2957457
Graph Matching Based Authorization Model for Efficient Secure XML Querying
XML is rapidly emerging as a standard for data representation and exchange over the World Wide Web and an increasing amount of sensitive business data is processed in the XML format. Therefore, it is critical to have control mechanisms to restrict a user to access only the parts of XML documents that he/she is authorized to access. In this paper, we propose the first DTD-based access control model that employs graph matching to analyze if an input query is fully acceptable, fully rejectable, or partially acceptable, and to rewrite for partially acceptable queries only if necessary, along with the features of optimization and speed-up for query rewriting by introducing an index structure.
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.
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.
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.
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.
623020
URSA: ubiquitous and robust access control for mobile ad hoc networks
Restricting network access of routing and packet forwarding to well-behaving nodes and denying access from misbehaving nodes are critical for the proper functioning of a mobile ad-hoc network where cooperation among all networking nodes is usually assumed. However, the lack of a network infrastructure, the dynamics of the network topology and node membership, and the potential attacks from inside the network by malicious and/or noncooperative selfish nodes make the conventional network access control mechanisms not applicable. We present URSA, a ubiquitous and robust access control solution for mobile ad hoc networks. URSA implements ticket certification services through multiple-node consensus and fully localized instantiation. It uses tickets to identify and grant network access to well-behaving nodes. In URSA, no single node monopolizes the access decision or is completely trusted. Instead, multiple nodes jointly monitor a local node and certify/revoke its ticket. Furthermore, URSA ticket certification services are fully localized into each node's neighborhood to ensure service ubiquity and resilience. Through analysis, simulations, and experiments, we show that our design effectively enforces access control in the highly dynamic, mobile ad hoc network.
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.
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.
619246
The impact of multihop wireless channel on TCP performance
This paper studies TCP performance in a stationary multihop wireless network using IEEE 802.11 for channel access control. We first show that, given a specific network topology and flow patterns, there exists an optimal window size W* at which TCP achieves the highest throughput via maximum spatial reuse of the shared wireless channel. However, TCP grows its window size much larger than W* leading to throughput reduction. We then explain the TCP throughput decrease using our observations and analysis of the packet loss in an overloaded multihop wireless network. We find out that the network overload is typically first signified by packet drops due to wireless link-layer contention, rather than buffer overflow-induced losses observed in the wired Internet. As the offered load increases, the probability of packet drops due to link contention also increases, and eventually saturates. Unfortunately the link-layer drop probability is insufficient to keep the TCP window size around W'*. We model and analyze the link contention behavior, based on which we propose link RED that fine-tunes the link-layer packet dropping probability to stabilize the TCP window size around W*. We further devise adaptive pacing to better coordinate channel access along the packet forwarding path. Our simulations demonstrate 5 to 30 percent improvement of TCP throughput using the proposed two techniques.
13148267
Fair scheduling in wireless packet networks
Fair scheduling of delay and rate-sensitive packet flows over a wireless channel is not addressed effectively by most contemporary wireline fair scheduling algorithms because of two unique characteristics of wireless media: (a) bursty channel errors, and (b) location-dependent channel capacity and errors. Besides, in packet cellular networks, the base station typically performs the task of packet scheduling for both downlink and uplink flows in a cell; however a base station has only a limited knowledge of the arrival processes of uplink flows.In this paper, we propose a new model for wireless fair scheduling based on an adaptation of fluid fair queueing to handle location-dependent error bursts. We describe an ideal wireless fair scheduling algorithm which provides a packetized implementation of the fluid model while assuming full knowledge of the current channel conditions. For this algorithm, we derive the worst-case throughput and delay bounds. Finally, we describe a practical wireless scheduling algorithm which approximates the ideal algorithm. Through simulations, we show that the algorithm achieves the desirable properties identified in the wireless fluid fair queueing model.