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.
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.
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.
41350051
Language engineering for the Semantic Web: a digital library for endangered languages
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.
45286677
AIMS: An Adaptive Interactive Modeling System for Supporting Engineering Decision Making
Engineering decision making is a two-phase process involving model formation and model utilization. Simulation models have been useful for decision support but, can be too slow for interactive applications. An integrated methodology is presented for inducing faster simulation models and using these models to support interactive design. In AIMS, both model formation and model utilization are controlled by a multiple objective optimizer, ISO. This knowledge processing framework is applied to combustion engine design.
1093389
TOPS: An intelligent associate for Turning Operation Planning
This article describes the development of a new modeling environment that supports the building of intelligent associates for turning operation planning. By intelligent associates, we mean a computer-based system that allows a process planner to assert a greater degree of control during a consultation than do traditional expert systems. Intelligent associates are able to assist process planners in a colleague-like manner while solving domain tasks. They relieve routine operations while supporting creative problem-solving. Multiple levels of human experience are supported, advising and constraining inexperienced planners while providing a flexible environment for experienced planners working on new planning strategies. Several Al-based techniques have been employed in the development of this new modeling environment. The utility of this environment is demonstrated by developing a turning operation planning intelligent associate (TOPS). TOPS assists a process planner by computing interactions and checking f...
35964038
Learning Engineering Models with the Minimum Description Length Principle
This paper discusses discovery of mathematical models from engineering data sets. KEDS, a Knowledge-based Equation Discovery System, identifies several potentially overlapping regions in the problem space, each associated with an equation of different complexity and accuracy. The minimum description length principle, together with the KEDS algorithm, is used to guide the partitioning of the problem space. The KEDSMDL algorithm has been tested on discovering models for predicting the performance efficiencies of an internal combustion engine.
1924192
The impact of multihop wireless channel on TCP throughput and loss
This paper studies TCP performance over multihop wireless networks that use the IEEE 802.11 protocol as the access method. Our analysis and simulations show that, given a specific network topology and flow patterns, there exists a TCP window size W*, at which TCP achieves best throughput via improved spatial channel reuse. However, TCP does not operate around W*, and typically grows its average window size much larger; this leads to decreased throughput and increased packet loss. The TCP throughput reduction can be explained by its loss behavior. Our results show that network overload is mainly signified by wireless link contention in multihop wireless networks. As long as the buffer size at each node is reasonably large (say, larger than 10 packets), buffer overflow-induced packet loss is rare and packet drops due to link-layer contention dominate. Link-layer drops offer the first sign for network overload. We further show that multihop wireless links collectively exhibit graceful drop behavior: as the offered load increases, the link contention drop probability also increases, but saturates eventually. In general, the link drop probability is insufficient to stabilize the average TCP window size around W*. Consequently, TCP suffers from reduced throughput due to reduced spatial reuse. We further propose two techniques, link RED and adaptive pacing, through which we are able to improve TCP throughput by 5% to 30% in various simulated topologies. Some simulation results are also validated by real hardware experiments.
611972
Tracking Causal Dependencies in an Active Object-Oriented Database
As active and deductive databases are applied to more complex domains (e.g. engineering design), the need to track the causality of data which has been derived by rules in the database becomes vital. Truth maintenance systems have been used in the area of artificial intelligence to track the causal dependencies of data derived from rules in knowledge-based systems. These same techniques can be applied to active object-oriented databases to provide the users with the means to track the relationships between data and rules. This paper describes the relevant features of a simple truth maintenance systems and puts forth a model of how truth maintenance systems can be integrated with an active object-oriented database, including the definition of new query operators to interpret the causal information for the end user.