15432335
A model for abstract process specification, verification and composition
An abstract business process contains a description the protocol that a business process engages in without revealing the internal computation of the process. This description provides the information necessary to compose the process with other Web services. BPEL supports this by providing distinct dialects for specifying abstract and executable processes. Unfortunately, BPEL does not prevent complex computations from being included in an abstract process. This complicates the protocol description, unnecessarily reveals implementation details, and makes it difficult to analyze correctness.
 We propose some restrictions on the data manipulation constructs that can be used in an abstract BPEL process. The restrictions permit a full description of a protocol while hiding computation. A restricted abstract process can easily be converted into an abstract BPEL process or expanded into an executable BPEL process. Based on these restrictions we propose a formal model for a business process and use it as the basis of an algorithm for demonstrating the correctness of a protocol described by a restricted abstract process. We then sketch an algorithm for synthesizing a protocol based on a formal specification of its outcome and the tasks available for its construction.
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.
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.
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.
12297349
Creating and using models for engineering design: a machine-learning approach
An adaptive and interactive modeling system (AIMS) that integrates simulation, optimization and machine learning to help engineers make design decisions is described. AIMS views engineering decision making as a two-phase process of creating and then using models. The competitive relation learner and the induce-and-select optimizer, AIMS's two main components, and their roles in both phases of decision-making are discussed. AIMS's role in supporting the design of a diesel engine that outputs power within the 440- to 460-kW range and consumes the least amount of fuel is also discussed.<<ETX>>
18977617
Design and analysis of an algorithm for fair service in error‐prone wireless channels
In order to support diverse communication‐intensive real‐time and non‐real‐time data flows over a scarce, varying and shared wireless channel with location‐dependent and bursty errors, we define a service model that has the following characteristics: short‐term fairness among flows which perceive a clean channel, long‐term fairness for flows with bounded channel error, worst‐case delay bounds for packets, short‐term throughput bounds for flows with clean channels and long‐term throughput bounds for all flows with bounded channel error, expanded schedulable region, and support for both delay sensitive and error sensitive data flows. We present the wireless fair service algorithm, and show through both analysis and simulation that it achieves the requirements of the service model in typical wireless network environments. The key aspects of the algorithm are the following: (a) an enhanced fair queueing based service scheme that supports decoupling of delay and bandwidth, (b) graceful service compensation for lagging flows and graceful service degradation for leading flows, (c) support for real‐time delay sensitive flows as well as non‐real‐time error sensitive flows, and (d) an implementation within the framework of the simple and robust CSMA/CA wireless medium access protocol.
2573296
Commutative cipher based en-route filtering in wireless sensor networks
Wireless sensor networks offer unprecedented capabilities to monitor the physical world by reporting the occurrence of interesting events. Unfortunately, such networks are vulnerable to event fabrication attacks, in which the compromised nodes inject bogus reports into the network, fabricating non-existent events "appearing" at arbitrary locations. Most existing security solutions to these attacks need to share symmetric keys among sensor nodes. In this paper, we propose a commutative cipher based en-route filtering scheme (CCEF) that drops fabricated reports en-route without symmetric key sharing. In CCEF, the source node establishes a secret association with the base station on a per-session basis, while the intermediate forwarding nodes are equipped with a witness key. Through the usage of a commutative cipher, a forwarding node can use the witness key to verify the authenticity of the reports without knowing the original session key. As a result, CCEF can achieve stronger security protection than the existing symmetric key sharing approach.
30203063
Discourse model for collaborative design
Abstract A Discourse Model, including a structure and a process, is developed that provides software support for collaborative engineering design. The model shares characteristics of other design systems in the literature, including frames, constraints, semantic networks, and libraries of sharable design objects. It contributes a new model for conflict-aware agents, dynamic identification and dissemination of agent interest sets, a virtual workspace language, automatic detection of conflict, and a unique protocol for negotiation that ensures that interested agents have an opportunity to participate. The model is implementation independent and applicable to many research and commercial design environments currently available. An example scenario is provided in the architecture/engineering/construction domain that illustrates collaboration during the conceptual design of a fire station.
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.