6732588
Efficient schema-based XML-to-Relational data mapping
Storing and querying XML documents using a RDBMS is a challenging problem since one needs to resolve the conflict between the hierarchical, ordered nature of the XML data model and the flat, unordered nature of the relational data model. This conflict can be resolved by the following XML-to-Relational mappings: schema mapping, data mapping and query mapping. In this paper, we propose: (i) a lossless schema mapping algorithm to generate a database schema from a DTD, which makes several improvements over existing algorithms, (ii) two linear data mapping algorithms based on DOM and SAX, respectively, to map ordered XML data to relational data. To our best knowledge, there is no published linear schema-based data mapping algorithm for mapping ordered XML data to relational data. Experimental results are presented to show that our algorithms are efficient and scalable.
14239575
Semantics based verification and synthesis of BPEL4WS abstract processes
We introduce a logic model to formally specify the semantics of workflows and their composite tasks described as BPEL4WS abstract processes. Based on the model, we present a set of inference rules to deduce the strongest postcondition and weakest precondition of a workflow and demonstrate that automatic workflow verification is possible due to the restrictions on data manipulation in an abstract process. We then sketch an algorithm that automatically synthesizes a workflow given its specification and a task library.
6486168
A Dataflow-Oriented Atomicity and Provenance System for Pipelined Scientific Workflows
Scientific workflows have gained great momentum in recent years due to their critical roles in e-Science and cyberinfrastructure applications. However, some tasks of a scientific workflow might fail during execution. A domain scientist might require a region of a scientific workflow to be "atomic". Data provenance, which determines the source data that are used to produce a data item, is also essential to scientific workflows. In this paper, we propose: (i) an architecture for scientific workflow management systems that supports both provenance and atomicity; (ii) a dataflow-oriented atomicity model that supports the notions of commit and abort; and (iii) a dataflow-oriented provenance model that, in addition to supporting existing provenance graphs and queries, also supports queries related to atomicity and failure.
16579446
Mining Correlation between Motifs and Gene Expression
One of the major challenges in the post-genomic era is to determine all DNA-binding transcription factors (TFs) and their regulatory binding sites (motifs) within the genomes. To discover the relationship between the motifs and changes in gene expression, we propose a new algorithm, co-miner (correlation miner). Correlation rules are generated based on the expression profiles of genes with significant expression change through the time course of gene expression. Thus, we may consider the change in gene expression to be causatively associated with the transcription binding sites in the upstream sequences. In addition, we introduce partition and constraint pushing techniques to improve the performance and demonstrate their effectiveness by our experiments. By applying co-miner to a yeast dataset, the relationships between motifs and gene expression revealed by co-miner are confirmed in the literature.
7682350
Incremental genetic K-means algorithm and its application in gene expression data analysis
BackgroundIn recent years, clustering algorithms have been effectively applied in molecular biology for gene expression data analysis. With the help of clustering algorithms such as K-means, hierarchical clustering, SOM, etc, genes are partitioned into groups based on the similarity between their expression profiles. In this way, functionally related genes are identified. As the amount of laboratory data in molecular biology grows exponentially each year due to advanced technologies such as Microarray, new efficient and effective methods for clustering must be developed to process this growing amount of biological data.ResultsIn this paper, we propose a new clustering algorithm, Incremental Genetic K-means Algorithm (IGKA). IGKA is an extension to our previously proposed clustering algorithm, the Fast Genetic K-means Algorithm (FGKA). IGKA outperforms FGKA when the mutation probability is small. The main idea of IGKA is to calculate the objective value Total Within-Cluster Variation (TWCV) and to cluster centroids incrementally whenever the mutation probability is small. IGKA inherits the salient feature of FGKA of always converging to the global optimum. C program is freely available at http://database.cs.wayne.edu/proj/FGKA/index.htm.ConclusionsOur experiments indicate that, while the IGKA algorithm has a convergence pattern similar to FGKA, it has a better time performance when the mutation probability decreases to some point. Finally, we used IGKA to cluster a yeast dataset and found that it increased the enrichment of genes of similar function within the cluster.
18131628
Automatic workflow verification and generation
Correctness is an important aspect of workflow management systems. However, most of the workflow literature focuses only on the modeling aspects and assumes that a workflow is correct if during the execution it respects the control and data dependency specified by the workflow designer. To address the correctness question properly we propose a new workflow model based on Hoare semantics that allows to: (1) automatically check if the desired outcome of a workflow can be produced by its actual implementation, (2) automatically synthesize a workflow implementation from the workflow specification and a given task library.In particular we: (1) formalize the semantics of workflows and tasks with pre-and postconditions, (2) for each control construct we provide a set of sound inference rules formalizing its semantics. While most of our workflow constructs are standard, two of them are new: the universal and the existential constructs. We then describe algorithms for automatically checking the correctness of workflows and for automatic workflow generation.
30892527
On Design and Implementation of Adaptive Data Classification Scheme for DSM Systems
Distributed Shared Memory (DSM) environment is built by using specific softwares, to combine a number of computer hardware resources into one computing environment. Such environment not only provides an easy way to execute parallel applications, but also combines resources to speedup execution of these applications. DSM systems need to maintain data consistency in memory, what usually leads to communication overhead. Therefore, there exist a number of strategies that can be used to overcome this overhead and improve overall performance. Prefetching strategies have been proven to show great performance in DSM systems, since they can reduce data access communication latencies from remote nodes. However, these strategies also transfer unnecessary prefetching pages to remote nodes. In this research paper, we focus on the analysis of data access pattern during execution of parallel applications. We propose an Adaptive Data Classification scheme to improve prefetching strategy, with the goal to improve overall performance. Adaptive Data Classification scheme classifies data according to the access behavior of pages, so that home node uses past history access patterns of remote nodes to decide whether it needs to transfer related pages to remote nodes. From experimental results, our method can improve the performance of prefetching strategies in DSM systems.
96635
IPv4 address allocation and the BGP routing table evolution
The IP address consumption and the global routing table size are two of the vital parameters of the Internet growth. In this paper we quantitatively characterize the IPv4 address allocations made over the past six years and the global BGP routing table size changes during the same period of time. About 63,000 address blocks have been allocated since the beginning of the Internet, of which about 18,000 address blocks were allocated during our study period, from November 1997 to August 2004. Among these 18,000 allocations, 90% of them started being announced into the BGP routing table within 75 days after the allocation, while 8% of them has not been used up to now. Among all the address blocks that have ever been used, 45% of them were split into fragments smaller than the original allocated blocks; without these fragementations, the current BGP table would have been about half of its current size. Furthermore, we found that the evolution of BGP routing table consists of both the appearance of new prefixes and the disappearance of old prefixes. While the change of the BGP routing table size only reflects the combined results of the two processes, the dynamics of either process is much higher than that of the BGP table size. Finally, we classify routing prefixes into covering and covered ones, and examine their evolution separately. For the covered prefixes, which account for almost half of the BGP table size, we infer their practical motives such as multihoming, load balancing, and traffic engineering, etc., via a classification method.
9604157
Conflict resolution in cooperative design
Design is increasingly becoming a cooperative endeavor carried out by multiple agents with diverse kinds of expertise. The development of tools and underlying theories for supporting cooperative design has lagged, however, behind the growing needs implied by this evolution. 
The goal of this thesis work is to provide a computational model for supporting a critical component of cooperative design; the run-time resolution of conflicts. Though the long-term goal is to support unrestricted conflict resolution among human agents, this thesis focuses on an important subset of this problem: the resolution of domain-level conflicts in routine design, using machine-based agents. 
This thesis proposes a model of conflict resolution in cooperative design that corresponds well to how human design experts actually perform cooperative design, based on analysis of their group problem solving activity. This model supports natural participation for human experts, both at development-time as domain experts asked to create machine-based agents, as well as at run-time as problem solving agents themselves. The conflict resolution model is elaborated into a detailed implemented computational theory that offers many insights into how the conflict resolution expert and design agents should operate. The model incorporates a considerable body of conflict resolution expertise applicable to a wide variety of domains, as well as techniques for acquiring further expertise and evaluating its completeness.
12858200
Building Robust Learning Systems by Combining Induction and Optimization
Each concept description language and search strategy has an inherent inductive bias, a preference for some hypotheses over others. No single inductive bias performs optimally on all problems. This paper describes a system that couples induction with optimization to carry out an efficient search of large regions of inductive bias space. Experimental results are reported demonstrating the system's capacity to choose optimal biases even for complex and noisy problems.
2709125
A two-tier data dissemination model for large-scale wireless sensor networks
Sink mobility brings new challenges to large-scale sensor networking. It suggests that information about each mobile sink's location be continuously propagated through the sensor field to keep all sensor nodes updated with the direction of forwarding future data reports. Unfortunately frequent location updates from multiple sinks can lead to both excessive drain of sensors' limited battery power supply and increased collisions in wireless transmissions. In this paper we describe TTDD, a Two-Tier Data Dissemination approach that provides scalable and efficient data delivery to multiple mobile sinks. Each data source in TTDD proactively builds a grid structure which enables mobile sinks to continuously receive data on the move by flooding queries within a local cell only. TTDD's design exploits the fact that sensor nodes are stationary and location-aware to construct and maintain the grid structures with low overhead. We have evaluated TTDD performance through both analysis and extensive simulation experiments. Our results show that TTDD handles multiple mobile sinks efficiently with performance comparable with that of stationary sinks.