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What is the Confusion Matrix?

A confusion matrix is a tool for assessing the quality of a classification model in Machine Learning. It checks how many of the predictions were correctly or incorrectly assigned to a class.

How to judge a Classification?

In the simplest case, a classification consists of two states. Suppose we want to investigate how well Corona tests reflect the infection status of a patient. In this case, the Corona test serves as a classifier of a total of two states: infected or non-infected.

These two classes can result in a total of four states, depending on whether the classification of the test was really correct:

  • True Positive: The rapid test classifies the person as infected and a subsequent PCR test confirms this result. Thus, the rapid test was correct.
  • False Positive: The rapid test is positive for a person, but a subsequent PCR test shows that the person is actually not infected, i.e. negative.
  • True Negative: The rapid test is negative and the person is actually not infected.
  • False Negative: The Corona rapid test classifies the tested person as healthy, i.e. negative, however, the person is infected and should therefore have a positive rapid test.

What is a Confusion Matrix?

The confusion matrix helps to evaluate and neutrally assess the quality of a learned classification. Furthermore, specific metrics can be calculated more easily with the help of the matrix. To build the confusion matrix, one needs the test set of the dataset. The classifier assigns the classes to the data points.

The matrix is composed of the error types already mentioned. The rows are the predicted classes for the test set and the columns are the actual labels of the test set:

Das Bild zeigt den allgemeinen Aufbau der Konfusionsmatrix.
Structure of the Confusion Matrix

Assume that our test set for the Corona rapid tests includes 200 individuals, broken down by cell as follows:

Das Bild zeigt eine beispielhafte Konfusionsmatrix für den Klassifikator "Corona Schnelltest".
Example with Corona Tests

Specifically, the matrix results in the following values:

  • True Positive = 120: A total of 120 people were classified as infected by the rapid test and actually carrying the virus.
  • False Positive = 20: 20 people are sick according to the rapid test, but are not actually infected.
  • False Negative = 40: 40 subjects tested negative by the rapid test, but are actually infected.
  • True Negative = 20: 20 people were negative, and the rapid test confirmed this.

The confusion matrix is therefore often used to determine which type of error occurs frequently in the classifier. Our exemplary Corona quick test is correct in 70 % of the cases ((120 + 20) / 200), which is not a bad value at first glance. However, a false negative error occurs in 20 % (40 / 200) of all cases. This means that in 20% of all cases, the person is shown as healthy, although he is actually sick and contagious. In the case of a viral disease, therefore, it is not only the accuracy that is decisive but also the false negative rate.

These ratios can be read easily from a confusion matrix and then calculated.

What ratios can be calculated from the Confusion Matrix?

Since each use case focuses on different metrics, some of these metrics have evolved over time. In this chapter, we briefly present the most important ones.


The sensitivity, or True Positive Rate, describes the cases in which positively classified data points were actually positive:

\(\) \[\frac{\text{True Positive}}{\text{True Positive + False Negative}}\]


Specificity, or True Negative Rate, measures all cases in which negatively classified data points were actually negative:

\(\) \[\frac{\text{True Negative}}{\text{True Negative + False Positive}}\]


Precision is the relative frequency of correctly, positively classified subjects:

\(\) \[\frac{\text{True Positive}}{\text{True Positive + False Positive}}\]


We already know the accuracy of other types of models. It describes the total number of correctly classified persons in relation to all classifications:

\(\) \[\frac{\text{True Positive + True Negative}}{\text{True Positive + True Negative + False Positive + False Negative}}\]

Error Rate

The error rate is the opposite of the accuracy, i.e. the percentage of false classifications:

\(\) \[\frac{\text{False Positive + False Negative}}{\text{True Positive + True Negative + False Positive + False Negative}}\]

How to create a Confusion Matrix in Python?

Once you have trained a classifier in Python, the truth matrix can be created using the “Scikit-Learn” module. To do this, we just need two arrays with the predicted classes for the test set and the actual labels for the test set. In our case, the classification model can distinguish between the classes “cat”, “ant” and “bird”. Accordingly, we expect a confusion matrix with three rows and three columns.

# Import Scikit-Learn
from sklearn.metrics import confusion_matrix

# True Labels of Testset
y_true = ["cat", "ant", "cat", "cat", "ant", "bird"]

# Predicted Labels of Testset
y_pred = ["ant", "ant", "cat", "cat", "ant", "cat"]

# Create Confusion Matrix
confusion_matrix(y_true, y_pred, labels=["ant", "bird", "cat"])

array([[2, 0, 0],
       [0, 0, 1],
       [1, 0, 2]], dtype=int64)

This matrix can now also be used to calculate the true positives, false positives, etc. from it. Classification with more than two classes, can be quite complicated by hand.

# Get Figures of a two-class Classification
tn, fp, fn, tp = confusion_matrix([0, 1, 0, 1], [1, 1, 1, 0]).ravel()
(tn, fp, fn, tp)

(0, 2, 1, 1)

# Get Figures of a multi-class Classification
confusion_matrix(y_true, y_pred, labels=["ant", "bird", "cat"]).ravel()

array([2, 0, 0, 0, 0, 1, 1, 0, 2], dtype=int64)

This is what you should take with you

  • The confusion matrix helps in the evaluation of classification models.
  • In most cases, it contains four fields: True Positive, True Negative, False Positive, and False Negative.
  • The fields can be used to calculate specific metrics that help evaluate the classifier.

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