1
|
Alwateer M, Bamaqa A, Farsi M, Aljohani M, Shehata M, Elhosseini MA. Transformative Approaches in Breast Cancer Detection: Integrating Transformers into Computer-Aided Diagnosis for Histopathological Classification. Bioengineering (Basel) 2025; 12:212. [PMID: 40150677 PMCID: PMC11939498 DOI: 10.3390/bioengineering12030212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2025] [Revised: 02/14/2025] [Accepted: 02/19/2025] [Indexed: 03/29/2025] Open
Abstract
Breast cancer (BC) remains a leading cause of cancer-related mortality among women worldwide, necessitating advancements in diagnostic methodologies to improve early detection and treatment outcomes. This study proposes a novel twin-stream approach for histopathological image classification, utilizing both histopathologically inherited and vision-based features to enhance diagnostic precision. The first stream utilizes Virchow2, a deep learning model designed to extract high-level histopathological features, while the second stream employs Nomic, a vision-based transformer model, to capture spatial and contextual information. The fusion of these streams ensures a comprehensive feature representation, enabling the model to achieve state-of-the-art performance on the BACH dataset. Experimental results demonstrate the superiority of the twin-stream approach, with a mean accuracy of 98.60% and specificity of 99.07%, significantly outperforming single-stream methods and related studies. Statistical analyses, including paired t-tests, ANOVA, and correlation studies, confirm the robustness and reliability of the model. The proposed approach not only improves diagnostic accuracy but also offers a scalable and efficient solution for clinical applications, addressing the challenges of resource constraints and increasing diagnostic demands.
Collapse
Affiliation(s)
- Majed Alwateer
- Department of Computer Science, College of Computer Science and Engineering, Taibah University, Yanbu 46421, Saudi Arabia; (M.A.); (M.A.)
| | - Amna Bamaqa
- Department of Computer Science and Informatics, Applied College, Taibah University, Madinah 41461, Saudi Arabia;
| | - Mohamed Farsi
- Department of Information Systems, College of Computer Science and Engineering, Taibah University, Yanbu 46421, Saudi Arabia;
| | - Mansourah Aljohani
- Department of Computer Science, College of Computer Science and Engineering, Taibah University, Yanbu 46421, Saudi Arabia; (M.A.); (M.A.)
| | - Mohamed Shehata
- Department of Bioengineering, Speed School of Engineering, University of Louisville, Louisville, KY 40292, USA;
| | - Mostafa A. Elhosseini
- Department of Information Systems, College of Computer Science and Engineering, Taibah University, Yanbu 46421, Saudi Arabia;
- Computers and Control Systems Engineering Department, Faculty of Engineering, Mansoura University, Mansoura 35516, Egypt
| |
Collapse
|
2
|
Salunkhe SY, Chavan MS. ZF-QDCNN: ZFNet and quantum dilated convolutional neural network based Alzheimer's disease detection using MRI images. NETWORK (BRISTOL, ENGLAND) 2025:1-45. [PMID: 39932952 DOI: 10.1080/0954898x.2025.2452288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 12/30/2024] [Accepted: 01/07/2025] [Indexed: 02/13/2025]
Abstract
Alzheimer's disease (AD) is a severe neurological disorder that leads to irreversible memory loss. In the previous research, the early-stage Alzheimer's often presents with subtle memory issues that are difficult to differentiate from normal age-related changes. This research designed a novel detection model called the Zeiler and Fergus Quantum Dilated Convolutional Neural Network (ZF-QDCNN) for AD detection using Magnetic Resonance Imaging (MRI). Initially, the input MRI images are taken from a specific dataset, which is pre-processed using a Gaussian filter. Then, the brain area segmentation is performed by utilizing the Channel-wise Feature Pyramid Network for Medicine (CFPNet-M). After segmentation, relevant features are extracted, and the classification of AD is performed using the ZF-QDCNN, which is the integration of the Zeiler and Fergus Network (ZFNet) with the Quantum Dilated Convolutional Neural Network (QDCNN). Moreover, the ZF-QDCNN model demonstrated promising performance, achieving an accuracy of 91.7%, a sensitivity of 90.7%, a specificity of 92.7%, and a f-measure of 91.8% in detecting AD. Additionally, the proposed ZF-QDCNN model effectively identifies and classifies Alzheimer's disease in MRI images, highlighting its potential as a valuable tool for early diagnosis and management of the condition.
Collapse
Affiliation(s)
- Sharda Yashwant Salunkhe
- Research Scholar, Shivaji University
- Department of E & C, Sharad Institute of Technology College of Engineering, Ichalkaranji, India
| | - Mahesh S Chavan
- Department of Electronics & Telecommunication, KIT's College of Engineering, Kolhapur, India
| |
Collapse
|
3
|
Abd El-Khalek AA, Balaha HM, Alghamdi NS, Ghazal M, Khalil AT, Abo-Elsoud MEA, El-Baz A. A concentrated machine learning-based classification system for age-related macular degeneration (AMD) diagnosis using fundus images. Sci Rep 2024; 14:2434. [PMID: 38287062 PMCID: PMC10825213 DOI: 10.1038/s41598-024-52131-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/14/2024] [Indexed: 01/31/2024] Open
Abstract
The increase in eye disorders among older individuals has raised concerns, necessitating early detection through regular eye examinations. Age-related macular degeneration (AMD), a prevalent condition in individuals over 45, is a leading cause of vision impairment in the elderly. This paper presents a comprehensive computer-aided diagnosis (CAD) framework to categorize fundus images into geographic atrophy (GA), intermediate AMD, normal, and wet AMD categories. This is crucial for early detection and precise diagnosis of age-related macular degeneration (AMD), enabling timely intervention and personalized treatment strategies. We have developed a novel system that extracts both local and global appearance markers from fundus images. These markers are obtained from the entire retina and iso-regions aligned with the optical disc. Applying weighted majority voting on the best classifiers improves performance, resulting in an accuracy of 96.85%, sensitivity of 93.72%, specificity of 97.89%, precision of 93.86%, F1 of 93.72%, ROC of 95.85%, balanced accuracy of 95.81%, and weighted sum of 95.38%. This system not only achieves high accuracy but also provides a detailed assessment of the severity of each retinal region. This approach ensures that the final diagnosis aligns with the physician's understanding of AMD, aiding them in ongoing treatment and follow-up for AMD patients.
Collapse
Affiliation(s)
- Aya A Abd El-Khalek
- Communications and Electronics Engineering Department, Nile Higher Institute for Engineering and Technology, Mansoura, Egypt
| | - Hossam Magdy Balaha
- BioImaging Lab, Department of Bioengineering, J.B. Speed School of Engineering, University of Louisville, Louisville, KY, USA
| | - Norah Saleh Alghamdi
- Department of Computer Sciences, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mohammed Ghazal
- Electrical, Computer, and Biomedical Engineering Depatrment, Abu Dhabi University, Abu Dhabi, UAE
| | - Abeer T Khalil
- Communications and Electronics Engineering Department, Faculty of Engineering, Mansoura University, Mansoura, Egypt
| | - Mohy Eldin A Abo-Elsoud
- Communications and Electronics Engineering Department, Faculty of Engineering, Mansoura University, Mansoura, Egypt
| | - Ayman El-Baz
- BioImaging Lab, Department of Bioengineering, J.B. Speed School of Engineering, University of Louisville, Louisville, KY, USA.
| |
Collapse
|
4
|
Farahat IS, Sharafeldeen A, Ghazal M, Alghamdi NS, Mahmoud A, Connelly J, van Bogaert E, Zia H, Tahtouh T, Aladrousy W, Tolba AE, Elmougy S, El-Baz A. An AI-based novel system for predicting respiratory support in COVID-19 patients through CT imaging analysis. Sci Rep 2024; 14:851. [PMID: 38191606 PMCID: PMC10774502 DOI: 10.1038/s41598-023-51053-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/29/2023] [Indexed: 01/10/2024] Open
Abstract
The proposed AI-based diagnostic system aims to predict the respiratory support required for COVID-19 patients by analyzing the correlation between COVID-19 lesions and the level of respiratory support provided to the patients. Computed tomography (CT) imaging will be used to analyze the three levels of respiratory support received by the patient: Level 0 (minimum support), Level 1 (non-invasive support such as soft oxygen), and Level 2 (invasive support such as mechanical ventilation). The system will begin by segmenting the COVID-19 lesions from the CT images and creating an appearance model for each lesion using a 2D, rotation-invariant, Markov-Gibbs random field (MGRF) model. Three MGRF-based models will be created, one for each level of respiratory support. This suggests that the system will be able to differentiate between different levels of severity in COVID-19 patients. The system will decide for each patient using a neural network-based fusion system, which combines the estimates of the Gibbs energy from the three MGRF-based models. The proposed system were assessed using 307 COVID-19-infected patients, achieving an accuracy of [Formula: see text], a sensitivity of [Formula: see text], and a specificity of [Formula: see text], indicating a high level of prediction accuracy.
Collapse
Affiliation(s)
- Ibrahim Shawky Farahat
- Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura, Egypt
| | | | - Mohammed Ghazal
- Electrical, Computer and Biomedical Engineering Department, Abu Dhabi University, Abu Dhabi, UAE
| | - Norah Saleh Alghamdi
- Department of Computer Sciences, College of Computer and Information Sciences, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ali Mahmoud
- Department of Bioengineering, University of Louisville, Louisville, USA
| | - James Connelly
- Department of Radiology, University of Louisville, Louisville, USA
| | - Eric van Bogaert
- Department of Radiology, University of Louisville, Louisville, USA
| | - Huma Zia
- Electrical, Computer and Biomedical Engineering Department, Abu Dhabi University, Abu Dhabi, UAE
| | - Tania Tahtouh
- College of Health Sciences, Abu Dhabi University, Abu Dhabi, UAE
| | - Waleed Aladrousy
- Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura, Egypt
| | - Ahmed Elsaid Tolba
- Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura, Egypt
- The Higher Institute of Engineering and Automotive Technology and Energy, Kafr El Sheikh, Egypt
| | - Samir Elmougy
- Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura, Egypt
| | - Ayman El-Baz
- Department of Bioengineering, University of Louisville, Louisville, USA.
| |
Collapse
|
5
|
Alharthi AG, Alzahrani SM. Do it the transformer way: A comprehensive review of brain and vision transformers for autism spectrum disorder diagnosis and classification. Comput Biol Med 2023; 167:107667. [PMID: 37939407 DOI: 10.1016/j.compbiomed.2023.107667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
Autism spectrum disorder (ASD) is a condition observed in children who display abnormal patterns of interaction, behavior, and communication with others. Despite extensive research efforts, the underlying causes of this neurodevelopmental disorder and its biomarkers remain unknown. However, advancements in artificial intelligence and machine learning have improved clinicians' ability to diagnose ASD. This review paper investigates various MRI modalities to identify distinct features that characterize individuals with ASD compared to typical control subjects. The review then moves on to explore deep learning models for ASD diagnosis, including convolutional neural networks (CNNs), autoencoders, graph convolutions, attention networks, and other models. CNNs and their variations are particularly effective due to their capacity to learn structured image representations and identify reliable biomarkers for brain disorders. Computer vision transformers often employ CNN architectures with transfer learning techniques like fine-tuning and layer freezing to enhance image classification performance, surpassing traditional machine learning models. This review paper contributes in three main ways. Firstly, it provides a comprehensive overview of a recommended architecture for using vision transformers in the systematic ASD diagnostic process. To this end, the paper investigates various pre-trained vision architectures such as VGG, ResNet, Inception, InceptionResNet, DenseNet, and Swin models that were fine-tuned for ASD diagnosis and classification. Secondly, it discusses the vision transformers of 2020th like BiT, ViT, MobileViT, and ConvNeXt, and applying transfer learning methods in relation to their prospective practicality in ASD classification. Thirdly, it explores brain transformers that are pre-trained on medically rich data and MRI neuroimaging datasets. The paper recommends a systematic architecture for ASD diagnosis using brain transformers. It also reviews recently developed brain transformer-based models, such as METAFormer, Com-BrainTF, Brain Network, ST-Transformer, STCAL, BolT, and BrainFormer, discussing their deep transfer learning architectures and results in ASD detection. Additionally, the paper summarizes and discusses brain-related transformers for various brain disorders, such as MSGTN, STAGIN, and MedTransformer, in relation to their potential usefulness in ASD. The study suggests that developing specialized transformer-based models, following the success of natural language processing (NLP), can offer new directions for image classification problems in ASD brain biomarkers learning and classification. By incorporating the attention mechanism, treating MRI modalities as sequence prediction tasks trained on brain disorder classification problems, and fine-tuned on ASD datasets, brain transformers can show a great promise in ASD diagnosis.
Collapse
Affiliation(s)
- Asrar G Alharthi
- Department of Computer Science, College of Computers and Information Technology, Taif University, Saudi Arabia.
| | - Salha M Alzahrani
- Department of Computer Science, College of Computers and Information Technology, Taif University, Saudi Arabia
| |
Collapse
|
6
|
Abbas Q, Hussain A, Baig AR. CAD-ALZ: A Blockwise Fine-Tuning Strategy on Convolutional Model and Random Forest Classifier for Recognition of Multistage Alzheimer's Disease. Diagnostics (Basel) 2023; 13:167. [PMID: 36611459 PMCID: PMC9818479 DOI: 10.3390/diagnostics13010167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/24/2022] [Accepted: 12/31/2022] [Indexed: 01/05/2023] Open
Abstract
Mental deterioration or Alzheimer's (ALZ) disease is progressive and causes both physical and mental dependency. There is a need for a computer-aided diagnosis (CAD) system that can help doctors make an immediate decision. (1) Background: Currently, CAD systems are developed based on hand-crafted features, machine learning (ML), and deep learning (DL) techniques. Those CAD systems frequently require domain-expert knowledge and massive datasets to extract deep features or model training, which causes problems with class imbalance and overfitting. Additionally, there are still manual approaches used by radiologists due to the lack of dataset availability and to train the model with cost-effective computation. Existing works rely on performance improvement by neglecting the problems of the limited dataset, high computational complexity, and unavailability of lightweight and efficient feature descriptors. (2) Methods: To address these issues, a new approach, CAD-ALZ, is developed by extracting deep features through a ConvMixer layer with a blockwise fine-tuning strategy on a very small original dataset. At first, we apply the data augmentation method to images to increase the size of datasets. In this study, a blockwise fine-tuning strategy is employed on the ConvMixer model to detect robust features. Afterwards, a random forest (RF) is used to classify ALZ disease stages. (3) Results: The proposed CAD-ALZ model obtained significant results by using six evaluation metrics such as the F1-score, Kappa, accuracy, precision, sensitivity, and specificity. The CAD-ALZ model performed with a sensitivity of 99.69% and an F1-score of 99.61%. (4) Conclusions: The suggested CAD-ALZ approach is a potential technique for clinical use and computational efficiency compared to state-of-the-art approaches. The CAD-ALZ model code is freely available on GitHub for the scientific community.
Collapse
Affiliation(s)
- Qaisar Abbas
- College of Computer and Information Sciences, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11432, Saudi Arabia
| | - Ayyaz Hussain
- Department of Computer Science, Quaid-i-Azam University, Islamabad 44000, Pakistan
| | - Abdul Rauf Baig
- College of Computer and Information Sciences, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11432, Saudi Arabia
| |
Collapse
|
7
|
Balaha HM, Hassan AES. A variate brain tumor segmentation, optimization, and recognition framework. Artif Intell Rev 2022. [DOI: 10.1007/s10462-022-10337-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
8
|
Baghdadi NA, Malki A, Magdy Balaha H, AbdulAzeem Y, Badawy M, Elhosseini M. An optimized deep learning approach for suicide detection through Arabic tweets. PeerJ Comput Sci 2022; 8:e1070. [PMID: 36092010 PMCID: PMC9455273 DOI: 10.7717/peerj-cs.1070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Many people worldwide suffer from mental illnesses such as major depressive disorder (MDD), which affect their thoughts, behavior, and quality of life. Suicide is regarded as the second leading cause of death among teenagers when treatment is not received. Twitter is a platform for expressing their emotions and thoughts about many subjects. Many studies, including this one, suggest using social media data to track depression and other mental illnesses. Even though Arabic is widely spoken and has a complex syntax, depressive detection methods have not been applied to the language. The Arabic tweets dataset should be scraped and annotated first. Then, a complete framework for categorizing tweet inputs into two classes (such as Normal or Suicide) is suggested in this study. The article also proposes an Arabic tweet preprocessing algorithm that contrasts lemmatization, stemming, and various lexical analysis methods. Experiments are conducted using Twitter data scraped from the Internet. Five different annotators have annotated the data. Performance metrics are reported on the suggested dataset using the latest Bidirectional Encoder Representations from Transformers (BERT) and Universal Sentence Encoder (USE) models. The measured performance metrics are balanced accuracy, specificity, F1-score, IoU, ROC, Youden Index, NPV, and weighted sum metric (WSM). Regarding USE models, the best-weighted sum metric (WSM) is 80.2%, and with regards to Arabic BERT models, the best WSM is 95.26%.
Collapse
Affiliation(s)
- Nadiah A. Baghdadi
- Nursing Management and Education Department, College of Nursing, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Amer Malki
- College of Computer Science and Engineering, Taibah University, Yanbu, Saudi Arabia
| | - Hossam Magdy Balaha
- Computers and Control Systems Engineering Department, Faculty of Engineering, Mansoura University, Mansoura, Egypt
| | - Yousry AbdulAzeem
- Computer Engineering Department, Misr Higher Institute for Engineering and Technology, Mansoura, Egypt
| | - Mahmoud Badawy
- Computers and Control Systems Engineering Department, Faculty of Engineering, Mansoura University, Mansoura, Egypt
| | - Mostafa Elhosseini
- College of Computer Science and Engineering, Taibah University, Yanbu, Saudi Arabia
- Computers and Control Systems Engineering Department, Faculty of Engineering, Mansoura University, Mansoura, Egypt
| |
Collapse
|