Global Visualization and Alignments of Whole Bacterial Genomes
We present a novel visualization technique to align whole bacterial genomes with millions of nucleotides. Our basic design combines the descriptive power of pixel-based visualizations with the interpretative strength of digital image-processing filters. The innovative use of pixel enhancement techniques on pixel-based visualizations brings out the best of the recursive data patterns and further enhances the effectiveness of the visualization techniques. The result is a fast, versatile, and cost-effective analysis tool to reveal hidden structures that might lead to the discovery of functional identifications as well as phenotypic changes of whole bacterial genomes. Nine different whole bacterial genomes obtained from public genome banks are used to demonstrate our designs and prove their viability. Although the design of the new visualization technique is targeted at analyzing genomic sequences, we show with examples that it can be used to study other types of sequential data sets with a priori orders.

title: Generating Graphs for Visual Analytics through Interactive Sketching
abstract: We introduce an interactive graph generator, GreenSketch, designed to facilitate the creation of descriptive graphs required for different visual analytics tasks. The human-centric design approach of GreenSketch enables users to master the creation process without specific training or prior knowledge of graph model theory. The customized user interface encourages users to gain insight into the connection between the compact matrix representation and the topology of a graph layout when they sketch their graphs. Both the human-enforced and machine-generated randomnesses supported by GreenSketch provide the flexibility needed to address the uncertainty factor in many analytical tasks. This paper describes more than two dozen examples that cover a wide variety of graph creations from a single line of nodes to a real-life small-world network that describes a snapshot of telephone connections. While the discussion focuses mainly on the design of GreenSketch, we include a case study that applies the technology in a visual analytics environment and a usability study that evaluates the strengths and weaknesses of our design approach

title: Multivariate Visualization with Data Fusion
abstract: We discuss a fusion-based visualization method to analyze a multivariate climate dataset and its metadata. The primary difference between a conventional visualization and a fusion-based visualization is that the former draws on a single image whereas the latter draws on multiple see-through layers, which are then overlaid on each other to form the final visualization. We propose optimized colormaps to highlight subtle features that would not be shown with conventional colormaps. We present fusion techniques that integrate multiple single-purpose visualization techniques into the same viewing space. Our highly flexible fusion approach allows scientists to explore multiple parameters concurrently by mixing and matching images without frequently reconstructing new visualizations from the data for every possible combination. Although our primary visualization application is climate modeling, we show with examples that our fundamental design - fusing layers of data images for multivariate visualization - can be generalized for other information visualization applications.

title: Organic data memory using the DNA approach
abstract: For very long-term storage and retrieval, encode information as artificial DNA strands and insert into living hosts. As vectors, bacteria, even some bugs and weeds, might be good for hundreds of millions of years.

title: Vector fields simplification-a case study of visualizing climate modeling and simulation data sets
abstract: In our study of regional climate modeling and simulation, we frequently encounter vector fields that are crowded with large numbers of critical points. A critical point in a flow is where the vector field vanishes. While these critical points accurately reflect the topology of the vector fields, in our study only a subset of them is worth further investigation. We present a filtering technique based on the vorticity of the vector fields to eliminate the less interesting and sometimes sporadic critical points in a multiresolution fashion. The neighboring regions of the preserved features, which are characterized by strong shear and circulation, are potential locations of weather instability. We apply our feature filtering technique to a regional climate modeling data set covering East Asia in the summer of 1991.

title: Data Signatures and Visualization of Scientific Data Sets
abstract: Today, as data sets used in computations grow in size and complexity, the technologies developed over the years to deal with scientific data sets have become less efficient and effective. Many frequently used operations, such as eigenvector computation, could quickly exhaust our desktop workstations once the data size reaches certain limits. On the other hand, the high-dimensional data sets we collect every day don't relieve the problem. Many conventional metric designs that build on quantitative or categorical data sets cannot be applied directly to heterogeneous data sets with multiple data types. While building new machines with more resources might conquer the data size problems, the complexity of today's computations requires a new breed of projection techniques to support analysis of the data and verification of the results. We introduce the concept of a data signature, which captures the essence of a scientific data set in a compact format, and use it to conduct analysis as if using the original. A time-dependent climate simulation data set demonstrates our approach and presents the results.

title: A blind watermarking technique for multiple watermarks
abstract: We propose a blind watermarking technique to embed multiple watermarks simultaneously. It allows the use of correlated key to embed multiple watermarks. A dual-key system is used to reduce the chance of the removal of watermark. Each embedded watermark can be decoded/detected by its own key. One direct approach and two iterative approaches are proposed to reduce the correlation effects among the noise-like keys. Experimental results show that multiple watermarks can be embedded without significant loss in PSNR and the watermark can be detected when the watermarked image is JPEG compressed.

title: Phylogenetic Web Profiler
abstract: Phylogenetic Web Profiler (PWP) is a web-based service designed to perform phylogenetic profiling of proteins against genomes. The current version offers a selection of 63 completed genomes and available plasmids as annotated in the PEDANT genome database. Unlike currently available applications, this tool offers several choices of ortholog prediction parameters including E-value cutoff, percent length difference tolerance, and annotation similarity. Additional features include tight integration with the PEDANT database and tools to analyze properties of predicted proteins. PWP should prove very useful for the analysis of functional-linkage between proteins.

title: Rate estimation for H.264/AVC spatial resolution reduction
abstract: The emergence of wireless networks has posed new challenges for multimedia content providers. In particular, many existing video contents have bit-rates and resolutions far exceeding the capability of wireless networks and mobile devices and they need to be adapted before transmission. In this paper, we propose a technique using /spl rho/-domain information to estimate the bit rate of down-sampled video in the H.264/AVC format. The bit rate is estimated in two stages. In the initialization stage, we use a low-complexity algorithm to estimate the /spl rho/-domain parameters for half and quarter resolutions, respectively. In the refinement stage, the estimation error is feed-forwarded to improve the estimation accuracy. Experimental results show that the proposed technique can estimate the bit rate accurately at a wide range of down-sampling ratios.

title: Novel blind multiple watermarking technique for images
abstract: Three novel blind watermarking techniques are proposed to embed watermarks into digital images for different purposes. The watermarks are designed to be decoded or detected without the original images. The first one, called single watermark embedding (SWE), is used to embed a watermark bit sequence into digital images using two secret keys. The second technique, called multiple watermark embedding (MWE), extends SWE to embed multiple watermarks simultaneously in the same watermark space while minimizing the watermark (distortion) energy. The third technique, called iterative watermark embedding (IWE), embeds watermarks into JPEG-compressed images. The iterative approach of IWE can prevent the potential removal of a watermark in the JPEG recompression process. Experimental results show that embedded watermarks using the proposed techniques can give good image quality and are robust in varying degree to JPEG compression, low-pass filtering, noise contamination, and print-and-scan.

title: On improving the iterative watermark embedding technique for JPEG-to-JPEG watermarking
abstract: We previously proposed an iterative technique called iterative watermark embedding (IWE) for watermark embedding in JPEG compressed domains. The proposed technique embeds the watermark successfully when the quality factor of the JPEG image is high, but when the quality factor is low, not all the bits of the watermark can be embedded. This is due to uneven distribution of capacities in different regions of the image. Moreover, the computation complexity of the iterative loop is high. In this paper we improve the technique using shuffling to equalize the capacities of different regions. Also, the iterative loop is replaced by a direct approach to reduce the computational complexity. We call this direct approach Direct JPEG Watermarking Embedding (DJWE). A Human Visual System (HVS) model is used to prioritize the DCT coefficients to achieve good visual quality. Experimental results show that the watermarks are robust against Gaussian noise attack and JPEG transcoding attacks.