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.
13757062
Faster solution to the maximum quartet consistency problem with constraint programming
Evolution is an important sub-area of study in biological science, whereby the evolutionary history, or phylogeny, would shed light on the genetic linkage and the functional correlation for the species under consideration. Many kinds of species data can be deployed for the task and many phylogeny reconstruction methods have been examined in the literature. A quartet approach is to build a local phylogeny for every 4 species, which is called a quartet for these 4 species, and then to assemble a phylogeny for the whole set of species satisfying the topological constraints imposed by these quartets built. In practice, those predicted quartets might not agree each other and the optimization problem, the well-known Maximum Quartet Consistency (MQC) problem, is to construct a phylogeny to satisfy a maximum number of the predicted quartets. An equivalent representation for the MQC problem through searching for a certain ultrametric matrix via Answer Set Programming has recently been proposed. This paper follows the approach and presents a number of optimization techniques to speed up the searching process. The experimental results on both the simulated and real datasets suggest that the new representation combined with Constraint Programming presents a unique perspective to the MQC problem.
7109499
Statistical learning for effective visual information retrieval
For effective retrieval of visual information, statistical learning plays a pivotal role. Statistical learning in such a context faces at least two major mathematical challenges: scarcity of training data, and imbalance of training classes. We present these challenges and outline our methods for addressing them: active learning, recursive subspace co-training, adaptive dimensionality reduction, class-boundary alignment, and quasi-bagging.
8499708
Cooperation models for service oriented multi-agent system
In the paper, the cooperation models for service oriented multi-agent system are formally and rigorously investigated and put forward. According to the service request forces and service offer manners, a number of elementary cooperation models and their atomic communication acts are identified. The rigorous semantics of the communication acts and the cooperation models and their constraints are formally defined and analyzed.
22669962
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 (Y.W. Chang et al., 1996). 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. Further, the decomposition property of a universal switch block provides a key insight into its layout implementation with a smaller silicon area. We also compare our universal switch blocks with others of the topology associated with Xilinx XC4000-type FPGAs. Experimental results demonstrate that our universal switch blocks improve routability at the chip level.
17315153
Randomness and universal machines
The present work investigates several questions from a recent survey of Miller and Nies related to Chaitin's @W numbers and their dependence on the underlying universal machine. Furthermore, the notion @W"U[X][email protected]?"p":"U"("p")"@7"@?"X2^-^|^p^| is studied for various sets X and universal machines U. A universal machine U is constructed such that for all x, @W"U[{x}]=2^1^-^H^(^x^). For such a universal machine there exists a co-r.e. set X such that @W"U[X] is neither left-r.e. nor Martin-Lof random. Furthermore, one of the open problems of Miller and Nies is answered completely by showing that there is a sequence U"n of universal machines such that the truth-table degrees of the @W"U"""n form an antichain. Finally, it is shown that the members of hyperimmune-free Turing degree of a given @P"1^0-class are not low for @W unless this class contains a recursive set.
1961392
Degrees of Weakly Computable Reals
This paper studies the degrees of weakly computable reals. It is shown that certain types of limit-recursive reals are Turing incomparable to all weakly computable reals except the recursive and complete ones. Furthermore, it is shown that an r.e. Turing degree is array-recursive iff every real in it is weakly computable.
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.
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.