Browsing by Subject "Complex networks"
Now showing 1 - 12 of 12
Results Per Page
Sort Options
Item Open Access Algorithms for effective querying of compound graph-based pathway databases(BioMed Central Ltd., 2009-11-16) Doğrusöz, Uğur; Çetintaş, Ahmet; Demir, Emek; Babur, ÖzgünBackground: Graph-based pathway ontologies and databases are widely used to represent data about cellular processes. This representation makes it possible to programmatically integrate cellular networks and to investigate them using the well-understood concepts of graph theory in order to predict their structural and dynamic properties. An extension of this graph representation, namely hierarchically structured or compound graphs, in which a member of a biological network may recursively contain a sub-network of a somehow logically similar group of biological objects, provides many additional benefits for analysis of biological pathways, including reduction of complexity by decomposition into distinct components or modules. In this regard, it is essential to effectively query such integrated large compound networks to extract the sub-networks of interest with the help of efficient algorithms and software tools. Results: Towards this goal, we developed a querying framework, along with a number of graph-theoretic algorithms from simple neighborhood queries to shortest paths to feedback loops, that is applicable to all sorts of graph-based pathway databases, from PPIs (protein-protein interactions) to metabolic and signaling pathways. The framework is unique in that it can account for compound or nested structures and ubiquitous entities present in the pathway data. In addition, the queries may be related to each other through "AND" and "OR" operators, and can be recursively organized into a tree, in which the result of one query might be a source and/or target for another, to form more complex queries. The algorithms were implemented within the querying component of a new version of the software tool PATIKAweb (Pathway Analysis Tool for Integration and Knowledge Acquisition) and have proven useful for answering a number of biologically significant questions for large graph-based pathway databases. Conclusion: The PATIKA Project Web site is http://www.patika.org. PATIKAweb version 2.1 is available at http://web.patika.org. © 2009 Dogrusoz et al; licensee BioMed Central Ltd.Item Open Access Analytic relationship of relative synchronizability to network structure and motifs(National Academy of Sciences, 2023-09-05) Lizier, J. T.; Bauer, F.; Atay, Fatihcan Mehmet; Jost, J.Synchronization phenomena on networks have attracted much attention in studies of neural, social, economic, and biological systems, yet we still lack a systematic understanding of how relative synchronizability relates to underlying network structure. Indeed, this question is of central importance to the key theme of how dynamics on networks relate to their structure more generally. We present an analytic technique to directly measure the relative synchronizability of noise-driven time-series processes on networks, in terms of the directed network structure. We consider both discrete-time autoregressive processes and continuous-time Ornstein–Uhlenbeck dynamics on networks, which can represent linearizations of nonlinear systems. Our technique builds on computation of the network covariance matrix in the space orthogonal to the synchronized state, enabling it to be more general than previous work in not requiring either symmetric (undirected) or diagonalizable connectivity matrices and allowing arbitrary self-link weights. More importantly, our approach quantifies the relative synchronization specifically in terms of the contribution of process motif (walk) structures. We demonstrate that in general the relative abundance of process motifs with convergent directed walks (including feedback and feedforward loops) hinders synchronizability. We also reveal subtle differences between the motifs involved for discrete or continuous-time dynamics. Our insights analytically explain several known general results regarding synchronizability of networks, including that small-world and regular networks are less synchronizable than random networks.Item Open Access Glycosaminoglycan-Mimetic Signals Direct the Osteo/Chondrogenic Differentiation of Mesenchymal Stem Cells in a Three-Dimensional Peptide Nanofiber Extracellular Matrix Mimetic Environment(American Chemical Society, 2016-02) Arslan, E.; Güler, Mustafa O.; Tekinay, A. B.Recent efforts in bioactive scaffold development focus strongly on the elucidation of complex cellular responses through the use of synthetic systems. Designing synthetic extracellular matrix (ECM) materials must be based on understanding of cellular behaviors upon interaction with natural and artificial scaffolds. Hence, due to their ability to mimic both the biochemical and mechanical properties of the native tissue environment, supramolecular assemblies of bioactive peptide nanostructures are especially promising for development of bioactive ECM-mimetic scaffolds. In this study, we used glycosaminoglycan (GAG) mimetic peptide nanofiber gel as a three-dimensional (3D) platform to investigate how cell lineage commitment is altered by external factors. We observed that amount of fetal bovine serum (FBS) presented in the cell media had synergistic effects on the ability of GAG-mimetic nanofiber gel to mediate the differentiation of mesenchymal stem cells into osteogenic and chondrogenic lineages. In particular, lower FBS concentration in the culture medium was observed to enhance osteogenic differentiation while higher amount FBS promotes chondrogenic differentiation in tandem with the effects of the GAG-mimetic 3D peptide nanofiber network, even in the absence of externally administered growth factors. We therefore demonstrate that mesenchymal stem cell differentiation can be specifically controlled by the combined influence of growth medium components and a 3D peptide nanofiber environment.Item Open Access Inhibition of VEGF mediated corneal neovascularization by anti-angiogenic peptide nanofibers(Elsevier, 2016-11) Senturk, B.; Cubuk, M. O.; Ozmen, M. C.; Aydin B.; Güler, Mustafa O.; Tekinay, A. B.Atypical angiogenesis is one of the major symptoms of severe eye diseases, including corneal neovascularization, and the complex nature of abnormal vascularization requires targeted methods with high biocompatibility. The targeting of VEGF is the most common approach for preventing angiogenesis, and the LPPR peptide sequence is known to strongly inhibit VEGF activity by binding to the VEGF receptor neuropilin-1. Here, the LPPR epitope is presented on a peptide amphiphile nanofiber system to benefit from multivalency and increase the anti-angiogenic function of the epitope. Peptide amphiphile nanofibers are especially useful for ocular delivery applications due to their ability to remain on the site of interest for extended periods of time, facilitating the long-term presentation of bioactive sequences. Consequently, the LPPR sequence was integrated into a self-assembled peptide amphiphile network to increase its efficiency in the prevention of neovascularization. Anti-angiogenic effects of the peptide nanofibers were investigated by using both in vitro and in vivo models. LPPR-PA nanofibers inhibited endothelial cell proliferation, tube formation, and migration to a greater extent than the soluble LPPR peptide in vitro. In addition, the LPPR-PA nanofiber system led to the prevention of vascular maturation and the regression of angiogenesis in a suture-induced corneal angiogenesis model. These results show that the anti-angiogenic activity exhibited by LPPR peptide nanofibers may be utilized as a promising approach for the treatment of corneal angiogenesis.Item Open Access IoT based smart office application for advanced indoor working environment and energy efficiency(IEEE, 2017) Batı, Arda Cankat; Coşkun, Ercan; Gözüaçık, Ömer; İlhan, Giray; Şahin, Fatih Alperen; Uncuoğlu, Uygar; Güngen, Murat Alp; Telli, A.Internet of Things is a complex network, consisting of many elements that communicate with each other constantly. The network includes various modules, sensors, and computers etc. which constantly share data with each other, and carry out independent actions. The system may include interfaces connecting the users to the system, such as mobile apps and websites. In our vision, a 'Smart Office' is an office which knows or can determine office users' needs, and acts according to this knowledge. Our main goal is to design an office which will make independent decisions to maintain optimal office environment. These decisions will be made according to manually set user preferences and sensor readings. With our smart office system, we are aiming to provide flexible and energy efficient working environment to the users.Item Open Access Neural networks based online learning(IEEE, 2017) Ergen, Tolga; Kozat, Süleyman SerdarIn this paper, we investigate online nonlinear regression and introduce novel algorithms based on the long short term memory (LSTM) networks. We first put the underlying architecture in a nonlinear state space form and introduce highly efficient particle filtering (PF) based updates, as well as, extended Kalman filter (EKF) based updates. Our PF based training method guarantees convergence to the optimal parameter estimation under certain assumptions. We achieve this performance with a computational complexity in the order of the first order gradient based methods by controlling the number of particles. The experimental results illustrate significant performance improvements achieved by the introduced algorithms with respect to the conventional methods.Item Open Access A non-atochastic learning approach to energy efficient mobility management(Institute of Electrical and Electronics Engineers Inc., 2016) Shen, C.; Tekin, C.; Van Der Schaar, M.Energy efficient mobility management is an important problem in modern wireless networks with heterogeneous cell sizes and increased nodes densities. We show that optimization-based mobility protocols cannot achieve long-Term optimal energy consumption, particularly for ultra-dense networks (UDNs). To address the complex dynamics of UDN, we propose a non-stochastic online-learning approach, which does not make any assumption on the statistical behavior of the small base station (SBS) activities. In addition, we introduce handover cost to the overall energy consumption, which forces the resulting solution to explicitly minimize frequent handovers. The proposed batched randomization with exponential weighting (BREW) algorithm relies on batching to explore in bulk, and hence reduces unnecessary handovers. We prove that the regret of BREW is sublinear in time, thus guaranteeing its convergence to the optimal SBS selection. We further study the robustness of the BREW algorithm to delayed or missing feedback. Moreover, we study the setting where SBSs can be dynamically turned ON and OFF. We prove that sublinear regret is impossible with respect to arbitrary SBS ON/OFF, and then develop a novel learning strategy, called ranking expert (RE), that simultaneously takes into account the handover cost and the availability of SBS. To address the high complexity of RE, we propose a contextual ranking expert (CRE) algorithm that only assigns experts in a given context. Rigorous regret bounds are proved for both RE and CRE with respect to the best expert. Simulations show that not only do the proposed mobility algorithms greatly reduce the system energy consumption, but they are also robust to various dynamics which are common in practical ultra-dense wireless networks.Item Open Access PETAL: a fully distributed location service for wireless ad hoc networks(Academic Press, 2017) Ilkhechi, A. R.; Korpeoglu, I.; Güdükbay, Uğur; Ulusoy, ÖzgürLocation service is an essential prerequisite for mobile wireless ad hoc networks (MANETs) in which the underlying routing protocol leverages physical location information of sender and receiver nodes. Fulfillment of this requirement is challenging partly due to the mobility and unpredictability of nodes in MANETs. Moreover, scalability and location information availability under various circumstances are also substantial factors in designing an effective location service paradigm. By and large, utilizing centralized or distributed location servers responsible for storing the location information of all, or a subset of participant mobile devices, is a method employed in a significant portion of location service schemes. However, from the fairness point of view, it is more suitable to employ a location service scheme that treats participant nodes fairly, without mandating an unlucky subset to undertake the responsibility of serving as location server(s). In this work, we propose a scalable and fully decentralized location service scheme (PETAL) in which the burden of location update and inquiry tasks is almost evenly distributed among the nodes, resulting in an improvement in resilience against individual node failures. PETAL does not require hashing which results in more complexity, it is resilient against swarm mobility pattern, it requires minimal periodic location update messages when nodes do not move, and finally it does not require too many parameter configurations on all nodes. Our simulation results reveal that PETAL performs efficiently, particularly in environments densely populated by wireless devices. © 2017 Elsevier LtdItem Open Access Poly-cyclodextrin cryogels with aligned porous structure for removal of polycyclic aromatic hydrocarbons (PAHs) from water(Elsevier, 2017-08) Topuz, F.; Uyar, TamerCyclodextrins (CDs) are sugar-based cyclic oligosaccharides, which form inclusion complexes with small guest molecules through their hydrophobic cavity. Here we successfully synthesized highly porous poly-cyclodextrin (poly-CD) cryogels, which were produced under cryogenic conditions by the cross-linking of amine-functional CDs with PEG-based diepoxide cross-linker. The poly-CD cryogels showed aligned porous network structures owing to the directional freezing of the matrix, of which the pore size and architecture exposed variations depending on the composition of the reactants. The cryogels were employed for the removal of genotoxic polycyclic aromatic hydrocarbons (PAHs) from aqueous solutions. They reached PAH sorption capacities as high as 1.25 mg PAH per gram cryogel. This high sorption performance is due to interactions between PAHs and the complete swollen network, and thus, is not restricted by interfacial adsorption. Given that the hydrophilic nature of the components, the sorption performance could only be attributed to the inclusion complex formation of CDs with PAH molecules. The poly-CD cryogels could be recycled with an exposure to ethanol and reused without any significant loss in the sorption capacity of PAHs.Item Open Access Regional model-based computerized ionospheric tomography using GPS measurements: IONOLAB-CIT(Wiley-Blackwell Publishing, Inc., 2015) Tuna, H.; Arıkan, Orhan; Arikan, F.Three-dimensional imaging of the electron density distribution in the ionosphere is a crucial task for investigating the ionospheric effects. Dual-frequency Global Positioning System (GPS) satellite signals can be used to estimate the slant total electron content (STEC) along the propagation path between a GPS satellite and ground-based receiver station. However, the estimated GPS-STEC is very sparse and highly nonuniformly distributed for obtaining reliable 3-D electron density distributions derived from the measurements alone. Standard tomographic reconstruction techniques are not accurate or reliable enough to represent the full complexity of variable ionosphere. On the other hand, model-based electron density distributions are produced according to the general trends of ionosphere, and these distributions do not agree with measurements, especially for geomagnetically active hours. In this study, a regional 3-D electron density distribution reconstruction method, namely, IONOLAB-CIT, is proposed to assimilate GPS-STEC into physical ionospheric models. The proposed method is based on an iterative optimization framework that tracks the deviations from the ionospheric model in terms of F2 layer critical frequency and maximum ionization height resulting from the comparison of International Reference Ionosphere extended to Plasmasphere (IRI-Plas) model-generated STEC and GPS-STEC. The suggested tomography algorithm is applied successfully for the reconstruction of electron density profiles over Turkey, during quiet and disturbed hours of ionosphere using Turkish National Permanent GPS Network.Item Open Access Replacement problem in Web caching(IEEE, 2003-06-07) Çakıroğlu, Seda; Arıkan, ErdalCaching has been recognized as an effective scheme for avoiding service bottleneck and reducing network traffic in World Wide Web. Our work focuses on the replacement problem in Web caching, which arises due to limited storage. We seek the best configuration for a fully connected network of N caches. The problem is formulated as a discrete optimization problem. A number of low complexity heuristics are studied to obtain approximate solutions. Performances are tested under fictitious probabilistic request sequences access logs of real Web traffic. LFD (longest-forward-distance), the classical optimal off-line paging algorithm, is observed not to be optimal. Instead a window scheme should be used. Under an unchanging request pattern, a simple static placement algorithm achieves the maximum hit rates using the arrival probabilities. Otherwise, for quick adaptation to changing requests and for better worst-case performances a randomized algorithm should be chosen. We also give an analysis of Web data to propose best heuristics for its characteristics. © 2003 IEEE.Item Open Access Simulating a wavelength-size 2-D lens with an accurate numerical method(IEEE, 2001) Boriskin, A. V.; Nosich, A. I.; Altıntaş, AyhanThe effect of a localized light source directivity improvement due to an arbitrarily shaped dielectric cylinder taken as a 2-D model of a dielectric lens is studied. The source is simulated by the field of a complex source-point (CSP). An efficient algorithm for the solution of 2-D problem of wave scattering by a smooth dielectric cylinder is developed, based on the concept of analytical regularization. The basic properties of the algorithm are studied. Numerical results for the accuracy of the algorithm and sample far-field characteristics such as the total radiated power, directivity and radiation patterns for various lens parameters are presented.