and test sets have?
  • Are the classes in the training set well balanced?


Using y_train.shape and y_test.shape we can see the training set has 273 samples and y_test has 69 samples.

We can check the balance of classes by counting the number of ones for each of the columns in the one-hot-encoded target, which shows the training set has 121 Adelie, 98 Gentoo and 54 Chinstrap samples.

Adelie       121
Chinstrap     54
Gentoo        98
dtype: int64

The dataset is not perfectly balanced, but it is not orders of magnitude out of balance either. So we will leave it as it is.

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

Keras for neural networks

For this lesson we will be using Keras to define and train our neural network models. 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:

from tensorflow import keras

For this class 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:

from numpy.random import seed
from tensorflow.random import set_seed

Build a neural network from scratch

Now we will build a neural network from scratch, and although this sounds like a daunting task, with Keras it is actually surprisingly straightforward.

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 let Keras now 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.

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:

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

The instantiation here has 2 parameters and a seemingly strange combination of parentheses, so let’s 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 hyperparameter tuning. The second parameter is the activation function to use, here we choose relu which is 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 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.

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

Because we chose the one-hot encoding, we use 3 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.

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

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

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.

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


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

model = keras.Model(inputs=inputs, outputs=output_layer)
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. 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 accordingly of neurons.
The name in quotes within the string Model: "model_1" may be different in your view; this detail is not important.

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 in 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 before a fitting 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.

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.

history =, 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:

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

Training loss curve of the neural network training

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 fast or slowly?
    • Is the graph look very jittery?
  2. Do you think the resulting trained network will work well on the test set?


  1. The loss curve should drop quite quickly in a smooth line with little jitter
  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.

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.

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


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.

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


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 tuning the hyperparameters.

We have created a test set 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.

from sklearn.metrics import confusion_matrix

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

matrix = confusion_matrix(true_species, predicted_species)
[[22  0  8]
 [ 5  0  9]
 [ 6  0 19]]

Unfortunately, this matrix is kinda hard to read. 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:

# 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. = 'True Label' = 'Predicted Label'

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.

sns.heatmap(confusion_df, annot=True)

Confusion matrix of the test set

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?


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

9. Tune hyperparameters

As we discussed before the design and training of a neural network comes with many hyper parameter choices. We will go into more depth of these hyperparameters 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.'my_first_model')

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

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

This loaded model can be used as before to predict.

# 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")


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 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.