Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
Browse
9 results
Search Results
Conference Object The Effect of Different Classifiers on Recursive Cluster Elimination in the Analysis of Transcriptomic Data(Institute of Electrical and Electronics Engineers Inc., 2023-10-11) Bulut, Nurten; Bakir-Güngör, Burcu; Qaqish, Bahjat F.; Yousef, MalikGene expression data with limited sample size and a large number of genes are frequently encountered in genetic studies. In such high-dimensional data, identification of genes that distinguish between disease states is a challenging task. Feature selection (FS) is a useful approach in dealing with high dimensionality. Support Vector Machines Recursive Cluster Elimination (SVM-RCE) is a technique for FS in high-dimensional data. The SVM-RCE approach has been utilized for identification of clusters of genes whose expression levels correlate with pathological state. A key step in SVM-RCE is the use of an SVM classifier to assign an area under the curve (AUC) score to each gene cluster based on its ability to predict class labels. In this study, we investigate the use of alternative classifiers in the cluster-scoring step. Specifically, we compare Support Vector Machines, Random Forest, XgBoost, Naive Bayes, and linear logistic regression. In addition to AUC score performance evaluation, the algorithms are compared in terms of the number of selected genes at different levels of clustering and in terms of the running time. © 2023 Elsevier B.V., All rights reserved.Article Citation - WoS: 52Citation - Scopus: 69Spectrum-Aware Bio-Inspired Routing in Cognitive Radio Sensor Networks for Smart Grid Applications(Elsevier Science Bv, 2017-03) Fadel, E.; Faheem, M.; Gungor, V. C.; Nassef, L.; Akkari, N.; Malik, M. G. A.; Akyildiz, I. F.Cognitive radio sensor networks (CRSNs) have been proposed to serve as a reliable, robust, and efficient communications infrastructure that can address both the existing and future energy management requirements of the smart grid. The existing and envisioned applications of CRSN-based smart grid include substation automation, overhead transmission line monitoring, home energy management, advanced metering infrastructure, wide-area situational awareness, demand response, outage management, distribution automation, asset management. To realize these applications, in this paper, honey bee mating optimization-based routing and cooperative channel assignment algorithms have been proposed. The developed framework significantly decreases the probability of packet loss and preserves high link quality among sensor nodes in harsh smart grid spectrum environments. The proposed approach performance has been evaluated in terms of packet delivery ratio, delay, and energy consumption demonstrating that it has successfully addressed the QoS requirements of most of the SG applications presented. (C) 2017 Elsevier B.V. All rights reserved.Article Citation - Scopus: 25Recursive Cluster Elimination Based Rank Function (SVM-RCE-R) Implemented in KNIME(F1000 Research Ltd, 2021-01-05) Yousef, Malik; Bakir-Güngör, Burcu; Jabeer, Amhar; Göy, Gökhan; Qureshi, Rehman A.; C Showe, Louise; C. Showe, LouiseIn our earlier study, we proposed a novel feature selection approach, Recursive Cluster Elimination with Support Vector Machines (SVM-RCE) and implemented this approach in Matlab. Interest in this approach has grown over time and several researchers have incorporated SVM-RCE into their studies, resulting in a substantial number of scientific publications. This increased interest encouraged us to reconsider how feature selection, particularly in biological datasets, can benefit from considering the relationships of those genes in the selection process, this led to our development of SVM-RCE-R. SVM-RCE-R, further enhances the capabilities of SVM-RCE by the addition of a novel user specified ranking function. This ranking function enables the user to stipulate the weights of the accuracy, sensitivity, specificity, f-measure, area under the curve and the precision in the ranking function This flexibility allows the user to select for greater sensitivity or greater specificity as needed for a specific project. The usefulness of SVM-RCE-R is further supported by development of the maTE tool which uses a similar approach to identify MicroRNA (miRNA) targets. We have also now implemented the SVM-RCE-R algorithm in Knime in order to make it easier to applyThe use of SVM-RCE-R in Knime is simple and intuitive and allows researchers to immediately begin their analysis without having to consult an information technology specialist. The input for the Knime implemented tool is an EXCEL file (or text or CSV) with a simple structure and the output is also an EXCEL file. The Knime version also incorporates new features not available in SVM-RCE. The results show that the inclusion of the ranking function has a significant impact on the performance of SVM-RCE-R. Some of the clusters that achieve high scores for a specified ranking can also have high scores in other metrics. © 2021 Elsevier B.V., All rights reserved.Article Citation - WoS: 74Citation - Scopus: 89QERP: Quality-Of (QoS) Aware Evolutionary Routing Protocol for Underwater Wireless Sensor Networks(IEEE-Inst Electrical Electronics Engineers Inc, 2018-09) Faheem, Muhammad; Tuna, Gurkan; Gungor, Vehbi CagriQuality-of-service (QoS) aware reliable data delivery is a challenging issue in underwater wireless sensor networks (UWSNs). This is clue to impairments of the acoustic transmission caused by excessive noise, extremely long propagation delays, high bit error rate, low bandwidth capacity, multipath effects, and interference. To address these challenges, meet the commonly used UWSN performance indicators, and overcome the inefficiencies of the existing clustering-based routing schemes, a novel QoS aware evolutionary cluster based routing protocol (QERP) has been proposed for UWSN-based applications. The proposed protocol improves packet delivery ratio, and reduces average end-to-end delay and overall network energy consumption. Our comparative performance evaluations demonstrate that QERP is successful in achieving low network delay, high packet delivery ratio, and low energy consumption.Article Citation - WoS: 10Citation - Scopus: 8Ensemble Feature Selection for Clustering Damage Modes in Carbon Fiber-Reinforced Polymer Sandwich Composites Using Acoustic Emission(Wiley-VCH Verlag GmbH, 2024-07-15) Gulsen, Abdulkadir; Kolukisa, Burak; Caliskan, Umut; Bakir-Gungor, Burcu; Gungor, Vehbi CagriAcoustic emission (AE) serves as a noninvasive technique for real-time structural health monitoring, capturing the stress waves produced by the formation and growth of cracks within a material. This study presents a novel ensemble feature selection methodology to rank features highly relevant with damage modes in AE signals gathered from edgewise compression tests on honeycomb-core carbon fiber-reinforced polymer. Two distinct features, amplitude and peak frequency, are selected for labeling the AE signals. An ensemble-supervised feature selection method ranks feature importance according to these labels. Using the ranking list, unsupervised clustering models are then applied to identify damage modes. The comparative results reveal a robust correlation between the damage modes and the features of counts and energy when amplitude is selected. Similarly, when peak frequency is chosen, a significant association is observed between the damage modes and the features of partial powers 1 and 2. These findings demonstrate that, in addition to the commonly used features, other features, such as partial powers, exhibit a correlation with damage modes. This article presents a novel ensemble feature selection methodology to rank features relevant to damage modes on acoustic emission signals in carbon fiber-reinforced polymer sandwich composites. Subsequently, ranked features are utilized in unsupervised clustering models to identify damage modes. The comparative results demonstrate that, along with common features, other features, like partial powers, have a robust correlation with damage modes.image (c) 2024 WILEY-VCH GmbHConference Object Citation - Scopus: 2Effect of Recursive Cluster Elimination With Different Clustering Algorithms Applied to Gene Expression Data(Institute of Electrical and Electronics Engineers Inc., 2023-10-11) Kuzudisli, Cihan; Bakir-Güngör, Burcu; Qaqish, Bahjat F.; Yousef, MalikFeature selection (FS) is an effective tool in dealing with high dimensionality and reducing computational cost. Support Vector Machines-Recursive Cluster Elimination (SVM-RCE) is one of several algorithms that have been developed for FS in high dimensional data. SVM-RCE involves a clustering step which originally is k-means. Using various performance metrics, three alternative algorithms are evaluated in this context; k-medoids, Hierarchical Clustering (HC), and Gaussian Mixture Model (GMM). Comparisons will be carried out on five publicly available gene expression datasets. The results show that k-means in SVM-RCE obtains higher performance than other tested algorithms in terms of classification performance. Additionally, HC shows a similar performance to k-means. Our findings show superiority of using k-means. This study can contribute to the development of SVM-RCE with different variations, leading to decrease in the number of selected genes, and an increase in prediction performance. © 2023 Elsevier B.V., All rights reserved.Article Citation - WoS: 64Citation - Scopus: 76EDHRP: Energy Efficient Event Driven Hybrid Routing Protocol for Densely Deployed Wireless Sensor Networks(Academic Press Ltd- Elsevier Science Ltd, 2015-12) Faheem, Muhammad; Abbas, Muhammad Zahid; Tuna, Gurkan; Gungor, Vehbi CagriEfficient management of energy resources is a challenging research area in Wireless Sensor Networks (WSNs). Recent studies have revealed that clustering is an efficient topology control approach for organizing a network into a connected hierarchy which balances the traffic load of the sensor nodes and improves the overall scalability and the lifetime of WSNs. Inspired by the advantages of clustering techniques, we have three main contributions in this paper. First, we propose an energy efficient cluster formation algorithm called Active Node Cluster Formation (ANCF). The core aim to propose ANCF algorithm is to distribute heavy data traffic and high energy consumption load evenly in the network by offering unequal size of clusters in the network. The developed scheme appoints each cluster head (CH) near to the sink and sensing event while the remaining set of the cluster heads (CHs) are appointed in the middle of each cluster to achieve the highest level of energy efficiency in dense deployment. Second, we propose a lightweight sensing mechanism called Active Node Sensing Algorithm (ANSA). The key aim to propose the ANSA algorithm is to avoid high sensing overlapping data redundancy by appointing a set of active nodes in each cluster with satisfy coverage near to the event. Third, we propose an Active Node Routing Algorithm (ANRA) to address complex inter and intra cluster routing issues in highly dense deployment based on the node dominating values. Extensive experimental studies conducted through network simulator NCTUNs 6.0 reveal that our proposed scheme outperforms existing routing techniques in terms of energy efficiency, end-to-end delay and data redundancy, congestion management and setup robustness. (C) 2015 Elsevier Ltd. All rights reserved.Article Citation - WoS: 53Citation - Scopus: 66Application of Biological Domain Knowledge Based Feature Selection on Gene Expression Data(MDPI, 2020-12-22) Yousef, Malik; Kumar, Abhishek; Bakir-Gungor, BurcuIn the last two decades, there have been massive advancements in high throughput technologies, which resulted in the exponential growth of public repositories of gene expression datasets for various phenotypes. It is possible to unravel biomarkers by comparing the gene expression levels under different conditions, such as disease vs. control, treated vs. not treated, drug A vs. drug B, etc. This problem refers to a well-studied problem in the machine learning domain, i.e., the feature selection problem. In biological data analysis, most of the computational feature selection methodologies were taken from other fields, without considering the nature of the biological data. Thus, integrative approaches that utilize the biological knowledge while performing feature selection are necessary for this kind of data. The main idea behind the integrative gene selection process is to generate a ranked list of genes considering both the statistical metrics that are applied to the gene expression data, and the biological background information which is provided as external datasets. One of the main goals of this review is to explore the existing methods that integrate different types of information in order to improve the identification of the biomolecular signatures of diseases and the discovery of new potential targets for treatment. These integrative approaches are expected to aid the prediction, diagnosis, and treatment of diseases, as well as to enlighten us on disease state dynamics, mechanisms of their onset and progression. The integration of various types of biological information will necessitate the development of novel techniques for integration and data analysis. Another aim of this review is to boost the bioinformatics community to develop new approaches for searching and determining significant groups/clusters of features based on one or more biological grouping functions.Article Citation - WoS: 12Citation - Scopus: 19An Approximate Spectral Clustering Ensemble for High Spatial Resolution Remote-Sensing Images(IEEE-Inst Electrical Electronics Engineers Inc, 2015-05) Tasdemir, Kadim; Moazzen, Yaser; Yildirim, IsaUnsupervised clustering of high spatial resolution remote-sensing images plays a significant role in detailed land-cover identification, especially for agricultural and environmental monitoring. A recently promising method is approximate spectral clustering (SC) which enables spectral partitioning for large datasets to extract clusters with distinct characteristics without a parametric model. It also facilitates the use of various information types via advanced similarity criteria. However, it requires an empirical selection of a similarity criterion optimal for the corresponding application. To address this challenge, we propose an approximate SC ensemble (ASCE2) which fuses partitionings obtained by different similarity representations. Contrary to existing spectral ensembles for remote-sensing applications, the proposed ASCE2 employs neural gas quantization instead of random sampling, advanced similarity criteria instead of traditional distance-based Gaussian kernel with different decay parameters, and a two-level ensemble. We evaluate the proposed ASCE2 with three measures (accuracy, adjusted Rand index, and normalized mutual information) using five remote-sensing images, two of which are commonly available. We apply the ASCE2 in two applications for agricultural monitoring: 1) land-cover identification to determine orchard fields using a WorldView-2 image (0.5-m spatial resolution) and 2) finding lands in good agricultural condition using multitemporal RapidEye images (5-m spatial resolution). Experimental results indicate a significant betterment of the resulting partitionings obtained by the proposed ensemble, with respect to the evaluation measures in these applications.