Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Conference Object Citation - Scopus: 2miRcorrNetPro: Unraveling Algorithmic Insights Through Cross-Validation in Multi-Omics Integration for Comprehensive Data Analysis(Institute of Electrical and Electronics Engineers Inc., 2023-12-05) Ünlü Yazici, Miray; Yousef, Malik; Marron, J. S.; Bakir-Güngör, Burcu; Yazici, Miray UnluHigh throughput -omics technologies facilitate the investigation of regulatory mechanisms of complex diseases. Along this line, scientists develop promising tools and methods to extend our understanding at the molecular and functional levels. To this end, miRcorrNet tool performs integrative analysis of MicroRNA (miRNA) and gene expression profiles via machine learning (ML) approach to identify significant miRNA groups and their associated target genes. In this study, we propose miRcorrNetPro tool, which extends miRcorrNet by tracking group scoring, ranking and other information through the cross-validation iterations. Heatmap visualizations enable deep novel insights into the collective behavior of clusters of groups in cellular signaling and hence facilitate detection of potential biomarkers for the disease under investigation. Although miRcorrNetPro is designed as a generic tool, here we present our findings and potential miRNA biomarkers for Breast Cancer (BRCA). The miRcorrNetPro tool and all other supplementary files are available at https://github.com/Miray-Unlu/miRcorrNetPro. © 2024 Elsevier B.V., All rights reserved.Book Part Citation - WoS: 5Citation - Scopus: 5Wireless MEMS for Smart Grids(Woodhead Publ Ltd, 2017) Tuna, G.; Gungor, V. C.; Dursun, B.Book Part Citation - WoS: 1Citation - Scopus: 4Understanding Communication via Diffusion: Simulation Design and Intricacies(Springer International Publishing AG, 2017) Acar, Bilal; Akkaya, Ali; Genc, Gaye; Yilmaz, H. Birkan; Kuran, M. Sukru; Tugcu, Tuna; Şükrü Kuran, M.Understanding Communication via Diffusion (CvD) is key to molecular communications research since it dominates the movement at the nano-scale. The researcher needs to properly understand the random diffusion of the molecules for the analysis of a molecular communication system. This chapter aims explaining the dynamics of diffusion from a communication engineer's perspective as well as providing useful hints for an effective simulation design by discussing some key intricacies. The chapter starts with a brief survey of simulators for molecular communications, followed by the basics of the simulation of Brownian motion and CvD. Several intricacies are addressed to help the researcher in simulation design, such as the number of replications required in terms of movement and bit sequence. We utilize this information further by discussing the design of more complex CvD systems such as tunnel-based approach that utilizes destroyer molecules and distributed simulator design based on HLA. Introduction of more complex CvD systems provides significant improvements in data rate and communications in general, bridging the gap between human-scale and nano-scale systems and enabling nanonetworking as a viable technology.Conference Object Citation - Scopus: 1Traffic Light Management Systems Using Reinforcement Learning(Institute of Electrical and Electronics Engineers Inc., 2022-09-07) Can, Sultan Kubra; Thahir, Adam Rizvi; Cos¸kun, Mustafa; Güngör, Vehbi Çağrı; Coskun, MustafaWhile reducing traffic congestion and decrease the number of traffic accidents in the intersections, most of the traffic light management approaches cannot adapt well to fast changing traffic dynamics and growing demands of the intersections with modern world developments. To overcome this problem, adaptive traffic controllers are developed, and detectors and sensors are added to systems to enable adoption and dynamism. Recently, reinforcement learning has shown its capability to learn the dynamics of complex environments, such as urban traffic. Although it was studied in single junction systems, one of the problems was the lack of consistency with how the real world system works. Most of the systems assume that the environment is fully observable or actions would be freely executed using simulators. This study aims to merge usefulness of reinforcement learning methods with real-world traffic constraints. Comparative performance evaluations show that the reinforcement learning algorithm (Advantage Actor-Critic (A2C)) converges well while staying stable under changing traffic dynamics. © 2022 Elsevier B.V., All rights reserved.Conference Object The Relationship Between TSH Levels, Maternal Characteristics and Racial Group of the Aneuploidy Screening(Institute of Electrical and Electronics Engineers Inc., 2022-09-07) Soylemez, Ummu Gülsüm; Kaymakçalan, Hande; Härkönen, Juho; Bakir-Güngör, Burcu; Celebiler, Hande KaymakcalanFirst-trimester maternal screening is a widely used test for detecting fetal aneuploidies and neural tube defects for over two decades. Human chorionic gonadotropin hormone (beta-hCG) and pregnancy-associated plasma protein A (PAPP-A) are two serum biomarkers that are analyzed in this screening. The thyroid hormone is a critical hormone for normal pregnancy and fetal development. During the first half of pregnancy, placental and fetal development depends on the thyroid hormone levels in the mother. Therefore, thyroid abnormalities in the mother can result in unfavorable pregnancy outcomes such as intrauterine growth restriction, miscarriage, hypertensive disorders, premature birth, and an increase in the risk of low IQ in the newborn. In this study, we analyzed the first-trimester screening data collected from 410 pregnant women who were seen at Yale University Hospital Prenatal Unit; and checked for possible correlations of TSH levels with maternal characteristics, racial group PAPP-A MoM levels. © 2022 Elsevier B.V., All rights reserved.Article Citation - WoS: 9Citation - Scopus: 11The Intersubband Optical Properties of a Two-Electron Quantum Dot-Quantum Well Heterostructure(Academic Press Ltd- Elsevier Science Ltd, 2015-10) Aydin, Rasit; Tas, Hatice; Sahin, MehmetIn this paper, both linear and third-order nonlinear optical properties of two-electron in a semiconductor core/shell/well/shell quantum dot (QD) heterostructure for cases with and without a hydrogenic donor impurity have been investigated in a detailed manner as depending on the structure parameters. For this purpose, first, the energy eigenvalues and corresponding wave functions of the structure have been computed as a function of the layer thicknesses by means of the self-consistent solution of the Poisson and Schrodinger equations in envelope function effective mass approximation. Second, using these energy eigenvalues and their wave functions obtained from the calculations, both linear and third-order nonlinear optical properties of the multi-shell QD (MSQD) with two-electron have been determined as a function of the photon energies and shell thicknesses. Also, all procedures mentioned above have been repeated for negatively charged donor impurity (D-) located in the center of the same structure. Finally, obtained results have been presented comparatively for cases with and without the impurity. (C) 2015 Elsevier Ltd. All rights reserved.Article Citation - WoS: 4Citation - Scopus: 5The Existence of Positive Solutions for a Semipositone Second-Order M-Point Boundary Value Problem(Dynamic Publishers, inc, 2015) Dogan, AbdulkadirIn this paper, we study the existence of positive solutions to boundary value problem {u '' + lambda f(t,u)=0, t is an element of(0,1); u(0)=Sigma(m-2)(i-1) alpha (i)u(xi(i)), u'(1) = Sigma (m-2)(i=1) beta(i) u'(xi(i)), where xi(i) is an element of(0, 1), 0 < xi(1) < xi(2) < ... < xi(m-2) < 1, alpha(i), beta(i) is an element of[0,infinity), lambda is positive parameter. By using Krasnoserskii's fixed point theorem, we provide sufficient conditions for the existence of at least one positive solution to the above boundary value problem.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.Conference Object Symmetric Electret-Based Vibration Energy Harvesters With Curved-Beam Hinges(IEEE, 2023-05-28) Hah, DooyoungBroadband power spectral characteristics are desirable in vibration energy harvesters, and it can be achieved by employing curved-beam hinges, which exhibit force-displacement nonlinearity. Via numerical analysis by using stochastic differential equations and colored-noise inputs, this study shows that a symmetric configuration of the curved-beam hinges in electret-based harvesters can produce higher (up to 8% more) power outputs than an asymmetric one. It also presents that the harvesters with curved-beam hinges can produce higher (up to 4.4 times) power outputs than those with straight hinges when the vibration magnitude is 0.05g.Conference Object Structural Integrity Analysis of a Two-Pole Synchronous Reluctance Machine With Non-Circular Shaft(IEEE, 2023-06-14) Tekgun, Didem; Tekgun, Burak; Alan, IrfanThis paper investigates the structural strength of a 6-inch diameter, two-pole, 4 kW line start synchronous reluctance machine (LS-SynRM) designed with a new non-circular shaft structure that serves as a pump motor. Flux paths on the rotor are widened while narrowing down the shaft of the motor on the q- axis to improve the motor efficiency. By using this method, a wider path is created for the flux in the d-axis. As a result, the inductance in the d-axis, the ratio of inductance between the d-axis and q-axis (referred to as saliency ratio), and the difference in inductance between the d-axis and q-axis are all amplified. To evaluate the structural strength of the machine, a series of analyses are conducted, including modal, harmonic, and static examination on the rotor using ANSYS Structural. The findings indicate that to prevent redundant deformations and undesirable vibrations because of resonance, the maximum safe limit for shaft size reduction is determined as 8 mm.