Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Article Citation - Scopus: 2Prediction of Colorectal Cancer Based on Taxonomic Levels of Microorganisms and Discovery of Taxonomic Biomarkers Using the Grouping-Scoring (G-S-M) Approach(Elsevier Ltd, 2025-03) Bakir-Güngör, Burcu; Temiz, Mustafa; Canakcimaksutoglu, Beyza; Yousef, MalikColorectal cancer (CRC) is one of the most prevalent forms of cancer globally. The human gut microbiome plays an important role in the development of CRC and serves as a biomarker for early detection and treatment. This research effort focuses on the identification of potential taxonomic biomarkers of CRC using a grouping-based feature selection method. Additionally, this study investigates the effect of incorporating biological domain knowledge into the feature selection process while identifying CRC-associated microorganisms. Conventional feature selection techniques often fail to leverage existing biological knowledge during metagenomic data analysis. To address this gap, we propose taxonomy-based Grouping Scoring Modeling (G-S-M) method that integrates biological domain knowledge into feature grouping and selection. In this study, using metagenomic data related to CRC, classification is performed at three taxonomic levels (genus, family and order). The MetaPhlAn tool is employed to determine the relative abundance values of species in each sample. Comparative performance analyses involve six feature selection methods and four classification algorithms. When experimented on two CRC associated metagenomics datasets, the highest performance metric, yielding an AUC of 0.90, is observed at the genus taxonomic level. At this level, 7 out of top 10 groups (Parvimonas, Peptostreptococcus, Fusobacterium, Gemella, Streptococcus, Porphyromonas and Solobacterium) were commonly identified for both datasets. Moreover, the identified microorganisms at genus, family, and order levels are thoroughly discussed via refering to CRC-related metagenomic literature. This study not only contributes to our understanding of CRC development, but also highlights the applicability of taxonomy-based G-S-M method in tackling various diseases. © 2025 Elsevier B.V., All rights reserved.Article Citation - WoS: 37Citation - Scopus: 35Performance Prediction and Adaptation for Database Management System Workload Using Case-Based Reasoning Approach(Pergamon-Elsevier Science Ltd, 2018-07) Raza, Basit; Kumar, Yogan Jaya; Malik, Ahmad Kamran; Anjum, Adeel; Faheem, MuhammadWorkload management in a Database Management System (DBMS) has become difficult and challenging because of workload complexity and heterogeneity. During and after execution of the workload, it is hard to control and handle the workload. Before executing the workload, predicting its performance can help us in workload management. By knowing the type of workload in advance, we can predict its performance in an adaptive way that will enable us to monitor and control the workload, which ultimately leads to performance tuning of the DBMS. This study proposes a predictive and adaptive framework named as the Autonomic Workload Performance Prediction (AWPP) framework. The proposed AWPP framework predicts and adapts the DBMS workload performance on the basis of information available in advance before executing the workload. The Case-Based Reasoning (CBR) approach is used to solve the workload management problem. The proposed CBR approach is compared with other machine learning techniques. To validate the AWPP framework, a number of benchmark workloads of the Decision Support System (DSS) and the Online Transaction Processing (OLTP) are executed on the MySQL DBMS. For preparation of training and testing data, we executed more than 1000 TPC-H and TPC-C like workloads on a standard data set. The results show that our proposed AWPP framework through CBR modeling performs better in predicting and adapting the DBMS workload. DBMSs algorithms can be optimized for this prediction and workload can be controlled and managed in a better way. In the end, the results are validated by performing post-hoc tests. (C) 2018 Elsevier Ltd. All rights reserved.Conference Object Citation - WoS: 16Citation - Scopus: 20Machine Learning Analysis of Inflammatory Bowel Disease-Associated Metagenomics Dataset(Institute of Electrical and Electronics Engineers Inc., 2018-09) Hacilar, Hilal; Nalbantoĝlu, Özkan Ufuk; Bakir-Güngör, BurcuThere is an ongoing interplay between humans and our microbial communities. The microorganisms living in our gut produce energy from our food, strengthen our immune system, break down foreign products, and release metabolites and hormones, which are significant for regulating our physiology. The shifts away from this 'healthy' gut microbiome is considered to be associated with many diseases. Inflammatory bowel diseases (IBD) including Crohn's disease and ulcerative colitis, are gut related disorders affecting the intestinal tract. Although some metagenomics studies are conducted on IBD recently, our current understanding of the precise relationships between the human gut microbiome and IBD remains limited. In this regard, the use of state-of-the art machine learning approaches became popular to address a variety of questions like early diagnosis of certain diseases using human microbiota. In this study, we investigate which subset of gut microbiota are mostly associated with IBD and if disease-associated biomarkers can be detected via applying state-of-the art machine learning algorithms and proper feature selection methods. © 2019 Elsevier B.V., All rights reserved.Book Part Citation - Scopus: 4Computational Detection of Pre-MicroRNAs(Humana Press Inc., 2021-08-26) Saçar Demirci, Müşerref DuyguMicroRNA (miRNA) studies have been one of the most popular research areas in recent years. Although thousands of miRNAs have been detected in several species, the majority remains unidentified. Thus, finding novel miRNAs is a vital element for investigating miRNA mediated posttranscriptional gene regulation machineries. Furthermore, experimental methods have challenging inadequacies in their capability to detect rare miRNAs, and are also limited to the state of the organism under examination (e.g., tissue type, developmental stage, stress-disease conditions). These issues have initiated the creation of high-level computational methodologies endeavoring to distinguish potential miRNAs in silico. On the other hand, most of these tools suffer from high numbers of false positives and/or false negatives and as a result they do not provide enough confidence for validating all their predictions experimentally. In this chapter, computational difficulties in detection of pre-miRNAs are discussed and a machine learning based approach that has been designed to address these issues is reviewed. © 2021 Elsevier B.V., All rights reserved.Article Citation - Scopus: 4CCPred: Global and Population-Specific Colorectal Cancer Prediction and Metagenomic Biomarker Identification at Different Molecular Levels Using Machine Learning Techniques(Elsevier Ltd, 2024-11) Bakir-Güngör, Burcu; Temiz, Mustafa; Inal, Yasin; Cicekyurt, Emre; Yousef, MalikColorectal cancer (CRC) ranks as the third most common cancer globally and the second leading cause of cancer-related deaths. Recent research highlights the pivotal role of the gut microbiota in CRC development and progression. Understanding the complex interplay between disease development and metagenomic data is essential for CRC diagnosis and treatment. Current computational models employ machine learning to identify metagenomic biomarkers associated with CRC, yet there is a need to improve their accuracy through a holistic biological knowledge perspective. This study aims to evaluate CRC-associated metagenomic data at species, enzymes, and pathway levels via conducting global and population-specific analyses. These analyses utilize relative abundance values from human gut microbiome sequencing data and robust classification models are built for disease prediction and biomarker identification. For global CRC prediction and biomarker identification, the features that are identified by SelectKBest (SKB), Information Gain (IG), and Extreme Gradient Boosting (XGBoost) methods are combined. Population-based analysis includes within-population, leave-one-dataset-out (LODO) and cross-population approaches. Four classification algorithms are employed for CRC classification. Random Forest achieved an AUC of 0.83 for species data, 0.78 for enzyme data and 0.76 for pathway data globally. On the global scale, potential taxonomic biomarkers include ruthenibacterium lactatiformanas; enzyme biomarkers include RNA 2′ 3′ cyclic 3′ phosphodiesterase; and pathway biomarkers include pyruvate fermentation to acetone pathway. This study underscores the potential of machine learning models trained on metagenomic data for improved disease prediction and biomarker discovery. The proposed model and associated files are available at https://github.com/TemizMus/CCPRED. © 2024 Elsevier B.V., All rights reserved.Article Citation - WoS: 7Citation - Scopus: 8Autonomic Workload Performance Tuning in Large-Scale Data Repositories(Springer London Ltd, 2018-09-04) Raza, Basit; Sher, Asma; Afzal, Sana; Malik, Ahmad Kamran; Anjum, Adeel; Kumar, Yogan Jaya; Faheem, MuhammadThe workload in large-scale data repositories involves concurrent users and contains homogenous and heterogeneous data. The large volume of data, dynamic behavior and versatility of large-scale data repositories is not easy to be managed by humans. This requires computational power for managing the load of current servers. Autonomic technology can support predicting the workload type; decision support system or online transaction processing can help servers to autonomously adapt to the workloads. The intelligent system could be designed by knowing the type of workload in advance and predict the performance of workload that could autonomically adapt the changing behavior of workload. Workload management involves effectively monitoring and controlling the workflow of queries in large-scale data repositories. This work presents a taxonomy through systematic analysis of workload management in large-scale data repositories with respect to autonomic computing (AC) including database management systems and data warehouses. The state-of-the-art practices in large-scale data repositories are reviewed with respect to AC for characterization, performance prediction and adaptation of workload. Current issues are highlighted at the end with future directions.