3234528
An Ontology-Based Multimedia Annotator for the Semantic Web of Language Engineering
The development of the Semantic Web, the next-generation Web, greatly relies on the availability of ontologies and powerful annotation tools. However, there is a lack of ontology-based annotation tools for linguistic multimedia data. Existing tools either lack ontology support or provide limited support for multimedia. To fill the gap, we present an ontology-based linguistic multimedia annotation tool, OntoELAN, which features: (1) the support for OWL ontologies; (2) the management of language profiles, which allow the user to choose a subset of ontological terms for annotation; (3) the management of ontological tiers, which can be annotated with language profile terms and, therefore, corresponding ontological terms; and (4) storing OntoELAN annotation documents in XML format based on multimedia and domain ontologies. To our best knowledge, OntoELAN is the first audio/video annotation tool in the linguistic domain that provides support for ontology-based annotation. It is expected that the availability of such a tool will greatly facilitate the creation of linguistic multimedia repositories as islands of the Semantic Web of language engineering.
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.
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.
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.
9604157
Conflict resolution in cooperative design
Design is increasingly becoming a cooperative endeavor carried out by multiple agents with diverse kinds of expertise. The development of tools and underlying theories for supporting cooperative design has lagged, however, behind the growing needs implied by this evolution. 
The goal of this thesis work is to provide a computational model for supporting a critical component of cooperative design; the run-time resolution of conflicts. Though the long-term goal is to support unrestricted conflict resolution among human agents, this thesis focuses on an important subset of this problem: the resolution of domain-level conflicts in routine design, using machine-based agents. 
This thesis proposes a model of conflict resolution in cooperative design that corresponds well to how human design experts actually perform cooperative design, based on analysis of their group problem solving activity. This model supports natural participation for human experts, both at development-time as domain experts asked to create machine-based agents, as well as at run-time as problem solving agents themselves. The conflict resolution model is elaborated into a detailed implemented computational theory that offers many insights into how the conflict resolution expert and design agents should operate. The model incorporates a considerable body of conflict resolution expertise applicable to a wide variety of domains, as well as techniques for acquiring further expertise and evaluating its completeness.
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.
1764244
Machine Learning in Engineering Automation
Abstract Engineers need intelligent tools to assist them with problems such as design, planning, monitoring, control, diagnosis, and analysis. Manual construction of these tools can be costly or impossible due to problems such as large amounts of data, lack of problem understanding, and the expense of knowledge engineering. Machine learning techniques hold promise for assisting in solutions to many of these problems, but engineering domains present significant challenges to learning systems, including: noisy data, continuous quantities, mathematical formulas, large problem spaces, incorporating multiple sources and forms of knowledge, and the need for user-system interaction. This paper describes a number of challenges to learning systems motivated by engineering applications and describes a taxonomy of engineering tasks for application of machine learning technology.
37627056
SWIFT: system workbench for integrating and facilitating teams
There have been many R&D efforts in recent years to develop computer environments that directly enhance group problem-solving productivity. An example of such efforts is the computer-based virtual teaming technology (VTT) developed at the knowledge-based Engineering Sytems Research Laboratory (KESRL). The core software environment for KESRL's VTT is called SWIFT and is based on the knowledge processing technology (KPT) previously developed at KESRL to support various engineering design tasks. SWIFT is a flexible environment which enables the rapid development of collaborative applications, linking workers in distributed environments, of many domains. The paper presents the overall system architecture of SWIFT, and introduces the current and future R&D efforts at KESRL in realizing SWIFT for significant industrial applications.<<ETX>>