242677
Model checking the secure electronic transaction (SET) protocol
We use model checking to establish five essential correctness properties of the secure electronic transaction (SET) protocol. SET has been developed jointly by Visa and MasterCard as a method to secure payment card transactions over open networks, and industrial interest in the protocol is high. Our main contributions are to firstly create a formal model of the protocol capturing the purchase request, payment authorization, and payment capture transactions. Together these transactions constitute the kernel of the protocol. We then encoded our model and the aforementioned correctness properties in the input language of the FDR model checker. Running FDR on this input established that our model of the SET protocol satisfies all five properties even though the cardholder and merchant, two of the participants in the protocol, may try to behave dishonestly in certain ways. To our knowledge, this is the first attempt to formalize the SET protocol for the purpose of model checking.
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.
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.
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.
11578218
A new model for packet scheduling in multihop wireless networks
The goal of packet scheduling disciplines is to achieve fair and maximum allocation of 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 model for packet scheduling 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.
6309018
Knowledge-based learning integrating acquisition and learning
Empirical learning algorithms are hampered by their inability to use domain knowledge to guide the induction of new rules. This paper describes knowledge-based learning, an approach to learning that selects the examples and relevant attributes for an empirical algorithm. Knowledge-based learning can be used for developing rules for engineering expert systems. Engineers often have some rules for problem solving, but also many experiences (examples) that facilitate solving problems. Knowledge-based learning systems are able to use both forms of knowledge.
24216233
CAQ: A machine learning tool for engineering
Abstract Machine learning algorithms developed from artificial intelligence (AI) research are rapidly finding useful applications in engineering domains. They are joining a family of tools that can help engineers summarize (or synthesize) massive amounts of data to support decision making. Traditional tools in this family, such as various statistical-based techniques, deal mostly with continuous (real) valued attributes — their results are relatively accurate, but often hard to interpret. On the other hand, logic-based learning tools, such as Michalski's AQ series of programs for learning concepts from examples, deal only with discrete valued attributes — their results are easier to comprehend, but not accurate for engineering applications which rarely deal solely with discrete valued attributes. Ideally, engineers need algorithms that work with a mix of attributes including those that take continuous values and those that take discrete values. Engineering problems also demand that learning algorithms be able to handle noise and produce concepts that are comprehensible. CAQ (Continuous AQ) is an algorithm designed to meet engineering requirements. This paper explains how CAQ combines continuous and discrete values, and shows that handling continuous attributes as real numbers instead of forcing them into a discrete representation leads to more efficient concept formation. Data from a turning process simulator used in support of machine operation planning in manufacturing are used to demonstrate the new algorithm.
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.
33554044
PEAS: a robust energy conserving protocol for long-lived sensor networks
In this paper we present PEAS, a robust energy-conserving protocol that can build long-lived, resilient sensor networks using a very large number of small sensors with short battery lifetime. PEAS extends the network lifetime by maintaining a necessary set of working nodes and turning off redundant ones. PEAS operations are based on individual node's observation of the local environment and do not require any node to maintain per neighbor node state. PEAS performance possesses a high degree of robustness in the presence of both node power depletions and unexpected failures. Our simulations and analysis show that PEAS can maintain an adequate working node density in the face of up to 38% node failures, and it can maintain roughly a constant overhead level under various deployment conditions ranging from sparse to very dense node deployment by using less than 1% of total energy consumption. As a result, PEAS can extend a sensor network's functioning time in linear proportion to the deployed sensor population.