VIPR: A Visual Interface Tool for Programming Semantic Web Rules

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.Semantic technologies have evolved from the initial purpose of supporting semantic integration, information exchange for the semantic web, towards a generic set of engineering tools for knowledge modelling, representation, inference. However, there is still much work required within the area of Semantic computing, the area highlights a key research challenge involving the complexity in engineering Semantic rules, associated dedicated models. Many existing tools focus on the creation of models, but concentrate on providing support for domain experts, isolating users with no knowledge engineering experience. This paper aims to address this issue by introducing a novel approach to enable the visual creation of Semantic web rules, for use within ontological models, context-aware applications. The developed tool, known as VIPR, aims to provide a user-friendly, interactive approach to aid in the creation of Semantic rules for ontologies. The work describes the design process involved in creating VIPR, presents the results of a comparative user evaluation. The research highlights the extent to which this tool has on improving the usability, intuitiveness of creating rules in an interactive environment, assesses how the tool can improve the learnability level for users with no prior knowledge engineering experience

Bioinformatics for High-throughput Virus Detection and Discovery

Pathogen detection is a challenging problem given that any given specimen may contain one or more of many different microbes. Additionally, a specimen may contain microbes that have yet to be discovered. Traditional diagnostics are ill-equipped to address these challenges because they are focused on the detection of a single agent or panel of agents. I have developed three innovative computational approaches for analyzing high-throughput genomic assays capable of detecting many microbes in a parallel and unbiased fashion. The first is a metagenomic sequence analysis pipeline that was initially applied to 12 pediatric diarrhea specimens in order to give the first ever look at the diarrhea virome. Metagenomic sequencing and subsequent analysis revealed a spectrum of viruses in these specimens including known and highly divergent viruses. This metagenomic survey serves as a basis for future investigations about the possible role of these viruses in disease. The second tool I developed is a novel algorithm for diagnostic microarray analysis called VIPR: Viral Identification with a PRobabilistic algorithm). The main advantage of VIPR relative to other published methods for diagnostic microarray analysis is that it relies on a training set of empirical hybridizations of known viruses to guide future predictions. VIPR uses a Bayesian statistical framework in order to accomplish this. A set of hemorrhagic fever viruses and their relatives were hybridized to a total of 110 microarrays in order to test the performance of VIPR. VIPR achieved an accuracy of 94% and outperformed existing approaches for this dataset. The third tool I developed for pathogen detection is called VIPR HMM. VIPR HMM expands upon VIPR\u27s previous implementation by incorporating a hidden Markov model: HMM) in order to detect recombinant viruses. VIPR HMM correctly identified 95% of inter-species breakpoints for a set of recombinant alphaviruses and flaviviruses Mass sequencing and diagnostic microarrays require robust computational tools in order to make predictions regarding the presence of microbes in specimens of interest. High-throughput diagnostic assays coupled with powerful analysis tools have the potential to increase the efficacy with which we detect pathogens and treat disease as these technologies play more prominent roles in clinical laboratories

Computational Tradespace Exploration, Analysis, and Decision-Making: A Proposed Framework for Organizational Self-Assessment

The ability to assess technical feasibility, project risk, technical readiness, and realistic performance expectations in early-phase conceptual design is a challenging mission-critical task for large procurement projects. At present, there is not a well-defined framework for evaluating current practices of organizations performing computational trade studies. One such organization is the US Army Ground Vehicle Systems Center (GVSC). When defining requirements and priorities for the next-generation autonomy-enabled ground vehicle system, GVSC is faced with the challenge of an increasingly complex programmatic tradespace due to emerging complexities of ground vehicle systems. This thesis aims to document and evaluate tradespace processes, methods, and tools within GVSC. A systematic review of the literature was conducted to investigate existing gaps, limitations, and potential growth opportunities related to tradespace activities reflecting the greater body of knowledge observed in the literature. Following this review, an interview-based study was developed through which a series of interviews with GVSC personnel was conducted and subsequently benchmarked against the baseline established in the literature. In addition to characterizing the current practices of tradespace exploration and analysis within GVSC, the analysis of the collected interview data revealed current capability gaps, areas of excellence, and potential avenues for improvement within GVSC. Through this thesis, other organizations can perform similar self-assessments to improve internal capabilities with respect to tradespace studies

Proposed Unified Visual Programming Language

Throughout time, computer scientists have edited their programs by keypunching, then typing and more recently by typing and `point-and-clicking'. The need for improving the editing of a computer program is driven mainly by the necessity to reduce errors and increase productivity. Furthermore facilitating the editing of a computer program can contribute in facilitating the apprenticeship of programming by novices. The awakening of visual programming languages (VPL) offers an opportunity to considerably reduce editing errors, but also to be a great tool for non-programmers. For instance, the programmer is not required any longer to remember the syntax or constructs of a language to type it; instead he/she builds up a program by pointing and clicking visual objects perhaps combined with typing. This could lead to a less error prone program and higher productivity since the programmer types less. There still are a lot of challenges to surmount to increase the usability and intuitiveness of VPLs, especially for large-scale general purpose programming. One of the main problems in VPLs is that of achieving scalability. This study aims at contributing to the area of visual programming languages, by proposing the framework for a visual programming language that is the unification of the best features of four existing VPLs. This unified VPL, or UVPL, is designed to better achieve scalability, which is lacking - in general - in current VPLs. This study provides as well a short survey of the four selected VPLs, and a set of metrics to evaluate visual programs.Computer Science Departmen

Capsules and Semantic Regions for Code Visualization and Direct Manipulation of Live Programs

JPie is a visual programming environment supporting live construction of Java applications. Class modifications, such as declaring instance variables and overriding methods, take effect immediately on existing instances of the class to encourage experimentation in an educational setting. Because programs are edited live, editing gestures must transform the program from one well-formed state to another, without intermediate ambiguous states. To accomplish this, JPie’s visual representation provides capsules, which represent logical code units, and semantic regions, which represent different aspects of a program. A capsule’s meaning depends upon its containing semantic region. Similarly, a gesture, which involves manipulation of a capsule, is interpreted on the basis of the semantic region in which it occurs. This paper describes how capsules and semantic regions visually expose the structure of JPie programs and support live program editing through natural atomic gestures

Vehicle Integrated Prognostic Reasoner (VIPR) 2010 Annual Final Report

Honeywell's Central Maintenance Computer Function (CMCF) and Aircraft Condition Monitoring Function (ACMF) represent the state-of-the art in integrated vehicle health management (IVHM). Underlying these technologies is a fault propagation modeling system that provides nose-to-tail coverage and root cause diagnostics. The Vehicle Integrated Prognostic Reasoner (VIPR) extends this technology to interpret evidence generated by advanced diagnostic and prognostic monitors provided by component suppliers to detect, isolate, and predict adverse events that affect flight safety. This report describes year one work that included defining the architecture and communication protocols and establishing the user requirements for such a system. Based on these and a set of ConOps scenarios, we designed and implemented a demonstration of communication pathways and associated three-tiered health management architecture. A series of scripted scenarios showed how VIPR would detect adverse events before they escalate as safety incidents through a combination of advanced reasoning and additional aircraft data collected from an aircraft condition monitoring system. Demonstrating VIPR capability for cases recorded in the ASIAS database and cross linking them with historical aircraft data is planned for year two

4D reduced TE (RTE) spiral phase contrast NRI for rapid quantification and visualization of blood flow and hemodynamics.

4D flow Phase Contrast MRI is a relatively new technique in MRI which is capable of deriving time-resolved three-dimensional velocity fields in a 3D volume noninvasively. 4D flow imaging is a 3D k-space acquisition where for the third dimension, an additional phase-encoding step is required. The velocity field can then be used to obtain flow waveform, wall shear stress, vascular compliance, blood pressure, and other hemodynamic information. A significant limitation of 4D flow methods has been the requisite long scan times, requiring the patient to remain motionless at times on the order of 10-20 minutes, depending on scan parameters. The scan times may become more prohibitive in case of 4D cardiovascular studies where respiratory gating with navigator echoes is required. In this thesis the feasibility of using a reduced TE stack of spirals k-space acquisition for 4D flow imaging are investigated. Starting with fundamentals of MRI, the basics of Phase contrast and 4D flow MRI are thoroughly discussed in Chapter 1-3 and subsequently experimental phantom results are reported in Chapter 4, pointing to the feasibility of performing highly accurate 4D velocity and flow measurement with the proposed pulse sequence under a variety of flow conditions and with substantial reductions in scan time when compared to conventional 4D flow. In phantom studies, results based on the root mean square error criterion indicate that 4D Reduced TE (RTE) Spiral PC MRI is capable of providing the same level of accuracy as conventional 4D conventional PC MRI but in a much shorter scan time (30% reduction in scan time when imaging an FOV of 100*100*60 mm3 and spatial resolution of 1.5*1.5*3 mm3). Moreover, the proposed method has the added advantage of achieving the shorter echo time of 2 ms versus 3.6 ms for conventional 4D flow at Q=50ml/s and 1.57 ms versus 3.2 ms at the higher flow rate of Q=150 ml/s leading to more accurate assessment of flow distal to narrowings. Statistical results indicate that at low flow rates performance of both methods are similar. At higher flow rates, however, 4D RTE spiral flow achieves better accuracy. Qualitative results in phantom studies also revealed that at higher flow rates, better flow visualization was achieved with4D RTE spiral flow compared with conventional 4D flow. In the second part of Chapter 4, we also report on application of the proposed sequence, in-vivo, to 5 healthy volunteers and 5 subjects with mild to moderate Aortic Stenosis (AS) disease. Results from the proposed method were statistically correlated with velocity profiles derived from conventional 4D flow and Doppler Ultrasound. Results indicate that 4D RTE Spiral is capable of providing the same level of accuracy in flow measurement as Conventional 4D flow MRI for imaging of the aortic valve, but on average resulted in a 30% reduction in scan time and 45% reduction in echo time. 4D RTE Spiral was also able to achieve an echo time of 1.68 ms versus 2.9 ms for that of conventional 4D flow MRI, permitting less signal dephasing in the presence of jet flows distal to occlusions. With Doppler Ultrasound adopted as the reference method, 4D RTE Spiral flow measured peak velocity and maximum pressure gradient with a higher level of accuracy when compared to Conventional 4D flow MRI. Both methods measured left-ventricular out flow tract (LVOT) diameter, Aortic Valve (AV) eject time and time to AV peak with same accuracy. It is concluded that 4D RTE Spiral flow MRI is an excellent technique for flow measurement in cardiac patients who are unable to tolerate longer scan times, currently required by conventional 4D flow methods

State v. Kerr Clerk\u27s Record Dckt. 44770

https://digitalcommons.law.uidaho.edu/idaho_supreme_court_record_briefs/7753/thumbnail.jp