Browsing by Author "Aydin, Zafer"
Now showing items 1-20 of 24
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Ceph-based Storage Server Application
Azginoglu, Nuh; Eren, Mehmet Akif; Celik, Mete; Aydin, Zafer (IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA, 2018)Ceph is a scalable and high performance distributed file system. In this study, a Ceph-based storage server was implemented and used actively. This storage system has been used as a disk of 40 virtual servers in 4 different ... -
Combining Classifiers for Protein Secondary Structure Prediction
Aydin, Zafer; Uzut, Ommu Gulsum (IEEE345 E 47TH ST, NEW YORK, NY 10017 USA, 2017)Protein secondary structure prediction is an important step in estimating the three dimensional structure of proteins. Among the many methods developed for predicting structural properties of proteins, hybrid classifiers ... -
Comparison of Machine Learning Classifiers for Protein Secondary Structure Prediction
Aydin, Zafer; Kaynar, Oguz; Gormez, Yasin; Isik, Yunus Emre (IEEE, 2018)Proteinlerin üç boyutlu yapılarının tahmin edilmesi teorik kimya ve biyoenformatik için önemli problemlerden biridir. Protein yapı tahmininin en önemli aşamalarından biri ise ikincil yapı tahminidir. Protein veritabanlarındaki ... -
Comparison of NR and UniClust Databases for Protein Secondary Structure Prediction
Aydin, Zafer; Kaynar, Oguz; Gormez, Yasin (IEEE, 2018)Proteinlerin üç boyutlu yapılarının tahmin edilmesi teorik kimya ve biyoenformatik için önemli problemlerden biridir. Üç boyutlu yapı tahminin en önemli aşamalarından biri ise ikincil yapı tahminidir. İkincil yapı ... -
A Continuously Benchmarked and Crowdsourced Challenge for Rapid Development and Evaluation of Models to Predict COVID-19 Diagnosis and Hospitalization
Yan, Yao; Schaffter, Thomas; Bergquist, Timothy; Yu, Thomas; Prosser, Justin; Aydin, Zafer; Jabeer, Amhar; Brugere, Ivan; Gao, Jifan; Chen, Guanhua; Causey, Jason; Yao, Yuxin; Bryson, Kevin; Long, Dustin R.; Jarvik, Jeffrey G.; Lee, Christoph, I; Wilcox, Adam; Guinney, Justin; Mooney, Sean (AMER MEDICAL ASSOC330 N WABASH AVE, STE 39300, CHICAGO, IL 60611-5885, 2021)IMPORTANCE Machine learning could be used to predict the likelihood of diagnosis and severity of illness. Lack of COVID-19 patient data has hindered the data science community in developing models to aid in the response ... -
Crowdsourcing digital health measures to predict Parkinson's disease severity: the Parkinson's Disease Digital Biomarker DREAM Challenge
Aydin, Zafer; Sieberts, Solveig K.; Schaff, Jennifer; Duda, Marlena; Pataki, Balint Armin; Sun, Ming; Snyder, Phil; Daneault, Jean-Francois; Parisi, Federico; Costante, Gianluca; Rubin, Udi; Banda, Peter; Chae, Yooree; Chaibub Neto, Elias; Dorsey, E. Ray; Chen, Aipeng; Elo, Laura L.; Espino, Carlos; Glaab, Enrico; Goan, Ethan; Golabchi, Fatemeh Noushin; Gormez, Yasin; Jaakkola, Maria K.; Jonnagaddala, Jitendra; Klen, Riku; Li, Dongmei; McDaniel, Christian; Perrin, Dimitri; Perumal, Thanneer M.; Rad, Nastaran Mohammadian; Rainaldi, Erin; Sapienza, Stefano; Schwab, Patrick; Shokhirev, Nikolai; Venalainen, Mikko S.; Vergara-Diaz, Gloria; Zhang, Yuqian; Wang, Yuanjia; Guan, Yuanfang; Brunner, Daniela; Bonato, Paolo; Mangravite, Lara M.; Omberg, Larsson (NATURE RESEARCHHEIDELBERGER PLATZ 3, BERLIN 14197, GERMANY, 2021)Consumer wearables and sensors are a rich source of data about patients' daily disease and symptom burden, particularly in the case of movement disorders like Parkinson's disease (PD). However, interpreting these complex ... -
Data Mining Techniques in Direct Marketing on Imbalanced Data using Tomek Link Combined with Random Under-sampling
Ümit Yilmaz; Zafer Aydin; V. Çağri Güngör; Cengiz Gezer (Association for Computing Machinery, 2021)Determining the potential customers is very important in direct marketing. Data mining techniques are one of the most important methods for companies to determine potential customers. However, since the number of potential ... -
A deep learning approach with Bayesian optimization and ensemble classifiers for detecting denial of service attacks
Gormez, Yasin; Aydin, Zafer; Karademir, Ramazan; Gungor, Vehbi C. (WILEY, 111 RIVER ST, HOBOKEN 07030-5774, NJ USA, 2020)Detecting malicious behavior is important for preventing security threats in a computer network. Denial of Service (DoS) is among the popular cyber attacks targeted at web sites of high-profile organizations and can ... -
The Determination of Distinctive Single Nucleotide Polymorphism Sets for the Diagnosis of Behçet's Disease
Isik, Yunus EMRE; Gormez, Yasin; Aydin, Zafer; Bakir-Gungor, Burcu (Institute of Electrical and Electronics Engineers Inc., 2021)Behçet's Disease (BD) is a multi-system inflammatory disorder in which the etiology remains unclear. The most probable hypothesis is that genetic tendency and environmental factors play roles in the development of BD. In ... -
Developing structural profile matrices for protein secondary structure and solvent accessibility prediction
Aydin, Zafer; Azginoglu, Nuh; Bilgin, Halil Ibrahim; Celik, Mete (OXFORD UNIV PRESS, GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND, 2019)Motivation: Predicting secondary structure and solvent accessibility of proteins are among the essential steps that preclude more elaborate 3D structure prediction tasks. Incorporating class label information contained in ... -
Dimensionality reduction for protein secondary structure and solvent accesibility prediction
Aydin, Zafer; Kaynar, Oguz; Gormez, Yasin (IMPERIAL COLLEGE PRESS, 57 SHELTON ST, COVENT GARDEN, LONDON WC2H 9HE, ENGLAND, 2018)Secondary structure and solvent accessibility prediction provide valuable information for estimating the three dimensional structure of a protein. As new feature extraction methods are developed the dimensionality of the ... -
Effect of interpolation on specular reflections in texture-based automatic colonic polyp detection
Kacmaz, Rukiye Nur; Yilmaz, Bulent; Aydin, Zafer (WILEY, 111 RIVER ST, HOBOKEN 07030-5774, NJ USA, 2020)Reflections of LED light cause unwanted noise effects called specular reflection (SR) on colonoscopic images. The aim of this study was to seek answers to the following two questions. (a) How are the texture features used ... -
Feature Selection for Protein Dihedral Angle Prediction
Aydin, Zafer; Kaynar, Oguz; Gormez, Yasin (IEEE345 E 47TH ST, NEW YORK, NY 10017 USA, 2017)Three-dimensional structure prediction has crucial importance for bioinformatics and theoretical chemistry. One of the main steps of three-dimensional structure prediction is dihedral (torsion) angle prediction. As new ... -
IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction
Gormez, Yasin; Sabzekar, Mostafa; Aydin, Zafer (WILEY111 RIVER ST, HOBOKEN 07030-5774, NJ, 2021)There is a close relationship between the tertiary structure and the function of a protein. One of the important steps to determine the tertiary structure is protein secondary structure prediction (PSSP). For this reason, ... -
Knowledge based response correction method for design of reconfigurable N-shaped microstrip patch antenna using inverse ANNs
Aoad, Ashrf; Simsek, Murat; Aydin, Zafer (WILEY, 2017)Artificial neural networks (ANNs) have been often used for engineering design problems. In this work, an inverse model of a reconfigurable N-shaped microstrip patch antenna which is formed by ANN is considered to find ... -
Lung cancer subtype differentiation from positron emission tomography images
Ayyildiz, Oguzhan; Aydin, Zafer; Yilmaz, Bulent; Karacavus, Seyhan; enkaya, Kubra; Icer, Semra; Tasdemir, Arzu; Kaya, Eser (TUBITAK SCIENTIFIC & TECHNICAL RESEARCH COUNCIL TURKEY, ATATURK BULVARI NO 221, KAVAKLIDERE, ANKARA, 00000, TURKEY, 2020)Lung cancer is one of the deadly cancer types, and almost 85% of lung cancers are nonsmall cell lung cancer (NSCLC). In the present study we investigated classification and feature selection methods for the differentiation ... -
Metabolic Imaging Based Sub-Classification of Lung Cancer
Bicakci, Mustafa; Ayyildiz, Oguzhan; Aydin, Zafer; Basturk, Alper; Karacavus, Seyhan; Yilmaz, Bulent (IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA, 2020)Lung cancer is one of the deadliest cancer types whose 84% is non-small cell lung cancer (NSCLC). In this study, deep learning-based classification methods were investigated comprehensively to differentiate two subtypes ... -
New modeling of reconfigurable microstrip antenna using hybrid structure of simulation driven and knowledge based artificial neural networks
Aoad, Ashrf; Aydin, Zafer (PAMUKKALE UNIV, CAMPUS INCILIPINAR, DENIZLI, 20020, TURKEY, 2020)Knowledge-based modeling has a critical role to embed existing knowledge to improve modeling performance. Since reconfigurable antenna can provide more operational frequencies than the classical antennas, a knowledge-based ... -
A noise-aware feature selection approach for classification
Sabzekar, Mostafa (SPRINGERONE NEW YORK PLAZA, SUITE 4600 , NEW YORK, NY 10004, UNITED STATES, 2021)A noise-aware version of support vector machines is utilized for feature selection in this paper. Combining this method and sequential backward search (SBS), a new algorithm for removing irrelevant features is proposed. ... -
NSEM: Novel Stacked Ensemble Method for Sentiment Analysis
Emre Isik, Yunus; Gormez, Yasin; Kaynar, Oguz; Aydin, Zafer (IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA, 2018)Today, people often share their ideas, opinions and feelings through forums, social media sites, blogs and similar platforms. For this reason, access to these data has become very easy. Increase in the number of shares ...
