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Yayın Discovering cis-regulatory modules by optimizing barbecues(Elsevier Science Bv, 2009-05-28) Mosig, Axel; Bıyıkoğlu, Türker; Prohaska, Sonja J.; Stadler, Peter F.Gene expression in eukaryotic cells is regulated by a complex network of interactions, in which transcription factors and their binding sites on the genomic DNA play a determining role. As transcription factors rarely, if ever, act in isolation, binding sites of interacting factors are typically arranged in close proximity forming so-called cis-regulatory modules. Even when the individual binding sites are known, module discovery remains a hard combinatorial problem, which we formalize here as the Best Barbecue Problem. It asks for simultaneously stabbing a maximum number of differently colored intervals from K arrangements of colored intervals. This geometric problem turns out to be an elementary, yet previously unstudied combinatorial optimization problem of detecting common edges in a family of hypergraphs, a decision version of which we show here to be NP-complete. Due to its relevance in biological applications, we propose algorithmic variations that are suitable for the analysis of real data sets comprising either many sequences or many binding sites. Being based on set systems induced by interval arrangements, our problem setting generalizes to discovering patterns of co-localized itemsets in non-sequential objects that consist of corresponding arrangements or induce set systems of co-localized items. In fact, our optimization problem is a generalization of the popular concept of frequent itemset mining.Yayın Imagined contact facilitates acculturation, sometimes: contradicting evidence from two sociocultural contexts(Educational Publishing Foundation-American Psychological Assoc, 2019-10) Bağcı Hemşinlioğlu, Sabahat Çiğdem; Piyale, Zeynep Ecem; Stathi, SofiaObjective: Imagined intergroup contact has been shown to be an effective tool to improve intergroup relationships in various settings, yet the application of the strategy among minority group members and across cultures has been scarce. The current research aimed to test imagined contact effects on minority group members' acculturation strategies (contact participation and culture maintenance), perceived discrimination, feelings of belongingness, and social acceptance across three studies conducted in the United Kingdom (Study 1) and Turkey (Studies 2 and 3). Method: The sample consisted of Eastern Europeans in Study 1 (N = 63) and Kurds in Study 2 and 3 (N = 66 and 210, respectively). Participants were randomly assigned to 1 of 2 conditions (control vs. imagined contact) and completed measures of acculturation, perceived discrimination, general belongingness, and social acceptance. Results: Findings showed that while imagined contact significantly reduced perceived discrimination and culture maintenance, and increased contact participation and social acceptance among Eastern Europeans (Study 1), it reduced social acceptance and contact participation among Kurds recruited from a conflict-ridden homogeneous setting (Study 2). With a larger and more heterogeneous sample of Kurds (Study 3), these effects occurred only among those with higher ingroup identification. Moreover, in all studies social acceptance mediated the effects of imagined contact on contact participation and perceived discrimination. Discussion. Findings offer important insights about the use of the imagined contact strategy among minority group members and imply the need to take into account the context-dependent nature of contact strategies.Yayın Automated cell nucleus detection for large-volume electron microscopy of neural tissue(IEEE, 2014-04-29) Tek, Faik Boray; Kroeger, Thorben; Hamprecht, Fred A.; Mikula, ShawnVolumetric electron microscopy techniques, such as serial block-face electron microscopy (SBEM), generate massive amounts of image data that are used for reconstructing neural circuits. Typically, this requires time-intensive manual annotation of cells and their connections. To facilitate this analysis, we study the problem of automated detection of cell nuclei in a new SBEM dataset that contains cerebral cortex, white matter, and striatum from an adult mouse brain. The dataset was manually annotated to identify the locations of all 3309 cell nuclei in the volume. We make both dataset and annotations available here. Using a hybrid approach that combines interactive learning, morphological processing, and object level feature classification, we demonstrate automated detection of cell nuclei at 92.4% recall and 95.1% precision. These algorithms are not RAM-limited and can scale to arbitrarily large datasets.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 When imagining intergroup contact mobilizes collective action: The perspective of disadvantaged and advantaged groups(Pergamon-Elsevier Science Ltd, 2019-03) Bağcı Hemşinlioğlu, Sabahat Çiğdem; Stathi, Sofia; Piyale, Zeynep EcemThe current studies aimed to reveal the potential role of imagined intergroup contact on collective action tendencies within a context of intergroup conflict. Study 1 (disadvantaged Kurds, N = 80) showed that imagined contact increased collective action tendencies and this effect was mediated by increased perceived discrimination and ethnic identification. Study 2 (advantaged Turks, N = 127) demonstrated that imagined contact also directly increased collective action tendencies, as well as perceived discrimination and relative deprivation among the advantaged group. No significant mediation emerged. At the same time, in line with literature, imagined contact led only the advantaged group members to display more positive outgroup attitudes. Findings suggest that in settings where ingroup identities and conflict are salient, imagined contact may not readily undermine motivation for social change among group members.Yayın A cooperative neural network control structure and its application for systems having dead-zone nonlinearities(Springer International Publishing Ag, 2022-03) Dinçmen, ErkinAn adaptive control structure utilizing two feed-forward neural networks (NN) is proposed to deal with systems having unknown nonlinearities. One of the networks is trained to mimic the nonlinear system dynamics. Its training will be repeated with periods in order to keep it an updated valid model of the system all the times since the parameters and/or nonlinearities of the system may change during time. The other network, which is the Controller NN, adapts itself continuously by collaborating with the Model NN. The stability-convergence analysis of both networks is performed via Lyapunov method. An example system is chosen to show the applicability of the control algorithm. This example system is created by combining a linear dynamics model with a dead-zone function to represent a nonlinear system to be controlled. It should be noted that the proposed control structure can be used in any nonlinear system without knowing the system dynamics. The only information required by Model NN is the training set consisting input-output data pairs of the system. The Model NN is trained offline with this training set, and afterward the Controller NN adapts its weights online continuously during the control task with the help of Model NN. The performances of PD and PID controllers are also given for comparison purposes.Yayın Thermo-microstretch elastic bodies and plane waves(IOP PUBLISHING LTD, 2011) İnan, Esin; Kırış, AhmetIn the present work, vibration problems of rectangular plates are considered for the determination of upper bounds to the unknown microstretch material properties. The frequencies are obtained by extending the Ritz method to this case. The analysis shows that some additional frequencies characterizing the microstretch effects appear among the classical frequencies. Furthermore, by the increasing values of the microstretch constants, the additional frequencies disappear and only the classical frequencies remain in the spectrum. Considering this phenomenon, an optimization problem is established for the identification of the upper bounds of microstretch elastic constants. In the second part of the work, thermal effects are considered and several theories are discussed. Finally, propagation of the plane waves is investigated.Yayın Real time electrocardiogram identification with multi-modal machine learning algorithms(Springer International Publishing AG, 2018) Waili, Tuerxun; Nor, Rizal Mohd; Sidek, Khairul Azami; Rahman, Abdul Wahab Bin Abdul; Güven, GökhanWeaknesses in conventional identification technologies such as identification cards, badges and RFID tags prompts attention to biometric form of identification. Biometrics like voice, brain signal and finger print are unique human traits that can be used for identification. In this paper we present an identification system based on Electrocardiogram (heart signal). There is a considerable number of research in the past with high accuracy for identification , however, most ignore the practical time required to identify an individual. In this study, we explored a more practical approach in identification by reducing the number of time required for identification. We explore ways to identity a person within 3-4 s using just 5 heart beats. We extracted few reliable features from each QRS complexes, combined effort of three algorithms to achieve 96% accuracy. This approach is more suitable and practical in real time applications where time for identification is important.Yayın Fingertip electrocardiogram and speech signal based biometric recognition system(Işık Üniversitesi, 2021-12-27) Güven, Gökhan; Güz, Ümit; Gürkan, Hakan; Işık Üniversitesi, Lisansüstü Eğitim Enstitüsü, Elektronik Mühendisliği Doktora ProgramıFingertip electrocardiogram and speech signal based biometric recognition system In this research work, we presented a one-dimensional CNN-based person identification system which depends on the combination of both speech and ECG modalities to improve the overall performance compared to traditional systems. The proposed method has two approach: one is to develop combination of textindependent speech and fingertip ECG fusion system, the other one is to develop a robust rejection algorithm to prevent unauthorized access to the fusion system. In addition to the system robustness, we have developed an ECG spike and inconsistent beats removing algorithm, which detect and remove the problems caused by either portable fingertip ECG devices or movements of the patients. First approach has been tested on 30, 45, 60, 75 and 90 people which were taken from LibriSpeech Corpus database and combination of both CYBHi and our private fingertip ECG database. The 3-fold cross validation test setup has been conducted while system working time was set to 10 seconds. In the first experiment, we achieved 90.22% accuracy rate for 90 people for ECG based system. For the speech based system, 97.94% accuracy rate has achieved for 90 people. For the combination of both system, 99.92% accuracy rate has been achieved. For the second approach, 90 people for ECG and Speech database were being used as genuine class, 26 people as imposter class, and after the performance evaluation in optimum rejection thresholds, 71.08% accuracy rate for imposters rejection and 71.05% accuracy rate for genuine recognition has achieved for ECG based system. For the speech based system, imposter class were 87.82% accurately rejected while genuine classes were 86.48% accurately identified. The combination of both system has achieved 91.68% accuracy for genuine identification rate whereas 96.05% accuracy for imposter rejection.Yayın Transforming tourism experience: AI-based smart travel platform(Association for Computing Machinery, 2023) Yöndem, Meltem Turhan; Özçelik, Şuayb Talha; Caetano, Inés; Figueiredo, José; Alves, Patrícia; Marreiros, Goreti; Bahtiyar, Hüseyin; Yüksel, Eda; Perales, FernandoIn this paper, we propose the development of a novel personalized tourism platform incorporating artificial intelligence (AI) and augmented reality (AR) technologies to enhance the smart tourism experience. The platform utilizes various data sources, including travel history, user activity, and personality assessments, combined with machine learning algorithms to generate tailored travel recommendations for individual users. We implemented fundamental requirements for the platform: secure user identification using blockchain technology and provision of personalized services based on user interests and preferences. By addressing these requirements, the platform aims to increase tourist satisfaction and improve the efficiency of the tourism industry. In collaboration with various universities and companies, this multinational project aims to create a versatile platform that can seamlessly integrate new smart tourism units, providing an engaging, educational, and enjoyable experience for users.
