Diabetes Prediction Using Machine

Learning Algorithms and Ontology

Hakim El Massari, Zineb Sabouri, Sajida Mhammedi

and Noreddine Gherabi∗

National School of Applied Sciences, Sultan Moulay Slimane University,

Lasti Laboratory, Khouribga, Morocco
E-mail: [email protected]; [email protected]
∗
Corresponding Author

Received 11 February 2022; Accepted 12 March 2022;

Publication 11 May 2022

Abstract
Diabetes is one of the chronic diseases, which is increasing from year to
year. The problems begin when diabetes is not detected at an early phase
and diagnosed properly at the appropriate time. Different machine learning
techniques, as well as ontology-based ML techniques, have recently played
an important role in medical science by developing an automated system that
can detect diabetes patients. This paper provides a comparative study and
review of the most popular machine learning techniques and ontology-based
Machine Learning classification. Various types of classification algorithms
were considered namely: SVM, KNN, ANN, Naive Bayes, Logistic regres-
sion, and Decision Tree. The results are evaluated based on performance
metrics like Recall, Accuracy, Precision, and F-Measure that are derived from
the confusion matrix. The experimental results showed that the best accuracy
goes for ontology classifiers and SVM.

Keywords: Machine learning, ontology, diabetes, prediction.

Journal of ICT Standardization, Vol. 10 2, 319–338.

doi: 10.13052/jicts2245-800X.10212
© 2022 River Publishers
320 H. El Massari et al.

1 Introduction
Diabetes is a group of the deadliest and metabolic diseases in which the
level of blood sugar in the human body is abnormally high. It impacts the
body’s capacity to produce the hormone insulin. High blood sugar commonly
causes many complications such as intensified thirst, increased hunger, and
frequent urination if diabetes goes untreated and undiagnosed at an early
stage. Therefore, early detection is the only way to avoid complications
by using the trending technology for ontology-based and machine learning.
Machine learning (ML) is one of the most rapidly developing fields
of computer science, with several applications. It refers to the process of
extracting useful information from a large set of data. ML techniques are
used in different areas such as medical diagnosis, marketing, industry, and
other scientific fields. ML algorithms have been widely used in medical
datasets and are best suited for medical data analysis. There are various
forms of ML, including classification, regression, and clustering. Depending
on the problem that we are trying to solve, each form has a distinct result
and impact. In our work, we focus on classification methods, which are
applied to classify a given dataset into predefined groups and to predict
future activities or information to that data due to its good accuracy and
performance. Classification algorithms are usually employed in the medical
domain especially in diagnosing the diseases such as diabetes. Therefore,
the commonly used machine learning classification [1] namely SVM, KNN,
ANN, Naive Bayes, Logistic regression, and Decision Tree are applied to
identify diabetes patients at an early period.
On the other side, Ontology is one of the most adopted approaches to
manage, organize and extract data during the previous decades. It is a data
representation method that has been successfully implemented in a variety
of fields, especially the medical domain. It is important in computer science
because of its capacity to represent diverse concepts and their relationships in
different disciplines. In actuality, no single ontology is sufficient to follow
the growing demands of today’s healthcare, and the ontologies must be
integrated with algorithms of machine learning to support data integration and
analysis [2]. In previous work, we already created and explored an ontology-
based model capable of predicting diabetes patients by using an ontology
classifier based on a decision tree algorithm.
In this study, we aim to make a comparative analysis among the
six popular classification techniques and ontology-based machine learn-
ing classification based on carefully chosen parameters such as Precision,
 Diabetes Prediction Using Machine Learning Algorithms and Ontology 321

Accuracy, F-Measure, and Recall, which are derived from the confusion
matrix.
The organization of the remainder of the paper is as follows: Section 2
represents the literature review of related classification algorithms in the field
of diabetes prediction. Section 3 we present technologies and methods used
in this comparative analysis. Section 4 we describe the performance metrics
used to evaluate the models. Section 5, we present results and discussion.
Finally, Section 6 presents future work and conclusions.

2 Related Works
Recently researchers have published a considerable amount of research to
identify diabetic patients based on symptoms by applying machine-learning
techniques. In [3], the authors propose a model that can predict is the patient
has diabetes or not. This model is based on the prediction precision of
powerful machine learning algorithms, which use certain measures such as
precision, recall, and F1-measure. The authors use Pima Indian Diabetes
(PIDD) dataset to predict diabetic onset based on diagnostics manner. The
results obtained using Logistic Regression (LR), Naı̈ve Bayes (NB), and K-
nearest Neighbor (KNN) algorithms were 94%, 79%, and 69% respectively.
In the paper [4], the authors use seven ML algorithms on the dataset to predict
diabetes, they found that the model with Logistic Regression and SVM were
better on diabetes prediction, they built a NN model with a different hidden
layer and observed the NN with two hidden layers provided 88.6% accuracy.
The study applied in the paper [5] uses several machine learning classi-
fication algorithms (Gaussian Naive Bayes, K-Nearest Neighbors, Artificial
Neural Network, Logistic Regression, Decision Tree, Random Forest, and
Support Vector Machine) on the PIID dataset. Logistic Regression got the
best accuracy result.
Sarwar et al. [6], discuss predictive analytics in healthcare, a number of
machine learning algorithms are used in this study. For experiment purposes,
a dataset of patient’s medical is obtained. The performance and accuracy of
the applied algorithms are discussed and compared
In the paper [7], the authors propose a diabetes prediction model for the
classification of diabetes including external factors responsible for diabetes
along with regular factors like Glucose, BMI, Age, Insulin, etc. Classification
accuracy is improved with the novel dataset compared with existing dataset.
On a dataset of 521 instances (80% and 20% for training testing respec-
tively), [8] authors applied 8 ML algorithms such as logistic regression,
322 H. El Massari et al.

support vector machines-linear, and nonlinear kernel, random forest, deci-

sion tree, adaptive boosting classifier, K-nearest neighbor, and naı̈ve bayes.
According to the results, the Random Forest classifier achieved 98% accuracy
compared to the other.
In [9], the researchers used machine-learning algorithms including Logis-
tic Regression, Gaussian Process, Adaptive Boosting (AdaBoost), Decision
Tree, K-Nearest Neighbors, Multilayer Perceptron, Support Vector Machine,
Bernoulli Naive Bayes, Bagging Classifier, Random Forest, and Quadratic
Discriminant Analysis. The Random Forest classifier performs better and
achieved a 98% accuracy, which is higher than the other three algorithms.
To predict diabetes at an early stage, the paper [10] proposes a novel
approach to diabetes prediction using significant attributes. Various tools are
used to determine attribute selection for clustering and prediction. The results
indicate a strong association of diabetes with body mass index (BMI) and
glucose level. Several techniques for predicting diabetes are used such as
artificial neural network (ANN), random forest, and K-means clustering for
the prediction of diabetes, and the ANN technique provided the best accuracy
Another method is used for diabetes prediction [11]. In this method the
authors propose a novel approach of machine learning algorithms applied in
hadoop based clusters for diabetes prediction. This approach is applied in
the Pima Indians Diabetes Database and Digestive Diseases and the results
obtained show that the ML algorithms produce the best accurate diabetes
predictive.
In this experimental analysis [12] four machine learning algorithms,
Random Forest, K-nearest neighbor, Support Vector Machine, and Linear
Discriminant Analysis are used in the predictive analysis of early-stage
diabetes. High accuracy of 87.66% goes to the Random Forest classifier.
In another way, the authors of the paper [13] have built models to
predict and classify diabetes complications. In this work, several supervised
classification algorithms were applied to predict and classify 8 diabetes
complications. The complications include some parameters such as metabolic
syndrome, dyslipidemia, nephropathy, diabetic foot, obesity, and retinopathy.
In [14], the authors present two approaches of machine learning to
predict diabetes patients. Random forest algorithm for the classification
approach, and XGBoost algorithm for a hybrid approach. The results show
that XGBoost outperforms in terms of an accuracy rate of 74.10%.
Authors in this article [15] tested machine learning algorithms such as
support vector machine, logistic regression, Decision Tree, Random Forest,
gradient boost, K-nearest neighbor, Naı̈ve Bayes algorithm. According to the
 Diabetes Prediction Using Machine Learning Algorithms and Ontology 323

results, Naı̈ve Base and Random Forest classifiers achieved 80% accuracy
compared to the other algorithms.

3 Technologies and Method

The experimentation is carried out using the methods and technologies
described in the next subsections. The process of developing this comparative
analysis is illustrated in Figure 1.

3.1 Dataset
The dataset called Pima Indians Diabetes Database (PIDD) is originally
from the National Institute of Diabetes and Digestive and Kidney Diseases.
The purpose is to expect based on diagnostic measurements whether a patient
has diabetes. It has 768 instances and 8 numerical attributes plus a class (preg,
plas, pres, skin, insu, mass, pedi, age, class).

Figure 1 Experimental flowchart.

324 H. El Massari et al.

Figure 2 Graphical representation of the ontology.

After the dataset pre-processing step using UCI Machine Learning, the
output file in CSV format will be transformed into ARFF format.

3.2 Machine Learning Algorithms

After preparing the dataset, we import it into Weka software, which contains
tools for data preparation, classification [16], clustering, association rule
exploration, visualization [17] and Similarity [18]. We used the six most com-
monly used classifiers to classify binary datasets (SVM, KNN, ANN, Logistic
Regression, Naı̈ve Bayes, Decision Tree). The results of the classifiers can be
found in Section 5.

3.3 Ontology Model

The approach used to classify the dataset using the ontology model was
published and detailed in our previous work [2], we recommend reading it
for more details. Here, we will give some details briefly.
The ontology was created by the open-source platform “Protégé”, a free
ontology editor and framework for building intelligent systems [19]. Figure 2
illustrates the graphical representation of our ontology generated by the
OntoGraph plugin.
The dataset is imported with the help of Cellfie, a Protégé plugin for
importing spreadsheet data into OWL ontologies. Then, we extracted gen-
erated rules from the Decision Tree algorithm and import them to Protégé
using the SWRLTab plugin. To execute SWRL rules and infer new ontology
axioms, we used the Pellet reasoner which has a more direct functionality
for working with OWL and SWRL rules. It uses the dataset and SWRL rules
to induce the inference and provides the final decision where is the patient is
 Diabetes Prediction Using Machine Learning Algorithms and Ontology 325

tested negative or positive. The results of the ontology classifier are presented
in Section 5.

4 Evaluation
In Machine Learning, performance measurement is an essential task. It is
critical to choose the right metrics to evaluate the machine learning model.
Therefore, metrics are used to determine how machine learning algorithms’
performance is measured and compared.
Different performance metrics are used to evaluate machine learning
algorithms such as Accuracy, Precision, Recall, F-Measure, ROC Area,
Kappa statistic, Root mean squared error, Root relative squared error, etc.
Almost all of the performance metrics are derived from the Confusion
Matrix and the numbers inside it. The Confusion Matrix is one of the most
intuitive and easiest metrics for determining the model’s correctness and
accuracy. It is used for classification problems with two or more types of
classes as output.
The confusion matrix is a table with two dimensions (“Actual” and
“Predicted”), and sets of “classes” in both dimensions. Our Actual classifi-
cations are columns and Predicted ones are Rows. For more understanding of
what the confusion matrix is all about and what it represents, let’s take a real
example from our study where we are predicting whether a patient is having
diabetes or not (1: tested positive 0: tested negative). Figure 3 illustrates the
confusion Matrix details, and Table 1 describes the terms associated with the
confusion matrix.
An ideal classification performance would only have no entries for FN
and FP (i.e., the number of FN equal number of FP equal zero).
Diverse measures can be derived from a confusion matrix such as Accu-
racy, Precision, Recall and F-Measure. The best value of accuracy, precision,
and recall is 1.0, whereas the worst is 0.0. Figure 3 illustrates how to compute
them from the confusion matrix.

Table 1 Terms associated with Confusion matrix

Terms Description
True Positives (TP) Number of patients correctly identified as Positive
True Negatives (TN) Number of patients correctly identified as Negative
False Positives (FP) Number of patients incorrectly identified as Positive
False Negatives (FN) Number of patients incorrectly identified as Negative
326 H. El Massari et al.

Figure 3 Confusion Matrix details.

Accuracy (ACC):
TP + TN
ACC =
TP + TN + FP + FN
Accuracy is computed as the number of all correct predictions divided
by the total number of the dataset, which is the number of patients that are
identified correctly in total in our case.
Precision (PREC):
TP
PREC =
TP + FP
PREC is computed as the number of correct positive predictions divided
by the total number of positive predictions.
Recall (REC):
TP
REC =
TP + FN
REC is computed as the number of correct positive predictions divided by
the total number of positives. It represents the relevant patients that have been
correctly detected, it is also called Sensitivity or true positive rate (TPR).
F-Measure:
P REC ∗ REC
F -Measure : = 2 ∗
P REC + REC
 Diabetes Prediction Using Machine Learning Algorithms and Ontology 327

Figure 4 Performance metrics: Accuracy, Precision, Recall.

F-Measure called also F-score, is a harmonic mean of precision and recall,

it provides the quality of prediction.
ROC – AUC Area:
AUC – ROC curve is a performance measurement for the classification
problems at various threshold settings. ROC is a probability curve and AUC
represents the degree or measure of separability. It tells how much the model
is capable of distinguishing between classes. If the value of AUC is high, the
model predicts classes indicated by 0 as value 0 and classes indicated by 1 as
value 1. By analogy, when the value of the AUC is high, the model is more
efficient and therefore we can distinguish patients with disease and without
disease.
There are other metrics like Mean Squared Error (MSE), Root Mean
Squared Error (RMSE), Mean Absolute Error (MAE), but generally are used
in regression problems. Therefore, this comparative study will rely on the
performance metrics explained above due to the dataset and algorithms used
categorized in classification problems. Also, the same metrics are used to
evaluate the quality of our ontology model.
In the next section, we present the result obtained from the classifiers
using Weka and Protégé software.

5 Results and Discussion

In this section, we present the result obtained from the evaluation of classi-
fiers used in this research including the result and statistics of the ontology
classifier.
This study is based on a set of criteria, on the one hand, no method applied
for feature selection or performance improvement for a fair comparison of
the performance of classification algorithms, on the other hand, we used two
modes test: cross-validation 10 times and percentage split (split 66.0% train,
328 H. El Massari et al.

Figure 5 Statistics of inferred concepts. (a) based on 10-fold cross-validation. (b) based on
66% split mode validation.

Table 2 Confusion matrix of ontology classier based on 10-fold cross-validation mode

Actual Class
Tested Positive and Negative Classification Positive Negative
Predicted class Positive TP: 449 FP: 104
Negative FN: 69 TN: 146

Table 3 Confusion matrix of ontology classier based on 66% split mode validation
Actual Class
Tested Positive and Negative Classification Positive Negative
Predicted class Positive TP: 160 FP: 37
Negative FN: 16 TN: 48

remainder test) in order to enrich the study and give more visibility to these
two modes.
According to the performance metrics explained in the previous section,
the results of the ontology classifier are shown in Tables 2 and 3, and Figure 5.
Furthermore, we present the result of Accuracy, Precision, Recall, F-Measure
in Figures 6–10 illustrating the graphic of each metric.
Table 4 summarizes the experimental results for ML and ontology
classifiers used in this study.
– Accuracy
In Figure 6 and Table 4, we obtained the highest value in terms of 10-
fold cross-validation mode for Ontology, SVM and Logistic Regression with
77.5%, 77.3%, 77.2% respectively. In split test mode, we obtained 80.1%,
79.7%, 79.3 for logistic regression, ontology and SVM consecutively.
 Diabetes Prediction Using Machine Learning Algorithms and Ontology 329

Figure 6 Comparison results of accuracy.

– Precision
The ontology classifier has the highest Precision of 81.2% for both test
modes. Followed by Naı̈ve Bayes and ANN. More details are shown in
Table 4 and Figure 7.

Figure 7 Comparison results of precision.

330 H. El Massari et al.

– Recall
From Figure 8 and Table 4, we notice that SVM had the highest value in
both test modes, followed by Ontology and Logistic Regression in the last
position.

Figure 8 Comparison results of recall.

– F-Measure
SVM and Ontology have the same metric of F-Measure with 83.3% and
∼85.8% for 10-fold cross-validation and split test mode. (See Figure 9 and
Table 4)

Figure 9 Comparison results of F-Measure.

 Diabetes Prediction Using Machine Learning Algorithms and Ontology 331

– ROC area
Table 4 and Figure 10 show that Logistic Regression, Naı̈ve Bayes, and
Ontology have the better value of the ROC Area.

Figure 10 Comparison results of ROC area.

Table 4 Statistics of the experimental results for ML and ontology classifiers

Accuracy Precision Recall F-Measure ROC Area
Folds-10 Split-66% Folds-10 Split-66% Folds-10 Split-66% Folds-10 Split-66% Folds-10 Split-66%
SVM 0,773 0,813 0,785 0,813 0,898 0,904 0,838 0,856 0,720 0,729
KNN 0,702 0,806 0,759 0,806 0,794 0,792 0,776 0,799 0,650 0,691
ANN 0,754 0,836 0,798 0,836 0,832 0,775 0,815 0,805 0,793 0,772
LR 0,772 0,828 0,793 0,828 0,880 0,893 0,834 0,859 0,832 0,855
NB 0,763 0,824 0,802 0,824 0,844 0,843 0,823 0,833 0,819 0,854
DT 0,738 0,809 0,790 0,809 0,814 0,854 0,802 0,831 0,751 0,796
Ontology 0,775 0,812 0,812 0,812 0,867 0,909 0,838 0,858 0,808 0,819

Discussion
In our measurements, we used two test mode options, and we noticed that
the percentage split was exceeded in the cross-validation test mode due to the
small data mass, for this we will base by following on a cross-validation 10
times.
332 H. El Massari et al.

In this benchmarking, we used classification machine learning algorithms

to retrieve the performance metrics obtained from the classifiers
We compared the ontology results to different machine learning algo-
rithms, and the experimental results show that the ontology classifier is con-
sidered the best with a high accuracy 77.5%, followed by the SVM algorithms
77.3% and logistic regression 77.2%. We conclude that the combination
of machine learning and ontological reasoning (i.e., using rules extracted
from machine learning algorithms and integrating them using SWRL into
the ontology) may give better results. Moreover, these comparison results
confirm how the knowledge representation and reasoning capabilities of
OWL ontology could provide additional benefits besides classification.
Moreover, the ontology classifier is an interpretable model, which can
thus provide information on how the process makes the decision. The results
of the ontology classifier are identical and comparable to those of the machine
learning classifiers. The results are also human interpretable and the rules can
be changed or added as needed.
Our comparative study is selective and unique in the way that we have
integrated for the first-time ontology with machine learning and precisely in
the field of the prediction of diabetic patients; it is therefore a first compara-
tive analysis of ML and ontology classifiers. No meaningful comparison was
made for this reason; on the other hand, researchers use different data and
other methods for selection and performance improvement.

6 Conclusion and Future Work

Machine learning techniques are widely used in all scientific fields and are
responsible for revolutionizing industries across the world. The field of health
has recently experienced great development in terms of the use of automatic
learning mechanisms and methods. These techniques have shown effective
results and could be useful in the management of chronic diseases such as
diabetes.
The Semantic Web, for its part, has proven its value and strength in
various fields, including the field of health, ontology as a part of the Semantic
Web comes with its ability to process concepts and relationships way humans
perceive interrelated concepts.
This comparative analysis summarizes the result obtained from the
most common classification machine learning methods and ontology-based
machine learning. The findings reveal that, even with no feature selection
applied, the ontology classification method has the highest accuracy. This
 Diabetes Prediction Using Machine Learning Algorithms and Ontology 333

leads us to a new search field that we suggest and encourage researchers to

contribute and create new ideas in the same context, to give more results
and comparison, for the purpose of prediction, recommendation, or make a
decision, etc.
From our side, we look forward to enhancing this comparative study by
applying new approaches to integrate rules of machine learning with the
ontology classification method, we also intend to use regression machine
learning algorithms

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Biographies

Hakim El Massari received his master degree from Normal Superior

School of Abdelmalek Essaadi University, Tétouan, Morocco, in 2014.
Currently, he is preparing his Ph.D. in computer science at the National
School of Applied Sciences, Sultan Moulay Slimane University, Khouribga,
Morocco. His research areas include Machine Learning, Deep Learning,
Big Data, Semantic Web, and Ontology. He can be contacted at email:
[email protected].
336 H. El Massari et al.

Zineb Sabouri received her in Computer Engineering degree from the

National School of Applied Sciences of Khouribga, Morocco. She worked
as a computer engineer in a multinational. Currently, she is a Phd Student in
computer science at Sultane Moulay Slimane University. Her area of interest
is Machine Learning, Intelligent Systems, Deep Learning, and Big Data.

Sajida Mhammedi received her Ms Degree in Computer Engineering from

Faculty of Science and Technologie, Beni Mellal Morocco, She worked as a
visiting researcher at the Sultane Moulay Slimane University, Her research
interests include Machine Learning, Semantic Web, recommendation sys-
tems, Ontology, and Big Data.
 Diabetes Prediction Using Machine Learning Algorithms and Ontology 337

Noreddine Gherabi is a professor of computer science with industrial and

academic experience. He holds a doctorate degree in computer science.
In 2013, he worked as a professor of computer science at Mohamed Ben
Abdellah University and since 2015 has worked as a research professor at
Sultan Moulay Slimane University, Morocco. Member of the International
Association of Engineers (IAENG).
Professor Gherabi having several contributions in information systems
namely: big data, semantic web, pattern recognition, intelligent systems . . . .
He has several papers (book chapters, international journals, and con-
ferences/workshops), and edited books. He has served on executive and
technical program committees and as a reviewer of numerous international
conferences and journals, he convened and chaired more than 30 confer-
ences and workshops. He is member of the editorial board of several other
renowned international journals:
• Co-editor in chief (Editorial Board) in the journal “The International
Journal of sports science and engineering for children” (IJSSEC).
• Associate Editor in the journal “International Journal of Engineering
Research and Sports Science”.
• Reviewer in several journals/Conferences
• Excellence Award, the best innovation in science and technology 2009
Last books in Springer :
• Intelligent Systems in Big Data, Semantic Web and Machine Learning
• Advances in Information, Communication and Cybersecurity
• Information Technology and Communication Systems
His research areas include Machine Learning, Deep Learning, Big
Data, Semantic Web, and Ontology. He can be contacted at email:
[email protected].