Visualizing Gene Clusters using Neighborhood Graphs in R

The visualization of cluster solutions in gene expression data analysis gives practitioners an understanding of the cluster structure of their data and makes it easier to interpret the cluster results. Neighborhood graphs allow for visual assessment of relationships between adjacent clusters. The number of clusters in gene expression data is for biological reasons rather large. As a linear projection of the data into 2 dimensions does not scale well in the number of clusters there is a need for new visualization techniques using non-linear arrangement of the clusters. The new visualization tool is implemented in the open source statistical computing environment R. It is demonstrated on microarray data from yeast

But a walking shadow: designing, performing and learning on the virtual stage

Representing elements of reality within a medium, or taking aspects from one medium and placing them in another is an act of remediation. The process of this act, however, is largely taken for granted. Despite the fact that available information enables a qualitative assessment of the history of multimedia and their influences on different fields of knowledge, there are still some areas that require more focused research attention. For example, the relationship between media evolution and new developments in scenographic practice is currently under investigation. This article explores the issue of immediacy as a condition of modern theatre in the context of digital reality. It discusses the opportunities and challenges that recent technologies present to contemporary practitioners and theatre design educators, creating a lot of scope to break with conventions. Here, we present two case studies that look into technology-mediated learning about scenography through the employment of novel computer visualization techniques. The first case study is concerned with new ways of researching and learning about theatre through creative exploration of design artefacts. The second case study investigates the role of the Immersive Virtual World Second Life™ (SL) in effective teaching of scenography, and in creating and experiencing theatrical performances

Vulnerability Clustering and other Machine Learning Applications of Semantic Vulnerability Embeddings

Cyber-security vulnerabilities are usually published in form of short natural language descriptions (e.g., in form of MITRE's CVE list) that over time are further manually enriched with labels such as those defined by the Common Vulnerability Scoring System (CVSS). In the Vulnerability AI (Analytics and Intelligence) project, we investigated different types of semantic vulnerability embeddings based on natural language processing (NLP) techniques to obtain a concise representation of the vulnerability space. We also evaluated their use as a foundation for machine learning applications that can support cyber-security researchers and analysts in risk assessment and other related activities. The particular applications we explored and briefly summarize in this report are clustering, classification, and visualization, as well as a new logic-based approach to evaluate theories about the vulnerability space.Comment: 27 pages, 13 figure

Weather, climate, and hydrologic forecasting for the US Southwest: A survey

As part of a regional integrated assessment of climate vulnerability, a survey was conducted from June 1998 to May 2000 of weather, climate, and hydrologic forecasts with coverage of the US Southwest and an emphasis on the Colorado River Basin. The survey addresses the types of forecasts that were issued, the organizations that provided them, and techniques used in their generation. It reflects discussions with key personnel from organizations involved in producing or issuing forecasts, providing data for making forecasts, or serving as a link for communicating forecasts. During the survey period, users faced a complex and constantly changing mix of forecast products available from a variety of sources. The abundance of forecasts was not matched in the provision of corresponding interpretive materials, documentation about how the forecasts were generated, or reviews of past performance. Potential existed for confusing experimental and research products with others that had undergone a thorough review process, including official products issued by the National Weather Service. Contrasts between the state of meteorologic and hydrologic forecasting were notable, especially in the former's greater operational flexibility and more rapid incorporation of new observations and research products. Greater attention should be given to forecast content and communication, including visualization, expression of probabilistic forecasts and presentation of ancillary information. Regional climate models and use of climate forecasts in water supply forecasting offer rapid improvements in predictive capabilities for the Southwest. Forecasts and production details should be archived, and publicly available forecasts should be accompanied by performance evaluations that are relevant to users

Designing Improved Sediment Transport Visualizations

Monitoring, or more commonly, modeling of sediment transport in the coastal environment is a critical task with relevance to coastline stability, beach erosion, tracking environmental contaminants, and safety of navigation. Increased intensity and regularity of storms such as Superstorm Sandy heighten the importance of our understanding of sediment transport processes. A weakness of current modeling capabilities is the ability to easily visualize the result in an intuitive manner. Many of the available visualization software packages display only a single variable at once, usually as a two-dimensional, plan-view cross-section. With such limited display capabilities, sophisticated 3D models are undermined in both the interpretation of results and dissemination of information to the public. Here we explore a subset of existing modeling capabilities (specifically, modeling scour around man-made structures) and visualization solutions, examine their shortcomings and present a design for a 4D visualization for sediment transport studies that is based on perceptually-focused data visualization research and recent and ongoing developments in multivariate displays. Vector and scalar fields are co-displayed, yet kept independently identifiable utilizing human perception\u27s separation of color, texture, and motion. Bathymetry, sediment grain-size distribution, and forcing hydrodynamics are a subset of the variables investigated for simultaneous representation. Direct interaction with field data is tested to support rapid validation of sediment transport model results. Our goal is a tight integration of both simulated data and real world observations to support analysis and simulation of the impact of major sediment transport events such as hurricanes. We unite modeled results and field observations within a geodatabase designed as an application schema of the Arc Marine Data Model. Our real-world focus is on the Redbird Artificial Reef Site, roughly 18 nautical miles offshor- Delaware Bay, Delaware, where repeated surveys have identified active scour and bedform migration in 27 m water depth amongst the more than 900 deliberately sunken subway cars and vessels. Coincidently collected high-resolution multibeam bathymetry, backscatter, and side-scan sonar data from surface and autonomous underwater vehicle (AUV) systems along with complementary sub-bottom, grab sample, bottom imagery, and wave and current (via ADCP) datasets provide the basis for analysis. This site is particularly attractive due to overlap with the Delaware Bay Operational Forecast System (DBOFS), a model that provides historical and forecast oceanographic data that can be tested in hindcast against significant changes observed at the site during Superstorm Sandy and in predicting future changes through small-scale modeling around the individual reef objects

Visualization techniques for heterogeneous and multidimensional simulated building performance data sets

The architecture, environment and construction industry is facing, on the one hand, ambitious environmental regulations for low carbon and net zero energy buildings, and on the other hand, the emergence of new techniques such as parametric assessment and cloud computing. As a result, there is a dramatic increase of performance analysis and collected data during the building design phase. However, previous research highlighted major weaknesses of current building performance simulation -BPS- software regarding its ability to represent and explore input and output data, to interact with it, and to extract valuable data patterns and analyses. Therefore, this research aims to identify suitable visualization techniques that might increase the usability and the knowledge extracted from building simulation dataset. To that end, an interdisciplinary approach has been set up. First, a literature review allowed to characterize the specificities of BPS dataset, namely their heterogeneous nature -discrete, ordinal, categorical, and continuous-, their different correlation levels and their medium size. Second, key tasks that should be performed by BPS tools to support the design process are identified: exploration, solutions generation and evaluation. Then, two data visualization techniques that accept the BPS dataset specificities and that enable to perform these key tasks were selected within the information visualization research field: Decision Tree and Parallel Coordinates. Third, these techniques were applied to an extensive BPS dataset, generated from a series of parametric building simulations based on a high-performance building to be, called the smart living building. Finally, a qualitative comparison between the selected visualization techniques was conducted so as to reveal their strengths and weaknesses. This comparison highlights Parallel Coordinates as the most promising approach

Modelling and visualizing sustainability assessment in urban environments

Major urban development projects extend over prolonged timescales (up to 25 years in the case of major regeneration projects), involve a large number of stakeholders, and necessitate complex decision making. Comprehensive assessment of critical information will involve a number of domains, such as social, economic and environmental, and input from a wide a range of stakeholders. This makes rigorous and holistic decision making, with respect to sustainability, exceptionally difficult without access to appropriate decision support tools. Assessing and communicating the key aspects of sustainability and often conflicting information remains a major hurdle to be overcome if sustainable development is to be achieved. We investigate the use of an integrated simulation and visualization engine and will test if it is effective in: 1) presenting a physical representation of the urban environment, 2) modelling sustainability of the urban development using a subset of indicators, here the modelling and the visualization need to be integrated seamlessly in order to achieve real time updates of the sustainability models in the 3D urban representation, 3) conveying the sustainability information to a range of stakeholders making the assessment of sustainability more accessible. In this paper we explore the first two objectives. The prototype interactive simulation and visualization platform (S-City VT) integrates and communicates complex multivariate information to diverse stakeholder groups. This platform uses the latest 3D graphical rendering techniques to generate a realistic urban development and novel visualization techniques to present sustainability data that emerge from the underlying computational model. The underlying computational model consists of two parts: traditional multicriteria evaluation methods and indicator models that represent the temporal changes of indicators. These models are informed from collected data and/or existing literature. The platform is interactive and allows real time movements of buildings and/or material properties and the sustainability assessment is updated immediately. This allows relative comparisons of contrasting planning and urban layouts. Preliminary usability results show that the tool provides a realistic representation of a real development and is effective at conveying the sustainability assessment information to a range of stakeholders. S-City VT is a novel tool for calculating and communicating sustainability assessment. It therefore begins to open up the decision making process to more stakeholders, reducing the reliance on expert decision makers

Investigating the use of background knowledge for assessing the relevance of statements to an ontology in ontology evolution

The tasks of learning and enriching ontologies with new concepts and relations have attracted a lot of attention in the research community, leading to a number of tools facilitating the process of building and updating ontologies. These tools often discover new elements of information to be included in the considered ontology from external data sources such as text documents or databases, transforming these elements into ontology compatible statements or axioms. While some techniques are used to make sure that statements to be added are compatible with the ontology (e.g. through conflict detection), such tools generally pay little attention to the relevance of the statement in question. It is either assumed that any statement extracted from a data source is relevant, or that the user will assess whether a statement adds value to the ontology. In this paper, we investigate the use of background knowledge about the context where statements appear to assess their relevance. We devise a methodology to extract such a context from ontologies available online, to map it to the considered ontology and to visualize this mapping in a way that allows to study the intersection and complementarity of the two sources of knowledge. By applying this methodology on several examples, we identified an initial set of patterns giving strong indications concerning the relevance of a statement, as well as interesting issues to be considered when applying such techniques