Early Detection of Alzheimer’s Disease

Jayant Harwalkar Hemankith Reddy M Shravani

Department of Computer Science Department of Computer Science Department of Computer Science
PES University PES University PES University
Bangalore, India Bangalore, India Bangalore, India
jayanthharwalkar@gmail.com hemankith@gmail.com hemankith@gmail.com
Neelesh S developed machine learning and deep learning model
Department of Computer Science which predicts AD risk.
PES University Despite the currently available biomarkers, electronic
Bangalore, India healthcare data, health records, and increase in
hemankith@gmail.com digitalization

Abstract—This document is a model and instructions for

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I. INTRODUCTION
Alzheimer’s disease(AD), a brain disorder, is
considered to be a form of dementia that slowly
destroys memory, thinking, and eventually, the ability to
perform daily tasks. It is caused by the loss and
degeneration of neurons in the brain mostly in the
cortex region. AD is caused by the formation of plagues
in which clumps of abnormal proteins are formed
outside the neuron which block the neuron connections,
disrupting signals, which leads to impairment of the
brain. AD can also be formed by tangles in which a
protein build-up occurs inside the neuron, affecting the
signal transition. In AD, the brain starts to shrink, the
gyri become narrow while the sulci widen. The risk of
getting this disease increases with age and it is mostly
seen in older people[].
AD can be diagnosed by doing a brain autopsy and
biopsy and there is no complete cure for the disease[].
Having an early detection improves the chances for
effective treatment and the ability of the individual to
participate in a wide variety of clinical trials. Treatment
is effective if given in the early stages. Currently, there
are no treatments to reverse the damage already caused
but proper medication can halt the further progression
of AD and prolong life[].
AD can be detected by performing scans like magnetic
resonance imaging(MRI), computed tomography(CT), or
positron emission tomography(PET)[3]. Researchers use
raw MRI brain scans, demographic images, and clinical
data to compare it with normal cognition by using a
of data, there is not enough information on how to use
this large-scale health data in the prediction of AD risk,
but there are few studies that demonstrate that
potential AD risk can be predicted when these resources
are combined with data-driven machine learning
models.[5]
II. LITERATURE REVIEW
As the person ages, the risk of getting Alzheimer’s
disease also increases which is one of the major health
issues. So early diagnosis and detection are necessary to
allow them to get efficient treatment.[] Considering the
amount of research that is made, machine learning
techniques, and branches of artificial intelligence are
widely used for this. Even with the existence of all these
methods, there are no instruments for detection.
However, certain, physical, neuropsychological,
physiological, and neurological tests can be used for the
identification of this disease.[12] One such method is by
using SVM for feature selection. There are many types
of classifications that uses SVM for feature extraction,
for example, it can be done using SPECT images which
use SPECT perfusion imaging to classify healthy patients’
images from those having AD. The approach is based on
linear programming formulation based on a linear
hyperplane which performs simultaneous feature
selection and classification. They also contain proximity
information regarding features and later generate a
classifier that not only selects the most relevant voxels
but also the most relevant areas for classification which
gives more robust classifiers that are better for
interpretation. This method has a specificity of 90 % and
a specificity of 84%, this is also proven to be better than
Fisher Linear Discriminant(FLD) and also statistical
parametric mapping(SPM) and also better than human
experts. The location of voxels is incorporated in the
problem, so the feature selection here depends on the
brain regions instead of separate non-connected voxels.
The voxel values that are taken as features outperform
the local approach of SPM.[6] Even though this
approach provided good results on Cohort 1, the results
weren’t great for inter-cohort as the accuracy dropped
to 74. This showed that the selected regions of the
considered refined atlas did not have good
generalisation ability.[7] One of the other methods is by
using CNN for prediction and classification. The
classification is done using two methods, the first one
contains CNN architecture on MRI scans based on 2D
and 3 D convolutions. The CNN architecture is built from
scratch. The second method consists of transfer learning
techniques like the VGG19 pre-trained model. The two
methods are evaluated using nine performance metrics.
The end-to-end framework is applied for this medical
image classification. Simple CNN architecture is applied
to 2D and 3D images of MRI. 2D and 3D convolutions-
based CNN architectures are used. This can be used
along with deep learning pre-trained models such as
VGG19. Standard CNN contains feature extraction,
feature reduction and classification so there is no need
to do extraction manually. The weights in initial layers
act as feature extractors, their values can be further
improved by iterative learning.[9]
III. DATASET
The data were obtained from the Alzheimer’s Disease
Neuroimaging Initiative (ADNI)database
(adni.loni.usc.edu). The ADNI is a long-term study that
uses indicators such as imaging, genetic, clinical, and
biochemical markers to follow and detect Alzheimer’s
disease early. The ADNI data repository has around 2220
patients’ imaging, clinical, and genetic data from four
investigations (ADNI3, ADNI2, ADNI1 and ADNI GO). The
image data (MRI scans) was used. ADNI provides
researchers with as they work on the progression of
Alzheimer’s disease. PET images, MRI images, genetics,
cognitive tests, CSF, and blood data are collected and
validated and these can be used by researchers as
predictors of the disease. The first goal is to detect AD at
the earliest stage (pre-dementia) and identify
biomarkers that can be used to track the disease’s
progression. Support breakthroughs in Alzheimer’s
disease intervention, prevention, and therapy by using
innovative diagnostic tools at the earliest possible stage
(when intervention may be most successful). ADNI has a
ground-breaking data-access policy, which makes data
available to all scientists worldwide without restriction.
We have acquired 2294 ADNI1 1.5T MRI scans which are
in the NiFTI format. The images are pre-classified into
CN, MCI or AD. Each of the images is of the shape 192 x
192 X 160.
IV. IMPLEMENTATION DETAILS
A. Architecture
The images from the database are fed to a pipeline
which consists of a series of pre-processing techniques.
PSO performs feature selection on the pre-processed
images. The resultant images will be stored in a
database and will be used by PSO to get optimal
parameters of the Convolutional Neural Network. This
produces an optimized architecture for CN. The CNN
model is trained, validated and tested.
B. Pre-processing
The pre-processing steps are:
(I) ADNI pipeline
(II) Registration
(III) Segmentation and Normalization
(IV) Skull Stripping
(V) Smoothing
(I) ADNI pipeline: The images in the dataset are
obtained from MRI machines, and the machines
use magnetic waves and radio waves to produce
the scans. There are parameters such as radio
frequency, magnetic frequency and uniformity of
the coil which can cause variations in the MRI
scans. To correct such variations in the images, the
ADNI pipeline is used. The following is done on the
MRI image as a part of this pipeline
(i) Post-Acquisition Correction: Scanners with
different acquisition parameters provide
considerable hurdles. Small changes in
acquisition parameters for quantitative
sequences have a significant impact on machine
learning models, thus rectifying these
inconsistencies is critical.
(ii) B1 Intensity Variation: B1 errors are one of the
problems in measuring MTR which expands to
the magnetization transfer ratio since this MTR
value changes with a change in the
magnetization transfer (MT) pulse amplitude.
These errors can also be caused due to
 nonuniformity in the radiofrequency and
incorrect transmitter output settings when
accounting for changing levels of RF coil loading.
These mistakes need to be corrected to obtain
images with no variations and loss of crucial
data.
(iii) Intensity Non-Uniformity: The quality of
acquired data can be affected by intensity non-
uniformity. The term ”intensity non-uniformity”
refers to anatomically unrelated intensity
variance in data. It can be caused by the radio-
frequency coil used, the acquisition pulse
sequence used, and the sample’s composition
and geometry. As a result, it is critical to correct
this variation, and a variety of approaches have
been offered to do so.
(II) Registration: The act of aligning images to be
analyzed is called registration of images, and it is a
critical phase in which data from several images
must be integrated everywhere. They can be taken
at various times, from various perspectives, and
with various sensors. Registration in medical
imaging allows you to merge data from multiple
modalities, such as CT, MR, SPECT, or PET, to get a
full picture of the patient. In our case, since the
MRI scans are taken from different angles, it is the
process of geometrically aligning all the images for
further analysis. It can be used to create a
correspondence between features in a set of
images and then infer correspondence away from
those features using a transformation model.
(III) Segmentation and Normalization: The division of
brain tissue, which can be split into tissue sections
such as cerebrospinal fluid (CSF) which cushions
the brain, grey matter (GM) where the actual
processing is done and white matter (WM) which
gives communication between different GM areas,
is the major focus of the brain magnetic resonance
imaging (MRI) image segmentation approach (CSF).
Various significant brain regions that could be
useful in identifying Alzheimer’s disease are found
and kept during image segmentation.
Normalization is the process of shifting and scaling
an image so that the pixels have a zero mean and
unit variance. By removing scale invariance, the
model can converge faster.
(IV) Skull Stripping: Skull stripping is a process wherein
the skull and the non-brain region of the image are
removed and only the brain portion of the image is
retained as we deal with only this region for
analysis of Alzheimer’s disease. Skull stripping is
one of the first steps in the process of diagnosing
brain disorders. In a brain MRI scan, it is the
method for differentiating brain tissue from non-
brain tissue. Even for experienced radiologists,
separating the brain from the skull is a time-
consuming process, with results that vary widely
from person to person. This is a pipeline that only
needs the input of a raw MRI picture and should
produce a segmented image of the brain after the
necessary pre-processing.
(V) Smoothing: Smoothing involves removing
redundant information and noise from the images.
It helps in the easy identification of trends and
patterns in the images. When the image is
produced in an MRI machine, it consists of
different kinds of noise which need to be removed
to obtain a clean image without loss of any crucial
information.
C. CNN parameter optimisation using PSO
The process of training is repetitive and continued
until the stop criteria are met. The steps to optimize PSO
are:
1) Feed the pre-processed images as input to the CNN
network. The images should be of the same size
and characteristics. For example, they should of the
same dimensions, scale, colour gamma, etc.,
2) Design of PSO parameters. The algorithm’s particle
population is generated. This involves setting the
values for the number of particles, number of
iterations, inertial weight, social constant, and
cognitive constant etc., Random values can be set
or can also be set according to some heuristic
3) With the parameters obtained by the PSO, the
parameters of CNN are initialised (parameters to be
set are given in the table below). CNN is ready to be
trained now.
4) Training and validation of CNN. The CNN reads,
processes, validates and tests the input images.
This step produces values for the objective
functions. The objective functions are AIC and
Recognition rate. These values are returned to the
PSO.
5) Calculate the objective function. The objective
function is calculated by PSO to obtain the optimal
values in the search space.
6) PSO parameters are updated. Both, the position of
the particles and the velocity of the particles that
characterize the particles, are updated by taking
into consideration Pbest and Gbest. The updated
position is with respect to its own They are updated
based on its own optimal position (Pbest) and the
 optimal position of the entire swarm in the search
space (Gbest).
7) This process continues until the end criteria are
met. The end criteria can be the number of
iterations or a threshold value.
8) It is then determined which architecture is optimal.
Here the Gbest particle represents the optimal
architecture.
To elaborate further on how the algorithm will work,
an example is presented. The particle structure can
consist of 8 positions as shown below. Each particle has
these 8 positions and each of these positions is
responsible for tuning one hyper-parameter. The hyper-
parameters to be optimized are given in the below
table.

TABLE I: Structure of Particle

X1 X2 X3 X4 X5 X6 X7 X8 X9 X10
TABLE II: Example Particle Structure

Particle Coordinate Hyper-Parameter Search Space

X1 Convolution layer number [1, 4]
X1 Filter number (1st layer) [32, 128]
X3 Filter size (1st layer) [1, 3]
X4 Filter number (2nd layer) [32, 128]
X5 Filter size (2nd layer) [1, 3]
X6 Filter number (3rd layer) [32, 128]
X7 Filter size (4th layer) [1, 3]
X8 Filter number (4th layer) [32, 128]
X9 Filter size (5th layer) [1, 3]
X10 Filter number (5th layer) [32, 128]

From Table II, it is observed that, the X1 coordinate

controls the hyper-parameter for convolution layer
number. If X1 = 4, it means that there will be 4
convolution layers. X2 and X3 control the hyper-
parameters filter number and size respectively. If X2 = 32
and X3 = 2, it implies that there will be 32 filters of size
5x5 (1 is mapped to 3x3, 2 to 5x5, 3 corresponds to 7x7,
and 4 implies 9x9). Similarly, X4 and X5 control filter
numbers and size for layer 2. The same goes for all the
remaining coordinates. X10 represents the batch size for
training.

TABLE III: Example particle generated by the algorithm

4 100 2 64 2 64 3 96 1 32