Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
Browse
Search Results
Now showing 1 - 2 of 2
Article Citation - WoS: 15Citation - Scopus: 19Campways: Constrained Alignment Framework for the Comparative Analysis of a Pair of Metabolic Pathways(Oxford University Press, 2013) Abaka, Gamze; Bıyıkoğlu, Türker; Erten, CesimMotivation: Given a pair of metabolic pathways, an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction, drug design and overall may enhance our understanding of cellular metabolism.Results: We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable, which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database, we demonstrate that when compared with a state-of-the-art alternative, the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms. © The Author 2013.Conference Object Citation - WoS: 1Citation - Scopus: 1Enabling Cooperation, Resource Allocation and Receiver Selection Across Cells: Complementary Fractional Frequency Reuse(Institute of Electrical and Electronics Engineers Inc., 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. © 2013 IEEE.