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Visual Integration of Quantitative Proteomic Data, Pathways, and Protein Interactions

IEEE TRANSACTIONS ON visualization AND COMPUTER GRAPHICS 2010年第4期16卷 609-620页

作者： Jianu, Radu Yu, Kebing Cao, Lulu Nguyen, Vinh Salomon, Arthur R. Laidlaw, David H. Brown Univ Dept Comp Sci Providence RI 02912 USA Brown Univ Dept Chem Providence RI 02912 USA Brown Univ Ctr Genom & Prote Providence RI 02912 USA Brown Univ Dept Mol Biol Cell Biol & Biochem Providence RI 02912 USA

We introduce several novel visualization and interaction paradigms for visual analysis of published protein-protein interaction networks, canonical signaling pathway models, and quantitative proteomic data. We evaluate them anecdotally with domain scientists to demonstrate their ability to accelerate the proteomic analysis process. Our results suggest that structuring protein interaction networks around canonical signaling pathway models, exploring pathways globally and locally at the same time, and driving the analysis primarily by the experimental data, all accelerate the understanding of protein pathways. Concrete proteomic discoveries within T-cells, mast cells, and the insulin signaling pathway validate the findings. The aim of the paper is to introduce novel protein network visualization paradigms and anecdotally assess the opportunity of incorporating them into established proteomic applications. We also make available a prototype implementation of our methods, to be used and evaluated by the proteomic community.

关键词： Biological (genome or protein) databases data and knowledge visualization graphs and networks interactive data exploration and discovery visualization techniques and methodologies

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Feature Level-Sets: Generalizing Iso-Surfaces to Multi-Variate Data

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IEEE TRANSACTIONS ON visualization AND COMPUTER GRAPHICS 2020年第2期26卷 1308-1319页

作者： Jankowai, Jochen Hotz, Ingrid Linkoping Inst Technol Dept Sci & Technol S-60233 Norrkoping Sweden

Iso-surfaces or level-sets provide an effective and frequently used means for feature visualization. However, they are restricted to simple features for uni-variate data. The approach does not scale when moving to multi-variate data or when considering more complex feature definitions. In this paper, we introduce the concept of traits and feature level-sets, which can be understood as a generalization of level-sets as it includes iso-surfaces, and fiber surfaces as special cases. The concept is applicable to a large class of traits defined as subsets in attribute space, which can be arbitrary combinations of points, lines, surfaces and volumes. It is implemented into a system that provides an interface to define traits in an interactive way and multiple rendering options. We demonstrate the effectiveness of the approach using multi-variate data sets of different nature, including vector and tensor data, from different application domains.

关键词： Tensile stress Data visualization Rendering (computer graphics) Transfer functions Geometry Feature extraction Multivariate visualization visualization techniques and methodologies approximation of surfaces and contours

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Accelerating volume rendering by ray leaping with back steps

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COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2010年第2期97卷 99-113页

作者： Celebi, Oemer Cengiz Cevik, Ulus Cukurova Univ Adana Turkey

The methods for visualizing sampled spatial scientific data are known as volume rendering, where images are generated by computing 2D projections of 3D volume data. Since all the discrete data cells participate in the generation of each image, rendering time grows linearly with the resolution and complexity of the dataset. Empty cells in the data, which do not contribute to the final image, are of the important factors that increase the rendering time. During recent years, researchers have highly concentrated on improving the performance of these methods to achieve real time rendering. Skipping the empty space provides significant speedup and known as space leaping which requires implementation of special data structures and pre-processing. This paper presents a simple and efficient technique, that we name "ray-leaping," for the acceleration of total rendering process and eliminates the need for special data structures and pre-processing. (C) 2009 Elsevier Ireland Ltd. All rights reserved.

关键词： Information visualization Volume visualization visualization techniques and methodologies Space leaping Ray leaping

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KelpFusion: A Hybrid Set visualization Technique

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IEEE TRANSACTIONS ON visualization AND COMPUTER GRAPHICS 2013年第11期19卷 1846-1858页

作者： Meulemans, Wouter Riche, Nathalie Henry Speckmann, Bettina Alper, Basak Dwyer, Tim TU Eindhoven NL-5600 MB Eindhoven Netherlands Microsoft Res Redmond WA 98052 USA Univ Calif Santa Barbara Santa Barbara CA 93106 USA Monash Univ Caulfield Vic 3145 Australia

We present KelpFusion: a method for depicting set membership of items on a map or other visualization using continuous boundaries. KelpFusion is a hybrid representation that bridges hull techniques such as Bubble Sets and Euler diagrams and line-and graph-based techniques such as LineSets and Kelp Diagrams. We describe an algorithm based on shortest-path graphs to compute KelpFusion visualizations. Based on a single parameter, the shortest-path graph varies from the minimal spanning tree to the convex hull of a point set. Shortest-path graphs aim to capture the shape of a point set and smoothly adapt to sets of varying densities. KelpFusion fills enclosed faces based on a set of simple legibility rules. We present the results of a controlled experiment comparing KelpFusion to Bubble Sets and LineSets. We conclude that KelpFusion outperforms Bubble Sets both in accuracy and completion time and outperforms LineSets in completion time.

关键词： Information visualization visualization techniques and methodologies

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Watertight Incremental Heightfield Tessellation

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IEEE TRANSACTIONS ON visualization AND COMPUTER GRAPHICS 2023年第9期29卷 3888-3899页

作者： Cornel, Daniel Zechmeister, Silvana Groeller, Eduard Waser, Jurgen VRVis Forsch GmbH A-1220 Vienna Austria TU Wien A-1040 Vienna Austria

In this article, we propose a method for the interactive visualization of medium-scale dynamic heightfields without visual artifacts. Our data fall into a category too large to be rendered directly at full resolution, but small enough to fit into GPU memory without pre-filtering and data streaming. We present the real-world use case of unfiltered flood simulation data of such medium scale that need to be visualized in real time for scientific purposes. Our solution facilitates compute shaders to maintain a guaranteed watertight triangulation in GPU memory that approximates the interpolated heightfields with view-dependent, continuous levels of detail. In each frame, the triangulation is updated incrementally by iteratively refining the cached result of the previous frame to minimize the computational effort. In particular, we minimize the number of heightfield sampling operations to make adaptive and higher-order interpolations viable options. We impose no restriction on the number of subdivisions and the achievable level of detail to allow for extreme zoom ranges required in geospatial visualization. Our method provides a stable runtime performance and can be executed with a limited time budget. We present a comparison of our method to three state-of-the-art methods, in which our method is competitive to previous non-watertight methods in terms of runtime, while outperforming them in terms of accuracy.

关键词： visualization techniques and methodologies heightfield rendering terrain rendering level of detail tessellation

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Automated thresholding and analysis of microCT scanned bread dough

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JOURNAL OF MICROSCOPY 2014年第2期256卷 100-110页

作者： Jensen, S. Samanta, S. Chakrabarti-Bell, S. Regenauer-Lieb, K. Siddique, K. H. M. Wang, S. CSIRO Kensington WA Australia CSIRO Food Futures Natl Res Flagship Canberra ACT Australia Univ Western Australia Sch Earth & Environm Crawley WA Australia Univ Western Australia Western Australian Geothermal Ctr Excellence Crawley WA Australia Univ Western Australia UWA Inst Agr Crawley WA Australia

Computer aided x-ray microtomography is an increasingly popular method to investigate the structure of materials. Continuing improvements in the technique are resulting in increasingly larger data sets. The analysis of these data sets generally involves executing a static workflow for multiple samples and is generally performed manually by researchers. Executing these processes requires a significant time investment. A workflow which is able to automate the activities of the user would be useful. In this work, we have developed an automated workflow for the analysis of microtomography scanned bread dough data sets averaging 5GB in size. Comparing the automated workflow with the manual workflow indicates a significant amount of the time spent (33% in the case of bread dough) on user interactions in manual method. Both workflows return similar results for porosity and pore frequency distribution. Finally, by implementing an automated workflow, users save the time which would be required to manually execute the workflow. This time can be spent on more productive tasks. Lay Description Technological advances in x-ray scanning techniques have resulted in larger, more complex microtomographic datasets. Processing these datasets can be both a time consuming and oftentimes repetitive task as datasets of similar materials tend to have similar characteristics. What if there was a better way to analyze these datasets? Our research has investigated using computer programming languages instead of researchers to automatically perform tasks involved in the analysis of microtomographic datasets of ten scanned bread dough samples. Our results highlighted the benefits of using computers to automate the analysis process, demonstrating that nearly 33% of the time required is due to researchers interacting with the analysis programs and not from the analysis itself. The quantitative data provided by the automated workflow are nearly identical to results found by researchers. This resear

关键词： Bread dough microstructure visualization systems and software visualization techniques and methodologies x-ray microtomography

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Are Metrics Enough? Guidelines for Communicating and Visualizing Predictive Models to Subject Matter Experts

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IEEE TRANSACTIONS ON visualization AND COMPUTER GRAPHICS 2024年第7期30卷 4137-4153页

作者： Suh, Ashley Appleby, Gabriel Anderson, Erik W. Finelli, Luca Chang, Remco Cashman, Dylan Tufts Univ Medford MA 02155 USA Novartis Pharmaceut Data Sci & AI CH-4033 Basel Switzerland

Presenting a predictive model's performance is a communication bottleneck that threatens collaborations between data scientists and subject matter experts. Accuracy and error metrics alone fail to tell the whole story of a model - its risks, strengths, and limitations - making it difficult for subject matter experts to feel confident in their decision to use a model. As a result, models may fail in unexpected ways or go entirely unused, as subject matter experts disregard poorly presented models in favor of familiar, yet arguably substandard methods. In this paper, we describe an iterative study conducted with both subject matter experts and data scientists to understand the gaps in communication between these two groups. We find that, while the two groups share common goals of understanding the data and predictions of the model, friction can stem from unfamiliar terms, metrics, and visualizations - limiting the transfer of knowledge to SMEs and discouraging clarifying questions being asked during presentations. Based on our findings, we derive a set of communication guidelines that use visualization as a common medium for communicating the strengths and weaknesses of a model. We provide a demonstration of our guidelines in a regression modeling scenario and elicit feedback on their use from subject matter experts. From our demonstration, subject matter experts were more comfortable discussing a model's performance, more aware of the trade-offs for the presented model, and better equipped to assess the model's risks - ultimately informing and contextualizing the model's use beyond text and numbers.

关键词： Data models Data visualization Predictive models Interviews Data science Guidelines Stakeholders Data communications aspects human factors modeling and prediction visualization techniques and methodologies

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Generating graphs for visual analytics through interactive sketching

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IEEE TRANSACTIONS ON visualization AND COMPUTER GRAPHICS 2006年第6期12卷 1386-1398页

作者： Wong, Pak Chung Foote, Harlan Mackey, Patrick Perrine, Ken Chin, George, Jr. Pacific NW Natl Lab Richland WA 99352 USA

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.

关键词： data and knowledge visualization information visualization visualization techniques and methodologies graphs and networks

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Graph signatures for visual analytics

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IEEE TRANSACTIONS ON visualization AND COMPUTER GRAPHICS 2006年第6期12卷 1399-1413页

作者： Wong, Pak Chung Foote, Harlan Chin, George, Jr. Mackey, Patrick Perrine, Ken Pacific NW Natl Lab Richland WA 99352 USA

We present a visual analytics technique to explore graphs using the concept of a data signature. A data signature, in our context, is a multidimensional vector that captures the local topology information surrounding each graph node. Signature vectors extracted from a graph are projected onto a low-dimensional scatterplot through the use of scaling. The resultant scatterplot, which reflects the similarities of the vectors, allows analysts to examine the graph structures and their corresponding real-life interpretations through repeated use of brushing and linking between the two visualizations. The interpretation of the graph structures is based on the outcomes of multiple participatory analysis sessions with intelligence analysts conducted by the authors at the Pacific Northwest National Laboratory. The paper first uses three public domain data sets with either well-known or obvious features to explain the rationale of our design and illustrate its results. More advanced examples are then used in a customized usability study to evaluate the effectiveness and efficiency of our approach. The study results reveal not only the limitations and weaknesses of the traditional approach based solely on graph visualization, but also the advantages and strengths of our signature-guided approach presented in the paper.

关键词： data and knowledge visualization information visualization visualization techniques and methodologies graphs and networks

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A Neuron Membrane Mesh Representation for visualization of Electrophysiological Simulations

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IEEE TRANSACTIONS ON visualization AND COMPUTER GRAPHICS 2012年第2期18卷 214-227页

作者： Lasserre, Sebastien Hernando, Juan Hill, Sean Schuermann, Felix de Miguel Anasagasti, Pedro Abou Jaoude, Georges Markram, Henry Ecole Polytech Fed Lausanne Blue Brain Project CH-1015 Lausanne Switzerland Univ Politecn Madrid CesViMa E-28040 Madrid Spain Ecole Polytech Fed Lausanne Lab Informat & Visualizat CH-1015 Lausanne Switzerland

We present a process to automatically generate three-dimensional mesh representations of the complex, arborized cell membrane surface of cortical neurons (the principal information processing cells of the brain) from nonuniform morphological measurements. Starting from manually sampled morphological points (3D points and diameters) from neurons in a brain slice preparation, we construct a polygonal mesh representation that realistically represents the continuous membrane surface, closely matching the original experimental data. A mapping between the original morphological points and the newly generated mesh enables simulations of electrophysiolgical activity to be visualized on this new membrane representation. We compare the new mesh representation with the state of the art and present a series of use cases and applications of this technique to visualize simulations of single neurons and networks of multiple neurons.

关键词： visualization techniques and methodologies curve surface solid and object representation data mapping neuronal network visualization

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