8131087
Multipath-Based Multicasting Strategies for Wormhole-Routed Star Graph Interconnection Networks
The star graph interconnection network has been recognized as an attractive alternative to the popular hypercube network. In this paper, we present a multipath-based multicast routing model for wormholerouted star graph networks, propose two efficient multipath routing schemes, and contrast the performance of the proposed schemes with the performance of the scheme presented in our previous work. Both of the two proposed schemes have been proven to be deadlock-free. The first scheme, simplemultipath routing, uses multiple independent paths for concurrent multicasting. The second scheme, two-phase multipath routing, includes two phases: source-to-relay and relay-to-destination. For each phase, multicasting is carried out using simple multipath routing. Experimental results show that, for short and medium messages with small message startup latencies, the proposed schemes reduce multicast latency more efficiently than other schemes.
29824463
Task migration in 2D wormhole-routed mesh multicomputers
In this paper, two simple task migration schemes are first proposed for 2D mesh, multicomputers with supporting X-Y wormhole routing in the one-port communication model. We next propose a hybrid task migration scheme which attempts to minimize the total transmission latency. Finally, we compare all of our proposed task migration schemes using performance analysis.
46178429
Task Migration in All-Port Wormhole-Routed 2D Mesh Multicomputer
In a mesh multicomputer, submeshes are scheduled to perform jobs according to some processor allocation schemes, each job assigned to occupy processors of one submesh with an appropriate size. In order to assign the region for the incoming jobs, a task compaction is needed to produce a larger contiguous free region. The overhead of task compaction is primarily relied on designing an efficient task migration scheme. In this paper, we aim at the 2D mesh multicomputers with supporting wormhole routing in all-port communication model as the target machine. First, a certain and a relieved constraints between two submeshes for task migration are proposed. We next propose two task migration schemes following one of the constraints in 2D mesh multicomputers. We also analyze and discuss the routing phases for task migration. Finally, we compare the proposed task migration schemes via performance analysis.
10869493
A dual-hamiltonian-path-based multicasting strategy for wormhole-routed star graph interconnection networks
Multicast is an important collective communication operation on multicomputer systems, in which the same message is delivered from a source node to an arbitrary number of destination nodes. The star graph interconnection network has been recognized as an attractive alternative to the popular hypercube network. In this paper, we first address a dual-hamiltonian-path-based routing model with two virtual channels based on two hamiltonian paths (HPs) and a network partitioning strategy for wormhole-routed star graph networks. Then, we propose three efficient multicast routing schemes on basis of such a model. All of the three proposed schemes are proved deadlock-free. The first scheme, network-selection-based dual-path routing, selects subnetworks that are constructed either by the first HP or by the second HP for dual-path routing. The second one, optimum dual-path routing, selects subnetworks with optimum routing path for dual-path routing. The third scheme, two-phase optimum dual-path routing, includes two phases, source-to-relay and relay-to-destination. Finally, experimental results are given to show that our proposed three routing schemes outperform the unicast-based, the HP, and the single-HP-based dual-path routing schemes significantly.
45055182
Mining frequent tree-like patterns in large datasets
Sequential pattern mining is crucial to data mining domains. This paper proposes a novel data mining approach for exploring hierarchical tree structures, named tree-like patterns, representing the relationships for a pair of items in a sequence. Using tree-like patterns, the relationships for a pair of items can be identified in terms of the cause and effect. A novel technique that efficiently counts support values for tree-like patterns using a queue structure is proposed. In addition, this paper addresses an efficient scheme for determining the frequency of a tree-like pattern in a sequence using a dynamic programming approach. Each tree-like pattern embedded in a sequence is considered to have a certain valuable meaning or the degree of importance used in different applications. Two addressed formulas are applied to determine the degree of significance for a specific sequence, which denotes the degree of consecutive items in a tree-like pattern for a sequence. The larger the degree of significance a tree-like pattern has, the more the tree-like pattern is compacted in the sequence. The characteristics differentiating the explored patterns from those obtained with other schemes are discussed. A simulation analysis of the proposed data mining approach is utilized to demonstrate its efficacy. Finally, the proposed approach is designed and implemented in a data mining system integrated into a novel e-learning platform.
41663574
Mining Frequent Tree-Like Patterns in Large Datasets
In this paper, we propose a novel data mining scheme to explore the frequent hierarchical structure patterns, named tree-like patterns, with the relationship of each item on a sequence. By tree-like patterns, we are clear to find out the relation of items between the cause and effect. Finally, we discuss the different characteristics to our mined patterns with others. As a consequence, we can find out that our addressed tree-like patterns can be widely used to explore a variety of different applications.
10160655
A Suboptimal Algorithm for De Novo Peptide Sequencing via Tandem Mass Spectrometry
Tandem mass spectrometry has emerged to be one of the most powerful high-throughput techniques for protein identification. Tandem mass spectrometry selects and fragments peptides of interest into N-terminal ions and C-terminal ions, and it measures the mass/charge ratios of these ions. The de novo peptide sequencing problem is to derive the peptide sequences from given tandem mass spectral data of k ion peaks without searching against protein databases. By transforming the spectral data into a matrix spectrum graph G = (V, E), where |V| = O(k(2)) and |E| = O(k(3)), we give the first polynomial time suboptimal algorithm that finds all the suboptimal solutions (peptides) in O(p|E|) time, where p is the number of solutions. The algorithm has been implemented and tested on experimental data. The program is available at http://hto-c.usc.edu:8000/msms/menu/denovo.htm.
2051959
Performance Evaluation of Forwarding Strategies for Location Management in Mobile Networks
This paper presents a methodology for evaluating the performance of forwarding strategies for location management in a personal communication services (PCS) mobile network. A forwarding strategy in the PCS network can be implemented by two mechanisms: a forwarding operation which follows a chain of databases to locate a mobile user and a resetting operation which updates the databases in the chain so that the current location of a mobile user can be known directly without having to follow a chain of databases. In this paper, we consider the PCS network as a server whose function is to provide services to the mobile user for ‘updating the location of the user as the user moves across a database boundary’ and ‘locating the mobile user’. We use a Markov chain to describe the behavior of the mobile user and analyze the best time when forwarding and resetting should be performed in order to optimize the service rate of the PCS network. We demonstrate the applicability of our approach with hexagonal and mesh coverage models for the PCS network and provide a physical interpretation of the result.
15833114
Exploring Gradient-Based Face Navigation Interfaces
We have created a gradient-based face navigation interface that allows users to explore a large face space based on an eigenface technique. This approach to synthesizing faces contrasts with more typical techniques for forming composite faces based on the blending of facial features. We compare three ways of moving through the face space, using two types of sliders and a face-wheel. These are adapted from typical color space interfaces since they are commonly used. However, eigenface dimensions do not have meaningful text labels, unlike primary colors, necessitating the use of faces themselves for the labels of the navigation axes. Results suggest that users can navigate with face-labelled axes. They find slider interfaces best suited to finding the neighborhood of a target face, but that the face-wheel is better for refinement once inside the neighborhood.
18749157
A case study in genome-level fragment assembly
MOTIVATION
We use the fact of two teams independently sequencing the one megabase genome of Borrelia burgdorferi as an opportunity to study the accuracy of genome-level assembly.


RESULTS
We compare the results of three different assembly programs (PHRAP, TIGR Assembler, and STROLL) on the DNA fragments used in both the Brookhaven and TIGR sequencing projects. We also describe the algorithms and data structures used in our assembly program STROLL, which was used in the Brookhaven Borrelia project.
1816267
From Region Encoding To Extended Dewey: On Efficient Processing of XML Twig Pattern Matching
Finding all the occurrences of a twig pattern in an XML database is a core operation for efficient evaluation of XML queries. A number of algorithms have been proposed to process a twig query based on region encoding labeling scheme. While region encoding supports efficient determination of structural relationship between two elements, we observe that the information within a single label is very limited. In this paper, we propose a new labeling scheme, called extended Dewey. This is a powerful labeling scheme, since from the label of an element alone, we can derive all the elements names along the path from the root to the element. Based on extended Dewey, we design a novel holistic twig join algorithm, called TJFast. Unlike all previous algorithms based on region encoding, to answer a twig query, TJFast only needs to access the labels of the leaf query nodes. Through this, not only do we reduce disk access, but we also support the efficient evaluation of queries with wildcards in branching nodes, which is very difficult to be answered by algorithms based on region encoding. Finally, we report our experimental results to show that our algorithms are superior to previous approaches in terms of the number of elements scanned, the size of intermediate results and query performance.