41181604
The Semantic Web: opportunities and challenges for next-generation Web applications
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.
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.
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.
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.
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.
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.
1236934
A Packet Scheduling Approach to QoS Support in Multihop Wireless Networks
Providing packet-level quality of service (QoS) is critical to support both rate-sensitive and delay-sensitive applications in bandwidth-constrained, shared-channel, multihop wireless networks. Packet scheduling has been a very popular paradigm to ensure minimum throughput and bounded delay access for packet flows. This work describes a packet scheduling approach to QoS provisioning in multihop wireless networks. Besides minimum throughput and delay bounds for each flow, our scheduling disciplines seek to achieve fair and maximum allocation of the shared wireless channel bandwidth. However, these two criteria can potentially be in conflict in a generic-topology multihop wireless network where a single logical channel is shared among multiple contending flows and spatial reuse of the channel bandwidth is possible. In this paper, we propose a new scheduling model that addresses this conflict. The main results of this paper are the following: (a) a two-tier service model that provides a minimum “fair” allocation of the channel bandwidth for each packet flow and additionally maximizes spatial reuse of bandwidth, (b) an ideal centralized packet scheduling algorithm that realizes the above service model, and (c) a practical distributed backoff-based channel contention mechanism that approximates the ideal service within the framework of the CSMA/CA protocol.
35964038
Learning Engineering Models with the Minimum Description Length Principle
This paper discusses discovery of mathematical models from engineering data sets. KEDS, a Knowledge-based Equation Discovery System, identifies several potentially overlapping regions in the problem space, each associated with an equation of different complexity and accuracy. The minimum description length principle, together with the KEDS algorithm, is used to guide the partitioning of the problem space. The KEDSMDL algorithm has been tested on discovering models for predicting the performance efficiencies of an internal combustion engine.
1764244
Machine Learning in Engineering Automation
Abstract Engineers need intelligent tools to assist them with problems such as design, planning, monitoring, control, diagnosis, and analysis. Manual construction of these tools can be costly or impossible due to problems such as large amounts of data, lack of problem understanding, and the expense of knowledge engineering. Machine learning techniques hold promise for assisting in solutions to many of these problems, but engineering domains present significant challenges to learning systems, including: noisy data, continuous quantities, mathematical formulas, large problem spaces, incorporating multiple sources and forms of knowledge, and the need for user-system interaction. This paper describes a number of challenges to learning systems motivated by engineering applications and describes a taxonomy of engineering tasks for application of machine learning technology.
896953
Sequential Aggregate Signatures and Multisignatures Without Random Oracles
We present the first aggregate signature, the first multisignature, and the first verifiably encrypted signature provably secure without random oracles. Our constructions derive from a novel application of a recent signature scheme due to Waters. Signatures in our aggregate signature scheme are sequentially constructed, but knowledge of the order in which messages were signed is not necessary for verification. The aggregate signatures obtained are shorter than Lysyanskaya et al. sequential aggregates and can be verified more efficiently than Boneh et al. aggregates. We also consider applications to secure routing and proxy signatures.