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HiPiler: visual exploration of Large Genome Interaction Matrices with Interactive Small Multiples

IEEE TRANSACTIONS ON visualIZATION AND COMPUTER GRAPHICS 2018年第1期24卷 522-531页

作者： Lekschas, Fritz Bach, Benjamin Kerpedjiev, Peter Gehlenborg, Nils Pfister, Hanspeter Harvard Univ Cambridge MA 02138 USA Harvard Med Sch Boston MA USA

This paper presents an interactive visualization interface HiPiler for the exploration and visualization of regions-of-interest in large genome interaction matrices. Genome interaction matrices approximate the physical distance of pairs of regions on the genome to each other and can contain up to 3 million rows and columns with many sparse regions. Regions of interest (ROls) can be defined, e.g., by sets of adjacent rows and columns, or by specific visual patterns in the matrix. However, traditional matrix aggregation or pan-and-zoom interfaces fail in supporting search, inspection, and comparison of ROls in such large matrices. In HiPiler, ROls are first-class objects, represented as thumbnail-like "snippets". Snippets can be interactively explored and grouped or laid out automatically in scatterplots, or through dimension reduction methods. Snippets are linked to the entire navigable genome interaction matrix through brushing and linking. The design of HiPiler is based on a series of semi-structured interviews with 10 domain experts involved in the analysis and interpretation of genome interaction matrices. We describe six exploration tasks that are crucial for analysis of interaction matrices and demonstrate how HiPiler supports these tasks. We report on a user study with a series of data exploration sessions with domain experts to assess the usability of HiPiler as well as to demonstrate respective findings in the data.

关键词： Interactive Small Multiples Matrix Comparison Biomedical visualization Genomics

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Building assessment with sub-pixel accuracy using satellite imagery

Building assessment with sub-pixel accuracy using satellite ...

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conference on visual data exploration and analysis III

作者： Meng, J Davenport, M MACDONALD DETTWILER & ASSOCIATES LTD RICHMONDBC V6V 2J3CANADA

ISBN: (纸本)0819420301

This paper describes a semi-automated building assessment method (SABAM) for estimating building edges with sub-pixel accuracy. The semi-automated approach is based on an earlier manual point method which determined building height using shadow length analysis. The manual method was then semi-automated using a sub-pixel edge detection algorithm to obtain more precise building edges and reduce human interpretation. Edge locations have been evaluated to within 1/100th of a pixel using gradient descent.

关键词： building analysis sub-pixel accuracy satellite imagery shadow analysis

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visual exploration of Local Interest Points in Sets of Time Series

Visual Exploration of Local Interest Points in Sets of Time ...

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IEEE conference on visual Analytics Science and Technology (vAST)

作者： Schreck, Tobias Sharalieva, Lyubka Wanner, Franz Bernard, Juergen Ruppert, Tobias von Landesberger, Tatiana Bustos, Benjamin Univ Konstanz Constance Germany

ISBN: (纸本)9781467347532;9781467347525

visual analysis of time series data is an important, yet challenging task with many application examples in fields such as financial or news stream data analysis. Many visual time series analysis approaches consider a global perspective on the time series. Fewer approaches consider visual analysis of local patterns in time series, and often rely on interactive specification of the local area of interest. We present initial results of an approach that is based on automatic detection of local interest points. We follow an overview-first approach to find useful parameters for the interest point detection, and details-on-demand to relate the found patterns. We present initial results and detail possible extensions of the approach.

关键词： time series data Time series visual analytics Corner detection SETTING automatic detection visualization exploration news

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Prefetching for visual data exploration 8

Prefetching for visual data exploration

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8th International conference on database Systems for Advanced Applications

作者： Doshi, PR Rundensteiner, EA Ward, MO Worcester Polytech Inst Dept Comp Sci Worcester MA 01609 USA

ISBN: (纸本)0769518958

Modern computer applications, from business decision support to scientific data analysis, utilize data visualization tools to support exploratory activities. visual exploration tools typically do not scale well when applied to huge data sets, partially because being interactive necessitates real-time responses. However we observe that interactive visual explorations exhibit several properties that can be exploited for data access optimization, including locality of exploration, contiguous queries, and significant delays between user operations. We thus apply semantic caching of active query sets on the client side to exploit some of the above characteristics. We also introduce several prefetching strategies, each exploiting characteristics of our visual exploration environment. We have incorporated caching and prefetching strategies into XmdvTool, a public-domain tool for visual exploration of multivariate data sets. Experimental studies using synthetic as well as real user traces are conducted. Our results demonstrate that these proposed optimization techniques achieve significant performance improvements in our exploratory analysis system.

关键词： Computer applications Computer science data analysis data visualization Delay Marketing and sales Navigation Performance analysis Prefetching Stock markets

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Annotations in Different Steps of visual Analytics 16

Annotations in Different Steps of Visual Analytics

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16th International Joint conference on Computer vision, Imaging and Computer Graphics Theory and Applications (vISIGRAPP) / 12th International conference on Information visualization Theory and Applications (IvAPP)

作者： Schmidt, Christoph Grundel, Bastian Schumann, Heidrun Rosenthal, Paul Univ Rostock Inst Visual & Analyt Comp Rostock Germany Ernst Moritz Arndt Univ Greifswald Eye Care Ctr Greifswald Germany

ISBN: (纸本)9789897584886

Annotations in visual Analytics (vA) have become a common means to support the analysis by integrating additional information into the vA system. Here, annotations often differ between the individual steps of vA. For example, during data preprocessing it may be necessary to add information on the data, such as redundancy or discrepancy information, while annotations, used during exploration, often refer to the externalization of findings and insights. Describing the particular needs for these step-dependent annotations is challenging. To tackle this issue, we examine the data preprocessing, data cleansing, and data exploration steps for the analysis of heterogeneous and error prone data in respect to the design of specific annotations. By that, we describe their peculiarities for each step in the analysis, and thus aim to improve the visual analytics approach on clinical data. We show the applicability of our annotation concept by integrating it into an existing visual analytics tool to analyze and annotate data from the ophthalmic domain. In interviews and application sessions with experts, we assess the usefulness of our annotation concept for the analysis of the visual acuity development for patients, undergoing a specific therapy.

关键词： Annotation visual Analytics Heterogeneous Clinical data data Preprocessing data Cleansing data exploration

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Fast training of Self Organizing Maps for the visual exploration of molecular compounds

Fast training of Self Organizing Maps for the visual explora...

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International Joint conference on Neural Networks

作者： Fiannaca, Antonino Di Fatta, Giuseppe Rizzo, Riccardo Urso, Alfonso Gaglio, Salvatore CNR ICAR I-00185 Rome Italy Univ Reading Sch Syst Engn Reading Berks England Univ Palermo DINFO Palermo Italy

ISBN: (纸本)9781424413799

visual exploration of scientific data in life science area is a growing research field due to the large amount of available data. The Kohonen's Self Organizing Map (SOM) is a widely used tool for visualization of multidimensional data. In this paper we present a fast learning algorithm for SOMs that uses a simulated annealing method to adapt the learning parameters. The algorithm has been adopted in a data analysis framework for the generation of similarity maps. Such maps provide an effective tool for the visual exploration of large and multi-dimensional input spaces. The approach has been applied to data generated during the High Throughput Screening of molecular compounds;the generated maps allow a visual exploration of molecules with similar topological properties. The experimental analysis on real world data from the National Cancer Institute shows the speed up of the proposed SOM training process in comparison to a traditional approach. The resulting visual landscape groups molecules with similar chemical properties in densely connected regions.

关键词： Self organizing maps

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Fly wing asymmetry: A case study in visualization

Fly wing asymmetry: A case study in Visualization

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conference on visual data exploration and analysis v

作者： Buchanan, JW Ferry, P McIntyre, G veryovka, O Univ Alberta Dept Comp Sci Edmonton AB T6G 2H1 Canada

ISBN: (纸本)0819427381

There are many visualization systems available to the scientific community. Unfortunately the use of such systems is not as wide spread as we would like. The visualization of a scientist's data involves expertise from the scientist and the visualizing expert. In this paper we document the interaction between a scientist and a team of graphics people. We discuss why standard visualization systems were not used and we present our prototype system for fly-wing asymmetry visualization In Biology organismal symmetry or lack thereof is being used as a measure of the quality of life forms. In this paper we present a system that was designed to facilitate the analysis of fly-wing data. The data used in this visualization was collected to test the hypothesis that old mothers produce lower quality offspring than young mothers. Thirteen landmarks at wing vein intersections were digitized three times on each wing and analyzed for asymmetry. The system that we present here complements the statistical analysis tools that are used for the formal analysis. In particular, our system has helped the scientist find outliers and gain an intuition for the data that has helped him decide which statistical analysis to perform.

关键词： visualization Statistical analysis Prototyping visual analytics Computing systems Organisms veins Biological research Biology Quality measurement

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Waltz - An exploratory visualization tool for volume data, using multiform abstract displays

Waltz - An exploratory visualization tool for volume data, u...

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conference on visual data exploration and analysis v

作者： Roberts, JC Univ Kent Comp Lab Canterbury Kent England

ISBN: (纸本)0819427381

Although, visualization is now widely used, misinterpretations still occur. There are three primary solutions intended to aid a user interpret data correctly. These are: displaying the data in different forms (Multiform visualization);simplifying (or abstracting) the structure of the viewed information;and linking objects and views together (allowing corresponding objects to be jointly manipulated and interrogated). These well-known visualization techniques, provide an emphasis towards the visualization display. We believe however that current visualization systems do not effectively utilise the display, for example, often placing it at the end of a long visualization process. Our visualization system, based on an adapted visualization model, allows a display method to be used throughout the visualization process, in which the user operates a 'Display (correlate) and Refine' visualization cycle. This display integration provides a useful exploration environment, where objects and views may be directly manipulated;a set of 'portions of interest' can be selected to generate a specialized dataset. This may subsequently be further displayed, manipulated and filtered.

关键词： visualization visualization system multiform manipulation abstraction

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visually Exploring Transportation Schedules

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IEEE TRANSACTIONS ON visualIZATION AND COMPUTER GRAPHICS 2016年第1期22卷 170-179页

作者： Palomo, Cesar Guo, Zhan Silva, Claudio T. Freire, Juliana NYU New York NY 10003 USA

Public transportation schedules are designed by agencies to optimize service quality under multiple constraints. However, real service usually deviates from the plan. Therefore, transportation analysts need to identify, compare and explain both eventual and systemic performance issues that must be addressed so that better timetables can be created. The purely statistical tools commonly used by analysts pose many difficulties due to the large number of attributes at trip- and station-level for planned and real service. Also challenging is the need for models at multiple scales to Search for patterns at different times and stations, since analysts do not know exactly where or when relevant patterns might emerge and need to compute statistical summaries for multiple attributes at different granularities. To aid in this analysis, we worked in close collaboration with a transportation expert to design TR-EX, a visual exploration tool developed to identify, inspect and compare spatio-temporal patterns for planned and real transportation service. TR-EX combines two new visual encodings inspired by Marey's Train Schedule: Trips Explorer for trip-level analysis of frequency, deviation and speed;and Stops Explorer for station-level study of delay, wait time, reliability and performance deficiencies such as bunching. To tackle overplotting and to provide a robust representation for a large numbers of trips and stops at multiple scales, the system supports variable kernel bandwidths to achieve the level of detail required by users for different tasks. We justify our design decisions based on specific analysis needs of transportation analysts. We provide anecdotal evidence of the efficacy of TR-EX through a series of case studies that explore NYC subway service, which illustrate how TR-EX can be used to confirm hypotheses and derive new insights through visual exploration.

关键词： Transportation schedules kernel density estimation visual exploration

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Matches, Mismatches, and Methods: Multiple-view Workflows for Energy Portfolio analysis

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IEEE TRANSACTIONS ON visualIZATION AND COMPUTER GRAPHICS 2016年第1期22卷 449-458页

作者： Brehmer, Matthew Ng, Jocelyn Tate, Kevin Munzner, Tamara Univ British Columbia Vancouver BC V5Z 1M9 Canada EnerNOC Inc Boston MA USA

The energy performance of large building portfolios is challenging to analyze and monitor, as current analysis tools are not scalable or they present derived and aggregated data at too coarse of a level. We conducted a visualization design study, beginning with a thorough work domain analysis and a characterization of data and task abstractions. We describe generalizable visual encoding design choices for time-oriented data framed in terms of matches and mismatches, as well as considerations for workflow design. Our designs address several research questions pertaining to scalability, view coordination, and the inappropriateness of line charts for derived and aggregated data due to a combination of data semantics and domain convention. We also present guidelines relating to familiarity and trust, as well as methodological considerations for visualization design studies. Our designs were adopted by our collaborators and incorporated into the design of an energy analysis software application that will be deployed to tens of thousands of energy workers in their client base.

关键词： Design study design methodologies time series data task and requirements analysis coordinated and multiple views

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