R. Daniel Bergeron

Multiresolution multidimensional wavelet brushing

Brushing is a data visualization technique that identifies and highlights data subsets. We introduce a form of brushing in which the brushed data is usually displayed at a different resolution than the non brushed data. The paper presents the rationale behind the multiresolution support of multivariate data visualization and describes the construction of multiresolution brushing using wavelet approximations. The idea is implemented in an enhanced version of XmdvTool. Real scientific data is used for demonstration and practical applications are suggested.

Stereophonic and surface sound generation for exploratory data analysis

The analysis and interpretation of very high dimensional data require the development and use of data presentation techniques that harness human perceptual powers. The University of Lowells Exploratory Visualization project (Exvis) aims at designing, implementing, and evaluating perceptually-based tools for data presentation using both visual and auditory domains. This paper describes several auditory data presentation techniques, including the generation of stereophonic sound with apparent depth and sound that appears to emanate from a two-dimensional area. Both approaches can produce sound with auditory texture.

Multivariate visualization using metric scaling

The authors present an efficient visualization approach to support multivariate data exploration through a simple but effective low dimensional data overview based on metric scaling. A multivariate dataset is first transformed into a set of dissimilarities between all pairs of data records. A graph configuration algorithm based on principal components is then wed to determine the display coordinates of the data records in the low dimensional data overview. This overview provides a graphical summary of the multivariate data with reduced data dimensions, reduced data size, and additional data semantics. It can be used to enhance multidimensional data brushing, or to arrange the layout of other conventional multivariate visualization techniques. Real life data is used to demonstrate the approach.

Specifying complex dialogs in ALGAE

The complexity and high development costs of user interfaces has led to research into the design of User Interface Management Systems (UIMSs). At the heart of a UIMS is a facility for specifying a dialog control component, which processes user actions and coordinates program responses. This paper describes a language called ALGAE, which allows the specification of multi-threaded, event driven dialogs.

Intra-genomic variation in the ribosomal repeats of nematodes.

Ribosomal loci represent a major tool for investigating environmental diversity and community structure via high-throughput marker gene studies of eukaryotes (e.g. 18S rRNA). Since the estimation of species’ abundance is a major goal of environmental studies (by counting numbers of sequences), understanding the patterns of rRNA copy number across species will be critical for informing such high-throughput approaches. Such knowledge is critical, given that ribosomal RNA genes exist within multi-copy repeated arrays in a genome. Here we measured the repeat copy number for six nematode species by mapping the sequences from whole genome shotgun libraries against reference sequences for their rRNA repeat. This revealed a 6-fold variation in repeat copy number amongst taxa investigated, with levels of intragenomic variation ranging from 56 to 323 copies of the rRNA array. By applying the same approach to four C. elegans mutation accumulation lines propagated by repeated bottlenecking for an average of ~400 generations, we find on average a 2-fold increase in repeat copy number (rate of increase in rRNA estimated at 0.0285-0.3414 copies per generation), suggesting that rRNA repeat copy number is subject to selection. Within each Caenorhabditis species, the majority of intragenomic variation found across the rRNA repeat was observed within gene regions (18S, 28S, 5.8S), suggesting that such intragenomic variation is not a product of selection for rRNA coding function. We find that the dramatic variation in repeat copy number among these six nematode genomes would limit the use of rRNA in estimates of organismal abundance. In addition, the unique pattern of variation within a single genome was uncorrelated with patterns of divergence between species, reflecting a strong signature of natural selection for rRNA function. A better understanding of the factors that control or affect copy number in these arrays, as well as their rates and patterns of evolution, will be critical for informing estimates of global biodiversity.

Interactive data exploration with a supercomputer

An experiment in exploratory data visualization using a massively parallel processor is described. In exploratory data visualization, it is typically not known what is being looked for: instead, the data are explored with a variety of visualization techniques that can illuminate its nature by demonstrating patterns in it. With this approach, the authors were able to find new features in some of their oldest datasets and to create more vivid presentations of familiar features in these datasets. Their experience has also led to a better understanding of the nature of the exploratory visualization and has resulted in some formal representations of the interaction process in this environment.<<ETX>>

Graphics Programming Using the Core System

This paper introduces the reader to the principal concepts of interactive graphics programming. These concepts are explained with examples using the Core Graphics System developed by the ACM-SIGGRAPH Graphics Standards Planning Committee (GSPC) [GSPC77]. The Core System is similar in concept to many existing packages. It is designed as a general purpose subroutine package that provides an interface between an application program and graphics hardware, such as line drawing plotters and interactive displays. The major goal of the Core System is to define this interface to be independent of the specific hardware available, so that the application can be used on different computer configurations with minimal changes to the application program. The Core System provides basic application-independent facilities for creating arbitrary views of twoand three-dimensional objects and for supporting interaction between the application program and its user. Higher level utility subroutine packages, using the Core System functions, might be developed to serve the needs of specific application areas, such as computer-aided design or cartography. Other papers in this issue of COMPUTING SURVEYS describe the history and methodology that underlie the Core System [NEWM78], provide an overview of its features

Test Data Sets for Evaluating Data Visualization Techniques

In this paper we take a step toward addressing a pressing general problem in the development of data visualization systems — how to measure their effectiveness. The step we take is to define a model for specifying the generation of test data that can be employed for standardized and quantitative testing of a system’s performance. These test data sets, in conjunction with appropriate testing procedures, can provide a basis for certifying the effectiveness of a visualization system and for conducting comparative studies to steer system development.

An Isosurface Continuity Algorithm for Super Adaptive Resolution Data

We present the chain-gang algorithm for isosurface rendering of super adap tive resolution (SAR) volume data in order to minimize (1) the space needed for storage of both the data and the isosurface and (2) the time taken for computation. The chain gang algorithm is able to resolve discontinuities in SAR data sets. Unnecessary computation is avoided by skipping over large sets of volume data deemed uninteresting. Memory space is saved by leaving the uninteresting voxels out of our octree data structure used to traverse the volume data. Our isosurface generation algorithm extends the Marching Cubes Algorithm in order to handle inconsistencies that can arise between abutting cells that are separated by both one and two levels of resolution.

Brushing techniques for exploring volume datasets

Describes several visualization techniques based on the notion of multi-resolution brushing to browse large 3D volume datasets. Our software is implemented using public-domain libraries, and is designed to run on average-equipped desktop computers such as a Linux machine with 32 MBytes of memory. Empirically, our system allows scientists to obtain information from a large dataset with over 8.3 million numbers in interactive time. We show that very large scientific volume datasets can be accessed and utilized without expensive hardware and software.