17978140
Completeness and realizability: conditions for automatic generation of workflows
In recent years, workflow technology has greatly facilitated business process modeling and reengineering in information systems. On one hand, the separation of an application's control structure from the implementation of its task programs simplifies and speeds up application development. On the other hand, the run-time system assists users in coordinating and scheduling tasks of a business process. As a result, the cost of doing business is reduced, and business enterprises become more responsive to new business requirements and opportunities, hence, become more competitive in the market. Several formal methods have been proposed for specifying and modeling workflows. However, most workflows are designed manually, which becomes a time-consuming and error-prone procedure when a workflow involves hundreds or thousands of task programs. A recent approach is to generate workflow automatically from a task library and a specification of the desired outcome. In this paper, we define the notions of positive and negative dependency graphs for a task library to represent the dependencies among tasks in the library. Based on these dependencies, we identified sufficient conditions for a task library to be complete, and the conditions for a workflow postcondition to be realizable from a task library. We also identified a sufficient and necessary condition for the completeness of a class of task libraries, called S-task libraries.
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.
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.
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.
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>>
18477384
Verifiable Shuffle of Large Size Ciphertexts
A shuffle is a permutation and rerandomization of a set of ciphertexts. Among other things, it can be used to construct mix-nets that are used in anonymization protocols and voting schemes. While shuffling is easy, it is hard for an outsider to verify that a shuffle has been performed correctly. We suggest two efficient honest verifier zero-knowledge (HVZK) arguments for correctness of a shuffle. Our goal is to minimize round-complexity and at the same time have low communicational and computational complexity. 
 
The two schemes we suggest are both 3-move HVZK arguments for correctness of a shuffle. We first suggest a HVZK argument based on homomorphic integer commitments, and improve both on round complexity, communication complexity and computational complexity in comparison with state of the art. The second HVZK argument is based on homomorphic commitments over finite fields. Here we improve on the computational complexity and communication complexity when shuffling large ciphertexts.
44527180
A Robust Data Delivery Protocol for Large Scale Sensor Networks
Recent technology advances in low-cost, low-power chip designs have made feasible the deployment of large-scale sensor networks. Although data forwarding has been among the first set of issues explored in sensor networking, how to reliably deliver sensing data through a vast field of small, vulnerable sensors remains a research challenge. In this paper we present GRAdient Broadcast (GRAB), a new set of mechanisms and protocols which is designed specifically for robust data delivery in spite of unreliable nodes and fallible wireless links. Similar to previous work [1], GRAB builds and maintains a cost field, providing each sensor in the network the direction to forward sensing data. Different from all the existing approaches, however, GRAB forwards data along an interleaved mesh from each source to the receiver. The width of the forwarding mesh is controlled by the amount of credit carried in each data message, allowing the degree of delivery robustness to be adjusted by the sender. GRAB design harnesses the advantage of large scale and relies on the collective efforts of multiple nodes to deliver data, without dependency on any individual ones. As demonstrated in our extensive simulation experiments, GRAB can successfully deliver above 90% of data with relatively low energy cost even under adverse conditions of up to 30% node failures compounded with 15% link packet losses.
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.
62571350
Impact of configuration errors on DNS robustness
During the past twenty years the Domain Name System (DNS) has sustained phenomenal growth while maintaining satisfactory performance. However, the original design focused mainly on system robustness against physical failures, and neglected the impact of operational errors such as misconfigurations. Our recent measurement effort revealed three specific types of misconfigurations in DNS today: lame delegation, diminished server redundancy, and cyclic zone dependency. Zones with configuration errors suffer from reduced availability and increased query delays up to an order of magnitude. Furthermore, while the original DNS design assumed that redundant DNS servers fail independently, our measurements show that operational choices made at individual zones can severely affect the availability of other zones. We found that, left unchecked, DNS configuration errors are widespread, with lame delegation affecting 15% of the DNS zones, diminished server redundancy being even more prevalent, and cyclic dependency appearing in 2% of the zones. We also noted that the degrees of misconfiguration vary from zone to zone, with most popular zones having the lowest percentage of errors. Our results indicate that DNS, as well as any other truly robust large-scale system, must include systematic checking mechanisms to cope with operational errors.