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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 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 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 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.
