Interactive Visualization Approach Research Articles

My Corporis Fabrica: an ontology-based tool for reasoning and querying on complex anatomical models.

BackgroundMultiple models of anatomy have been developed independently and for different purposes. In particular, 3D graphical models are specially useful for visualizing the different organs composing the human body, while ontologies such as FMA (Foundational Model of Anatomy) are symbolic models that provide a unified formal description of anatomy. Despite its comprehensive content concerning the anatomical structures, the lack of formal descriptions of anatomical functions in FMA limits its usage in many applications. In addition, the absence of connection between 3D models and anatomical ontologies makes it difficult and time-consuming to set up and access to the anatomical content of complex 3D objects.ResultsFirst, we provide a new ontology of anatomy called My Corporis Fabrica (MyCF), which conforms to FMA but extends it by making explicit how anatomical structures are composed, how they contribute to functions, and also how they can be related to 3D complex objects. Second, we have equipped MyCF with automatic reasoning capabilities that enable model checking and complex queries answering. We illustrate the added-value of such a declarative approach for interactive simulation and visualization as well as for teaching applications.ConclusionsThe novel vision of ontologies that we have developed in this paper enables a declarative assembly of different models to obtain composed models guaranteed to be anatomically valid while capturing the complexity of human anatomy. The main interest of this approach is its declarativity that makes possible for domain experts to enrich the knowledge base at any moment through simple editors without having to change the algorithmic machinery. This provides MyCF software environment a flexibility to process and add semantics on purpose for various applications that incorporate not only symbolic information but also 3D geometric models representing anatomical entities as well as other symbolic information like the anatomical functions.

GlyphLink: An interactive visualization approach for semantic graphs

Graph analysis by data visualization involves achieving a series of topology-based tasks. When the graph data belongs to a data domain that contains multiple node and link types, as in the case of semantic graphs, topology-based tasks become more challenging. To reduce visual complexity in semantic graphs, we propose an approach which is based on applying relational operations such as selecting and joining nodes of different types. We use node aggregation to reflect the relational operations to the graph. We introduce glyphs for representing aggregated nodes. Using glyphs lets us encode connectivity information of multiple nodes with a single glyph. We also use visual parameters of the glyph to encode node attributes or type specific information. Rather than doing the operations in the data abstraction layer and presenting the user with the resulting visualization, we propose an interactive approach where the user can iteratively apply the relational operations directly on the visualization. We present the efficiency of our method by the results of a usability study that includes a case study on a subset of the International Movie Database. The results of the controlled experiment in our usability study indicate a statistically significant contribution in reducing the completion time of the evaluation tasks.

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

BackgroundSystem-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes/proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. While many enrichment analysis tools and gene-set libraries databases have been developed, there is still room for improvement.ResultsHere, we present Enrichr, an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. We applied Enrichr to analyze nine cancer cell lines by comparing their enrichment signatures to the enrichment signatures of matched normal tissues. We observed a common pattern of up regulation of the polycomb group PRC2 and enrichment for the histone mark H3K27me3 in many cancer cell lines, as well as alterations in Toll-like receptor and interlukin signaling in K562 cells when compared with normal myeloid CD33+ cells. Such analyses provide global visualization of critical differences between normal tissues and cancer cell lines but can be applied to many other scenarios.ConclusionsEnrichr is an easy to use intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists. Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr.

Adaptive visualization for exploratory information retrieval

As the volume and breadth of online information is rapidly increasing, ad hoc search systems become less and less efficient to answer information needs of modern users. To support the growing complexity of search tasks, researchers in the field of information developed and explored a range of approaches that extend the traditional ad hoc retrieval paradigm. Among these approaches, personalized search systems and exploratory search systems attracted many followers. Personalized search explored the power of artificial intelligence techniques to provide tailored search results according to different user interests, contexts, and tasks. In contrast, exploratory search capitalized on the power of human intelligence by providing users with more powerful interfaces to support the search process. As these approaches are not contradictory, we believe that they can re-enforce each other. We argue that the effectiveness of personalized search systems may be increased by allowing users to interact with the system and learn/investigate the problem in order to reach the final goal. We also suggest that an interactive visualization approach could offer a good ground to combine the strong sides of personalized and exploratory search approaches. This paper proposes a specific way to integrate interactive visualization and personalized search and introduces an adaptive visualization based search system Adaptive VIBE that implements it. We tested the effectiveness of Adaptive VIBE and investigated its strengths and weaknesses by conducting a full-scale user study. The results show that Adaptive VIBE can improve the precision and the productivity of the personalized search system while helping users to discover more diverse sets of information.

Understanding ecosystem services trade-offs with interactive procedural modeling for sustainable urban planning

Given the accelerating rate of urbanization worldwide, the sustainable provision of urban ecosystem services becomes increasingly important for the growing number of city dwellers. Attempts to increase a single ecosystem service however often lead to reduction or losses of others. For making sound decisions about sustainable urban development, knowledge and awareness of the interactions between ecosystem services are thus necessary. In this paper, we show how interactive rulers embedded in a 3D GIS-based procedural modeling environment can assist in making urban ecosystem services trade-offs explicit for sustainable urban planning. The interactive rulers are slider bars that offer stakeholders the possibility to explore trade-offs in ecosystem services reflected in different urban designs. The approach is illustrated in a case study in Abu Dhabi, Masdar City, a new city designed from scratch. An interactive 3D visualization approach links parametric shape grammars for the design of generative urban patterns and the reporting of urban ecosystem services. We show how various urban design scenarios can be generated in an interactive manner allowing a balance between the esthetics of the urban designs and a set of indicators describing the provision of relevant ecosystem services. With this approach, the space for actions and behavioral alternatives become explicit – a crucial step for sustainable urban planning which calls for innovative strategies to adapt to these uncertain and rapid changes.

PRM75 Parallel Sets as Interactive Visualization Approach for Analyzing Markov Models

PRM75 Parallel Sets as Interactive Visualization Approach for Analyzing Markov Models

Spark: A navigational paradigm for genomic data exploration

Biologists possess the detailed knowledge critical for extracting biological insight from genome-wide data resources, and yet they are increasingly faced with nontrivial computational analysis challenges posed by genome-scale methodologies. To lower this computational barrier, particularly in the early data exploration phases, we have developed an interactive pattern discovery and visualization approach, Spark, designed with epigenomic data in mind. Here we demonstrate Spark's ability to reveal both known and novel epigenetic signatures, including a previously unappreciated binding association between the YY1 transcription factor and the corepressor CTBP2 in human embryonic stem cells.

Interactive Ray Tracing of Large Models Using Voxel Hierarchies

AbstractWe propose an efficient approach for interactive visualization of massive models with CPU ray tracing. A voxel‐based hierarchical level‐of‐detail (LOD) framework is employed to minimize rendering time and required system memory. In a pre‐processing phase, a compressed out‐of‐core data structure is constructed, which contains the original primitives of the model and the LOD voxels, organized into a kd‐tree. During rendering, data is loaded asynchronously to ensure a smooth inspection of the model regardless of the available I/O bandwidth. With our technique, we are able to explore data sets consisting of hundreds of millions of triangles in real‐time on a desktop PC with a quad‐core CPU.

Interactive, Graph-based Visual Analysis of High-dimensional, Multi-parameter Fluorescence Microscopy Data in Toponomics

In Toponomics, the function protein pattern in cells or tissue (the toponome) is imaged and analyzed for applications in toxicology, new drug development and patient-drug-interaction. The most advanced imaging technique is robot-driven multi-parameter fluorescence microscopy. This technique is capable of co-mapping hundreds of proteins and their distribution and assembly in protein clusters across a cell or tissue sample by running cycles of fluorescence tagging with monoclonal antibodies or other affinity reagents, imaging, and bleaching in situ. The imaging results in complex multi-parameter data composed of one slice or a 3D volume per affinity reagent. Biologists are particularly interested in the localization of co-occurring proteins, the frequency of co-occurrence and the distribution of co-occurring proteins across the cell. We present an interactive visual analysis approach for the evaluation of multi-parameter fluorescence microscopy data in toponomics. Multiple, linked views facilitate the definition of features by brushing multiple dimensions. The feature specification result is linked to all views establishing a focus+context visualization in 3D. In a new attribute view, we integrate techniques from graph visualization. Each node in the graph represents an affinity reagent while each edge represents two co-occurring affinity reagent bindings. The graph visualization is enhanced by glyphs which encode specific properties of the binding. The graph view is equipped with brushing facilities. By brushing in the spatial and attribute domain, the biologist achieves a better understanding of the function protein patterns of a cell. Furthermore, an interactive table view is integrated which summarizes unique fluorescence patterns. We discuss our approach with respect to a cell probe containing lymphocytes and a prostate tissue section.

MetSign: a computational platform for high-resolution mass spectrometry-based metabolomics.

Data analysis in metabolomics is currently a major challenge, particularly when large sample sets are analyzed. Herein, we present a novel computational platform entitled MetSign for high-resolution mass spectrometry-based metabolomics. By converting the instrument raw data into mzXML format as its input data, MetSign provides a suite of bioinformatics tools to perform raw data deconvolution, metabolite putative assignment, peak list alignment, normalization, statistical significance tests, unsupervised pattern recognition, and time course analysis. MetSign uses a modular design and an interactive visual data mining approach to enable efficient extraction of useful patterns from data sets. Analysis steps, designed as containers, are presented with a wizard for the user to follow analyses. Each analysis step might contain multiple analysis procedures and/or methods and serves as a pausing point where users can interact with the system to review the results, to shape the next steps, and to return to previous steps to repeat them with different methods or parameter settings. Analysis of metabolite extract of mouse liver with spiked-in acid standards shows that MetSign outperforms the existing publically available software packages. MetSign has also been successfully applied to investigate the regulation and time course trajectory of metabolites in hepatic liver.

Flowstrates: An Approach for Visual Exploration of Temporal Origin‐Destination Data

AbstractMany origin‐destination datasets have become available in the recent years, e.g. flows of people, animals, money, material, or network traffic between pairs of locations, but appropriate techniques for their exploration still have to be developed. Especially, supporting the analysis of datasets with a temporal dimension remains a significant challenge. Many techniques for the exploration of spatio‐temporal data have been developed, but they prove to be only of limited use when applied to temporal origin‐destination datasets. We present Flowstrates, a new interactive visualization approach in which the origins and the destinations of the flows are displayed in two separate maps, and the changes over time of the flow magnitudes are represented in a separate heatmap view in the middle. This allows the users to perform spatial visual queries, focusing on different regions of interest for the origins and destinations, and to analyze the changes over time provided with the means of flow ordering, filtering and aggregation in the heatmap. In this paper, we discuss the challenges associated with the visualization of temporal origin‐destination data, introduce our solution, and present several usage scenarios showing how the tool we have developed supports them.

Interactive 3D visualization for wireless sensor networks

Wireless sensor networks open up a new realm of ubiquitous computing applications based on distributed large-scale data collection by embedded sensor nodes that are wirelessly connected and seamlessly integrated within the environment. 3D visualization of sensory data is a challenging issue, however, due to the large number of sensors used in typical deployments, continuous data streams, and constantly varying network topology. This paper describes a practical approach for interactive 3D visualization of wireless sensor network data. A regular 3D grid is reconstructed using scattered sensor data points and used to generate view-dependent 2D slices that are consequently rendered with commodity graphics hardware leading to smooth visualization over space and time. Furthermore, the use of efficient space partitioning data structures and the independent processing of sensor data points facilitates interactive rendering for large number of sensors while accommodating constantly changing network topology. The practical value of the proposed method is demonstrated and results obtained for visualizing time-varying temperature distributions in an urban area are presented.

ActiviTree: Interactive Visual Exploration of Sequences in Event-Based Data Using Graph Similarity

The identification of significant sequences in large and complex event-based temporal data is a challenging problem with applications in many areas of today's information intensive society. Pure visual representations can be used for the analysis, but are constrained to small data sets. Algorithmic search mechanisms used for larger data sets become expensive as the data size increases and typically focus on frequency of occurrence to reduce the computational complexity, often overlooking important infrequent sequences and outliers. In this paper we introduce an interactive visual data mining approach based on an adaptation of techniques developed for web searching, combined with an intuitive visual interface, to facilitate user-centred exploration of the data and identification of sequences significant to that user. The search algorithm used in the exploration executes in negligible time, even for large data, and so no pre-processing of the selected data is required, making this a completely interactive experience for the user. Our particular application area is social science diary data but the technique is applicable across many other disciplines.

Interactive Visual Analysis of Perfusion Data

Perfusion data are dynamic medical image data which characterize the regional blood flow in human tissue. These data bear a great potential in medical diagnosis, since diseases can be better distinguished and detected at an earlier stage compared to static image data. The wide-spread use of perfusion data is hampered by the lack of efficient evaluation methods. For each voxel, a time-intensity curve characterizes the enhancement of a contrast agent. Parameters derived from these curves characterize the perfusion and have to be integrated for diagnosis. The diagnostic evaluation of this multi-field data is challenging and time-consuming due to its complexity. For the visual analysis of such datasets, feature-based approaches allow to reduce the amount of data and direct the user to suspicious areas. We present an interactive visual analysis approach for the evaluation of perfusion data. For this purpose, we integrate statistical methods and interactive feature specification. Correlation analysis and Principal Component Analysis (PCA) are applied for dimensionreduction and to achieve a better understanding of the inter-parameter relations. Multiple, linked views facilitate the definition of features by brushing multiple dimensions. The specification result is linked to all views establishing a focus+context style of visualization in 3D. We discuss our approach with respect to clinical datasets from the three major application areas: ischemic stroke diagnosis, breast tumor diagnosis, as well as the diagnosis of the coronary heart disease (CHD). It turns out that the significance of perfusion parameters strongly depends on the individual patient, scanning parameters, and data pre-processing.

An Interactive Ontology Visualization Approach for the Networked Home Environment

Ontologies are broadly used in the context of networked home environments. With ontologies it is possible to define and store context information, as well as to model different kinds of physical environments. Ontologies are central to networked home environments as they carry the meaning. However, ontologies and the OWL language is complex. Several ontology visualization approaches have been developed to enhance the understanding of ontologies. The domain of networked home environments sets some special requirements for the ontology visualization approach. The visualization tool presented here, visualizes ontologies in a domain- specific way. It represents effectively the physical structures and spatial relationships of networked home environments. In addition, it provides extensive interaction possibilities for editing and manipulating the visualization. The tool shortens the gap from beginner to intermediate OWL ontology reader by visualizing instances in their actual locations and making OWL ontologies more interesting and concrete, and above all easier to comprehend. Keywords—Ontologies, visualization, interaction.

The multimod application framework: A rapid application development tool for computer aided medicine

This paper describes a new application framework (OpenMAF) for rapid development of multimodal applications in computer-aided medicine. MAF applications are multimodal in data, in representation, and in interaction. The framework supports almost any type of biomedical data, including DICOM datasets, motion-capture recordings, or data from computer simulations (e.g. finite element modeling). The interactive visualization approach (multimodal display) helps the user interpret complex datasets, providing multiple representations of the same data. In addition, the framework allows multimodal interaction by supporting the simultaneous use of different input–output devices like 3D trackers, stereoscopic displays, haptics hardware and speech recognition/synthesis systems. The Framework has been designed to run smoothly even on limited power computers, but it can take advantage of all hardware capabilities. The Framework is based on a collection of portable libraries and it can be compiled on any platform that supports OpenGL, including Windows, MacOS X and any flavor of Unix/linux.

Visualization and Analysis of Large Data Collections: a Case Study Applied to Confocal Microscopy Data

In this paper we propose an approach in which interactive visualization and analysis are combined with batch tools for the processing of large data collections. Large and heterogeneous data collections are difficult to analyze and pose specific problems to interactive visualization. Application of the traditional interactive processing and visualization approaches as well as batch processing encounter considerable drawbacks for such large and heterogeneous data collections due to the amount and type of data. Computing resources are not sufficient for interactive exploration of the data and automated analysis has the disadvantage that the user has only limited control and feedback on the analysis process. In our approach, an analysis procedure with features and attributes of interest for the analysis is defined interactively. This procedure is used for off-line processing of large collections of data sets. The results of the batch process along with "visual summaries" are used for further analysis. Visualization is not only used for the presentation of the result, but also as a tool to monitor the validity and quality of the operations performed during the batch process. Operations such as feature extraction and attribute calculation of the collected data sets are validated by visual inspection. This approach is illustrated by an extensive case study, in which a collection of confocal microscopy data sets is analyzed.

CareVis: Integrated visualization of computerized protocols and temporal patient data

Currently, visualization support for patient data analysis is mostly limited to the representation of directly measured data. Contextual information on performed treatment steps is an important source to find reasons and explanations for certain phenomena in the measured patient data, but is mostly spared out in the analysis process. This work aims to fill this gap via integrating classical data visualization and visualization of treatment information. We considered temporal as well as logical data aspects and applied a user-centered development approach that was guided by user input gathered via a user study, design reviews, and prototype evaluations. Furthermore, we investigated the novel PlanningLine glyph, that is used to represent plans in the temporal domain, via a comparative empirical user study. Our interactive visualization approach CareVis provides multiple simultaneous views to cover different aspects of the complex underlying data structure of treatment plans and patient data. The tightly coupled views use visualization methods well-known to domain experts and are designed to facilitate users' tasks. The views are based on the concepts of clinical algorithm maps and LifeLines which have been extended in order to cope with the powerful and expressive plan representation language Asbru. Initial feedback of physicians was encouraging and is accompanied by empirical evidence which verifies that PlanningLines are well suited to manage temporal uncertainty. The interactive integration of different visualization methods forms a novel way of combining, relating, and analyzing different kinds of medical data and information that otherwise would be separated.

H-MDS: a new approach for interactive visualization with multidimensional scaling in the hyperbolic space

We introduce a novel projection-based visualization method for high-dimensional data sets by combining concepts from MDS and the geometry of the hyperbolic spaces. This approach hyperbolic multi-dimensional scaling (H-MDS) is a synthesis of two important concepts for explorative data analysis and visualization: (i) multi-dimensional scaling uses proximity or pair distance data to generate a low-dimensional, spatial presentation of the data; (ii) previous work on the “hyperbolic tree browser” demonstrated the extraordinary advantages for an interactive display of graph-like data in the two-dimensional hyperbolic space ( H 2) . In the new approach, H-MDS maps proximity data directly into the H 2 . This removes the restriction to “quasi-hierarchical”, graph-based data—a major limitation of (ii). Since a suitable distance function can convert all kinds of data to proximity (or distance-based) data, this type of data can be considered the most general. We review important properties of the hyperbolic space and, in particular, the circular Poincaré model of the H 2 . It enables effective human–computer interaction: by mouse dragging the “focus”, the user can navigate in the data without loosing the context. In H 2 the “fish-eye” behavior originates not simply by a non-linear view transformation but rather by extraordinary, non-Euclidean properties of the H 2 . Especially, the exponential growth of length and area of the underlying space makes the H 2 a prime target for mapping hierarchical and (now also) high-dimensional data. Several high-dimensional mapping examples including synthetic and real-world data are presented. Since high-dimensional data produce “ring”-shaped displays, we present methods to enhance the display by modulating the dissimilarity contrast. This is demonstrated for an application for unstructured text: i.e., by using multiple film critiques from news:rec.art.movies.reviews and www.imdb.com, each movie is placed within the H 2 —creating a “space of movies” for interactive exploration.

Registration and alignment of three-dimensional images: an interactive visual approach.

A three-dimensional registration and alignment algorithm was developed to align single photon emission computed tomography examinations and magnetic resonance images. Operators manipulated images interactively with real-time visual feedback, with use of both internal and surface features to achieve accurate alignment. Operators aligned five brain phantom examinations (accuracy, 1.6 pixels; consistency, 0.7 pixels) and eight patient brain examinations (consistency, 0.5 pixels).