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Yayın Design and analysis of classifier learning experiments in bioinformatics: survey and case studies(IEEE Computer Soc, 2012-12) İrsoy, Ozan; Yıldız, Olcay Taner; Alpaydın, Ahmet İbrahim EthemIn many bioinformatics applications, it is important to assess and compare the performances of algorithms trained from data, to be able to draw conclusions unaffected by chance and are therefore significant. Both the design of such experiments and the analysis of the resulting data using statistical tests should be done carefully for the results to carry significance. In this paper, we first review the performance measures used in classification, the basics of experiment design and statistical tests. We then give the results of our survey over 1,500 papers published in the last two years in three bioinformatics journals (including this one). Although the basics of experiment design are well understood, such as resampling instead of using a single training set and the use of different performance metrics instead of error, only 21 percent of the papers use any statistical test for comparison. In the third part, we analyze four different scenarios which we encounter frequently in the bioinformatics literature, discussing the proper statistical methodology as well as showing an example case study for each. With the supplementary software, we hope that the guidelines we discuss will play an important role in future studies.Yayın A novel biometric identification system based on fingertip electrocardiogram and speech signals(Elsevier Inc., 2022-03) Güven, Gökhan; Güz, Ümit; Gürkan, HakanIn this research work, we propose a one-dimensional Convolutional Neural Network (CNN) based biometric identification system that combines speech and ECG modalities. The aim is to find an effective identification strategy while enhancing both the confidence and the performance of the system. In our first approach, we have developed a voting-based ECG and speech fusion system to improve the overall performance compared to the conventional methods. In the second approach, we have developed a robust rejection algorithm to prevent unauthorized access to the fusion system. We also presented a newly developed ECG spike and inconsistent beats removal algorithm to detect and eliminate the problems caused by portable fingertip ECG devices and patient movements. Furthermore, we have achieved a system that can work with only one authorized user by adding a Universal Background Model to our algorithm. In the first approach, the proposed fusion system achieved a 100% accuracy rate for 90 people by taking the average of 3-fold cross-validation. In the second approach, by using 90 people as genuine classes and 26 people as imposter classes, the proposed system achieved 92% accuracy in identifying genuine classes and 96% accuracy in rejecting imposter classes.Yayın Progressive damage analyses of masonry buildings by dynamic analyses(Springer International Publishing AG, 2020-08) Aras, Fuat; Akbaş, Tolga; Ekşi, Hızır; Çeribaşı, SeyitThis study investigates the effects of prescribed damage on the walls of masonry buildings by experimental and numerical methods. Ambient vibration survey method was applied to an existing, two-story, unreinforced masonry building to determine its dynamic characteristics, such as mode shapes and natural frequencies. Then, the walls on two exterior sides of the building were demolished, and dynamic testing was repeated for the damaged building. As the next step, the amount of damage on the building was increased by more impacts, and the dynamic characteristics of the heavily damaged building were identified. The results obtained from the undamaged, damaged and heavily damaged building were compared, and the damage effect on the natural frequencies of the building was noted. Besides, finite element analyses of the undamaged, damaged and heavily damaged buildings were performed. It was found that, the numerical models, constructed with code-based material properties, do not sufficiently represent the dynamic behavior of masonry buildings. Secondly, as the result of the sustained damage, while the experimental and the numerical modal analyses revealed the decrease in the dominant frequencies of the building, the difference between them increases with the severity of the damage. With the framework presented in this study, the behavior of masonry buildings can better be determined and used for analysis purposes.Yayın Projected changes in extreme temperature and precipitation indices over CORDEX-MENA domain(MDPI AG, 2021-05) Öztürk, Tuğba; Saygılı Aracı, Fatma Sibel; Kurnaz, Mehmet LeventIn this study, projected changes in climate extreme indices defined by the Expert Team on Climate Change Detection and Indices were investigated over Middle East and North Africa. Changes in the daily maximum and minimum temperature-and precipitation-based extreme indices were analyzed for the end of the 21st century compared to the reference period 1971–2000 using regional climate model simulations. Regional climate model, RegCM4.4 was used to downscale two different global climate model outputs to 50 km resolution under RCP4.5 and RCP8.5 scenarios. Results generally indicate an intensification of temperature-and precipitation-based extreme indices with increasing radiative forcing. In particular, an increase in annual minimum of daily minimum temperatures is more pronounced over the northern part of Mediterranean Basin and tropics. High increase in warm nights and warm spell duration all over the region with a pronounced increase in tropics are projected for the period of 2071–2100 together with decrease or no change in cold extremes. According to the results, a decrease in total wet-day precipitation and increase in dry spells are expected for the end of the century.Yayın A nonparametric approach for optimal reliability allocation in health services(Emerald Group Publishing Limited, 2016-02-01) Aksezer, Sezgin ÇağlarReliability evaluation of healthcare services has been a challenging task for both operations managers and system engineers working in the respective field. The purpose of this paper is to develop a data envelopment analysis-based reliability allocation model. Design/methodology/approach – A two-phase optimization scheme for the reliability evaluation and allocation of homogeneous system entities, namely, hospitals, operating in a healthcare network is proposed. First, reliability evaluation is performed nonparametrically through the frontier estimation technique data envelopment analysis by considering several failure modes and failure free discharged patients as the inputs and output of the service system. Subsequently, optimal reliability allocation that maximizes the overall network reliability subject to a budget constraint is carried out by utilizing weights of the inputs and output calculated on the Pareto optimal frontier, which is constructed from the most reliable hospitals operating in the network. Findings – The popular performance assessment methodology DEA is found to be an invaluable reliability assessment and allocation tool, where optimal weights of the associated envelopment model, under certain budget restrictions, are used to maximize overall network reliability. Originality/value – An empirical illustration of the proposed model is presented on a set of hospital network data from Turkey. Modeling implications can be carried out on similar service operations where identification of the critical performance indicator costs is possible.Yayın Significance map pruning and other enhancements to SPIHT image coding algorithm(Elsevier Science, 2003-10) Bayazıt, UluğThis paper proposes several enhancements to the Set Partitioning in Hierarchical Trees (SPIHT) image coding algorithm without changing the original algorithm's general skeleton. First and foremost, a method for significance map pruning based on a rate-distortion criterion is introduced. Specifically, the (Type A) sets of wavelet coefficients with small ratios of estimated distortion reduction to estimated rate contribution are deemed insignificant and effectively pruned. Even though determining such sets requires the computational complexity of the encoder to increase considerably with respect to the original SPIHT encoder, the original SPIHT decoder may still be used to decode the generated bitstream with a low computational complexity. The paper also proposes three low complexity enhancements by more sophisticated use of the adaptive arithmetic coder. Simulation results demonstrate that all these enhancements yield modest compression gains at moderate to high rates.Yayın Least minimum symbol error rate based post-distortion for adaptive mobile VLC transmission with receiver selection(Elsevier B.V., 2021-08) Miramirkhani, Farshad; Karbalayghareh, Mehdi; Mitra, RangeetIn the context of beyond-5G indoor communication systems, visible light communication (VLC) has emerged as a viable supplement for existing RF-based systems and as an enabler for high datarate communications. However, the existing indoor VLC systems are limited by detrimental outages caused by fluctuations in the VLC channel-gain due to user-mobility. Furthermore, the nonlinear characteristics of the light-emitting diode (LED) degrade the performance of VLC systems in the highpower regime by warping the input constellation. Additional performance-limits are introduced by inter-symbol interference (ISI) due to finite modulation-bandwidth of LEDs, and reflections from walls. In this paper, a random Fourier feature (RFF) based post-distorter is considered for mitigating the LED nonlinearity, and relevant expressions for the signal to noise ratio (SNR) are derived for a direct current biased optical orthogonal frequency division multiplexing (DCO-OFDM) system. Based on the derived expressions for SNR, the effects of user-mobility and ISI are mitigated by a DCO-OFDM based adaptive VLC transmission technique, which varies the transmission-rate/modulation-order under a specified error-rate constraint. Simulations are presented over channels obtained by ray-tracing, which indicates that the proposed algorithm achieves superior data-rates with a significantly lower error-rate.Yayın Affective theory of mind in human aging: is there any relation with executive functioning?(Routledge, 2019-04) Yıldırım, Elif; Soncu Büyükişcan, Ezgi; Gürvit, İbrahim HakanTheory of Mind (ToM) refers to the ability to make inferences on other’s mental or emotional states. Although there is evidence suggesting that impaired executive functions due to aging could have a negative impact on cognitive ToM, there is still controversy about the effect of age and age-related executive dysfunctions on affective ToM. To investigate affective ToM in healthy aging and its relationship with executive functions, we examined Reading Mind in the Eyes Test (RMET) performance and executive functions among young and older adults. There was no significant difference between age groups regarding their RMET scores. While affective ToM was correlated to executive functioning within the younger group, short term memory was found to be associated with RMET performance among older participants. Furthermore, within the older group, women performed better than men. Our findings suggest a preserved ability of affective ToM in healthy aging, which appears to be independent of executive functioning.Yayın Cognitive reserve and aging: impacts on theory of mind and executive functions(Routledge, 2025-03) Şandor, Serra; Hıdıroğlu Ongun, Ceren; Yıldırım, ElifAim: This study examines the effects of cognitive reserve (CR) on Executive Functions (EF) and Theory of Mind (ToM). While CR is suggested to mitigate age-related cognitive decline, its relationship with social cognition remains limited and inconsistent in the literature. It was hypothesized that the effect of CR on ToM might be indirect, mediated by EF and working memory. Methods: 225 cognitively healthy participants were included. CR was measured with the Cognitive Reserve Index Questionnaire, EF with verbal fluency and the Stroop Test, and WM using digit span tasks. Structural Equation Modeling was used to analyze the relationships among CR, EF, WM, and SC, controlling for age and gender. Results: CR was significantly associated with both RMET and FPRT performances. Mediation analysis revealed the direct effects of CR on RMET performance, while the effects on FPRT performance were mediated by executive functions. WM had a partial mediating effect on EF and ToM, but did not directly influence FPRT. Education was most strongly associated with RMET performance, while leisure activities were linked to FPRT performance. Conclusion: These findings suggest that CR indirectly supports ToM by enhancing EF and highlight the importance of interventions aimed at strengthening executive control to support social cognition in aging.
