Ahmed Shalaby

Dr. Ahmed Shalaby

University of Louisville, USA
orcid

Research Focus & Metrics

Academic Career Length

14Years (2013-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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28 March 2021 in Sensors
Verified
Journal Article
Open access
PDF file
MSMohamed Shaban
Mohamed Shaban
RSReem Salim
Reem Salim
HKHadil Abu Khalifeh
Hadil Abu Khalifeh
AKAdel Khelifi
Adel Khelifi
Ahmed ShalabyAhmed Shalaby
Ahmed Shalaby
Ayman El-BazAyman El-Baz
Ayman El-Baz
Oil leaks onto water surfaces from big tankers, ships, and pipeline cracks cause considerable damage and harm to the marine environment. Synthetic Aperture Radar (SAR) images provide an approximate representation for target scenes, including sea and land surfaces, ships, oil spills, and look-alikes. Detection and segmentation of oil spills from SAR images are crucial to aid in leak cleanups and protecting the environment. This paper introduces a two-stage deep-learning framework for the identification of oil spill occurrences based on a highly unbalanced dataset. The first stage classifies patches based on the percentage of oil spill pixels using a novel 23-layer Convolutional Neural Network. In contrast, the second stage performs semantic segmentation using a five-stage U-Net structure. The generalized Dice loss is minimized to account for the reduced oil spill representation in the patches. The results of this study are very promising and provide a comparable improved precision and Dice score compared to related work.

25 February 2020 in IEEE Access
Verified
Journal Article
Open access
MOHAMMED GHAZALMOHAMMED GHAZAL
MOHAMMED GHAZAL
SASamr Samir Ali
Samr Samir Ali
MHMahmoud Ali H.
Mahmoud Ali H.
Ahmed ShalabyAhmed Shalaby
Ahmed Shalaby
Ayman El-BazAyman El-Baz
Ayman El-Baz
Diabetic retinopathy (DR) is a disease that forms as a complication of diabetes. It is particularly dangerous since it often goes unnoticed and can lead to blindness if not detected early. Despite the clear importance and urgency of such an illness, there is no precise system for the early detection of DR so far. Fortunately, such system could be achieved using deep learning including convolutional neural networks (CNNs), which gained momentum in the field of medical imaging due to its capability of being effectively integrated into various systems in a manner that significantly improves the performance. This paper proposes a computer aided diagnostic (CAD) system for the early detection of non-proliferative DR (NPDR) using CNNs. The proposed system is developed for the optical coherence tomography (OCT) imaging modality. Throughout this paper, all aspects of deployment of the proposed system are studied starting from the preprocessing stage required to extract input retina patches to train the CNN without resizing the image, to the use of transfer learning principals and how to effectively combine features in order to optimize performance. This is done through investigating several scenarios for the system setup and then selecting the best one, which from the results revealed to be a two pre-trained CNNs based system, in which one of these CNNs is independently fed by nasal retina patches and the other one by temporal retina patches. The proposed transfer learning based CAD system achieves a promising accuracy of 94%.

7 April 2021 in Sensors
Verified
Journal Article
Open access
PDF file
Sarah AyyadSarah Ayyad
Sarah Ayyad
Mohamed ShehataMohamed Shehata
Mohamed Shehata
Ahmed ShalabyAhmed Shalaby
Ahmed Shalaby
MEMohamed Abou El-Ghar
Mohamed Abou El-Ghar
MOHAMMED GHAZALMOHAMMED GHAZAL
MOHAMMED GHAZAL
Ayman El-BazAyman El-Baz
Ayman El-Baz
Prostate cancer is one of the most identified cancers and second most prevalent among cancer-related deaths of men worldwide. Early diagnosis and treatment are substantial to stop or handle the increase and spread of cancer cells in the body. Histopathological image diagnosis is a gold standard for detecting prostate cancer as it has different visual characteristics but interpreting those type of images needs a high level of expertise and takes too much time. One of the ways to accelerate such an analysis is by employing artificial intelligence (AI) through the use of computer-aided diagnosis (CAD) systems. The recent developments in artificial intelligence along with its sub-fields of conventional machine learning and deep learning provide new insights to clinicians and researchers, and an abundance of research is presented specifically for histopathology images tailored for prostate cancer. However, there is a lack of comprehensive surveys that focus on prostate cancer using histopathology images. In this paper, we provide a very comprehensive review of most, if not all, studies that handled the prostate cancer diagnosis using histopathological images. The survey begins with an overview of histopathological image preparation and its challenges. We also briefly review the computing techniques that are commonly applied in image processing, segmentation, feature selection, and classification that can help in detecting prostate malignancies in histopathological images.

11 January 2022 in Diagnostics
Verified
Journal Article
Open access
PDF file
MAMohamed Ali
Mohamed Ali
YEYaser ElNakieb
Yaser ElNakieb
Ahmed ElnakibAhmed Elnakib
Ahmed Elnakib
Ahmed ShalabyAhmed Shalaby
Ahmed Shalaby
MHMahmoud Ali H.
Mahmoud Ali H.
Ayman El-BazAyman El-Baz
Ayman El-Baz
This study proposes a Computer-Aided Diagnostic (CAD) system to diagnose subjects with autism spectrum disorder (ASD). The CAD system identifies morphological anomalies within the brain regions of ASD subjects. Cortical features are scored according to their contribution in diagnosing a subject to be ASD or typically developed (TD) based on a trained machine-learning (ML) model. This approach opens the hope for developing a new CAD system for early personalized diagnosis of ASD. We propose a framework to extract the cerebral cortex from structural MRI as well as identifying the altered areas in the cerebral cortex. This framework consists of the following five main steps: (i) extraction of cerebral cortex from structural MRI; (ii) cortical parcellation to a standard atlas; (iii) identifying ASD associated cortical markers; (iv) adjusting feature values according to sex and age; (v) building tailored neuro-atlases to identify ASD; and (vi) artificial neural networks (NN) are trained to classify ASD. The system is tested on the Autism Brain Imaging Data Exchange (ABIDE I) sites achieving an average balanced accuracy score of 97±2%. This paper demonstrates the ability to develop an objective CAD system using structure MRI and tailored neuro-atlases describing specific developmental patterns of the brain in autism.

2 January 2023 in Bioengineering
Verified
Journal Article
Open access
PDF file
YEYaser ElNakieb
Yaser ElNakieb
MAMohamed Ali
Mohamed Ali
Ahmed ElnakibAhmed Elnakib
Ahmed Elnakib
Ahmed ShalabyAhmed Shalaby
Ahmed Shalaby
MHMahmoud Ali H.
Mahmoud Ali H.
Ayman El-BazAyman El-Baz
Ayman El-Baz
In addition to the standard observational assessment for autism spectrum disorder (ASD), recent advancements in neuroimaging and machine learning (ML) suggest a rapid and objective alternative using brain imaging. This work presents a pipelined framework, using functional magnetic resonance imaging (fMRI) that allows not only an accurate ASD diagnosis but also the identification of the brain regions contributing to the diagnosis decision. The proposed framework includes several processing stages: preprocessing, brain parcellation, feature representation, feature selection, and ML classification. For feature representation, the proposed framework uses both a conventional feature representation and a novel dynamic connectivity representation to assist in the accurate classification of an autistic individual. Based on a large publicly available dataset, this extensive research highlights different decisions along the proposed pipeline and their impact on diagnostic accuracy. A large publicly available dataset of 884 subjects from the Autism Brain Imaging Data Exchange I (ABIDE-I) initiative is used to validate our proposed framework, achieving a global balanced accuracy of 98.8% with five-fold cross-validation and proving the potential of the proposed feature representation. As a result of this comprehensive study, we achieve state-of-the-art accuracy, confirming the benefits of the proposed feature representation and feature engineering in extracting useful information as well as the potential benefits of utilizing ML and neuroimaging in the diagnosis and understanding of autism.

7 December 2021 in Sensors
Verified
Journal Article
Open access
PDF file
YEYaser ElNakieb
Yaser ElNakieb
MAMohamed Ali
Mohamed Ali
Ahmed ElnakibAhmed Elnakib
Ahmed Elnakib
Ahmed ShalabyAhmed Shalaby
Ahmed Shalaby
Ahmed SolimanAhmed Soliman
Ahmed Soliman
Ayman El-BazAyman El-Baz
Ayman El-Baz
Autism spectrum disorder (ASD) is a combination of developmental anomalies that causes social and behavioral impairments, affecting around 2% of US children. Common symptoms include difficulties in communications, interactions, and behavioral disabilities. The onset of symptoms can start in early childhood, yet repeated visits to a pediatric specialist are needed before reaching a diagnosis. Still, this diagnosis is usually subjective, and scores can vary from one specialist to another. Previous literature suggests differences in brain development, environmental, and/or genetic factors play a role in developing autism, yet scientists still do not know exactly the pathology of this disorder. Currently, the gold standard diagnosis of ASD is a set of diagnostic evaluations, such as the Autism Diagnostic Observation Schedule (ADOS) or Autism Diagnostic Interview–Revised (ADI-R) report. These gold standard diagnostic instruments are an intensive, lengthy, and subjective process that involves a set of behavioral and communications tests and clinical history information conducted by a team of qualified clinicians. Emerging advancements in neuroimaging and machine learning techniques can provide a fast and objective alternative to conventional repetitive observational assessments. This paper provides a thorough study of implementing feature engineering tools to find discriminant insights from brain imaging of white matter connectivity and using a machine learning framework for an accurate classification of autistic individuals. This work highlights important findings of impacted brain areas that contribute to an autism diagnosis and presents promising accuracy results. We verified our proposed framework on a large publicly available DTI dataset of 225 subjects from the Autism Brain Imaging Data Exchange-II (ABIDE-II) initiative, achieving a high global balanced accuracy over the 5 sites of up to 99% with 5-fold cross validation. The data used was slightly unbalanced, including 125 autistic subjects and 100 typically developed (TD) ones. The achieved balanced accuracy of the proposed technique is the highest in the literature, which elucidates the importance of feature engineering steps involved in extracting useful knowledge and the promising potentials of adopting neuroimaging for the diagnosis of autism.