PubMed İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397
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Article Citation - WoS: 2Citation - Scopus: 4RCE-IFE: Recursive Cluster Elimination With Intra-Cluster Feature Elimination(PeerJ Inc, 2025-02-07) Kuzudisli, Cihan; Bakir-Gungor, Burcu; Qaqish, Bahjat; Yousef, MalikThe computational and interpretational difficulties caused by the ever-increasing dimensionality of biological data generated by new technologies pose a significant challenge. Feature selection (FS) methods aim to reduce the dimension, and feature grouping has emerged as a foundation for FS techniques that seek to detect strong correlations among features and identify irrelevant features. In this work, we propose the Recursive Cluster Elimination with Intra-Cluster Feature Elimination (RCE-IFE) method that utilizes feature grouping and iterates grouping and elimination steps in a supervised context. We assess dimensionality reduction and discriminatory capabilities of RCE-IFE on various high-dimensional datasets from different biological domains. For a set of gene expression, MicroRNA (miRNA) expression, and methylation datasets, the performance of RCE-IFE is comparatively evaluated with RCE-IFE-SVM (the SVM-adapted version of RCE-IFE) and SVM-RCE. On average, RCE-IFE attains an area under the curve (AUC) of 0.85 among tested expression datasets with the fewest features and the shortest running time, while RCE-IFE-SVM (the SVM-adapted version of RCE-IFE) and SVM-RCE achieve similar AUCs of 0.84 and 0.83, respectively. RCE-IFE and SVM-RCE yield AUCs of 0.79 and 0.68, respectively when averaged over seven different metagenomics datasets, with RCE-IFE significantly reducing feature subsets. Furthermore, RCE-IFE surpasses several state-of-the-art FS methods, such as Minimum Redundancy Maximum Relevance (MRMR), Fast Correlation-Based Filter (FCBF), Information Gain (IG), Conditional Mutual Information Maximization (CMIM), SelectKBest (SKB), and eXtreme Gradient Boosting (XGBoost), obtaining an average AUC of 0.76 on five gene expression datasets. Compared with a similar tool, Multi-stage, RCE-IFE gives a similar average accuracy rate of 89.27% using fewer features on four cancer-related datasets. The comparability of RCE-IFE is also verified with other biological domain knowledge-based Grouping-Scoring-Modeling (G-S-M) tools, including mirGediNET, 3Mint, and miRcorrNet. Additionally, the biological relevance of the selected features by RCE-IFE is evaluated. The proposed method also exhibits high consistency in terms of the selected features across multiple runs. Our experimental findings imply that RCE-IFE provides robust classifier performance and significantly reduces feature size while maintaining feature relevance and consistency.Article Citation - WoS: 24Citation - Scopus: 27PANOGA: a Web Server for Identification of SNP-Targeted Pathways From Genome-Wide Association Study Data(Oxford Univ Press, 2014-01-11) Bakir-Gungor, Burcu; Egemen, Ece; Sezerman, Osman UgurGenome-wide association studies (GWAS) have revolutionized the search for the variants underlying human complex diseases. However, in a typical GWAS, only a minority of the single-nucleotide polymorphisms (SNPs) with the strongest evidence of association is explained. One possible reason of complex diseases is the alterations in the activity of several biological pathways. Here we present a web server called Pathway and Network-Oriented GWAS Analysis to devise functionally important pathways through the identification of SNP-targeted genes within these pathways. The strength of our methodology stems from its multidimensional perspective, where we combine evidence from the following five resources: (i) genetic association information obtained through GWAS, (ii) SNP functional information, (iii) protein-protein interaction network, (iv) linkage disequilibrium and (v) biochemical pathways.Article Citation - WoS: 4Citation - Scopus: 7Network Anomaly Detection Using Deep Autoencoder and Parallel Artificial Bee Colony Algorithm-Trained Neural Network(PeerJ Inc, 2024-10-08) Hacilar, Hilal; Dedeturk, Bilge Kagan; Bakir-Gungor, Burcu; Gungor, Vehbi CagriCyberattacks are increasingly becoming more complex, which makes intrusion detection extremely difficult. Several intrusion detection approaches have been developed in the literature and utilized to tackle computer security intrusions. Implementing machine learning and deep learning models for network intrusion detection has been a topic of active research in cybersecurity. In this study, artificial neural networks (ANNs), a type of machine learning algorithm, are employed to determine optimal network weight sets during the training phase. Conventional training algorithms, such as back- propagation, may encounter challenges in optimization due to being entrapped within local minima during the iterative optimization process; global search strategies can be slow at locating global minima, and they may suffer from a low detection rate. In the ANN training, the Artificial Bee Colony (ABC) algorithm enables the avoidance of local minimum solutions by conducting a high-performance search in the solution space but it needs some modifications. To address these challenges, this work suggests a Deep Autoencoder (DAE)-based, vectorized, and parallelized ABC algorithm for training feed-forward artificial neural networks, which is tested on the UNSW-NB15 and NF-UNSW-NB15-v2 datasets. Our experimental results demonstrate that the proposed DAE-based parallel ABC-ANN outperforms existing metaheuristics, showing notable improvements in network intrusion detection. The experimental results reveal a notable improvement in network intrusion detection through this proposed approach, exhibiting an increase in detection rate (DR) by 0.76 to 0.81 and a reduction in false alarm rate (FAR) by 0.016 to 0.005 compared to the ANN-BP algorithm on the UNSWNB15 dataset. Furthermore, there is a reduction in FAR by 0.006 to 0.0003 compared to the ANN-BP algorithm on the NF-UNSW-NB15-v2 dataset. These findings underscore the effectiveness of our proposed approach in enhancing network security against network intrusions.Article Citation - WoS: 9Citation - Scopus: 15MicroBiomeGSM: The Identification of Taxonomic Biomarkers From Metagenomic Data Using Grouping, Scoring and Modeling (G-S-M) Approach(Frontiers Media S.A., 2023-11-22) Bakir-Gungor, Burcu; Temiz, Mustafa; Jabeer, Amhar; Wu, Di; Yousef, MalikNumerous biological environments have been characterized with the advent of metagenomic sequencing using next generation sequencing which lays out the relative abundance values of microbial taxa. Modeling the human microbiome using machine learning models has the potential to identify microbial biomarkers and aid in the diagnosis of a variety of diseases such as inflammatory bowel disease, diabetes, colorectal cancer, and many others. The goal of this study is to develop an effective classification model for the analysis of metagenomic datasets associated with different diseases. In this way, we aim to identify taxonomic biomarkers associated with these diseases and facilitate disease diagnosis. The microBiomeGSM tool presented in this work incorporates the pre-existing taxonomy information into a machine learning approach and challenges to solve the classification problem in metagenomics disease-associated datasets. Based on the G-S-M (Grouping-Scoring-Modeling) approach, species level information is used as features and classified by relating their taxonomic features at different levels, including genus, family, and order. Using four different disease associated metagenomics datasets, the performance of microBiomeGSM is comparatively evaluated with other feature selection methods such as Fast Correlation Based Filter (FCBF), Select K Best (SKB), Extreme Gradient Boosting (XGB), Conditional Mutual Information Maximization (CMIM), Maximum Likelihood and Minimum Redundancy (MRMR) and Information Gain (IG), also with other classifiers such as AdaBoost, Decision Tree, LogitBoost and Random Forest. microBiomeGSM achieved the highest results with an Area under the curve (AUC) value of 0.98% at the order taxonomic level for IBDMD dataset. Another significant output of microBiomeGSM is the list of taxonomic groups that are identified as important for the disease under study and the names of the species within these groups. The association between the detected species and the disease under investigation is confirmed by previous studies in the literature. The microBiomeGSM tool and other supplementary files are publicly available at: https://github.com/malikyousef/microBiomeGSM.Article Citation - WoS: 25Citation - Scopus: 28Identification of Possible Pathogenic Pathways in Behcet's Disease Using Genome-Wide Association Study Data From Two Different Populations(Nature Publishing Group, 2014-09-17) Bakir-Gungor, Burcu; Remmers, Elaine F.; Meguro, Akira; Mizuki, Nobuhisa; Kastner, Daniel L.; Gul, Ahmet; Sezerman, Osman U.Behcet's disease (BD) is a multi-system inflammatory disorder of unknown etiology. Two recent genome-wide association studies (GWASs) of BD confirmed a strong association with the MHC class I region and identified two non-HLA common genetic variations. In complex diseases, multiple factors may target different sets of genes in the same pathway and thus may cause the same disease phenotype. We therefore hypothesized that identification of disease-associated pathways is critical to elucidate mechanisms underlying BD, and those pathways may be conserved within and across populations. To identify the disease-associated pathways, we developed a novel methodology that combines nominally significant evidence of genetic association with current knowledge of biochemical pathways, protein-protein interaction networks, and functional information of selected SNPs. Using this methodology, we searched for the disease-related pathways in two BD GWASs in Turkish and Japanese case-control groups. We found that 6 of the top 10 identified pathways in both populations were overlapping, even though there were few significantly conserved SNPs/genes within and between populations. The probability of random occurrence of such an event was 2.24E -39. These shared pathways were focal adhesion, MAPK signaling, TGF-beta signaling, ECM-receptor interaction, complement and coagulation cascades, and proteasome pathways. Even though each individual has a unique combination of factors involved in their disease development, the targeted pathways are expected to be mostly the same. Hence, the identification of shared pathways between the Turkish and the Japanese patients using GWAS data may help further elucidate the inflammatory mechanisms in BD pathogenesis.Article Citation - WoS: 42Citation - Scopus: 42HomSI: A Homozygous Stretch Identifier From Next-Generation Sequencing Data(Oxford Univ Press, 2013-12-03) Gormez, Zeliha; Bakir-Gungor, Burcu; Sagiroglu, Mahmut SamilIn consanguineous families, as a result of inheriting the same genomic segments through both parents, the individuals have stretches of their genomes that are homozygous. This situation leads to the prevalence of recessive diseases among the members of these families. Homozygosity mapping is based on this observation, and in consanguineous families, several recessive disease genes have been discovered with the help of this technique. The researchers typically use single nucleotide polymorphism arrays to determine the homozygous regions and then search for the disease gene by sequencing the genes within this candidate disease loci. Recently, the advent of next-generation sequencing enables the concurrent identification of homozygous regions and the detection of mutations relevant for diagnosis, using data from a single sequencing experiment. In this respect, we have developed a novel tool that identifies homozygous regions using deep sequence data. Using*.vcf (variant call format) files as an input file, our program identifies the majority of homozygous regions found by microarray single nucleotide polymorphism genotype data.Letter Epistatic Interactions Between Autoimmunity and Genetic Thrombophilia' Reply(Nature Publishing Group, 2015-01-14) Bakir-Gungor, Burcu; Remmers, Elaine F.; Meguro, Akira; Mizuki, Nobuhisa; Kastner, Daniel L.; Gul, Ahmet; Sezerman, Osman UgurArticle Citation - WoS: 25Citation - Scopus: 31Discovering Potential Taxonomic Biomarkers of Type 2 Diabetes From Human Gut Microbiota via Different Feature Selection Methods(Frontiers Media S.A., 2021-08-25) Bakir-Gungor, Burcu; Bulut, Osman; Jabeer, Amhar; Nalbantoglu, O. Ufuk; Yousef, MalikHuman gut microbiota is a complex community of organisms including trillions of bacteria. While these microorganisms are considered as essential regulators of our immune system, some of them can cause several diseases. In recent years, next-generation sequencing technologies accelerated the discovery of human gut microbiota. In this respect, the use of machine learning techniques became popular to analyze disease-associated metagenomics datasets. Type 2 diabetes (T2D) is a chronic disease and affects millions of people around the world. Since the early diagnosis in T2D is important for effective treatment, there is an utmost need to develop a classification technique that can accelerate T2D diagnosis. In this study, using T2D-associated metagenomics data, we aim to develop a classification model to facilitate T2D diagnosis and to discover T2D-associated biomarkers. The sequencing data of T2D patients and healthy individuals were taken from a metagenome-wide association study and categorized into disease states. The sequencing reads were assigned to taxa, and the identified species are used to train and test our model. To deal with the high dimensionality of features, we applied robust feature selection algorithms such as Conditional Mutual Information Maximization, Maximum Relevance and Minimum Redundancy, Correlation Based Feature Selection, and select K best approach. To test the performance of the classification based on the features that are selected by different methods, we used random forest classifier with 100-fold Monte Carlo cross-validation. In our experiments, we observed that 15 commonly selected features have a considerable effect in terms of minimizing the microbiota used for the diagnosis of T2D and thus reducing the time and cost. When we perform biological validation of these identified species, we found that some of them are known as related to T2D development mechanisms and we identified additional species as potential biomarkers. Additionally, we attempted to find the subgroups of T2D patients using k-means clustering. In summary, this study utilizes several supervised and unsupervised machine learning algorithms to increase the diagnostic accuracy of T2D, investigates potential biomarkers of T2D, and finds out which subset of microbiota is more informative than other taxa by applying state-of-the art feature selection methods.</p>Article Citation - WoS: 4Citation - Scopus: 5CSA-DE-LR: Enhancing Cardiovascular Disease Diagnosis With a Novel Hybrid Machine Learning Approach(PeerJ Inc, 2024-07-18) Dedeturk, Beyhan Adanur; Dedeturk, Bilge Kagan; Bakir-Gungor, BurcuCardiovascular diseases (CVD) are a leading cause of mortality globally, necessitating the development of efficient diagnostic tools. Machine learning (ML) and metaheuristic algorithms have become prevalent in addressing these challenges, providing promising solutions in medical diagnostics. However, traditional ML approaches often need to be improved in feature selection and optimization, leading to suboptimal performance in complex diagnostic tasks. To overcome these limitations, this study introduces a new hybrid method called CSA-DE-LR, which combines the clonal selection algorithm (CSA) and differential evolution (DE) with logistic regression. This integration is designed to optimize logistic regression weights efficiently for the accurate classification of CVD. The methodology employs three optimization strategies based on the F1 score, the Matthews correlation coefficient (MCC), and the mean absolute error (MAE). Extensive evaluations on benchmark datasets, namely Cleveland and Statlog, reveal that CSA-DELR outperforms state-of-the-art ML methods. In addition, generalization is evaluated using the Breast Cancer Wisconsin Original (WBCO) and Breast Cancer Wisconsin Diagnostic (WBCD) datasets. Significantly, the proposed model demonstrates superior efficacy compared to previous research studies in this domain. This study's findings highlight the potential of hybrid machine learning approaches for improving diagnostic accuracy, offering a significant advancement in the fields of medical data analysis and CVD diagnosis.Article Citation - Scopus: 4Aguhyper: A Hyperledger-Based Electronic Health Record Management Framework(PeerJ Inc, 2024-05-22) Dedeturk, Beyhan Adanur; Bakir-Gungor, BurcuThe increasing importance of healthcare records, particularly given the emergence of new diseases, emphasizes the need for secure electronic storage and dissemination. With these records dispersed across diverse healthcare entities, their physical maintenance proves to be excessively time-consuming. The prevalent management of electronic healthcare records (EHRs) presents inherent security vulnerabilities, including susceptibility to attacks and potential breaches orchestrated by malicious actors. To tackle these challenges, this article introduces AguHyper, a secure storage and sharing solution for EHRs built on a permissioned blockchain framework. AguHyper utilizes Hyperledger Fabric and the InterPlanetary Distributed File System (IPFS). Hyperledger Fabric establishes the blockchain network, while IPFS manages the off -chain storage of encrypted data, with hash values securely stored within the blockchain. Focusing on security, privacy, scalability, and data integrity, AguHyper ' s decentralized architecture eliminates single points of failure and ensures transparency for all network participants. The study develops a prototype to address gaps identi fi ed in prior research, providing insights into blockchain technology applications in healthcare. Detailed analyses of system architecture, AguHyper ' s implementation con fi gurations, and performance assessments with diverse datasets are provided. The experimental setup incorporates CouchDB and the Raft consensus mechanism, enabling a thorough comparison of system performance against existing studies in terms of throughput and latency. This contributes signi fi cantly to a comprehensive evaluation of the proposed solution and offers a unique perspective on existing literature in the fi eld.