A model-based reasoning architecture for system-level fault diagnosis

This dissertation presents a model-based reasoning architecture with a two fold purpose: to detect and classify component faults from observable system behavior, and to generate fault propagation models so as to make a more accurate estimation of current operational risks. It incorporates a novel approach to system level diagnostics by addressing the need to reason about low-level inaccessible components from observable high-level system behavior. In the field of complex system maintenance it can be invaluable as an aid to human operators. The first step is the compilation of the database of functional descriptions and associated fault-specific features for each of the system components. The system is then analyzed to extract structural information, which, in addition to the functional database, is used to create the structural and functional models. A fault-symptom matrix is constructed from the functional model and the features database. The fault threshold levels for these symptoms are founded on the nominal baseline data. Based on the fault-symptom matrix and these thresholds, a diagnostic decision tree is formulated in order to intelligently query about the system health. For each faulty candidate, a fault propagation tree is generated from the structural model. Finally, the overall system health status report includes both the faulty components and the associated at risk components, as predicted by the fault propagation model.Ph.D.Committee Chair: Vachtsevanos, George; Committee Member: Liang, Steven; Committee Member: Michaels, Thomas; Committee Member: Vela, Patricio; Committee Member: Wardi, Yora

An Independent Component Analysis Based Tool for Exploring Functional Connections in the Brain

This thesis describes the use of independent component analysis (ICA) as a measure of voxel similarity, which allows the user to find and view statistically independent maps of correlated voxel activity. The tool developed in this work uses a specialized clustering technique, designed to find and characterize clusters of activated voxels, to compare the independent component spatial maps across patients. This same method is also used to compare SPM results across patients

Applying Science Models for Search

The paper proposes three different kinds of science models as value-added services that are integrated in the retrieval process to enhance retrieval quality. The paper discusses the approaches Search Term Recommendation, Bradfordizing and Author Centrality on a general level and addresses implementation issues of the models within a real-life retrieval environment.Comment: 14 pages, 3 figures, ISI 201

National Mesothelioma Virtual Bank: A standard based biospecimen and clinical data resource to enhance translational research

Background: Advances in translational research have led to the need for well characterized biospecimens for research. The National Mesothelioma Virtual Bank is an initiative which collects annotated datasets relevant to human mesothelioma to develop an enterprising biospecimen resource to fulfill researchers' need. Methods: The National Mesothelioma Virtual Bank architecture is based on three major components: (a) common data elements (based on College of American Pathologists protocol and National North American Association of Central Cancer Registries standards), (b) clinical and epidemiologic data annotation, and (c) data query tools. These tools work interoperably to standardize the entire process of annotation. The National Mesothelioma Virtual Bank tool is based upon the caTISSUE Clinical Annotation Engine, developed by the University of Pittsburgh in cooperation with the Cancer Biomedical Informatics Grid™ (caBIG™, see http://cabig.nci.nih.gov). This application provides a web-based system for annotating, importing and searching mesothelioma cases. The underlying information model is constructed utilizing Unified Modeling Language class diagrams, hierarchical relationships and Enterprise Architect software. Result: The database provides researchers real-time access to richly annotated specimens and integral information related to mesothelioma. The data disclosed is tightly regulated depending upon users' authorization and depending on the participating institute that is amenable to the local Institutional Review Board and regulation committee reviews. Conclusion: The National Mesothelioma Virtual Bank currently has over 600 annotated cases available for researchers that include paraffin embedded tissues, tissue microarrays, serum and genomic DNA. The National Mesothelioma Virtual Bank is a virtual biospecimen registry with robust translational biomedical informatics support to facilitate basic science, clinical, and translational research. Furthermore, it protects patient privacy by disclosing only de-identified datasets to assure that biospecimens can be made accessible to researchers. © 2008 Amin et al; licensee BioMed Central Ltd

ViCTree: an automated framework for taxonomic classification from protein sequences

Motivation: The increasing rate of submission of genetic sequences into public databases is providing a growing resource for classifying the organisms that these sequences represent. To aid viral classification, we have developed ViCTree, which automatically integrates the relevant sets of sequences in NCBI GenBank and transforms them into an interactive maximum likelihood phylogenetic tree that can be updated automatically. ViCTree incorporates ViCTreeView, which is a JavaScript-based visualisation tool that enables the tree to be explored interactively in the context of pairwise distance data. Results: To demonstrate utility, ViCTree was applied to subfamily Densovirinae of family Parvoviridae. This led to the identification of six new species of insect virus. Availability: ViCTree is open-source and can be run on any Linux- or Unix-based computer or cluster. A tutorial, the documentation and the source code are available under a GPL3 license, and can be accessed at http://bioinformatics.cvr.ac.uk/victree_web/

Report on the first Twente Data Management Workshop on XML Databases and Information Retrieval

The Database Group of the University of Twente initiated a new series of workshops called Twente Data Management workshops (TDM), starting with one on XML Databases and Information Retrieval which took place on 21 June 2004 at the University of Twente. We have set ourselves two goals for the workshop series: i) To provide a forum to share original ideas as well as research results on data management problems; ii) To bring together researchers from the database community and researchers from related research fields