Browsing by Author "Moustafa, Ahmed"

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A Systematic Review of Graph Neural Network in Healthcare-Based Applications: Recent Advances, Trends, and Future Directions
(Scopus, 2024-01-16) Saha, Arpa; Hasan, Md. Zahid; Noori, Sheak Rashed Haider; Moustafa, Ahmed
Graph neural network (GNN) is a formidable deep learning framework that enables the analysis and modeling of intricate relationships present in data structured as graphs. In recent years, a burgeoning interest has arisen in exploiting the latent capabilities of GNN for healthcare-based applications, capitalizing on their aptitude for modeling complex relationships and unearthing profound insights from graph-structured data. However, to the best of our knowledge, no study has systemically reviewed the GNN studies conducted in the healthcare domain. This study has furnished an all-encompassing and erudite overview of the prevailing cutting-edge research on GNN in healthcare. Through analysis and assimilation of studies, current research trends, recurrent challenges, and promising future opportunities in GNN for healthcare applications have been identified. China emerged as the leading country to conduct GNN-based studies in the healthcare domain, followed by the USA, UK, and Turkey. Among various aspects of healthcare, disease prediction and drug discovery emerge as the most prominent areas of focus for GNN application, indicating the potential of GNN for advancing diagnostic and therapeutic approaches. This study proposed research questions regarding diverse aspects of GNN in the healthcare domain and addressed them through an in-depth analysis. This study can provide practitioners and researchers with profound insights into the current landscape of GNN applications in healthcare and can guide healthcare institutes, researchers, and governments by demonstrating the ways in which GNN can contribute to the development of effective and efficient healthcare systems
AMP-RNNpro: a two-stage approach for identification of antimicrobials using probabilistic features
(Scopus, 2024-06-05) Shaon, Md. Shazzad Hossain; Karim, Tasmin; Sultan, Md. Fahim; Ali, Md. Mamun; Ahmed, Kawsar; Hasan, Md. Zahid; Moustafa, Ahmed; Bui, Francis M.; Al-Zahrani, Fahad Ahmed
Antimicrobials are molecules that prevent the formation of microorganisms such as bacteria, viruses, fungi, and parasites. The necessity to detect antimicrobial peptides (AMPs) using machine learning and deep learning arises from the need for efficiency to accelerate the discovery of AMPs, and contribute to developing effective antimicrobial therapies, especially in the face of increasing antibiotic resistance. This study introduced AMP-RNNpro based on Recurrent Neural Network (RNN), an innovative model for detecting AMPs, which was designed with eight feature encoding methods that are selected according to four criteria: amino acid compositional, grouped amino acid compositional, autocorrelation, and pseudo-amino acid compositional to represent the protein sequences for efficient identification of AMPs. In our framework, two-stage predictions have been conducted. Initially, this study analyzed 33 models on these feature extractions. Then, we selected the best six models from these models using rigorous performance metrics. In the second stage, probabilistic features have been generated from the selected six models in each feature encoding and they are aggregated to be fed into our final meta-model called AMP-RNNpro. This study also introduced 20 features with SHAP, which are crucial in the drug development fields, where we discover AAC, ASDC, and CKSAAGP features are highly impactful for detection and drug discovery. Our proposed framework, AMP-RNNpro excels in the identification of novel Amps with 97.15% accuracy, 96.48% sensitivity, and 97.87% specificity. We built a user-friendly website for demonstrating the accurate prediction of AMPs based on the proposed approach
Amp-rnnpro: A Two-stage Approach for Identification of Antimicrobials Using Probabilistic Features
(Springer Nature, 2024-06-05) Shaon, Md. Shazzad Hossain; Karim, Tasmin; Sultan, Md. Fahim; Ali, Md. Mamun; Ahmed, Kawsar; Hasan, Md. Zahid; Moustafa, Ahmed; Bui, Francis M.; Al-Zahrani, Fahad Ahmed
Antimicrobials are molecules that prevent the formation of microorganisms such as bacteria, viruses, fungi, and parasites. The necessity to detect antimicrobial peptides (AMPs) using machine learning and deep learning arises from the need for efficiency to accelerate the discovery of AMPs, and contribute to developing effective antimicrobial therapies, especially in the face of increasing antibiotic resistance. This study introduced AMP-RNNpro based on Recurrent Neural Network (RNN), an innovative model for detecting AMPs, which was designed with eight feature encoding methods that are selected according to four criteria: amino acid compositional, grouped amino acid compositional, autocorrelation, and pseudo-amino acid compositional to represent the protein sequences for efficient identification of AMPs. In our framework, two-stage predictions have been conducted. Initially, this study analyzed 33 models on these feature extractions. Then, we selected the best six models from these models using rigorous performance metrics. In the second stage, probabilistic features have been generated from the selected six models in each feature encoding and they are aggregated to be fed into our final meta-model called AMP-RNNpro. This study also introduced 20 features with SHAP, which are crucial in the drug development fields, where we discover AAC, ASDC, and CKSAAGP features are highly impactful for detection and drug discovery. Our proposed framework, AMP-RNNpro excels in the identification of novel Amps with 97.15% accuracy, 96.48% sensitivity, and 97.87% specificity. We built a user-friendly website for demonstrating the accurate prediction of AMPs based on the proposed approach which can be accessed at http://13.126.159.30/.