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Yayın Enabling cooperation, resource allocation and receiver selection across cells: complementary fractional frequency reuse(IEEE, 2013) Bakşi, Saygın; Kaya, Onur; Bıyıkoğlu, TürkerFor a multi-cell multiple access channel, we develop a comprehensive cooperative communication framework: we propose a novel complementary fractional frequency reuse (FFR) strategy tailored specifically for pairwise user cooperation, also taking into account cell sectoring. This strategy allows the cell edge users not only to pool their resources and cooperate across cells, but also to choose the best receiver. We divide the users into cooperating inner and outer user pairs, and assign each pair orthogonal resources using OFDMA. We employ pairwise bidirectional cooperation based on block Markov superposition encoding among user pairs. We derive the achievable rates, while taking into account the geometry dependent interference at the users and the receiver. We find the jointly optimal power allocation, partner selection and receiver selection strategies that maximize the sum rate of the system. We then propose a heuristic matching algorithm, which operates based only on user and receiver locations. We compare the performance of our proposed strategies with several non-cooperative models, and demonstrate that the sum rate can nearly be doubled, while using the same resources.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 Optimal and near-optimal partner selection algorithms in cooperative OFDMA(IEEE, 2012) Bakşi, Saygın; Kaya, Onur; Bıyıkoğlu, TürkerWe obtain the jointly optimal power allocation and partner selection policies, that maximize the sum rate of a cooperative OFDMA system with mutually cooperating pairs of users. We show that the power allocation and partner selection steps can be performed sequentially, and the latter step can be formulated as a maximum weighted matching problem on an undirected graph, which can be solved in polynomial time. We further propose practical algorithms, and compare their performances to the optimal matching algorithm, and demonstrate that very simple and low complexity algorithms based on user-user and user-receiver distances may provide near-optimum rate performance. Moreover, we observe that algorithms that achieve superior sum-rate performance, surprisingly pair the cell edge users, with the strong users near the base station.Yayın Semiregular trees with minimal Laplacian spectral radius(Elsevier Inc, 2010-04-15) Bıyıkoğlu, Türker; Leydold, JosefA semiregular tree is a tree where all non-pendant vertices have the same degree. Among all semiregular trees with fixed order and degree, a graph with minimal (adjacency/Laplacian) spectral radius is a caterpillar. Counter examples show that the result cannot be generalized to the class of trees with a given (non-constant) degree sequence.
