9960122
Dynamic Zone-Balancing of Topology-Aware Peer-to-Peer Networks
Building a topology-aware peer-to-peer overlay network can bring many advantages, such as providing locality-aware connectivity and reducing routing path length. While its benefits on performance have been recognized, an uneven overlay zone distribution has emerged. Recent work has shown that topology-aware neighbor selection during construction can aggravate the unbalance of zone distribution while it reduces routing path length. The imbalance in zone sizes may lead to performance decrease and an unfair load distribution. 
 
In this paper, we present an even topology-aware peer-to-peer network based on De Bruijn Graph by developing a dynamic zone-balancing approach.
1677219
Application of Smodels in Quartet Based Phylogeny Construction
Evolution is an important sub-area of study in biological science, where given a set of taxa, the goal is to reconstruct their evolutionary history, or phylogeny. One very recent approach is to predict a local phylogeny for every subset of 4 taxa, called a quartet topology, and then to assemble a phylogeny for the whole set of taxa satisfying these predicted quartet topologies. In general, the predicted quartet topologies might not always agree with each other, and thus the objective function becomes to satisfy a maximum number of them. This is the well known Maximum Quartet Consistency (MQC) problem. In the past, the MQC problem has been solved by dynamic programming and the so-called fixed-parameter method. Recently, we have proposed to solve the MQC in answer set programming. In this note, we summarize the theoretical results of this approach and report new experimental results for the purpose of comparison, which show that our approach in answer set programming is favored over the existing approaches based on dynamic programming and fixed-parameter method. In particular, some of the hard instances (where the error ratio is high) that were not reported to be solved in other approaches can now be solved in our approach.
2388375
Congestion control via online sampling
We consider the congestion control problem in a communication network with multiple traffic sources, each modeled as a fully-controllable stream of fluid traffic. The controlled traffic shares a common bottleneck node with high-priority cross traffic described by a Markov-modulated fluid (MMF). Each controlled source is assumed to have a unique round-trip delay. We wish to maximize a linear combination of the throughput, delay, traffic loss rate, and a fairness metric at the bottleneck node. We introduce an online sampling-based burst-level congestion control scheme capable of performing effectively under rapidly-varying cross traffic by making explicit use of the provided MMF model of that variation. The control problem is posed as a finite-horizon Markov decision process and is solved heuristically using a technique called hindsight optimization. We provide a detailed derivation of our congestion control algorithm based on this technique. The distinguishing feature of our scheme relative to conventional congestion control schemes is that we exploit a stochastic model of the cross traffic. Our empirical study shows that our control scheme significantly outperforms the conventional proportional-derivative (PD) controller, achieving higher utilization, lower delay, and lower loss under reasonable fairness. The performance advantage of our scheme over the PD scheme grows as the rate variance of cross traffic increases, underscoring the effectiveness of our control scheme under variable cross traffic.
18105952
Adapting Prime Number Labeling Scheme for Directed Acyclic Graphs
Directed Acyclic Graph(DAG) could be used for modeling subsumption hierarchies. Several labeling schemes have been proposed or tailored for indexing DAG in order to efficiently explore relationships in such hierarchy. However few of them can satisfy all the requirements in response time, space, and effect of updates simultaneously. In this paper, the prime number labeling scheme is extended for DAG. The scheme invests intrinsic mapping between integer divisibility and subsumption hierarchy, which simplifies the transitive closure computations and diminishes storage redundancy, as well as inherits the dynamic labeling ability from original scheme. Performance is further improved by introducing some optimization techniques. Our extensive experimental results show that prime number labeling scheme for DAG outperforms interval-based and prefix-based labeling schemes in most cases.
17031172
Predictive buffer control in delivering remotely stored video using proxy servers
We study the problem of using proxy servers to stream video stored at a geographically separate location. The separation of the server and the storage introduces a non-negligible delay in retrieving video frames in real time. We assume an additive-increase/multiplicative-decrease transport protocol to support the streaming process and develop an effective scheme to achieve consistent, high streaming quality. The heart of the scheme is the control of buffer occupancy at the proxy server. We model the buffer as a bilinear dynamical system disturbed by a point process with stochastic state-dependent intensity. We first develop a buffer controller that does not exploit this model. Then, using the buffer model, we construct a second controller based on an optimal-control analysis for the case without retrieval delay. Extending these two controllers, we subsequently synthesize two controllers based on prediction of future system states using the model, taking into account both the delay and the state-dependent disturbance intensity. Our empirical study illustrates the effectiveness of the streaming scheme. We further find that the controllers exploiting the buffer model demonstrate performance significantly superior to that of the model-free controller in overcoming the adverse impact of the retrieval delay. We also conduct limited experiments to study the impact of variable retrieval delays.
16585637
Learning with non-metric proximity matrices
Many emerging applications formulate non-metric proximity matrices (non-positive semidefinite), and hence cannot fit into the framework of kernel machines. A popular approach to this problem is to transform the spectrum of the similarity matrix so as to generate a positive semidefinite kernel matrix. In this paper, we explore four representative transformation methods: denoise, flip, diffusion, and shift. Theoretically, we discuss a generalization problem where the test data are not available during transformation, and thus propose an efficient algorithm to address the problem of updating the cross-similarity matrix between test and training data. Extensive experiments have been conducted to evaluate the performance of these methods on several real-world (dis)similarity matrices with semantic meanings.
1432738
SGDB: a database of synthetic genes re-designed for optimizing protein over-expression
Here we present the Synthetic Gene Database (SGDB): a relational database that houses sequences and associated experimental information on synthetic (artificially engineered) genes from all peer-reviewed studies published to date. At present, the database comprises information from more than 200 published experiments. This resource not only provides reference material to guide experimentalists in designing new genes that improve protein expression, but also offers a dataset for analysis by bioinformaticians who seek to test ideas regarding the underlying factors that influence gene expression. The SGDB was built under MySQL database management system. We also offer an XML schema for standardized data description of synthetic genes. Users can access the database at , or batch downloads all information through XML files. Moreover, users may visually compare the coding sequences of a synthetic gene and its natural counterpart with an integrated web tool at , and discuss questions, findings and related information on an associated e-forum at .
6081408
Universal Cupping Degrees
Cupping nonzero computably enumerable (c.e. for short) degrees to 0′ in various structures has been one of the most important topics in the development of classical computability theory. An incomplete c.e. degree a is cuppable if there is an incomplete c.e. degree b such that a∪b=0′, and noncuppable if there is no such degree b. Sacks splitting theorem shows the existence of cuppable degrees. However, Yates(unpublished) and Cooper [3] proved that there are noncomputable noncuppable degrees. After that, Harrington and Shelah were able to employ the cupping/noncupping properties to show that the theory of the c.e. degrees under relation ≤ is undecidable. Cuppable and noncuppable degrees were further studied later. See Harrington [7], Miller [10], Fejer and Soare [6], Ambos-Spies, Lachlan and Soare [1], etc..
26204913
Nonisolated degrees and the jump operator
Abstract Say that a d.c.e. degree d is nonisolated if for any c.e. degree a d , there is another c.e. degree c such that a c d . In this paper, we investigate the relationship between the nonisolated degrees and the jump operator. We prove that there is a high nonisolated d.c.e. degree such that all c.e. degrees below it are bounded by a low d.c.e. degree.
28215274
A formal fuzzy reasoning system and reasoning mechanism based on propositional modal logic
We establish in this paper a fuzzy propositional modal logic, FPML, and the associated semantics, fuzzy Kripke semantics. We prove that FPML is sound and complete. Furthermore, we set up a formalized reasoning mechanism based on FPML.
6594297
Generic Universal Switch Blocks
A switch block M with W terminals on each side is said to be universal if every set of nets satisfying the dimension constraint (i.e., the number of nets on each side of M is at most W) is simultaneously routable through M. In this paper, we present an algorithm to construct N-sided universal switch blocks with W terminals on each side. Each of our universal switch blocks has (/sub 2//sup N/) W switches and switch-block flexibility N-1 (i.e., F/sub S/=N-1). We prove that no switch block with less than (/sub 2//sup N/)W switches can be universal. We also compare our universal switch blocks with others of the topology associated with Xilinx XC4000-type FPGAs. To explore the area performance of the universal switch blocks, we develop a detailed router for hierarchical FPGAs (HFPGAs) with 5-sided switch blocks. Experimental results demonstrate that our universal switch blocks improve routability at the chip level. Based on extensive experiments, we also provide key insights into the interactions between switch-block architectures and routing.