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Article
Multimodal Early Alzheimer’s Detection, a Genetic Algorithm
Approach with Support Vector Machines
Ana G. Sánchez-Reyna 1,† , José M. Celaya-Padilla 1,† , Carlos E. Galván-Tejada 1 , Huizilopoztli Luna-García 1 ,
Hamurabi Gamboa-Rosales 1 , Andres Ramirez-Morales 2 , Jorge I. Galván-Tejada 1, *
and on behalf of the Alzheimer’s Disease Neuroimaging Initiative ‡

1 Unidad Académica de Ingeniería Eléctrica, Universidad Autónoma de Zacatecas, Jardín Juárez 147,
Centro Historico, Zacatecas 98000, Mexico; ing.agsreyna19@gmail.com (A.G.S.-R.);
jose.celaya@uaz.edu.mx (J.M.C.-P.); ericgalvan@uaz.edu.mx (C.E.G.-T.); hlugar@uaz.edu.mx (H.L.-G.);
hamurabigr@uaz.edu.mx (H.G.-R.)
2 Department of Physics, Kyungpook National University, 80 Daehak-ro, Daegu 41566, Korea;
andres@knu.ac.kr
* Correspondence: gatejo@uaz.edu.mx
† These authors contributed equally to this work.
‡ Membership of the Alzheimer’s Disease Neuroimaging Initiative is provided in the acknowledgments.


 Abstract: Alzheimer’s disease (AD) is a neurodegenerative disease that mainly affects older adults.
Citation: Sánchez-Reyna, A.G.; Currently, AD is associated with certain hypometabolic biomarkers, beta-amyloid peptides, hy-
Celaya-Padilla, J.M.; Galvan-Tejada, perphosphorylated tau protein, and changes in brain morphology. Accurate diagnosis of AD, as
C.E.; Luna-García, H.; Gamboa- well as mild cognitive impairment (MCI) (prodromal stage of AD), is essential for early care of the
Rosales, H.; Ramirez-Morales, A.; disease. As a result, machine learning techniques have been used in recent years for the diagnosis
Galvan-Tejada, J.I.; Alzheimer’s of AD. In this research, we propose a novel methodology to generate a multivariate model that
Disease Neuroimaging Initiative. combines different types of features for the detection of AD. In order to obtain a robust biomarker,
Multimodal Early Alzheimer’s ADNI baseline data, clinical and neuropsychological assessments (1024 features) of 106 patients
Detection, a Genetic Algorithm
were used. The data were normalized, and a genetic algorithm was implemented for the selection of
Approach with Support Vector
the most significant features. Subsequently, for the development and validation of the multivariate
Machines. Healthcare 2021, 9, 971.
classification model, a support vector machine model was created, and a five-fold cross-validation
https://doi.org/10.3390/
with an AUC of 87.63% was used to measure model performance. Lastly, an independent blind test
healthcare9080971
of our final model, using 20 patients not considered during the model construction, yielded an AUC
Academic Editors: Yimin Zhou and of 100%.
Zuguo Chen
Keywords: Alzheimer’s disease; support vector machine; genetic algorithm
Received: 1 July 2021
Accepted: 26 July 2021
Published: 31 July 2021
1. Introduction
Publisher’s Note: MDPI stays neutral Alzheimer’s disease is one of the most common neurodegenerative diseases, mainly
with regard to jurisdictional claims in
affecting older adults. According to the World Health Organization [1] and Alzheimer’s
published maps and institutional affil-
Disease International [2], in 2018, dementia affected approximately 50 million people
iations.
worldwide, with an estimate of 75 million by 2030 and approximately 150 million by 2050.
Moreover, there is a co-occurrence of AD with several chronic diseases, such as diabetes
mellitus, which aggravate the treatment and outcome [3].
Although Alzheimer’s disease has no cure, there are pharmacological treatments to
Copyright: © 2021 by the authors. control the symptoms. Diagnosing AD in the mild stages allows the use of treatments that
Licensee MDPI, Basel, Switzerland. might delay the progression of the disease. Late AD detection, however, may lower the
This article is an open access article effectiveness of a given treatment. Hence, early detection is imperative for maximum effi-
distributed under the terms and
ciency [4]. There are efforts devoted to study Alzheimer’s disease, such as the Alzheimer’s
conditions of the Creative Commons
Disease Neuroimaging Initiative (ADNI) [5], which has documented a database of medical
Attribution (CC BY) license (https://
images, data from biological markers (biomarkers), and clinical and neuropsychological
creativecommons.org/licenses/by/
assessments of patients since 2004; these data are publicly available for scientific research.
4.0/).

Healthcare 2021, 9, 971. https://doi.org/10.3390/healthcare9080971 https://www.mdpi.com/journal/healthcare


Healthcare 2021, 9, 971 2 of 19

Typically, biomarkers to diagnose AD are extracted from the analyses of medical


images such as MRI and PET [6,7]. Moreover, blood metabolites have been studied as
possible biomarkers in the AD diagnosis [8]. Others techniques utilize speech data, which
contain features extracted from the spectrogram of the patient’s voice [9]. Recently, the com-
bination of clinical and neuropsychological assessments to extract biomarkers has attracted
attention, since these assessments are economic, easy to apply and compute their effec-
tiveness and are accessible in places where blood and medical images tests are difficult to
find [10–12]. These characteristics make the clinical and neuropsychological assessments
useful for early AD detection. This paper focuses on the latter assessments.
Several medical investigations are based on the use of multivariate models, that is,
the use of multiple features (biomarkers in this work) and their correlation. Through
machine learning (ML), artificial intelligence (AI) assists in creating a multivariate model
that aims to describe a given disease; the model is trained/fitted using well-characterized
data, empowering the model to infer properties of data not considered during the training
phase. In recent years, the use of ML in the area of medicine has played an important role
in the diagnosis, prediction and classification of diseases. ML has improved the processing
of medical images from different specialties and diagnosing with good precision various
diseases such as breast cancer, skin cancer, colon cancer, cerebral microbleeds, diabetes
disease and cardiovascular disease, in conjunction with others [13–15]. In the present work,
the use of ML for early AD detection, is explored.
One of the main challenges in the development of new biomarkers, for multifactorial
diseases, is the reduction of the data dimensionality. Copious sources of information, such
as clinical, imaging, metabolomic, etc., are readily available; the latter requires great efforts
to generate methodologies that reduce the number of features/dimensionality for the
efficient development of biomarkers. A promising approach to tackle this dimensionality
reduction challenge is the use of genetic algorithms. The genetic algorithms are techniques
of evolutionary computation, with low computational requirements, for finding solutions
to complex search and optimization problems [16]. Inspired by the Darwinian theory of
evolution, a genetic algorithm evolves iteratively a population of chromosomes (solutions)
and their genes, through a process of selection, crossover, and mutation, where the fittest
solutions (best biomarkers in the present case) prevail.
Specifically, this work proposes the use of ADNI-related features, gene indexes,
and clinical and neuropsychological assessments as features to build ML models based on
support vector machines to describe AD. Support vector machines are chosen as they offer
high accuracy and work well in high dimensional spaces [17]. In addition, we propose the
use of a genetic algorithm to select the most robust models to obtain biomarkers for the
detection of AD at an early stage of the disease between MCI and cognitive normal patients.
We expect that the combination of genetic algorithms and support vector machines will
benefit the early detection of AD. This paper is organized as follows: Section 2 discusses the
criteria that could be used to diagnose AD and addresses related work. Section 3 describes
the methodology used to build a model to classify subjects with AD vs. MCI and cognitive
normal (CN) (see Figure 1). Section 4 presents the results obtained from the models, while
Section 5 addresses the discussion, where the results of the final model are presented and
compared with other studies, a zoomed view of the figures for the results of this section
can be found in Appendix A. Finally, Sections 6 and 7 present the conclusions and future
work, respectively.

2. Alzheimer’s Disease Diagnosis and Related Work


2.1. Alzheimer’s Disease Diagnosis
It is possible to diagnose AD by combining clinical and neuropsychological assess-
ments, in conjunction with medical imaging. For example, the analysis of cerebrospinal
fluid (CSF) biomarkers with respect to neuropsychological assessments is used to deter-
mine the degree of degeneration of cognitive and behavioral functioning. This class of
studies encloses the Mini-Mental State Examination (MMSE) [18], which is a set of stan-
Healthcare 2021, 9, 971 3 of 19

dardized questions used internationally to measure cognitive impairment. The MMSE


score is calculated by tallying the number of questions answered correctly; a lower score
indicates greater cognitive impairment. The Alzheimer’s Disease Assessment Scale (ADAS)
Cognitive Subscale with 11 items (ADAS-Cog 11) [19] and its variant with 2 additional
items (ADAS-Cog 13) [20] are sub-scales of the ADAS for differentiating between normal
and impaired cognitive functioning and assessing the severity of cognitive symptoms
of dementia. The Geriatric Depression Scale (GDS) [21], which is a test that indicates
the presence of depression in older adults, and the Functional Activities Questionnaire
(FAQ) [22], which measures functional changes in adults using a scale of instrumental
activities, are also key assessments in diagnosing AD. Additionally, there are estimations
for the global scaling of dementia that clinically evaluate and classify its progression and
severity, such as the Global Deterioration Scale [23], which assesses the degree of deterio-
ration of cognitive function, and the Clinical Dementia Rating (CDR), which is a staging
instrument for classifying the severity of dementia. The CDR produces a global score
(CDGLOBAL) that determines the stage of dementia and a sum-of-boxes score (CDRSB)
that measures the severity of dementia. An algorithm is used to calculate the CDGLOBAL
score, while the CDRSB score is calculated by summing each of the domain box scores [24]
(see Table 1). In terms of medical imaging, magnetic resonance imaging (MRI) and positron
emission tomography (PET) are the most commonly used. This work studies clinical and
neuropsychological assessments and laboratory analysis for the diagnosis of AD. Some
considered examples are listed in Table 1.

Table 1. Examples of clinical and neuropsychological assessments and laboratory analysis for the
diagnosis of AD considered in this work.

Assessments Score Range Score Stages of Cognitive Function


MMSE 0–30 24–30 Normal cognitive
19–23 Mild dementia
10–18 Moderate dementia
<9 Severe dementia
Higher scores suggest greater
ADAS-Cog 11 0–70 severity of the cognitive symptoms
of dementia
Higher scores suggest greater
ADAS-Cog 13 0–85 severity of the cognitive symptoms
of dementia
GDS 0–15 0–4 Normal
5–8 Mild depression
9–11 Moderate depression
12–15 Severe depression
Global Deterioration Scale * 1–7 1 Normal cognitive
2 Age associated memory impairment
3 MCI
4 Mild dementia
5 Moderate dementia
6 Moderately severe dementia
7 Severe dementia
CDGLOBAL 0–3 0 No dementia
0.5 Questionable dementia
1 MCI
2 Moderate cognitive impairment
3 Severe cognitive impairment
* The Global Deterioration Scale assessment is not used by ADNI.
Healthcare 2021, 9, 971 4 of 19

2.2. Related Work


Machine learning methodologies have been applied successfully in the context of the
study of AD. For example, Daoqiang Zhang et al. [6] built an ML model by combining:
ADNI baseline features from three modalities, using data from MRI (to measure brain
atrophy), hypometabolism, and certain CSF proteins to classify patients with AD (or MCI)
vs. CN. They used a multiple-kernel support vector machine [25] model to classify patients,
resulting in an accuracy of 93.2%, a sensitivity of 93% and a specificity of 93.3% to classify
AD vs. CN. To classify MCI vs. CN, a classification accuracy of 76.4%, a sensitivity of
81.8% and a specificity of 66% were reported. Hassan et al. [26] combined non-imaging
biomarkers, a CSF biomarker and clinical data to generate and compare three ML models.
The goal was to classify CN vs. MCI patients. The best ML model, was the J48 decision
trees [27], classifying the patients with an accuracy of 96.92%, area under the receiver
operating characteristic curve (AUC) of 0.985, sensitivity of 100% and specificity of 95.74%.
More recently, in 2019, Stamate et al. [28], conducted a study with clinical and cognitive
data in combination with blood metabolite data for the classification of CN vs. AD patients.
Three different ML models were compared, obtaining XGBoost [29] as the best model with
an AUC of 0.88.

3. Methodology
The proposed methodology for this study consists of six stages, as shown in Figure 1.
In the first stage, the used datasets are described (Figure 1A). In the second stage, the dataset
of interest is created by selecting the subjects according to a given inclusion criteria
(Figure 1B). In the third stage, data preprocessing is applied, and verification and treat-
ment of the empty fields and data transformation are performed (Figure 1C). In the fourth
stage, feature selection is implemented by means of a genetic algorithm (Figure 1D). Then,
a representative set of biomarkers are studied using support vector machine classifiers
(Figure 1E). Finally, a validation test is done considering different metrics (accuracy, sensi-
tivity, specificity and AUC) to determine the performance of our model (Figure 1F).

Data Subject Data pre- Feature


Classification Validation
acquisition selection processing selection

Blind test

Genetic ●
Accuracy
algorithm ●
Support ●
Sensitivity

ADNI ●
Inclusion ●
Data ●
Forward Vector ●
Specificity
Dataset criteria normalization selection Machine ●
Area under

Backward (SVM)
the ROC
elimination
curve

(A) (B) (C) (D) (E) (F)

Figure 1. Flowchart of the proposed methodology. The green squares refer to the data processing
methodology, while the white squares detail the task involved in each step. (A) The different datasets
(gene indexes and clinical and neuropsychological assessments) are obtained from the ADNI database.
(B) Each dataset is analyzed and new data sets are created by selecting subjects according to the
criteria described in Table 2. (C) A preprocessing of the data is applied: handle the empty fields and
perform data transformations. (D) The use of genetic algorithms is implemented to extract the main
data features. (E) Using the main features for Alzheimer’s detection in patients, several models are
generated using the support vector machines. (F) The validation of our results is carried out using
different metrics (accuracy, sensitivity, specificity and AUC) to determine which of the models has
the best performance.

3.1. ADNI Database


The data used in this study were obtained from the ADNI database (adni.loni.usc.edu;
accessed on 7 September 2020). The ADNI was launched in 2003 as a public–private
partnership, led by the Principal Investigator Michael W.Weiner, MD. The primary goal
of ADNI has been to test whether serial MRI, PET, other biological markers, and clinical
and neuropsychological assessments can be combined to measure the progression of
Healthcare 2021, 9, 971 5 of 19

MCI and early AD. For up-to-date information, see www.adni-info.org; accessed on 7
September 2020.

3.2. Data Selection


An exhaustive analysis of the ADNI database was carried out, and more than 200 datasets
were analyzed, containing over 314 observations and 2279 features. A filter was imple-
mented to determine which of these features may be used in the proposed study. A reduced
dataset was generated with only those patients and features that met the conditions indi-
cated in Table 2, the dataset called “upennbiomk3” was taken as the initial dataset [5,30],
which has information of 106 patients from the ADNI1 study with two or more visits each.
The objective of this study is to analyze and observe the relationship of the data for the
classification and/or diagnosis of the disease.
Table 2. Inclusion criteria.

Inclusion Criteria
1. Patients should have visit codes of baseline (bl), 12 months (m12), 24 months (m24) or 36 months (m36).
2. Verify and check the participant roster ID (RID) to ensure that the measurements were from the same
patient in the different datasets.
3. In case of examinations and evaluation scales, only the final score was taken, avoiding
redundant information.
4. The age of the patients should be between 53 and 95 years at the enrolment date.
5. No distinction of gender, education, ethnicity, race, marital status was performed.
6. Patients should have biological, clinical and neuropsychological assessments.
7. Patients with duplicated records were merged using the 1st non-empty record.

The resulting filtered dataset (FDS), after applying the above inclusion criteria of Table 2,
contains information corresponding to 106 patients (42 Female/64 Male), age (75.95 ± 6.02),
clinical and neuropsychological evaluations and diagnoses (CN = 36, MCI = 52, AD = 18).

Data Preprocessing
The FDS dataset, fulfilling the visit code “bl” requirement, comprises 103 observations
(42 Female/61 Male) and excludes 3 patients lacking this visit code. For the qualitative
features, a nominal scale was made; thus, the feature used for the diagnosis of the patient
(DX) remained as a binary variable. When the patient’s diagnosis is CN or MCI, a “0”
label was assigned, otherwise, if the patient’s diagnosis is AD, a “1” was assigned. Once
the dataset was composed of only numerical variables, a filter was performed to drop
features missing more than 6.8% of the values. Thus, the final dataset size consists of
103 observations and 927 features. From this point, two versions of FDS were ccreated
under the following criteria:
• Dataset 1 (D1): The missing values in a given feature were substituted with the mean
value of this feature to complete the records (103 observations and 927 features).
• Dataset 2 (D2): From the above dataset D1, the neuropsychological features are
eliminated, leaving a grand total of (103 observations and 904 features).
In D2, neuropsychological features were removed in an attempt to find new features
that would aid in the diagnosis of AD, given these neuropsychological features were found
to have a high correlation with AD during the experimentation described in Section 3.3.1.
Subsequently, the datasets were scaled to transform their features. In this case, a
z-score transformation was applied, that is, the mean and the standard deviation of each
feature are transformed to zero and one, respectively. The transformed values, zi , are
expressed as [31],
x − x̄
zi = i , (1)
σ
where xi are the raw values, x̄ is their mean and σ is their standard deviation of each feature
in the dataset.
Healthcare 2021, 9, 971 6 of 19

Finally, for both D1 and D2, 80% of the data was used for training and testing, and the
remaining (20%) was saved for an independent blind test.

3.3. Model Generation


ML is a part of AI, which allows statistical models to learn from the interaction between
the input data and their processes [32], achieving the identification of complex patterns
within the data to classify, identify, optimize or predict future behaviors. ML models learn
through previous experience and extraction of generic knowledge from data, being able to
improve themselves autonomously, achieving excellent performance in making predictions.
With this motivation, this paper describes a methodology that aims to generate ML models
that allow the detection of AD at an early stage. Therefore, it is necessary to select features
in D1 and D2 that help build a robust model that combines information from different
sources such as gene indexes and clinical and neuropsychological assessments.
The flow chart for the model generation is presented in Figure 2. First, the data are
split into two subsets containing 80% of the data for training and testing, leaving the
remaining 20% for blind testing. Using the 80% subset, the feature selection procedure is
performed by means of a genetic algorithm. Next, with the best selected features, a model
that describes the data is generated. To assess the train/test performance of this model, a
k-fold cross-validation [33] is carried out. Later, using the whole 80% subset, the model is
trained to generate the final model. Finally, the remaining 20% of the data (blind dataset) is
used as unseen samples to assess the performance of the model on new subjects. In the
following subsections, each stage is presented.

20%

Train Blind
DATA
Feature Selection

Cross-validation Test
Best Model
GA

80%

Full train

Figure 2. Flowchart of the proposed methodology for the model generation and validation.

3.3.1. Feature Selection


Due to the large number of features (more than 900) in the datasets D1 and D2,
constructing models, which are capable of solving classification problems, becomes a very
complex computational task. Therefore, the use of genetic algorithms is proposed. Namely,
the GALGO [34] genetic algorithm (GA) is employed here, since it is efficient for selecting
the best subset of features in high dimensional datasets. For this study, GA creates an
initial population of chromosomes constituted of random sets of features. The fitness of
the chromosomes is evaluated by comparing their ability to correctly detect AD subjects.
Depending on the obtained fitness score, the process stops if the chromosome score is
higher than the predefined goal and this chromosome is selected. On the other hand,
if the process continues, the chromosome population is replicated and the chromosomes
crossover and mutate; in this manner, the fittest chromosomes will produce next generation
offspring. This step is repeated until a chromosome is found that meets the previously
established criteria. The considered GA parameters are described in Table 3.
Healthcare 2021, 9, 971 7 of 19

The GA was used to select the best subset of features from the FDS. The GA fitness of
the chromosomes is calculated, employing support vector machines as binary classifiers.
The support vector machine (SVM) model, introduced by Vladimir Vapnik [25], was
chosen since it is robust and could be used to solve binary classification ML problems.
The SVM model uses the theory of Structural Risk Minimization to maximize its prediction
accuracy and procures avoiding data overfitting [35]. The SVM classification is carried
out by mapping the original feature space, with kernel functions, to a hyperspace where a
hyperplane is constructed, which separates the data of one class from the other [25,34].
For this study, an SVM [36] with a radial kernel was used as a classification method
in the feature genetic search; the specific parameters of the model are shown in Table 3.
The top-50 most frequent features are obtained. This ranking is then used in the next step to
build the final model. The features appearing more frequently in this selection suggest that
they are of importance to the classification of AD patients, see Figure 3 (see Figure A1 for a
zoomed view). Subsequently, a model refinement was carried out by means of forward
selection and backwards elimination to select the most compact and accurate model (see
Table 4) [37].

Table 3. GA input parameters. The genetic selection parameters are as follows: The chromosome size
is set according to the recommendation found in Reference [34]. The number of solutions is defined
to avoid bias. The number of generations is set to allow most of the models to converge (see Figure 4
or Figure A2 for a zoomed view). The goal fitness is defined to obtain a minimum performance
required. The SVM hyper-parameters are as follows: The cost C is set to control the trade-off between
decision and classification error and to avoid overfitting. A small γ value restricts the curvature of
the decision boundary. A radial basis function is selected as the SVM kernel since it yields good
out-of-box performance [38].

Parameter Value
Genetic selection Classifier SVM
Chromosome size 5
Max solutions 300
Max generations 200
Goal fitness 0.9
SVM Cost C 1
Gamma γ 0.2
Kernel Radial

Figure 3. Gene frequency and rank in the models determined by implementing GA using the
parameters in Table 3 for the selection of the top features in the dataset. (A) Gene frequency shows
the number of times that a feature has been present in the models. (B) Gene rank shows the stability
and frequency of each feature within the models, ordered by rank. For a zoomed view see Figure A1.
Healthcare 2021, 9, 971 8 of 19

Table 4. Most important features for classification of patients with Alzheimer’s obtained through the GA.

Multivariate
Dataset Version Model Name Final Model Length Features
Model Type
D1 ADvsMCI/CN-m1 SVM 2 MMSE, CDRSB
CDGLOBAL,
D2 ADvsMCI/CN-m2 SVM 2
CDRSB

The forward selection algorithm creates models by adding one feature at a time and
keeps this feature in the model only if it contributes to the overall model accuracy. The for-
ward selection process generates models that allow obtaining a high level of classification
accuracy; however, this process can add a large number of features, which could overfit the
data. To avoid the latter, a backwards elimination process was carried out; in this process,
one feature is removed one at a time if the performance does not drop considerably. On the
other hand, if the performance of the model decreases, the feature is kept. Figure 5 (see
Figure A3 for a zoomed view) shows the performance of the models obtained during the
forward selection process; for more details, please refer to the results in Section 4.

Figure 4. Evolution of the maximum fitness score across generations. The horizontal axis represents
a given generation, whilst the vertical axis represents the fitness score. The average fitness, plotted
with a blue solid line, considers all models. The average unfinished fitness, plotted with a cyan solid
line, considers all searches that failed for a given generation and represents the average worst case
expectation. The established GA goal fitness is plotted with the red dotted line. For a zoomed view
see Figure A2.

Figure 5. Performance of the most compact and accurate models after using the forward selection
methodology. The horizontal axis represents the features ordered by rank. The vertical axis shows
the classification accuracy. For a zoomed view see Figure A3.
Healthcare 2021, 9, 971 9 of 19

3.4. Model Training and Validation


Once the feature selection process was completed, a SVM classification model was
created to study D1 and D2 containing only the best features; a linear kernel was chosen
given its simplicity and expected good performance [39]. The SVM model was validated
following a five-fold cross-validation strategy on the 80% dataset (see Table 5), and the
best penalty cost for each model was found to be C = 1 for the ADvsMCI/CN-m1 model
and C = 10 for the ADvsMCI/CN-m2 model. Next, using the whole 80% training dataset,
the model was fitted and used as the final model. Lastly, with the final model, a blind
validation test was performed on the 20% blind dataset in order to measure its correctness in
diagnosing AD in new unseen subjects (see Table 6), allowing to simulate a real-life scenario.

Table 5. Performance metrics obtained by k-fold cross-validation of the ADvsMCI/CN-m1 model.

AD vs. MCI/CN
Process Metrics Average Error
Training AUC 0.9079 0.0437
Specificity 0.9882 0.0156
Sensitivity 0.8276 0.0890
Accuracy 0.9631 0.0185
Testing AUC 0.8763 0.1024
Specificity 0.9811 0.0307
Sensitivity 0.7715 0.1957
Accuracy 0.9433 0.0444

Table 6. Training metrics and blind test validation of SVM models.

Model Name Model Name


ADvsMCI/CN-m1 ADvsMCI/CN-m2
Training (80%) Blind Test (20%) Training (80%) Blind Test (20%)
AUC 0.9231 AUC 1 AUC 0.9088 AUC 1
Specificity 1 Specificity 1 Specificity 0.9714 Specificity 1
Sensitivity 0.8461 Sensitivity 1 Sensitivity 0.8461 Sensitivity 1
Accuracy 0.9759 Accuracy 1 Accuracy 0.9518 Accuracy 1
Eighty percent of the dataset was used to train the model, and blind test validation was performed on the
remaining 20%.

3.5. Performance Analysis


The performance of these models was measured through the classification metrics:
accuracy, sensitivity and specificity (see Table 6). These metrics establish which of the models
is the best for identifying Alzheimer’s patients and which features are the most significant to
obtain the best results in each phase. Sensitivity, defined in Equation (2), refers to the correct
identification of patients with dementia (true positive). Specificity, defined in Equation (3),
refers to the correct identification of patients without dementia (true negative). Accuracy is
the percentage of cases that the model has classified correctly and is defined in Equation (4).

Tp
Sensitivity = (2)
Tp + Fn

Tn
Speci f icity = (3)
Tn + Fp
Tp + Tn
Accuracy(1 − Error ) = (4)
Tp + Tn + Fp + Fn
where
Tp = True positive, number of subjects with dementia correctly classified.
Fp = False positive, number of healthy subjects incorrectly classified.
Tn = True negative, number of healthy subjects correctly classified.
Healthcare 2021, 9, 971 10 of 19

Fn = False negative, number of subjects with dementia classified as healthy.


The AUC [40] has been used to measure the performance of a classifier as well.
The AUC describes how good a model is at making a prediction, and the AUC value ranges
from 0 to 1; 0 for an incorrect prediction of 0% and 1 for a 100% correct prediction. This
metric is computed with the sensitivity and specificity. The simplest way to calculate the
AUC is to use trapezoidal integration [40].

4. Results
The obtained models and the classification metrics are presented in Tables 4–6. It is
observed that the ADvsMCI/CN-m1 model and the ADvsMCI/CN-m2 model performed
equally in the blind test. This test reproduces the conditions in a real-life scenario to
diagnose AD in new unseen patients. Consequently, to choose the best model, an addi-
tional comparison of the length of the models, their features and the method of calculat-
ing their scores (MMSE, CDRSB, CDGLOBAL), was performed: The ADvsMCI/CN-m1
model contains only two features, MMSE and CDRSB, and has scores that are easier to
calculate than the CDGLOBAL assessment. Furthermore, in clinical and research areas,
the MMSE and CDRSB are more widely used to stage the severity of dementia. Therefore,
the ADvsMCI/CN-m1 model was established as the best performing model for classifying
AD patients.
Figures 3–5 (see Appendix A for a zoomed view), show the results obtained from the
application of the GA considering the GA parameters in Table 3. The selected top features,
for the development of the most representative model, are found by this GA configuration.
Figure 3 (see Figure A1 for a zoomed view) shows the results of the feature occurrences
in the models. The horizontal axis in Figure 3A shows the features. The left-vertical axis
shows the gene frequency, that is, the number of times a feature has been present in the
models. The right-vertical axis shows the corresponding percentage in relation to the total
number of models. Figure 3B shows the GA outcome rank stabilization, and this graph
shows the frequency (vertical axis) of the best features found by the GA algorithm in a
rank-descent fashion (horizontal axis), where the solid colors represent stable features
that always aid in the classification. For a zoomed view of the figures, please refer to
Appendix A and feature selection in Section 3.3.1 for more details. The inclusion procedure,
applied to the FDS dataset, included 103 patients and 927 features. The feature selection
was implemented using a GA, which evolved a total of 200 generations, and it was repeated
300 times. Figure 3 shows the stability ranking of the first 50 features found through this
GA. The features are ordered from the most to the least frequent appearance.
Figure 4 (see Figure A2 for a zoomed view) shows the fitness of the evolved models,
where the blue line represents the mean fitness considering all models and the red line
represents the generation in which the average fitness reaches the goal fitness. Analyzing
this figure, it was determined that the GA parameters in (Table 3) are appropriate, since
the number of generations needed to find an optimal model is less than 50 generations
on average.
With the ranked features (Figure 3), a forward selection procedure was used to create
a representative model to classify AD vs. MCI/CN. Figure 5 (see Figure A3 for a zoomed
view) demonstrates how the performance increased as features were added; the model was
then reduced by a backward elimination process to select the most compact model with
the highest classification accuracy and the lowest number of features.
Subsequently, multivariate SVM classification models were created with a linear
kernel, using the features obtained from the feature selection process by the GA, and refined
by forward selection and backward elimination (see Table 4). The final SVM models have
only two features each. To evaluate their performance and choose the most optimal model,
they were subjected to cross-validation and blind tests.
The models in Table 4 were subjected to a five-fold cross-validation. Eighty percent of
the FDS data were used for this process, which was separated to train and test for each of
the models. The results obtained from training and testing the five-fold cross-validation
Healthcare 2021, 9, 971 11 of 19

of the ADvsMCI/CN-m1 model are shown in Table 5. This table reports the mean of the
classification metrics for the five folds and the error that refers to the standard deviation of
the obtained results.
For measuring the performance of the model in a new environment, the model was
trained using the whole training dataset (80%) and subsequently validated by its perfor-
mance on the blind test dataset (20%). The results of this blind test validation are presented
in Table 6.
According to the results obtained in the blind test (Table 6), each of the classification
metrics used to measure the performance of the models had a value of 1. To validate these
results, the data were plotted using only the two features of each model to observe the
correlation of the data (see Figure 6). The plots show that the data are linearly separable.
This suggests that the use of a linear kernel in the SVM models for this study is appropriate.

Figure 6. Correlation of the features of each model during training (80% training data) and blind
test (20% blind subset). (A) Shows the correlation of ADvsMCI/CN-m1 model features in training;
(B) shows the correlation of ADvsMCI/CN-m1 model features in the blind test; (C) shows the correla-
tion of ADvsMCI/CN-m2 model features in training; (D) shows the correlation of ADvsMCI/CN-m2
model features in the blind test. In these plots, the model support vectors are represented with “X”;
the points represented with “O” are the remaining data. The red color classifies the data where
Alzheimer’s disease is present, while the black color classifies MCI/CN.

5. Discussion
The proposed methodology demonstrates the effectiveness of using genetic algorithms
and support vector machines systems for the classification of AD vs MCI/CN using multi-
source information.
Healthcare 2021, 9, 971 12 of 19

The methodology combined data (gene indexes and clinical and neuropsychological
assessments) from the ADNI1 study in its baseline stage of 103 patients.
Subsequently, in the normalization stage, the features were scaled (z-score transforma-
tion) for use in patient classification. Using the features, the genetic algorithms generated
200 generations for 300 solutions in order to find the best performing multivariate model.
As the models evolved, the average accuracy was plotted as depicted in Figure 4, the models
reached their best performance within the first fifteen generations. Hence, 200 generations
were defined as an optimal parameter, since no more generations were needed. The final
model was refined using forward selection and backward elimination. The SVM models
were constructed with the features obtained in Table 4.
The performance of the final model was evaluated using a cross-validation and a blind
test to simulate a real-world scenario. The cross-validation model was trained and tested
using 80% of the FDS dataset (see Table 4), while for the blind test, the model was trained
using 80% of the FDS dataset and validated using the remaining 20% of the unseen data.
The final SVM model to classify AD vs. MCI / CN was ADvsMCI/CN-m1, which obtained
a sensitivity of 100% and a specificity of 100% in the blind test. The value of both validation
metrics suggests that the model is robust. From over 900 features, the ADvsMCI/CN-m1
model included the following two features: MMSE and CDRSB.
The features included in the final model have been previously used as individual
diagnostic features, such as the MMSE proposed by [18] and the CDRSB proposed by [24].
Our model combines individual prediction performance into a multivariate model capable
of improving early diagnosis of AD. It was also observed that the CDRSB feature, which
represents one of the scores of the CDR assessment, appears in both models, proving to be
an important assessment in the classification of patients with some degree of dementia and
healthy patients.
The model proposed by Zhang et al. [6] has a good performance for the classification
of AD vs. CN patients. Nevertheless, in this model, most of the used features are extracted
from medical images of patients (MRI and PET). The proposed model obtained in the
present work avoids the use of features from medical images and obtains a performance
as good as the one proposed by Zhang et al.; the latter empowers the proposed model, in
this paper, with the advantage to be available in places where the access to medical images
studies is limited.
Additionally, the proposed models in this study avoid the use of features obtained
from laboratory tests to diagnose/classify patients between CN and MCI (or AD). This
leads to a natural reduction of the required features. Our models show similar performance
to the models proposed by Hassan et al. [26] and Stamate et al. [28], where the number of
features is higher than fifteen. Using fewer features could be advantageous for patients
who are vulnerable to laboratory tests or biopsies. It is hoped that the models proposed in
this study are a viable alternative for this type of patient.

6. Conclusions
The proposed methodology in this study selects the most relevant features of AD data
(gene indexes and clinical and neuropsychological assessment) through the use of genetic
algorithms. These features were used to generate supervised classification algorithms
with an SVM architecture. The efficiency of the generated models was evaluated by a
cross-validation and a blind test, selecting the model with the highest sensitivity, specificity,
and whose features exhibited a good performance during the blind test, for early detection
of AD, between subjects with AD and MCI or CN subjects.
The novelty of this study is that it uses only non-imaging biomarkers, and yet a
similar performance to those derived from medical images is reached. The obtained models
integrated features that were previously individually validated by the research community.
Therefore, the proposed multivariate study combines individual predictions into a more
robust biomarker to detect early Alzheimer’s disease.
Healthcare 2021, 9, 971 13 of 19

7. Future Work
For future work we, propose to combine features extracted directly from MRI and use
them with the biomarkers obtained in this study to predict the likelihood of a CN patient
evolving into an AD patient. We will also investigate the possibility of replacing those
features that come from CSF analyses and blood-based metabolomics tests (since these
analyses are considered invasive techniques) with features obtained from MRI and develop
more robust ML models for the classification of patients with AD.

Author Contributions: A.G.S.-R. and J.M.C.-P. performed the study. A.G.S.-R. and J.M.C.-P. per-
formed the study design and data analysis. A.G.S.-R., J.M.C.-P., C.E.G.-T., J.I.G.-T., A.R.-M., H.G.-R.
and H.L.-G. contributed to materials and methods used in this study. J.I.G.-T., C.E.G.-T., J.M.C.-P.
and A.R.-M. performed statistical analysis with critical feedback to the authors. H.L.-G. and A.R.-M.
contributed with critical feedback on the methodology and manuscript writing. A.R.-M., H.G.-R.,
J.I.G.-T. and C.E.G.-T. provided technical feedback from the results. All authors interpreted findings
from the analysis and drafted the manuscript. All authors have read and agreed to the published
version of the manuscript.
Funding: This research received no external funding.
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not applicable.
Data Availability Statement: The data presented in this study are available on request from corre-
sponding author.
Acknowledgments: Data collection and sharing for this study was funded by the Alzheimer’s Dis-
ease Neuroimaging Initiative (ADNI) (National Institutes of Health Grant U01 AG024904) and DOD
ADNI (Department of Defense award number W81XWH-12-2-0012). ADNI is funded by the National
Institute on Aging, the National Institute of Biomedical Imaging and Bioengineering, and through
generous contributions from the following: AbbVie, Alzheimer’s Association; Alzheimer’s Drug
Discovery Foundation; Araclon Biotech; BioClinica, Inc.; Biogen; Bristol-Myers Squibb Company;
CereSpir, Inc.; Cogstate; Eisai Inc.; Elan Pharmaceuticals, Inc.; Eli Lilly and Company; EuroImmun; F.
Hoffmann-La Roche Ltd and its affiliated company Genentech, Inc.; Fujirebio; GE Healthcare; IXICO
Ltd.; Janssen Alzheimer Immunotherapy Research and Development, LLC.; Johnson & Johnson
Pharmaceutical Research and Development LLC.; Lumosity; Lundbeck; Merck & Co., Inc.; Meso
Scale Diagnostics, LLC.; NeuroRx Research; Neurotrack Technologies; Novartis Pharmaceuticals
Corporation; Pfizer Inc.; Piramal Imaging; Servier; Takeda Pharmaceutical Company; and Transition
Therapeutics. The Canadian Institutes of Health Research is providing funds to support ADNI
clinical sites in Canada. Private sector contributions are facilitated by the Foundation for the Na-
tional Institutes of Health (www.fnih.org; accessed on 7 August 2020). The grantee organization is
the Northern California Institute for Research and Education, and the study is coordinated by the
Alzheimer’s Therapeutic Research Institute at the University of Southern California. ADNI data are
disseminated by the Laboratory for Neuro Imaging at the University of Southern California. Andres
Ramirez-Morales acknowledges support from the National Research Foundation (NRF) of Korea,
Grants 2018R1A6A1A06024970, 2019R1I1A3A01058933, 2020R1I1A1A01066423. (Data used in prepa-
ration of this article were obtained from the Alzheimer’s Disease Neuroimaging Initiative (ADNI)
database (adni.loni.usc.edu; accessed on 7 September 2020). As such, the investigators within the
ADNI contributed to the design and implementation of ADNI and/or provided data but did not par-
ticipate in analysis or writing of this report. A complete listing of ADNI investigators can be found at:
http://adni.loni.usc.edu/wp-content/uploads/how_to_apply/ADNI_Acknowledgement_List.pdf;
(accessed on 7 September 2020).
Conflicts of Interest: The authors declare no conflict of interest.
Healthcare 2021, 9, 971 14 of 19

Abbreviations
The following abbreviations are used in this manuscript:

AD Alzheimer’s disease
ADAS Alzheimer’s Disease Assessment Scale
ADAS-Cog 11 ADAS-Cognitive Subscale with 11 items
ADAS-Cog 13 ADAS-Cognitive Subscale with 13 items
ADNI Alzheimer’s Disease Neuroimaging Initiative
AI Artificial Intelligence
AUC Area Under the Receiver Operating Characteristic Curve
bl Baseline
CDGLOBAL Clinical Dementia Rating Global Score
CDR Clinical Dementia Rating
CDRSB Clinical Dementia Rating sum-of-boxes score
CN Cognitive Normal
CSF Cerebrospinal Fluid
D1 Dataset 1
D2 Dataset 2
Fn False Negative
Fp False Positive
FAQ Functional Activities Questionnaire
FDS Filtered Dataset
GA GALGO Genetic Algorithm
GDS Geriatric Depression Scale
m12 12 Months
m24 24 Months
m36 36 Months
MCI Mild Cognitive Impairment
ML Machine Learning
MMSE Mini-Mental State Examination
MRI Magnetic Resonance Imaging
PET Positron Emission Tomography
RID Participant Roster ID
SVM Support Vector Machine
Tn True Negative
Tp True Positive
Healthcare 2021, 9, 971 15 of 19

Appendix A

Figure A1. Gene frequency and rank in the models determined by implementing GA using the
parameters in Table 3 for the selection of the top features in the dataset. (A) Gene frequency shows
the number of times that a feature has been present in the models. (B) Gene rank shows the stability
and frequency of each feature within the models, ordered by rank.
Healthcare 2021, 9, 971 16 of 19

Figure A2. Evolution of the maximum fitness score across generations. The horizontal axis represents
a given generation, whilst the vertical axis represents the fitness score. The average fitness, plotted
with a blue solid line, considers all models. The average unfinished fitness, plotted with a cyan solid
line, considers all searches that failed for a given generation and represents the average worst-case
expectation. The established GA goal fitness is plotted with the red dotted line.
Healthcare 2021, 9, 971 17 of 19

Figure A3. Performance of the most compact and accurate models after using the forward selection
methodology. The horizontal axis represents the features ordered by rank. The vertical axis shows
the classification accuracy.
Healthcare 2021, 9, 971 18 of 19

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