13993895
A formal framework for agent itinerary specification, security reasoning and logic analysis
Mobile agent technology supports object migration from one site to another autonomously and proactively, performing its designated location-dependent tasks. Although the concept of proactive mobility has recently been demonstrated in several research prototypes, there is a lack of formal treatment of such mobility from the perspective of a distributed programming language. How to specify, model and reason about travel itineraries of mobile agents is fundamentally important for the development of secure and reliable mobile agent systems. In this paper, first, we introduce an itinerary language, MAIL, to model the mobile behavior of proactive agents. The language is structured and compositional so that an itinerary can be constructed recursively from primitive itineraries. We then define the operational semantics of the language in terms of a set of inference rules and prove that MAIL is expressive enough for most migration patterns. Finally, we show that MAIL is amenable to formal methods to reason about mobility and verify correctness and safety properties.
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.
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.
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.
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.
5343942
Knowledge-Based Equation Discovery in Engineering Domains
Machine learning techniques that can compress datasets into relationships that underlie the data have great utility for engineers. Most model discovery systems are not well suited to discovering comprehensible models in engineering domains. In this paper we present KEDS, a Knowledge-based Equation Discovery System, which uses a model-driven approach to discover equations and thereby build models from engineering data.
527997
Statistical en-route filtering of injected false data in sensor networks
In a large-scale sensor network individual sensors are subject to security compromises. A compromised node can inject into the network large quantities of bogus sensing reports which, if undetected, would be forwarded to the data collection point (i.e. the sink). Such attacks by compromised sensors can cause not only false alarms but also the depletion of the finite amount of energy in a battery powered network. We present a statistical en-route filtering (SEF) mechanism that can detect and drop such false reports. SEF requires that each sensing report be validated by multiple keyed message authentication codes (MACs), each generated by a node that detects the same event. As the report is forwarded, each node along the way verifies the correctness of the MACs probabilistically and drops those with invalid MACs at earliest points. The sink further filters out remaining false reports that escape the en-route filtering. SEF exploits the network scale to determine the truthfulness of each report through collective decision-making by multiple detecting nodes and collective false-report-detection by multiple forwarding nodes. Our analysis and simulations show that, with an overhead of 14 bytes per report, SEF is able to drop 80/spl sim/90% injected false reports by a compromised node within 10 forwarding hops, and reduce energy consumption by 50% or more in many cases.
1262760
Providing robust and ubiquitous security support for mobile ad-hoc networks
Providing security support for mobile ad-hoc networks is challenging for several reasons: (a) wireless networks are susceptible to attacks ranging from passive eavesdropping to active interfering, occasional break-ins by adversaries may be inevitable in a large time window; (b) mobile users demand "anywhere, anytime" services; (c) a scalable solution is needed for a large-scale mobile network. In this paper, we describe a solution that supports ubiquitous security services for mobile hosts, scales to network size, and is robust against break-ins. In our design, we distribute the certification authority functions through a threshold secret sharing mechanism, in which each entity holds a secret share and multiple entities in a local neighborhood jointly provide complete services. We employ localized certification schemes to enable ubiquitous services. We also update the secret shares to further enhance robustness against break-ins. Both simulations and implementation confirm the effectiveness of our design.
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.
1919911
Robust rate adaptation for 802.11 wireless networks
Rate adaptation is a mechanism unspecified by the 802.11 standards, yet critical to the system performance by exploiting the multi-rate capability at the physical layer.I n this paper, we conduct a systematic and experimental study on rate adaptation over 802.11 wireless networks. Our main contributions are two-fold. First, we critique five design guidelines adopted by most existing algorithms. Our study reveals that these seemingly correct guidelines can be misleading in practice, thus incur significant performance penalty in certain scenarios. The fundamental challenge is that rate adaptation must accurately estimate the channel condition despite the presence of various dynamics caused by fading, mobility and hidden terminals. Second, we design and implement a new Robust Rate Adaptation Algorithm (RRAA)that addresses the above challenge. RRAA uses short-term loss ratio to opportunistically guide its rate change decisions, and an adaptive RTS filter to prevent collision losses from triggering rate decrease. Our extensive experiments have shown that RRAA outperforms three well-known rate adaptation solutions (ARF, AARF, and SampleRate) in all tested scenarios, with throughput improvement up to 143%.