Browsing by Author "Alkhnbashi, Omer S"

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An Integrated Multimodal-Based CAD System for Breast Cancer Diagnosis.
(2024-11-05) Alkhnbashi, Omer S
Simple Summary: Diagnosis of breast cancer goes through multiple processes. Recently, a variety of system-aided diagnosis (CAD) systems have been proposed as Primary systems for initial diagnosis based on mammogram screenings. This paper enhances the diagnosis accuracy by using mammograms of both sides of the patient’s breasts instead of the infected side only. In addition, the paper boosts CAD accuracy by adding patient information and medical history along with mammogram images’ features. The proposed multimodal approach will serve as the nucleus for future work at both data and system levels to diagnose breast cancer and other diseases caused by various factors. Abstract: Breast cancer has been one of the main causes of death among women recently, and it has been the focus of attention of many specialists and researchers in the health field. Because of its seriousness and spread speed, breast cancer-resisting methods, early diagnosis, diagnosis, and treatment have been the points of research discussion. Many computers-aided diagnosis (CAD) systems have been proposed to reduce the load on physicians and increase the accuracy of breast tumor diagnosis. To the best of our knowledge, combining patient information, including medical history, breast density, age, and other factors, with mammogram features from both breasts in craniocaudal (CC) and mediolateral oblique (MLO) views has not been previously investigated for breast tumor classification. In this paper, we investigated the effectiveness of using those inputs by comparing two combination approaches. The soft voting approach, produced from statistical information-based models (decision tree, random forest, K-nearest neighbor, Gaussian naive Bayes, gradient boosting, and MLP) and an image-based model (CNN), achieved 90% accuracy. Additionally, concatenating statistical and image-based features in a deep learning model achieved 93% accuracy. We found that it produced promising results that would enhance the CAD systems. As a result, this study finds that using both sides of mammograms outperformed the result of using only the infected side. In addition, integrating the mammogram features with statistical information enhanced the accuracy of the tumor classification. Our findings, based on a novel dataset, incorporate both patient information and four-view mammogram images, covering multiple classes: normal, benign, and malignant.
Genomics of rare diseases in the Greater Middle East.
(2025-02-03) Chekroun, Ikram; Almarri, Mohamed A; Uddin, Mohammed; Alkhnbashi, Omer S; Ali, Fahad R; Alsheikh-Ali, Alawi; Abou Tayoun, Ahmad N
The Greater Middle East (GME) represents a concentrated region of unparalleled genetic diversity, characterized by an abundance of distinct alleles, founder mutations and extensive autozygosity driven by high consanguinity rates. These genetic hallmarks present a unique, yet vastly untapped resource for genomic research on Mendelian diseases. Despite this immense potential, the GME continues to face substantial challenges in comprehensive data collection and analysis. This Perspective highlights the region's unique position as a natural laboratory for genetic discovery and explores the challenges that have stifled progress thus far. Importantly, we propose strategic solutions, advocating for an all-inclusive research approach. With targeted investment and focused efforts, the latent genetic wealth in the GME can be transformed into a global hub for genomic research that will redefine and advance our understanding of the human genome.
SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions
(2024-10-14) Alkhnbashi, Omer S
Bacteria employ CRISPR-Cas systems for defense by integrating invader-derived sequences, termed spacers, into the CRISPR array, which constitutes an immunity memory. While spacer deletions occur randomly across the array, newly acquired spacers are predominantly integrated at the leader end. Consequently, spacer arrays can be used to derive the chronology of spacer insertions. Reconstruction of ancestral spacer acquisitions and deletions could help unravel the coevolution of phages and bacteria, the evolutionary dynamics in microbiomes, or track pathogens. However, standard reconstruction methods produce misleading results by overlooking insertion order and joint deletions of spacers. Here, we present SpacerPlacer, a maximum likelihood-based ancestral reconstruction approach for CRISPR array evolution. We used SpacerPlacer to reconstruct and investigate ancestral deletion events of 4565 CRISPR arrays, revealing that spacer deletions occur 374 times more frequently than mutations and are regularly deleted jointly, with an average of 2.7 spacers. Surprisingly, we observed a decrease in the spacer deletion frequency towards both ends of the reconstructed arrays. While the resulting trailer-end conservation is commonly observed, a reduced deletion frequency is now also detectable towards the variable leader end. Finally, our results point to the hypothesis that frequent loss of recently acquired spacers may provide a selective advantage.