Classification of Autism Spectrum Disorder Using

Convolutional Neural Networks

KEYWORDS ABSTRACT
Autism spectrum The current ASD diagnosis method which is based on clinical
disorder (ASD), interviews and observations of behaviors, characteristics, and
convolutional neural abilities, exabits some limitations. Additionally, considering the
network (CNN), current challenges in identifying the causes and mechanisms
deep learning, associated with ASD, there is an essential need for automated
resting-state functional techniques capable of providing an accurate classification between
magnetic resonance ASD and typically developed (TD). In this paper, a convolutional
imaging (rs-fMRI) neural network capable of differentiating ASD from TD is proposed.
The proposed network consists of 3 main stages. The preprocessing
as the 1st stage, then converting 4D functional MRI images into 2D and
labelling them as ASD or TD. Finally, the CNN, as the 3 rd stage, to
classify images into ASD or TD. This network employs the well-known
autism brain-imaging data exchange (ABIDE) dataset of the resting-
state functional magnetic resonance imaging (fMRI) of total 141
subjects of 5- to- 18 years old. The same network was trained and
tested using a sub-group of 18 subjects of 5- to- 10 years old and
achieved accuracy of 99% and 98% respectively.

1 INTRODUCTION restricted and repetitive behaviors (including

Health control for differentiating children with
autism from typically developed (TD) ones, has
been an important tool in the research field for
many years. Autism spectrum disorder (ASD) is
one of the major neurodevelopmental disorders
affecting children nowadays. Approximately,
1.5M children in Egypt have been identified with
some form of ASD and the statistics have shown,
alas, a significantly increasing percentage [1].
ASD is gene-environmental factors and occurs
four times more frequently in boys than in girls.
It is a multi-factorial neurodevelopmental
disorder, which is characterized by serious
impairments regarding two main aspects: social
and communication impairments and
stereotyped behaviors. There are many
symptoms associated with ASD, including (but
not limited to) social isolation, defects in joint
attention, and linguistic problems (such as
linguistic idiosyncrasies and neologisms) [2],
fixing on certain routines), and some repeated
movements. It must be noted that no single
behavior seems to be specifically related to
autism. Behaviors that appear to have and
elevated pattern of occurrence and their severity
must be considered. ASD also includes autistic
disorder, Asperger syndrome, and pervasive
developmental disorder not otherwise specified
(PDD-NOS) [3]. The available ASD diagnosis
techniques include clinical interviews and
behavior observations using standard rating
scales, as well as, genetic labs. The current ASD
diagnosis method, which is based on clinical
interviews and observations of behaviors,
characteristics, and abilities against the expected
developmental growth of a typical child exabits
some limitations. It also highly depends on the
doctor’s experience and may require a relatively
long period of observation and evaluation to
make a decision. In addition, it is incapable of

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finding out the underlying biological factors
behind the observed behavioral symptoms and
thus providing the proper treatment. Therefore,
applying classification techniques to
neuroimaging data obtained from magnetic
resonance imaging (MRI) and functional
magnetic resonance imaging (fMRI) for
differentiating ASD from non-ASD (TD) must be a
high priority in the neuroscientific research field.
The growing rapidly field of machine learning has
demonstrated outstanding success various
application domains and in the ASD domain, in
particular. The experimental results have shown
that the deep learning method is superior over
other traditional methods in the fields of image
processing, computer vision, bioinformatics, and
many more. This highlights how rapidly the
revolution of deep learning has refocused
medical image processing research [4].
Therefore, considering the current challenges in
identifying the causes and mechanisms
associated with ASDs, there is an essential need
for automated techniques capable of providing
an accurate classification between ASD and TD.
The application of classification techniques to
neuroimaging data obtained from structural
MRI, diffusion tensor imaging (DTI), (fMRI), and
magnetoencephalography for differentiating
ASD from TD has been a neuroscientific research
topic for years. The fMRI has a higher spatial
resolution and reasonable temporal resolution
compared to other neuroimaging techniques.
These advantages facilitate brain imaging
considering various aspects.
First, neuroimaging data can be analyzed
considering different approaches such as brain
activity and brain connectivity. The brain
connectivity includes three main categories:
structural brain connectivity, functional brain
connectivity, and effective/ causal brain
connectivity. A PubMed search regarding the
usage of the autism-brain-imaging data
exchange (ABIDE) dataset since its inception in
2013 has resulted in many publications [5 - 13].
Authors in [5] used a probabilistic neural
network to classify ASD from TD with 90%
accuracy. A 3D convolutional neural network
Electronic copy available at: https://ssrn.com/abstract=4057055
(CNN) algorithm with different architectures was
applied to classify ASD using health controls and
achieved accuracies between 45% and 73.3% as
reported in [6], [7], [8] and [9].
In the work proposed by Wang et al. [10], two
scenarios were applied to evaluate the
performance of a graphical CNN. In the first, the
CNN was applied to the k-voted functional
connectivity matrices. In the second one, the
performance related to the number of frames
was evaluated by applying the same steps as
those of the first scenario but with different
number of frames per individual. Accuracies
71.6% and 98.8% were achieved for scenarios
one and two, respectively.
In [11], Plitt et al. used over 10 different neural
network algorithms to classify ASD using health
controls. However, the best accuracy they
achieved was 76.67%. Also, they concluded that
the L2-regularized logistic regression (L2LR) and
the linear-support vector machine (L-SVM) were
the best classifiers. Statistical analysis is used in
[12] to classify ASD from TD with a 60% accuracy.
Most of the above studies showed that ASD
appears in the brain as abnormal patterns in the
default-mode network regions and in some
other regions such as the fusiform gyri,
cerebellum, amygdala, insula, and thalamus.
Second, the magnetoencephalography (MEG) is
used to investigate early responses in functional
connectivity during processing of angry, neutral,
and happy faces as reported in [13]. Their results
showed that ASD is related to abnormal patterns
in the limbic and paralimbic regions such as the
amygdala, insula, and ventromedial prefrontal
cortex of the social brain. Another neuroimaging
technique was used by Kana et al. [14]. They
employed diffusion tensor imaging and found a
decreased amount of white matter underlying
the temporal lobe in people with autism. Many
research studies were conducted to investigate
abnormal brain connectivity patterns related to
ASD. In one of these studies [15], the study
investigated the abnormal functional
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connectivity of sleeping toddlers with autism 2 METHODOLOGY
using fMRI. Their results showed abnormal
functional connectivity of the Broca’s area and
the Wernicke’s area with 72% sensitivity and
84% specificity. In [16], the authors investigated
the abnormal functional connectivity patterns of
ASD from large-scale resting-state (rs-)-fMRI
data and found hypo-connectivity of sensory-
motor regions during mental switching and
cognitive flexibility tasks as well as a hyper-
connectivity of prefrontal and parietal cortices
during high-level cognitive functions.
The comic strip vignettes was used by [14] during
fMRI to investigate the abnormal causal
correlates of physical and intentional causality of
ASD. They found a low functional connectivity
during intension causality tasks and high
functional connectivity during physical causality
tasks. They also identified 18 regions of interest
(ROI) related to ASD. Subsequently, In [17],
Deshpande et al. used these identified 18 ROIs
and applied support vector machine to classify
ASD from TD with a 95.9% accuracy. Finally, in
[18], authors conducted a physiological study of
the abnormal neural self-representation of Figure 1: Flow chart of the proposed
adults with autism, which showed that the algorithm.
activation of their ventromedial prefrontal
cortex is similar during self-representation and
other types of representation. However, a
hypoactivation of the middle cingulate cortex As shown in Figure 1, the proposed method is
was observed during self-representation. divided into 3 main steps. The first step is the
In this paper, a CNN architecture capable of preprocessing step which was used to remove
classifying ASD from TD is proposed. The sources of artifacts, as well as, noises that may
architecture is evaluated using the ABIDE be generated because of the different brain
dataset for different age scales and subjects’ dimension between the used subjects. The
numbers. This paper is organized as follows: different allocation of the brain inside the
previous work conducted on classification using scanners, or the movement of the brain during
different techniques is introduced in section 1. the experiment. Finally, the time delay may be
The proposed method and the dataset are
generated between the slices.
described in section 2. Finally, results are
discussed in section 3 and the paper is concluded Then, the 4D functional MRI images are
in section 4. converted into 2D and labelled as ASD or TD.

The 3rd step is to use the CNN to classify images

into ASD or TD.

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2.1 DATASET
The ABIDE dataset consists of 4D rs-fMRI of
2,226 subjects in total with an age range
between 5 and 64 years. In this dataset, there is
a male gender majority (more than 80% of the
ABIDE I dataset are males). The ABDIE dataset
generally consists of two sub-sets, namely ABIDE
I and ABIDE II, which have been independently
collected from more than 24 international brain-
imaging laboratories employing different
scanning protocols and parameters. The ABIDE
dataset is summarized in Table 1.
Table 1: ABDIE I and II dataset classifications.
Source ABIDE I ABIDE II Total
No. of ASD 539 521 1,060
No. of TD 573 593 1,166
Total 1,112 1,114
In this research, to minimize the errors, which
may be generated as a result of the different
scanning protocols and parameters used, as
much as possible, we used the data samples
were generated by the University of California,
Los Angeles (UCLA) Lab only, for a 5- to 18-year-
old age range of 141 subjects in total (78 ASD and
63 TD), (19 females and 122 males).
Figure 2: Flow chart of the preprocessing
stage.
Electronic copy available at: https://ssrn.com/abstract=4057055
2.2 PREPROCESSING
The block diagram of the preprocessing step is
shown in Figure 2. The SPM12 is the software
tool used to preprocess the 4D rs-fMRI data. The
slice timing correction is initially used to remove
the inhomogeneity resulted from the time delay
between the slices. Next, re-alignment is applied
for automatic comparison and reorientation
(i.e., applying displacements and rotations so
that both the structural and functional scans are
approximately aligned to each other and to the
canonical MNI template). Then, co- registration
was applied to achieve the same goal of the
realignment phase, but to a different modality
using a different function such as the mutual
information function. In addition, segmentation
is applied to separate the different brain tissue
classes using tissue probability maps, which
quantify the probability of the presence of a
certain tissue type for each voxel. Normalization
is also applied to fit the size and the shape of the
functional/- structural images to a standard
template.
Finally, smoothing is applied, which has two
purposes: to decrease the noise since each voxel
is much noisier than the voxel average and to
decrease the inter-subject variability by
averaging every voxel with a weighted sum of its
neighbors using the weighting defined by the
Gaussian kernel. Using SPM12, the original and
the preprocessed images are compared with a
standard brain template as a reference, as
shown in Figure 3.
2.3 Data Conversion
The performance of individual identification can
be improved with the increase in the number of
fMRI frames [10]. As a result, 4D rs-fMRIs were
converted into 2D by splitting the slices and
volumes. Also, by using try and error method, we
found that selecting 20 slices and 100 volumes
which are located into the middle of the 34 slices
& 120 volumes, respectively, achieved the best
accuracy.
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 2.4 Convolutional Neural Network
The typical CNN architecture for image
processing consists of a series of layers of
convolution filters [4]. The layers and options are
specified in Table 2.

Table 2: CNN Parameters.

No. of convolutional layers 3

No. of max- pooling layers 2
No. of fully connected layers 2
No. of classification layers 1
Padding 1
Stride 2×2
Convolutional kernels 3×8/- 16/- 32
No. of epochs 15
Learning rate 0.0001

The convolutional layer equation is given as

follows [19]:

𝒙𝒋 𝒍 = 𝒇 (∑𝒊∈𝑴𝒋 𝒙𝒊 𝒍−𝟏 ∗ 𝒌𝒊𝒋 𝒍 + 𝒃𝒋 𝒍 ) (1)

where 𝑥𝑗 𝑙 is the outputs of the current layer,

𝑥𝑖 𝑙−1 is the outputs of the previous layer which
is the inputs of the current layer, 𝑘𝑖𝑗 𝑙 is the
kernel of current layer, 𝑏𝑗 𝑙 is the biases for the
current layer, and 𝑀𝑗 is the selection of input
maps.

The activation function, which is applied after

the convolutional layer, is the rectified linear unit
(ReLU). It effectively removes the negative
values from an activation map by setting them to
zero.

Then, the down sampling layer is used because it

Figure 3: The 1st three images are the original
functional images, the 2nd three are the
preprocessed ones, and the final three
images are the standard brain template.
enables increasing the number of filters in the
deeper convolutional layers without increasing
the required amount of computations per layer.
This also helps in controlling the overfitting; less
parameters result is a lower possibility of
overfitting. This layer can be presented as
follows:
𝒙𝒋 𝒍 = 𝒅𝒐𝒘𝒏(𝒙𝒋 𝒍−𝟏 ) (2)

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where 𝑑𝑜𝑤𝑛(. ) is a sub-sampling function, 𝑥𝑗 𝑙 is
the outputs of the current layer, and 𝑥𝑖 𝑙−1 is the
outputs of the previous layer which is the inputs
of the current layer. The most common down-
sampling technique is max-pooling, which
summarizes the pixels of the stride size into 1
pixel of their maximum value. This can be
represented as follows:
𝒇(𝒙𝒍 ) = 𝒎𝒂𝒙(𝟎, 𝒙𝒍 ) (3)
The padding, P, is typically applied during the
convolution operations to ensure that the input
and the output feature maps have the same
dimensions (when P = 0, the dimensions are the
same). This can be calculated as follows:
𝑭−𝟏
𝑷= 𝟐
(4)
Where P is the amount of padding, and F is the
dimension of the filter/ kernel.
Also, the size of the output feature maps can be
calculated using the following equation:
𝑵−𝑭
𝑴= +𝟏 (5)
𝑺 Table 3: Confusion matrix
with ASD are functionally organized differently,
contributing to their clinical symptoms in distinct
ways. So, in a follow-up study and as per the
early ASD detection for an individual to facilitate
his/- her treatment, the same CNN architecture
was re-applied to the same data source (UCLA I
and II) but for a different age range (5-10 years
old) of 18 subjects of males only in total (7 ASD
and 11 TD). The data for both studies was divided
70% for training, and the other 30% was used for
random tests. Also, it is ensured that the there is
no repeated data either between the training
and testing samples or between themselves.
Figure 4 shows the accuracy progress and the
loss during the training phase of the proposed
network for the UCLA data of 5- to 10-year-old
children. The obtained accuracy is 98.3%, which
is calculated using the following equation and
summarized in Table 3:
𝑻𝑷+𝑻𝑵
𝑨𝒄𝒄𝒖𝒓𝒂𝒄𝒚 = 𝑻𝑷+𝑭𝑷+𝑻𝑵+𝑭𝑵
(6)

where N is the dimension of the input feature Actual

maps, F is the dimension of the filter, M is the Positive Negative
dimension of the output feature map, and S is Predicted Positive 𝑇𝑃 𝐹𝑃
the stride length. Negative 𝐹𝑁 𝑇𝑁

The processes of one forward pass, loss function

where: 𝑇𝑃 (true positive) is the no. of positive
calculation, one backward pass, and parameter
predicted cases, which are actually positive, 𝑇𝑁
updating constitute one training iteration. The
(true negative) is the no. of negative predicted
CNN training process is a sequential process
requiring many iterations (epochs) to optimize cases, which are actually negative, 𝐹𝑃 (false
the network parameters. In every epoch, a positive) is the no. of positive predicted cases,
subset of samples is randomly selected from the which are actually negative (type I error), and 𝐹𝑁
training data, and it is presented to the network (false negative) is the no. of negative predicted
to update its parameters using the backward cases, which are actually positive (type II error).
propagation, until the system reaches The system’s performance was measured using
saturation. the following equations:
3 RESULTS AND DISCUSSION 𝑻𝑷
𝑺𝒆𝒏𝒔𝒊𝒕𝒊𝒗𝒊𝒕𝒚 = 𝑻𝑷+𝑭𝑵
= 99.6% (7)
First, we applied the proposed CNN architecture 𝑻𝑵
using 141 subjects. The ASD occurs four times 𝑺𝒑𝒆𝒄𝒊𝒇𝒊𝒄𝒊𝒕𝒚 = 𝑻𝑵+𝑭𝑷
= 97.4% (8)
more frequently in boys than in girls. Authors in 𝑻𝑷
𝑷𝒓𝒆𝒄𝒊𝒔𝒊𝒐𝒏 = = 95.9% (9)
[20] found that the brains of females and males 𝑻𝑷+𝑭𝑷

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 Figure 4: Accuracy vs. loss during the training phase.
In contrast, [21] used CNN to classify the
histograms of the gray matter volumes
estimated from T1-weighted MRIs of ASD and
TD. In [22], CNN was used to classify the mean
and standard deviation of nine different
statistical measures within each ROI in ASD and
TD. Authors in [8] and [23] used CNN to classify
the mean time-series within each ROI in ASD and
TD. A feature-fused CNN was used to classify the
outputs of two sub-CNN networks in ASD and TD,
[9]. Two scenarios were done by Wang et. al. in
[10]. The results obtained using the proposed
CNN model are compared with those obtained
from other previously reported CNN models, as
shown in Table 4.
4 TOOLS AND TIME CONSUPTION
The proposed architecture was trained and
tested using Matlab in an Intel i7-8550U CPU (1.8
GHz), RADEON GRAPHICS, 8GB RAM. The
computation time was 18 min.
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5 CONCLUSION
In this work, a CNN architecture for classifying
ASD using rs-MRI data was proposed. The
proposed network consists of 14 layers in total (1
input layer, 3 convolutional layers, 3 ReLU layers,
2 max-pooling layers followed by 2 fully
connected layers, 2 soft-max layers, and 1
classification layer) and it was used to predict the
output. Finally, a classification layer was
employed to generate the predicted class. The
proposed architecture was applied on two data
samples from the UCLA lab and published in the
ABIDE dataset, 5- to 18-year-old and 5- to 10-
year-old samples. The achieved accuracy was
99.9% and 98.3%, respectively.
By comparing the results obtained from the
proposed CNN algorithm with those obtained
from other previously reported CNN algorithms,
the superior performance of the proposed
algorithm was verified.
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Table 4: Comparison between the proposed CNN architecture and other previously reported CNNs

Authors Data size Algorithm Frame# Accuracy

Xiaoxiao et al. [24] 130 subjects CNN _ 89%
Tamilarasi et al. [25] 300 subjects CNN _ 89.2
You et al. [9] 184 subjects CNN _ 68.5%
Wang et al. [10] 100 subjects CNN 100 per individual 98.8%
Proposed architecture 141 subjects CNN 2000 per individual 99.8%

Notes in Bioinformatics), 2018, vol. 11072

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