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Location - Computer Science Building (S3)

Location of the Institute for Computer Graphics: Computer Science Building (Science Park 3)

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Research

The Institute of Computer Graphics carries out research in a modern field that has been coined "visual computing". Our core disciplines cover the imaging, processing, visualization and displaying of visual data. These are enabled by new fields and technologies, such as light fields, projector-camera systems, responsive optics, mobile computing, and visual analytics.

Please select one of the following topics or years for detailed information.















Visualization

Guided Visual Exploration of Genomic Stratifications in Cancer


Cancer is a heterogeneous disease, and molecular profiling of tumors from large cohorts has enabled characterization of new tumor subtypes. This is a prerequisite for improving personalized treatment and ultimately achieving better patient outcomes. Potential tumor subtypes can be identified with methods such as unsupervised clustering or network-based stratification, which assign patients to sets based on high-dimensional molecular profiles. Detailed characterization of identified sets and their interpretation, however, remain a time-consuming exploratory process.
To address these challenges, we combined 'StratomeX', an interactive visualization tool that is freely available at >?http://www.caleydo.org/, with exploration tools to efficiently compare multiple patient stratifications, to correlate patient sets with clinical information or genomic alterations and to view the differences between molecular profiles across patient sets. Although we focus on cancer genomics here, StratomeX can also be applied in other disease cohorts.

Streit, M., Lex, A., Gratzl, S., Partl, P., Schmalstieg, D., Pfister, HP., Park, PJ., Gehlenborg, N., Guided Visual Exploration of Genomic Stratifications in Cancer, Nature Methods, 11, 884-885, 2014

Domino: Extracting, Comparing, and Manipulating Subsets across Multiple Tabular Datasets


Answering questions about complex issues often requires analysts to take into account information contained in multiple interconnected datasets. A common strategy in analyzing and visualizing large and heterogeneous data is to divide the data into meaningful subsets. In a next step, interesting subsets are selected and the associated data as well as the relationships between the subsets are visualized. However, neither the extraction and manipulation, nor the comparison of subsets is well supported by state-of-the-art techniques.
In this paper we present Domino, a novel multiform visualization technique for effectively representing subsets and the relationships between them. By providing comprehensive tools to arrange, combine, and extract subsets, Domino allows users to create both common visualization techniques and advanced visualizations tailored to specific use cases. In addition to the novel technique, we present an implementation that enables analysts to manage the wide range of options that our approach offers. Innovative interactive features such as placeholders and live previews support the rapid creation of complex analysis setups. We introduce the technique and the implementation using a simple example and demonstrate scalability and effectiveness in a use case from the field of cancer genomics.

Gratzl, S., Gehlenborg, N., Lex, A., Pfister, HP. and Streit, M., Domino: Extracting, Comparing, and Manipulating Subsets across Multiple Tabular Datasets, IEEE Transactions on Visualization and Computer Graphics (InfoVis 2014), 2014.

Opening the Black Box: Strategies for Increased User Involvement in Existing Algorithm Implementations


An increasing number of interactive visualization tools stress the integration with computational software like MATLAB and R to access a variety of proven algorithms for many purposes. In many cases, however, the algorithms are used as black boxes that run to completion in isolation which contradicts the needs of interactive data exploration. This paper structures, formalizes, and discusses possibilities to enable user involvement in ongoing computations. Based on a structured characterization of needs regarding intermediate feedback and control, the main contribution is a formalization and comparison of strategies for achieving user involvement for algorithms with different characteristics. In the context of integration, we describe considerations for implementing these strategies either as part of the visualization tool or as part of the algorithm, and we identify requirements and guidelines for the design of algorithmic APIs. To assess the practical applicability, we provide a survey of frequently used algorithm implementations within R regarding the fulfillment of these guidelines. While echoing previous calls for analysis modules which support data exploration more directly, we conclude that a range of pragmatic options for enabling user involvement in ongoing computations exists on both the visualization and algorithm side and should be used.

Mühlbacher, T., Piringer, H., Gratzl, S., Sedlmair, M., and Streit, M., Opening the Black Box: Strategies for Increased User Involvement in Existing Algorithm Implementations, IEEE Transactions on Visualization and Computer Graphics (VAST 2014), 2014.

ConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug Discovery


Large scale data analysis is nowadays a crucial part of drug discovery. Biologists and chemists need to quickly explore and evaluate potentially effective yet safe compounds based on many datasets that are in relationship with each other. However, there is a is a lack of tools that support them in these processes. To remedy this, we developed ConTour, an interactive visual analytics technique that enables the exploration of these complex, multi-relational datasets. At its core ConTour lists all items of each dataset in a column. Relationships between the columns are revealed through interaction: selecting one or multiple items in one column highlights and re-sorts the items in other columns. Filters based on relationships enable drilling down into the large data space. To identify interesting items in the first place, ConTour employs advanced sorting strategies, including strategies based on connectivity strength and uniqueness, as well as sorting based on item attributes. ConTour also introduces interactive nesting of columns, a powerful method to show the related items of a child column for each item in the parent column. Within the columns, ConTour shows rich attribute data about the items as well as information about the connection strengths to other datasets. Finally, ConTour provides a number of detail views, which can show items from multiple datasets and their associated data at the same time. We demonstrate the utility of our system in case studies conducted with a team of chemical biologists, who investigate the effects of chemical compounds on cells and need to understand the underlying mechanisms.

Partl, C., Lex, A., Streit, M., Strobelt, H., Wassermann, AM., Pfister, HP. and Schmalstieg, D., ConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug Discovery, IEEE Transactions on Visualization and Computer Graphics (VAST 2014), 2014.

Furby: Fuzzy Force-Directed Bicluster Visualization


Background: Cluster analysis is widely used to discover patterns in multi-dimensional data. Clustered heatmaps are the standard technique for visualizing one-way and two-way clustering results. In clustered heatmaps, rows and/or columns are reordered, resulting in a representation that shows the clusters as contiguous blocks. However, for biclustering results, where clusters can overlap, it is not possible to reorder the matrix in this way without duplicating rows and/or columns.
Results: We present Furby, an interactive visualization technique for analyzing biclustering results. Our contribution is twofold. First, the technique provides an overview of a biclustering result, showing the actual data that forms the individual clusters together with the information which rows and columns they share. Second, for fuzzy clustering results, the proposed technique additionally enables analysts to interactively set the thresholds that transform the fuzzy (soft) clustering into hard clusters that can then be investigated using heatmaps or bar charts. Changes in the membership value thresholds are immediately reflected in the visualization. We demonstrate the value of Furby by loading biclustering results applied to a multi-tissue dataset into the visualization.
Conclusions: The proposed tool allows analysts to assess the overall quality of a biclustering result. Based on this high-level overview, analysts can then interactively explore the individual biclusters in detail. This novel way of handling fuzzy clustering results also supports analysts in finding the optimal thresholds that lead to the best clusters.

Streit, M., Gratzl, S., Gillhofer, M., Mayr, A., Mitterecker, A. and Hochreiter, S., Furby: Fuzzy Force-Directed Bicluster Visualization, BMC Bioinformatics, 15(Suppl 6):S4, 2014.

Show Me the Invisible: Visualizing Hidden Content


Content on computer screens is often inaccessible to users because it is hidden, e.g., occluded by other windows, outside the viewport, or overlooked. In search tasks, the efficient retrieval of sought content is important. Current software, however, only provides limited support to visualize hidden occurrences and rarely supports search synchronization crossing application boundaries. To remedy this situation, we introduce two novel visualization methods to guide users to hidden content.
Our first method generates awareness for occluded or out-of-viewport content using see-through visualization. For content that is either outside the screen's viewport or for data sources not opened at all, our second method shows off-screen indicators and an on-demand smart preview. To reduce the chances of overlooking content, we use visual links, i.e., visible edges, to connect the visible content or the visible representations of the hidden content. We show the validity of our methods in a user study, which demonstrates that our technique enables a faster localization of hidden content compared to traditional search functionality and thereby assists users in information retrieval tasks.

Geymayer, T., Steinberger, M., Lex, A., Streit, M., and Schmalstieg, D., Show Me the Invisible: Visualizing Hidden Content, ACM SIGCHI Conference on Human Factors in Computing Systems (CHI 2014), 2014.

Characterizing Cancer Subtypes using the Dual Analysis Approach in Caleydo


The comprehensive analysis and characterization of cancer subtypes is an important problem to which significant resources have been devoted in recent years. In this paper we integrate the dual analysis method, which uses statistics to describe both the dimensions and the rows of a high dimensional dataset, into StratomeX, a Caleydo view tailored to cancer subtype analysis. We introduce significant difference plots for showing the elements of a candidate cancer subtype that differ significantly from other subtypes, thus enabling analysts to characterize cancer subtypes. We also enable analysts to investigate how samples relate to the subtype they are assigned and to the other groups. Our approach gives analysts the ability to create well-defined candidate subtypes based on statistical properties. We demonstrate the utility of our approach in three case studies, where we show that we are able to reproduce findings from a published cancer subtype characterization.

Turkay, C., Lex, A., Streit, M., Pfister, HP. and Hauser, H., Characterizing Cancer Subtypes using the Dual Analysis Approach in Caleydo, Computer Graphics and Applications, 34(2), 38-47, 2014

LineUp: Visual Analysis of Multi-Attribute Rankings


Rankings are a popular and universal approach to structure otherwise unorganized collections of items by computing a rank for each item based on the value of one or more of its attributes. This allows us, for example, to prioritize tasks or to evaluate the performance of products relative to each other. While the visualization of a ranking itself is straightforward, its interpretation is not because the rank of an item represents only a summary of a potentially complicated relationship between its attributes and those of the other items. It is also common that alternative rankings exist that need to be compared and analyzed to gain insight into how multiple heterogeneous attributes affect the rankings. Advanced visual exploration tools are needed to make this process efficient. In this paper we present a comprehensive analysis of requirements for the visualization of multi-attribute rankings. Based on these considerations, we propose a novel and scalable visualization technique - LineUp - that uses bar charts. This interactive technique supports the ranking of items based on multiple heterogeneous attributes with different scales and semantics. It enables users to interactively combine attributes and flexibly refine parameters to explore the effect of changes in the attribute combination. This process can be employed to derive actionable insights into which attributes of an item need to be modified in order for its rank to change. Additionally, through integration of slope graphs, LineUp can also be used to compare multiple alternative rankings on the same set of items, for example, over time or across different attribute combinations. We evaluate the effectiveness of the proposed multi-attribute visualization technique in a qualitative study. The study shows that users are able to successfully solve complex ranking tasks in a short period of time.

Gratzl, S., Lex, A., Gehlenborg, N., Pfister, HP. and Streit, M., LineUp: Visual Analysis of Multi-Attribute Rankings, IEEE Transactions on Visualization and Computer Graphics (InfoVis 2013), 19(12), pp. 2277-2286, 2013

Entourage: Visualizing Relationships between Biological Pathways using Contextual Subsets


Biological pathway maps are highly relevant tools for many tasks in molecular biology. They reduce the complexity of the overall biological network by partitioning it into smaller manageable parts. While this reduction of complexity is their biggest strength, it is, at the same time, their biggest weakness. By removing what is deemed not important for the primary function of the pathway, biologists lose the ability to follow and understand cross-talks between pathways. Considering these cross-talks is, however, critical in many analysis scenarios, such as, judging effects of drugs. In this paper we introduce entourage, a novel visualization technique that provides contextual information lost due to the artificial partitioning of the biological network, but at the same time limits the presented information to what is relevant to the analyst's task. We use one pathway map as the focus of an analysis and allow a larger set of contextual pathways. For these context pathways we only show the contextual subsets, i.e., the parts of the graph that are relevant to a selection. Entourage suggests related pathways based on similarities and highlights parts of a pathway that are interesting in terms of mapped experimental data. We visualize interdependencies between pathways using stubs of visual links, which we found effective yet not obtrusive. By combining this approach with visualization of experimental data, we can provide domain experts with a highly valuable tool. We demonstrate the utility of Entourage with case studies conducted with a biochemist who researches the effects of drugs on pathways. We show that the technique is well suited to investigate interdependencies between pathways and to analyze, understand, and predict the effect that drugs have on different cell types.

Lex, A., Partl, C., Kalkofen, D., Streit, M., Gratzl, S., Wassermann, A.M., Schmalstieg, D. and Pfister, HP., Entourage: Visualizing Relationships between Biological Pathways using Contextual Subsets, IEEE Transactions on Visualization and Computer Graphics (InfoVis 2013), 19(12), pp. 2536-2545, 2013

Rendering Gigaray Light Fields


We present a caching framework with a novel probability-based prefetching and eviction strategy applied to atomic cache units that enables interactive rendering of gigaray light fields. Further, we describe two new use cases that are supported by our framework: panoramic light fields, including a robust imaging technique and an appropriate parameterization scheme for real-time rendering and caching; and light-field-cached volume rendering, which supports interactive exploration of large volumetric datasets using light-field rendering. We consider applications such as light-field photography and the visualization of large image stacks from modern scanning microscopes.

Birklbauer, C., Opelt, S. and Bimber, O., Rendering Gigaray Light Fields, In proceedings of Eurographics (Computer Graphics Forum), 32(2), 469-478, 2013

Light-Field Supported Fast Volume Rendering


Advances in imaging technology leads to a continues increase of image data sets. Modern scanning microscopes, for instance, produce image stacks with a megapixel lateral resolution and many hundreds to thousands slices in axial direction. This trend will continue – resulting in very large volumetric data sets that are difficult to explore interactively, since the complexity of volume rendering is proportional to spatial and lateral resolution of the data. Light-field rendering is a fast and simple image-based rendering method that requires pre-computed image data. For volume rendering, each costly computed image is discarded after changing the viewing parameters, while it becomes idle if the viewing parameters are not changed and the visualization does not need to be updated. We combine light-field rendering and volume rendering with two goals: We recycle previously rendered images and use the idle times for filling a cached-managed light field. The final images are then composed from light-field rendering and from volume rendering – depending on the state of the light-field cache. This leads to a significant increase in rendering performance and to the ability of exploring large volumetric datasets interactively.

Birklbauer, C. and Bimber, O., Light-Field Supported Fast Volume Rendering, ACM Siggraph (poster), 2012

enRoute: Dynamic Path Extraction from Biological Pathway Maps for In-Depth Experimental Data Analysis


Pathway maps are an important source of information when analyzing functional implications of experimental data on biological processes. Associating large quantities of data with nodes on a pathway map and allowing in depth-analysis at the same time, however, is a challenging task. While a wide variety of approaches for doing so exist, they either do not scale beyond a few experiments or fail to represent the pathway appropriately. To remedy this, we introduce enRoute, a new approach for interactively exploring experimental data along paths that are dynamically extracted from pathways. By showing an extracted path side-by-side with experimental data, enRoute can present large amounts of data for every pathway node. It can visualize hundreds of samples, dozens of experimental conditions, and even multiple datasets capturing different aspects of a node at the same time. Another important property of this approach is its conceptual compatibility with arbitrary forms of pathways. Most notably, enRoute works well with pathways that are manually created, as they are available in large, public pathway databases. We demonstrate enRoute with pathways from the well-established KEGG database and expression as well as copy number datasets from humans and mice with more than 1,000 experiments at the same time. We validate enRoute in case studies with domain experts, who used enRoute to explore data for glioblastoma multiforme in humans and a model of steatohepatitis in mice.

Partl, C., Lex, A., Streit, M., Kalkofen, D., Kashofer, K. and Schmalstieg, D., enRoute: Dynamic Path Extraction from Biological Pathway Maps for In-Depth Experimental Data Analysis, In proceedings of the IEEE Symposium on Biological Data Visualization (BioVis'12), 2012.

Partl, C., Lex, A., Streit, M., Kalkofen, D., Kashofer, K. and Schmalstieg, D., enRoute: Dynamic Path Extraction from Biological Pathway Maps for Exploring Heterogeneous Experimental Datasets, BMC Bioinformatics, 14(Suppl 19):S3, 2013.

StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization


Identification and characterization of cancer subtypes are important areas of research that are based on the integrated analysis of multiple heterogeneous genomics datasets. Since there are no tools supporting this process, much of this work is done using ad-hoc scripts and static plots, which is inefficient and limits visual exploration of the data. To address this, we have developed StratomeX, an integrative visualization tool that allows investigators to explore the relationships of candidate subtypes across multiple genomic data types such as gene expression, DNA methylation, or copy number data. StratomeX represents datasets as columns and subtypes as bricks in these columns. Ribbons between the columns connect bricks to show subtype relationships across datasets. Drill-down features enable detailed exploration. StratomeX provides insights into the functional and clinical implications of candidate subtypes by employing small multiples, which allow investigators to assess the effect of subtypes on molecular pathways or outcomes such as patient survival. As the configuration of viewing parameters in such a multi-dataset, multi-view scenario is complex, we propose a meta visualization and configuration interface for dataset dependencies and data-view relationships.
StratomeX is developed in close collaboration with domain experts. We describe case studies that illustrate how investigators used the tool to explore subtypes in large datasets and demonstrate how they efficiently replicated findings from the literature and gained new insights into the data.

Lex, A., Streit, M., Schulz, H.-J., Partl, C., Schmalstieg, D., Park, P. J. and Gehlenborg, N., StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization, Computer Graphics Forum (EuroVis 2012), vol. 31, no. 3, pp. 1175-1184, 2012.

Procedural Texture Synthesis for Zoom-Independent Visualization of Multivariate Data


We propose a method for visualizing multivariate data in a view-dependent manner using a synthesized texture. The texture is generated using procedural random-phase Gabor noise and a specially constructed transfer function that is based on statistical properties of the noise. The procedural nature of texture synthesis allows us to alter the noise according to current viewing conditions by modifying its parameters. As a consequence, the textures are alias-free and data values can be interpreted at any scale. We show the applications of our method for displaying multivariate 2D weather data and for encoding additional information on top of a video without using color, thus leaving this communication channel for other purposes. We achieve simultaneous display of color and texture information by modifying the value component using the HSV color model, which allows us to ensure sufficient contrast for texture perception while keeping hue and saturation components intact. We provide the results of a user study, which shows significant advantage of our method over current methods with similar goals.

Klebnikov, R., Kainz, B., Steinberger, M., Streit, M. and Schmalstieg, D., Procedural Texture Synthesis for Zoom-Independent Visualization of Multivariate Data, Computer Graphics Forum (EuroVis'12), vol. 31, no. 3, pp. 1355-1364, 2012.

Model-Driven Design for the Visual Analysis of Heterogeneous Data



As heterogeneous data from different sources are being increasingly linked, it becomes difficult for users to understand how the data are connected, to identify what means are suitable to analyze a given data set, or to find out how to proceed for a given analysis task. We target this challenge with a new model-driven design process that effectively codesigns aspects of data, view, analytics, and tasks. We achieve this by using the workflow of the analysis task as a trajectory through data, interactive views, and analytical processes. The benefits for the analysis session go well beyond the pure selection of appropriate data sets and range from providing orientation or even guidance along a preferred analysis path to a potential overall speedup, allowing data to be fetched ahead of time. We illustrate the design process for a biomedical use case that aims at determining a treatment plan for cancer patients from the visual analysis of a large, heterogeneous clinical data pool. As an example for how to apply the comprehensive design approach, we present Stack’n’flip, a sample implementation which tightly integrates visualizations of the actual data with a map of available data sets, views, and tasks, thus capturing and communicating the analytical workflow through the required data sets.

Streit, M., Schulz, H.-J., Lex, A., Schmalstieg, D. and Schumann, H., Model-Driven Design for the Visual Analysis of Heterogeneous Data,
IEEE Transactions on Visualization and Computer Graphics, vol. 18, no. 6, pp.998-1010, 2012.

Visualizing Uncertainty in Biological Expression Data


Expression analysis of ∼omics data using microarrays has become a standard procedure in the life sciences. However, microarrays are subject to technical limitations and errors, which render the data gathered likely to be uncertain. While a number of approaches exist to target this uncertainty statistically, it is hardly ever even shown when the data is visualized using for example clustered heatmaps. Yet, this is highly useful when trying not to omit data that is “good enough” for an analysis, which otherwise would be discarded as too unreliable by established conservative thresholds. Our approach addresses this shortcoming by first identifying the margin above the error threshold of uncertain, yet possibly still useful data. It then displays this uncertain data in the context of the valid data by enhancing a clustered heatmap. We employ different visual representations for the different kinds of uncertainty involved. Finally, it lets the user interactively adjust the thresholds, giving visual feedback in the heatmap representation, so that an informed choice on which thresholds to use can be made instead of applying the usual rule-of-thumb cut-offs. We exemplify the usefulness of our concept by giving details for a concrete use case from our partners at the Medical University of Graz, thereby demonstrating our implementation of the general approach.

Holzhüter, C., Lex, A., Schmalstieg, D., Schulz H.-J., Schumann, H. and Streit, M., Visualizing Uncertainty in Biological Expression Data, In proceedings of the SPIE Conference on Visualization and Data Analysis (VDA'12), 2012.

Light-Field Caching


With the continuously increasing sensor resolutions of cameras, light field imaging is becoming a more and more practical extension to conventional digital photography. It complements postprocessing by synthetic aperture control, refocusing, as well as perspective and field-of-view changes. For being a true alternative to classical 2D imaging, however, the spatial resolution of light fields must be in the same megapixel-order as the resolution of today’s digital images. The additional angular resolution must also be adequately high to prevent sampling artifacts (in particular for synthetic re-focussing). This will quickly cause gigabytes rather than megabytes of data that have to be rendered with limited graphics memory. We describe a light-field caching framework that makes it possible to render very large light fields in real-time.

Opelt, S. and Bimber, O., Light-Field Caching, ACM Siggraph (poster), 2011

 

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