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  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>Use of machine learning methods and virtual reality to analyze genetic characteristics⋆</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Yevgeniya Daineko</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Almira Burkutbayeva</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>International Information Technology University</institution>
          ,
          <addr-line>Manas st 34/1 050040 Almaty</addr-line>
          ,
          <country country="KZ">Kazakhstan</country>
        </aff>
      </contrib-group>
      <abstract>
        <p>Recent advancements in computer vision and virtual reality (VR) have introduced new possibilities for diagnosing genetic disorders based on facial feature analysis-phenotypic characteristics. This study provides an overview of practical implementations of VR in medicine, as well as facial image processing methods, including preprocessing, key point detection, and classification using machine learning algorithms such as Support Vector Machines (SVM) and Convolutional Neural Networks (CNN). The potential integration of VR into clinical practice is examined, including the development of interactive training scenarios for physicians and the application of 3D modeling for analyzing rare genetic syndromes. The study discusses the prospects of implementing VR simulations for testing facial anomaly recognition algorithms and remote patient diagnosis. Additionally, key challenges related to algorithm accuracy, the accessibility of VR solutions, and the need for inclusive datasets are highlighted. The integration of VR and machine learning into the diagnostic process enhances the accuracy of medical decision-making and expands the potential of personalized medicine.</p>
      </abstract>
      <kwd-group>
        <kwd>eol&gt;machine learning</kwd>
        <kwd>genetic disorder diagnosis</kwd>
        <kwd>facial feature analysis</kwd>
        <kwd>virtual reality</kwd>
        <kwd>VR simulations</kwd>
        <kwd>3D modeling</kwd>
        <kwd>CNN</kwd>
        <kwd>medical diagnostics</kwd>
      </kwd-group>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>1. Introduction</title>
      <p>Virtual reality technologies open up wide opportunities for the rehabilitation of patients with
various impairments, providing significant advantages over traditional methods. VR provides full
immersion in a virtual environment, simulating conditions close to real ones, which improves the
perception of exercises, stimulates participation and simplifies the implementation of complex
tasks.</p>
      <p>One of the key advantages is the individualization of therapy. Unlike traditional methods, it
creates realistic scenarios tailored to individual patient needs, taking into account their cognitive
and physical capabilities. In addition, VR creates a safe space, minimizing the risk of injury, which
is especially important for patients with impaired motor coordination, such as after a stroke or
with Parkinson's disease. For example, a stroke survivor relearning hand coordination can engage
in VR-based exercises that simulate everyday tasks, such as picking up objects or preparing a meal,
in a risk-free environment. Similarly, patients with Parkinson’s disease can practice movement
control through virtual balance and gait training exercises, helping them regain confidence in their
mobility.</p>
      <p>VR technologies allow for an objective assessment of rehabilitation progress, recording
parameters such as speed and accuracy of movements, which simplifies the adjustment of the
treatment program. Additionally, One of the most compelling aspects of VR-based rehabilitation is
its ability to boost patient motivation through gamification. VR overcomes this challenge by
integrating interactive, game-like elements into therapy sessions, making the process more
engaging - especially for children with cognitive impairments.</p>
      <p>Another advantage of VR is its potential for remote rehabilitation. Patients who live in rural
areas, have mobility limitations, or struggle with transportation can access therapy sessions from
home using VR headsets. This increased accessibility reduces barriers to consistent treatment,
leading to better long-term recovery outcomes. VR technologies show high potential for the
rehabilitation of patients after stroke, with Parkinson's disease and children with cognitive
disorders, combining safety, effectiveness and an innovative approach.</p>
      <p>This article is devoted to the development a novel VR-based respiratory rehabilitation system
that integrates Strelnikova breathing exercises into an interactive virtual environment using Meta
Quest 3.</p>
      <p>
        In recent years, there has been a rapid increase in interest in the application of virtual reality
(VR) and computer vision technologies in medicine. The number of publications on the topic of "VR
technology in medicine" in the PubMed database increased from 58 in 2017 to 145 in the first half of
2021 [
        <xref ref-type="bibr" rid="ref1">1, 2</xref>
        ].
      </p>
      <p>Modern methods for diagnosing genetic diseases require significant resources, time, and the
involvement of highly qualified specialists. Moreover, traditional approaches based on genetic
testing and clinical analysis involve high financial costs, limiting accessibility for patients in certain
regions and social groups. For example, according to a study by Smith et al. (2021), the cost of
genetic testing in some countries ranges from $500 to $2,000 per patient, creating a substantial
financial burden on healthcare systems [3]. In Almaty, in major private medical laboratories such
as Invivo and Invitro, the cost of testing for major hereditary diseases is 328,730 tenge [4]. Whole
Genome Sequencing with a geneticist’s report costs 538,040 tenge and 690,000 ₸, respectively [5]</p>
      <p>Traditionally, genetic research faces challenges related to processing vast amounts of
information and the complexity of determining relationships between genes, proteins, and other
biomolecules. Analytical procedures often lack clarity in identifying hidden patterns and dynamic
processes. Furthermore, such procedures can take considerable time, sometimes, with results
requiring several days to weeks, significantly delaying treatment initiation and reducing its
effectiveness.</p>
      <p>The integration of VR and computer vision offers the possibility of creating interactive and
immersive environments in which researchers can:
1. Interactively visualize multidimensional genetic data in a three-dimensional space,
facilitating a deeper understanding of their structure and relationships.
2. Detect anomalies and patterns using computer vision algorithms adapted for the specificity
of biological data.</p>
      <p>The use of VR and machine learning methods not only automates the analysis process but also
enables the creation of interactive tools for physicians and researchers. A study by Ivanov et al.
(2023) demonstrated that the implementation of VR technologies in the genetic disease diagnostic
process can reduce analysis time by up to 40% compared to traditional methods [6].</p>
      <p>Thus, the integration of VR and computer vision into medical diagnostics represents a
promising direction that can reduce diagnostic costs through process automation, shorten the
waiting time for analysis results, accelerate treatment initiation, and improve diagnostic accuracy
through machine learning algorithms and immersive technologies.</p>
      <p>The motivation for this research is high, as the application of VR and computer vision in genetic
studies can significantly accelerate the discovery of new genetic patterns and relationships, which
is of great value for both fundamental science and practical medicine. A better understanding of
the genetic characteristics of individual patients contributes to the development of personalized
treatment approaches, which is a key focus of modern medicine.</p>
      <p>The aim of this review is to explore the potential of virtual reality and computer vision for the
automated analysis of facial phenotypic features associated with genetic diseases. The following
sections analyze existing VR and machine learning technologies in medical diagnostics, identify
key computer vision methods applicable to facial anomaly analysis, and examine successful case
studies of implementing these technologies in clinical practice.</p>
    </sec>
    <sec id="sec-2">
      <title>2. Overview of Technologies and Methods</title>
      <p>Virtual reality (VR) is actively being implemented in medical practice, offering new opportunities
for diagnostics, surgical planning, and professional training. VR enables the creation of interactive
3D models of a patient's anatomical structures, allowing physicians to thoroughly examine specific
cases before performing surgical interventions. For instance, the Surgical Theater platform is used
for neurosurgical planning, enabling the development of interactive 3D and VR models [7]. At the
Stanford Simulation and Virtual Reality Center for Neurosurgery, this technology is employed to
create 360-degree virtual models of patients’ brains, enhancing surgical planning and improving
treatment efficiency.</p>
      <p>Also, numerical modeling plays a significant role in simulating biological systems. For example,
[8] conducted a study using ANSYS Fluent to simulate blood flow in coronary arteries,
demonstrating the importance of computational fluid dynamics (CFD) in cardiovascular analysis
and supporting the broader integration of modeling technologies into medical research.</p>
      <p>Additionally, VR is used in the rehabilitation of patients after strokes and injuries. Specialized
programs allow patients to control their movements in a virtual environment, which contributes to
motor function recovery. According to a study by Dolganov and Karpova, the use of VR in
conjunction with standard rehabilitation programs in the acute phase of a stroke improves upper
limb function and reduces limitations in daily activities [9]. In another case, these technologies
have demonstrated effectiveness in rehabilitation and biofeedback therapy for patients with
impaired fine motor skills after an ischemic stroke [10].</p>
      <p>Machine learning methods, combined with computer vision, play a crucial role in facial data
analysis for diagnosing various diseases, including genetic syndromes. The key algorithms include
neural networks, Support Vector Machines (SVM), and the k-Nearest Neighbors (kNN) algorithm.
Additionally, convolutional neural networks (CNN) enable automatic recognition and classification
of facial features due to their ability to extract complex patterns from data and process spatial
dependencies [11]. First of all, the architecture consists of a Convolutional Layer that highlights
spatial features such as edges, textures, and shapes by applying filters to the input data (Figure 2).
Then comes the Pooling Layer, which reduces the dimension of the data, preserving the most
significant features, which reduces computational complexity. The third Fully Connected Layer
converts selected features into classes or results, for example, for the diagnosis of syndromes.</p>
      <p>SVM is widely used for high-accuracy data classification and regression tasks, particularly when
dealing with limited datasets. However, it has limitations—it is computationally intensive for large
datasets and sensitive to the choice of kernel and its parameters. The core principle of SVM is
finding a hyperplane that best separates data points into different classes [12]. Key components of
an SVM model include:
1. Hyperplane – a decision boundary that maximally separates different classes in
multidimensional space.
2. Support vectors – data points closest to the hyperplane that determine its position.
3. Regularization parameter (C) – balances the margin maximization between classes and
classification error minimization.
4. Kernel functions – transform data into higher-dimensional space where classes become
linearly separable. Examples include linear, polynomial, and Radial Basis Function (RBF)
kernels.</p>
      <p>Advanced CNN models such as ResNet and Inception offer improved accuracy in medical image
analysis, exceeding 90% in certain diagnostic tasks [13]. ResNet is a deep network with residual
connections that solve the problem of gradient attenuation. Inception uses multiscale convolutions,
which allows to identify features of different levels of complexity at the same time. This makes the
model universal for analyzing various types of data. EfficientNet optimizes accuracy and
computational costs by using compound scaling, i.e. changing the depth, width, and resolution of
the network at the same time.</p>
      <p>Various methods are employed for 3D facial scanning, each with its advantages and limitations.
Light Detection and Ranging (LiDAR) utilizes laser pulses to measure distances to objects, creating
highly accurate three-dimensional models [14]. This method provides superior precision and detail,
making it particularly useful for tasks that require precise facial geometry reconstruction.
However, LiDAR technology is expensive and often requires specialized equipment and controlled
scanning environments. Additionally, LiDAR devices can be sensitive to bright sunlight or
atmospheric interference, affecting their performance in outdoor conditions. The second method
-photogrammetry, is based on analyzing multiple images of an object taken from different angles.
These images are then processed using specialized software to create a 3D model [15]. Compared to
LiDAR, photogrammetry is more accessible, as it requires only standard photographic equipment.
However, its accuracy and level of detail may be lower than that of LiDAR, especially if the image
quality is poor or the number of captured photos is insufficient. Additionally, the processing time
for generating a model can be computationally intensive and time-consuming.</p>
      <p>Third method - 3D Reconstruction Deep learning techniques enable the reconstruction of 3D
facial models from 2D images. Algorithms such as CNNs are trained on large datasets to predict
three-dimensional facial structures based on two-dimensional photographs [16]. These approaches
are rapidly evolving and have shown promising results, allowing the generation of 3D models
without the need for specialized scanning equipment. However, the accuracy of such models
depends on the quality and diversity of training data, as well as the complexity of the neural
network architecture.</p>
    </sec>
    <sec id="sec-3">
      <title>3. Challenges and Risks</title>
      <p>Despite the rapid development of computer vision and VR technologies, their application in
medical diagnostics faces several challenges. First and foremost, the accuracy and reliability of
algorithms capable of identifying facial features characteristic of genetic disorders are crucial.
Achieving this requires large datasets and thorough model validation. The limited availability of
datasets for rare syndromes poses difficulties in model generalization. Studies indicate that machine
learning models can exhibit bias based on ethnicity, gender, and age, primarily due to imbalanced
training datasets [17].</p>
      <p>One key recommendation is the implementation of bias mitigation techniques and the
development of more inclusive datasets. This is particularly important in regions with diverse
ethnic compositions, such as Kazakhstan and Central Asia, where ethnic characteristics may
influence the expression of facial features. Research suggests that data augmentation can improve
algorithm accuracy by up to 15% [18].</p>
      <p>Secondly, high-precision VR devices and computer vision systems can be expensive, limiting
their use in low-resource regions. The cost of specialized hardware and software may hinder
widespread adoption, making affordability a key challenge for integrating these technologies into
clinical settings. Thirdly, medical professionals must understand how AI-driven algorithms make
decisions to build trust in automated diagnostic methods. The interpretability and transparency of
these algorithms are essential for their acceptance in medical practice.</p>
      <p>Additionally, the use of facial images in medical diagnostics raises ethical and legal concerns.
Strict data privacy regulations, such as the General Data Protection Regulation (GDPR), must be
adhered to when collecting and processing biometric data. Violations of privacy in facial image
data handling can have significant consequences for patients and their families. Addressing these
ethical concerns is critical for ensuring the responsible deployment of AI and VR technologies in
medical diagnostics.</p>
    </sec>
    <sec id="sec-4">
      <title>4. Phenotypic Features in Diagnosis</title>
      <p>Phenotypic manifestations refer to a set of external traits that arise from the interaction of genes
influencing growth, development, and the function of tissues and organs. Human facial structures
are shaped by complex genetic interactions, which determine not only basic proportions but also
unique facial characteristics. For instance, mutations in genes involved in morphogenesis, such as
TCF4 or FGFR2, can lead to craniofacial deformities.</p>
      <p>One well-known example is Down syndrome, which results from trisomy of 21st chromosome.
It is characterized by a flat facial profile, almond-shaped eyes, a short nose, and distinctive hand
features. These physical traits help physicians diagnose the condition at an early stage.</p>
      <p>Another case is Marfan syndrome, caused by a mutation in the FBN1 gene. This disorder is
associated with tall stature, long fingers (arachnodactyly), and distinct facial features such as a
narrow lower jaw. Marfan syndrome is also linked to systemic complications, including
cardiovascular abnormalities.</p>
      <p>According to the American Journal of Medical Genetics, approximately 60% of genetic
syndromes exhibit distinct external phenotypic features [19]. These findings emphasize the crucial
role of facial analysis in diagnosis, particularly for rare diseases where genetic testing may not
always be available. Thus, machine learning (ML) and computer vision provide new opportunities
for automated diagnosis, enabling the identification of patterns associated with specific genetic
conditions.</p>
    </sec>
    <sec id="sec-5">
      <title>5. Successful Cases in Disease Diagnosis and Specialist Training</title>
      <p>One of the most successful cases in computer vision-based genetic diagnostics is DeepGestalt, a
system that utilizes convolutional neural networks (CNNs) for facial image analysis. It has been
tested on over 10,000 images, achieving 91% accuracy [20]. Another notable example is Face2Gene,
which is widely used in clinical practice. This system enables the diagnosis of genetic disorders
based on facial images by leveraging large annotated databases. These databases contain
phenotypic markers, including facial characteristics and other manifestations of genetic syndromes.
According to clinical trials, Face2Gene has demonstrated an accuracy of 89% for Down syndrome
and 82% for Noonan syndrome [11]. Both systems rely on large biometric datasets, allowing them
to learn from diverse phenotypic patterns and improve diagnostic precision.</p>
      <p>In the field of medical training, the VR-NRP platform was developed for neonatal resuscitation
training [21]. It provides a realistic and interactive VR environment, where medical professionals
can practice life-saving techniques on newborns, increasing their confidence and efficiency in
realworld scenarios. Another example is a mixed reality system for medical procedures, such as central
venous catheter insertion [22]. This technology allows remote experts to guide local practitioners
through medical procedures, enhancing training quality and reducing errors. Additionally, the
SONIA system provides interactive VR-based neuroanatomy training [23]. It enables students and
educators to explore complex brain structures, improving comprehension and knowledge retention.</p>
    </sec>
    <sec id="sec-6">
      <title>6. Computer Vision Image Analysis Methods and Virtual Reality</title>
    </sec>
    <sec id="sec-7">
      <title>Integration</title>
      <p>Various types of data are used for genetic disease analysis, each contributing to different aspects of
facial feature recognition and classification:
1. 2D Photographs constitute the primary data type for most machine learning-based facial
analysis systems. Modern research in machine learning for facial image processing relies on
publicly available datasets such as Labeled Faces in the Wild (LFW) and CelebA [24]. These
datasets provide high-quality images that are widely used for training and testing deep
learning models.
2. 3D Images allow for a more precise analysis by creating volumetric models of facial
structures. For example, FaceBase is a database containing 3D facial scans of individuals
with craniofacial anomalies. Additionally, the 3D Facial Alignment in the Wild (3DFAW)
dataset includes 3D face scans captured in various expressions and lighting conditions,
making it valuable for developing robust models resistant to external factors.
3. Biometric Data – key facial landmarks, such as the distance between critical facial points,
are used to build models for facial structure analysis and disease detection.</p>
      <p>Stages of Data Processing:
 Preprocessing – This step involves noise removal, image normalization, and facial
alignment, ensuring consistency across the dataset.
 Augmentation – Since high-quality medical datasets are often limited, augmentation is used
to expand training data. This includes image transformations such as rotation, scaling, and
noise addition. Tools like Albumentations and TensorFlow ImageDataGenerator are widely
applied to enhance model robustness, particularly in scenarios with small datasets.
 Data Cleaning – The removal of duplicate images and mislabeling corrections ensures that
only high-quality and accurately labeled data are used for training.</p>
      <p>Facial landmark detection involves identifying specific facial points, such as the eyes, nose, and
mouth, to determine the structure of the face. This process consists of preliminary face localization
using models like MTCNN (Multi-task Cascaded Convolutional Neural Network) or Haar-Cascade.
A multi-task cascaded deep convolutional neural network (Figure 4) is a method consisting of three
convolutional networks that work in stages: first, coarse detection, then refinement, and finally
localization of key points. MTCNN, implemented in PyTorch or TensorFlow, detects faces and
simultaneously identifies the eyes, nose, and mouth. It is particularly effective for handling
variations in pose, lighting, and occlusion. Haar-Cascade, on the other hand, analyzes pixel
groupings to detect potential face regions by applying pretrained feature classifiers. Although
Haar-Cascade is computationally efficient, it is generally less accurate compared to deep
learningbased models like MTCNN.</p>
      <p>The second stage involves detecting key points, such as the corners of the eyes, the tip of the
nose, and the mouth. Convolutional neural networks trained on annotated datasets such as 300-W,
where facial landmarks were manually labeled, are used for this task [26]. For more diverse
conditions, including images taken from different angles, the Annotated Facial Landmarks in the
Wild (AFLW) dataset is applied. Feature extraction refers to identifying significant image
characteristics, including: geometric features – distances between key facial points; gradients and
textures – methods such as Histogram of Oriented Gradients (HOG) and Local Binary Patterns
(LBP). On one hand, HOG extracts gradient directions in small image regions to derive
texturebased characteristics. On the other hand, LBP compares pixel values within a small window,
generating binary patterns [27]. Tools such as OpenCV, a library used for preprocessing, face
localization, and feature analysis, and Dlib, which predicts 68 facial landmarks for structural
analysis, are widely used for implementing these methods.</p>
      <p>Various metrics are used to assess the efficiency of developed models, including accuracy, recall,
and the F-measure. Validation is performed on test datasets that were not used during the training
process to ensure objective evaluation. Additionally, cross-validation methods are applied to
enhance the reliability of the results.</p>
      <p>The integration of computer vision and VR into medical practice enhances diagnostic accuracy
and training efficiency, providing new tools for analyzing and visualizing complex medical data.
Thus, the combination of VR, computer vision, and advanced 3D scanning methods opens new
perspectives for medical diagnostics and treatment, contributing to greater precision and efficiency
in medical procedures.</p>
    </sec>
    <sec id="sec-8">
      <title>7. Prospects for future research</title>
      <p>Despite significant advancements in computer vision and VR, several unresolved challenges require
further investigation:
1. Enhancing the accuracy of facial feature recognition algorithms – Developing more
balanced datasets that consider ethnic and age diversity among patients.
2. Creating more accessible VR systems that can be implemented in clinical settings.
3. Developing VR interfaces that enable interaction with patient biometric data for more
precise diagnostics.
4. Analyzing the impact of VR simulations on clinical decision-making and diagnostic
accuracy.</p>
      <p>Further research in VR and computer vision could greatly improve the precision and
accessibility of genetic disease diagnostics while also enhancing medical education. The integration
of these technologies into clinical practice will contribute to the development of personalized
medicine and improve the overall quality of healthcare services.</p>
    </sec>
    <sec id="sec-9">
      <title>8. Conclusion</title>
      <p>This study provides a comprehensive review of modern approaches to the analysis of facial
phenotypic features associated with genetic diseases using machine learning and computer vision.
Key image processing techniques, including preprocessing, key point detection, and classification
using deep learning models, have been examined. Additionally, the role of VR in medical
diagnostics, patient rehabilitation, and physician training has been analyzed.</p>
      <p>The application of VR and computer vision in facial data analysis enhances diagnostic accuracy,
automates the recognition of genetic syndromes, and enables the development of interactive
educational tools for medical professionals. The use of advanced machine learning algorithms, such
as CNN, ResNet, and Inception, demonstrates high effectiveness in facial recognition and anomaly
classification tasks.</p>
      <p>The integration of VR into the diagnosis and treatment of genetic diseases can be implemented
in the following ways:
1. VR Simulations for Facial Anomaly Recognition Testing. Utilization of 3D modeling of facial
structures for analyzing phenotypic features of rare genetic disorders.
2. VR in Clinical Practice. Development of VR applications that allow physicians to interact
with 3D facial models of patients in real-time. Creation of VR platforms for telemedicine,
enabling remote consultations and diagnostics.
3. VR-Based Training and Simulations. Immersive VR training systems for teaching physicians
methods for diagnosing genetic diseases. Development of virtual case studies with real
patient data to enhance the qualification of medical specialists.</p>
    </sec>
    <sec id="sec-10">
      <title>Declaration on Generative AI</title>
      <p>The author(s) have not employed any Generative AI tools.
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