Sequence Surveyor: leveraging overview for scalable genomic alignment visualization

In this paper, we introduce overview visualization tools for large-scale multiple genome alignment data. Genome alignment visualization and, more generally, sequence alignment visualization are an important tool for understanding genomic sequence data. As sequencing techniques improve and more data become available, greater demand is being placed on visualization tools to scale to the size of these new datasets. When viewing such large data, we necessarily cannot convey details, rather we specifically design overview tools to help elucidate large-scale patterns. Perceptual science, signal processing theory, and generality provide a framework for the design of such visualizations that can scale well beyond current approaches. We present Sequence Surveyor, a prototype that embodies these ideas for scalable multiple whole-genome alignment overview visualization. Sequence Surveyor visualizes sequences in parallel, displaying data using variable color, position, and aggregation encodings. We demonstrate how perceptual science can inform the design of visualization techniques that remain visually manageable at scale and how signal processing concepts can inform aggregation schemes that highlight global trends, outliers, and overall data distributions as the problem scales. These techniques allow us to visualize alignments with over 100 whole bacterial-sized genomes.     

平行散点图:基于GPU的可视化分析方法

提出一种分析多维数据集之间关系的信息可视化方法--平行散点图.结合平行坐标、散点图方法,综合了焦点 背景、多视角、多视图、刷子等交互与可视化策略,使人有效地观察与分析多维数据集之间的连接关系;利用统一渲染GPU对粒子、线段、公告牌等的绘制与输出功能,在千万级数据集上达到较强的深度感与交互级的绘制性能;提出GPU上基于空间填充曲线的聚类算法,可交互式地降低连接线的视觉杂乱度;将连接、聚类与可视化整合为一个基于GPU的系统,在千万级数据集上达到交互级的可视化分析.     

Visualizing a Sequence of a Thousand Graphs (or Even More)

The visualization of dynamic graphs demands visually encoding at least three major data dimensions: vertices, edges, and time steps. Many of the state‐of‐the‐art techniques can show an overview of vertices and edges but lack a data‐scalable visual representation of the time aspect. In this paper, we address the problem of displaying dynamic graphs with a thousand or more time steps. Our proposed interleaved parallel edge splatting technique uses a time‐to‐space mapping and shows the complete dynamic graph in a static visualization. It provides an overview of all data dimensions, allowing for visually detecting time‐varying data patterns; hence, it serves as a starting point for further data exploration. By applying clustering and ordering techniques on the vertices, edge splatting on the links, and a dense time‐to‐space mapping, our approach becomes visually scalable in all three dynamic graph data dimensions. We illustrate the usefulness of our technique by applying it to call graphs and US domestic flight data with several hundred vertices, several thousand edges, and more than a thousand time steps.     

Cycle Plot Revisited: Multivariate Outlier Detection Using a Distance‐Based Abstraction

The cycle plot is an established and effective visualization technique for identifying and comprehending patterns in periodic time series, like trends and seasonal cycles. It also allows to visually identify and contextualize extreme values and outliers from a different perspective. Unfortunately, it is limited to univariate data. For multivariate time series, patterns that exist across several dimensions are much harder or impossible to explore. We propose a modified cycle plot using a distance‐based abstraction (Mahalanobis distance) to reduce multiple dimensions to one overview dimension and retain a representation similar to the original. Utilizing this distance‐based cycle plot in an interactive exploration environment, we enhance the Visual Analytics capacity of cycle plots for multivariate outlier detection. To enable interactive exploration and interpretation of outliers, we employ coordinated multiple views that juxtapose a distance‐based cycle plot with Cleveland's original cycle plots of the underlying dimensions. With our approach it is possible to judge the outlyingness regarding the seasonal cycle in multivariate periodic time series.     

Measuring Privacy and Utility in Privacy‐Preserving Visualization

In previous work, we proposed a technique for preserving the privacy of quasi‐identifiers in sensitive data when visualized using parallel coordinates. This paper builds on that work by introducing a number of metrics that can be used to assess both the level of privacy and the amount of utility that can be gained from the resulting visualizations. We also generalize our approach beyond parallel coordinates to scatter plots and other visualization techniques. Privacy preservation generally entails a trade‐off between privacy and utility: the more the data are protected, the less useful the visualization. Using a visually‐oriented approach, we can provide a higher amount of utility than directly applying data anonymization techniques used in data mining. To demonstrate this, we use the visual uncertainty framework for systematically defining metrics based on cluster artifacts and information theoretic principles. In a case study, we demonstrate the effectiveness of our technique as compared to standard data‐based clustering in the context of privacy‐preserving visualization.     

Time‐Series Plots Integrated in Parallel‐Coordinates Displays

We present a natural extension of two‐dimensional parallel‐coordinates plots for revealing relationships in time‐dependent multi‐attribute data by building on the idea that time can be considered as the third dimension. A time slice through the visualization represents a certain point in time and can be viewed as a regular parallel‐coordinates display. A vertical slice through one of the axes of the parallel‐coordinates display would show a time‐series plot. For a focus‐and‐context Integration of both views, we embed time‐series plots between two adjacent axes of the parallel‐coordinates plot. Both time‐series plots are drawn using a pseudo three‐dimensional perspective with a single vanishing point. An independent parallel‐coordinates panel that connects the two perspectively displayed time‐series plots can move forward and backward in time to reveal changes in the relationship between the time‐dependent attributes. The visualization of time‐series plots in the context of the parallel‐coordinates plot facilitates the exploration of time‐related aspects of the data without the need to switch to a separate display. We provide a consistent set of tools for selecting and contrasting subsets of the data, which are important for various application domains.     

Visual Coherence for Large‐Scale Line‐Plot Visualizations

Displaying a large number of lines within a limited amount of screen space is a task that is common to many different classes of visualization techniques such as time‐series visualizations, parallel coordinates, link‐node diagrams, and phase‐space diagrams. This paper addresses the challenging problems of cluttering and overdraw inherent to such visualizations. We generate a 2×2 tensor field during line rasterization that encodes the distribution of line orientations through each image pixel. Anisotropic diffusion of a noise texture is then used to generate a dense, coherent visualization of line orientation. In order to represent features of different scales, we employ a multi‐resolution representation of the tensor field. The resulting technique can easily be applied to a wide variety of line‐based visualizations. We demonstrate this for parallel coordinates, a time‐series visualization, and a phase‐space diagram. Furthermore, we demonstrate how to integrate a focus+context approach by incorporating a second tensor field. Our approach achieves interactive rendering performance for large data sets containing millions of data items, due to its image‐based nature and ease of implementation on GPUs. Simulation results from computational fluid dynamics are used to evaluate the performance and usefulness of the proposed method.     

Angular histograms: frequency-based visualizations for large, high dimensional data

Parallel coordinates is a popular and well-known multivariate data visualization technique. However, one of their inherent limitations has to do with the rendering of very large data sets. This often causes an overplotting problem and the goal of the visual information seeking mantra is hampered because of a cluttered overview and non-interactive update rates. In this paper, we propose two novel solutions, namely, angular histograms and attribute curves. These techniques are frequency-based approaches to large, high-dimensional data visualization. They are able to convey both the density of underlying polylines and their slopes. Angular histogram and attribute curves offer an intuitive way for the user to explore the clustering, linear correlations and outliers in large data sets without the over-plotting and clutter problems associated with traditional parallel coordinates. We demonstrate the results on a wide variety of data sets including real-world, high-dimensional biological data. Finally, we compare our methods with the other popular frequency-based algorithms.     

平行坐标及其在聚类分析中的应用

平行坐标对多维数据的表达是数据可视化的重要方法之一。它实现了多维数据在二维平面上的表示。利用平行坐标对数据进行分析处理的技术已经取得了很大的进展,如刷(Brushing)技术、交换坐标轴、抽象等。这些分析技术已经应用到数据挖掘的很多领域,尤其在聚类分析中,平行坐标对数据集的定性分析使聚类结果的合理性得到证明。     

基于图像变形技术的平行坐标可视化

针对传统的平行坐标可视化方法不适于处理大量高维数据等不足,将基于控制点的图像变形技术引入到可视化中,首先利用学习集中的数据建立控制点到目标点的变形函数,求出方程的参数,再将测试集中的数据通过变形函数映射到平行坐标系中,实验结果表明,通过图像变形原理能较好地实现高维数据的分类和可视化效果,优于传统的平行坐标方法。     

基于平行坐标的贝叶斯可视化分类方法

结合信息可视化与机器学习技术,提出一种基于多元数据平行坐标图表示的贝叶斯可视化分类方法。该方法基于类条件概率密度估计对平行坐标图表示进行优化,最后对变换后的各变量值加权求和,用贝叶斯法则分类。这种方法通过平行坐标来使不可见的数据和算法变得可见,从而易于利用专家领域知识,分类结果容易理解,特别适合应用到疾病诊断等医学领域的模式识别问题。     

一种针对类别数据分析的平行坐标改进方法

针对类别数据在传统平行坐标系中的映射重叠问题，提出类别统计和数据累积式偏移映射的平行坐标改进方法。该方法首先统计多维数据中的各类别数据的频次，使用直方图表示其记录数，将直方图与平行坐标相结合提出改进平行坐标。然后提出一种类别数据的数据累积式偏移算法，将映射在一点的数据均匀分布在坐标轴上的一定区域中，区域的范围根据数据记录数确定。最后设计实现可视化分析系统，通过改进平行坐标实现对数据集的筛选、条件交叉分析、类别间数据分析和维度间数据分析；通过联动视图和弦图两种方式实现每两个维度间的对比分析；通过字云显示每一维度的频次分布。案例数据集实验结果表明，该方法能在平行坐标中实现各维度中类别间的对比、各维度中记录数排序，以及对筛选数据集的分析，展示类别型数据维度间的关联关系。     

Brushing dimensions--a dual visual analysis model for high-dimensional data

In many application fields, data analysts have to deal with datasets that contain many expressions per item. The effective analysis of such multivariate datasets is dependent on the user's ability to understand both the intrinsic dimensionality of the dataset as well as the distribution of the dependent values with respect to the dimensions. In this paper, we propose a visualization model that enables the joint interactive visual analysis of multivariate datasets with respect to their dimensions as well as with respect to the actual data values. We describe a dual setting of visualization and interaction in items space and in dimensions space. The visualization of items is linked to the visualization of dimensions with brushing and focus+context visualization. With this approach, the user is able to jointly study the structure of the dimensions space as well as the distribution of data items with respect to the dimensions. Even though the proposed visualization model is general, we demonstrate its application in the context of a DNA microarray data analysis.     

A Visual Analysis Approach for Community Detection of Multi-Context Mobile Social Networks

The problem of detecting community structures of a social network has been extensively studied over recent years, but most existing methods solely rely on the network structure and neglect the context information of the social relations.The main reason is that a context-rich network offers too much flexibility and complexity for automatic or manual modulation of the multifaceted context in the analysis process.We address the challenging problem of incorporating context information into the community analysis with a novel visual analysis mechanism.Our approach consists of two stages: interactive discovery of salient context, and iterative context-guided community detection.Central to the analysis process is a context relevance model (CRM) that visually characterizes the influence of a given set of contexts on the variation of the detected communities, and discloses the community structure in specific context configurations.The extracted relevance is used to drive an iterative visual reasoning process, in which the community structures are progressively discovered.We introduce a suite of visual representations to encode the community structures, the context as well as the CRM.In particular, we propose an enhanced parallel coordinates representation to depict the context and community structures, which allows for interactive data exploration and community investigation.Case studies on several datasets demonstrate the efficiency and accuracy of our approach.     

MultiClusterTree: Interactive Visual Exploration of Hierarchical Clusters in Multidimensional Multivariate Data

Visual analytics of multidimensional multivariate data is a challenging task because of the difficulty in understanding metrics in attribute spaces with more than three dimensions. Frequently, the analysis goal is not to look into individual records but to understand the distribution of the records at large and to find clusters of records with similar attribute values. A large number of (typically hierarchical) clustering algorithms have been developed to group individual records to clusters of statistical significance. However, only few visualization techniques exist for further exploring and understanding the clustering results. We propose visualization and interaction methods for analyzing individual clusters as well as cluster distribution within and across levels in the cluster hierarchy. We also provide a clustering method that operates on density rather than individual records. To not restrict our search for clusters, we compute density in the given multidimensional multivariate space. Clusters are formed by areas of high density. We present an approach that automatically computes a hierarchical tree of high density clusters. To visually represent the cluster hierarchy, we present a 2D radial layout that supports an intuitive understanding of the distribution structure of the multidimensional multivariate data set. Individual clusters can be explored interactively using parallel coordinates when being selected in the cluster tree. Furthermore, we integrate circular parallel coordinates into the radial hierarchical cluster tree layout, which allows for the analysis of the overall cluster distribution. This visual representation supports the comprehension of the relations between clusters and the original attributes. The combination of the 2D radial layout and the circular parallel coordinates is used to overcome the overplotting problem of parallel coordinates when looking into data sets with many records. We apply an automatic coloring scheme based on the 2D radial layout of the hierarchical cluster tree encoding hue, saturation, and value of the HSV color space. The colors support linking the 2D radial layout to other views such as the standard parallel coordinates or, in case data is obtained from multidimensional spatial data, the distribution in object space.     

鲁棒最小二乘孪生支持向量机及其稀疏算法

最小二乘孪生支持向量机通过求解两个线性规划问题来代替求解复杂的二次规划问题,具有计算简单和训练速度快的优势。然而,最小二乘孪生支持向量机得到的超平面易受异常点影响且解缺乏稀疏性。针对这一问题,基于截断最小二乘损失提出了一种鲁棒最小二乘孪生支持向量机模型,并从理论上验证了模型对异常点具有鲁棒性。为使模型可处理大规模数据,基于表示定理和不完全Cholesky分解得到了新模型的稀疏解,并提出了适合处理带异常点的大规模数据的稀疏鲁棒最小二乘孪生支持向量机算法。数值实验表明,新算法比已有算法分类准确率、稀疏性、收敛速度分别提高了1.97%~37.7%、26~199倍和6.6~2 027.4倍。     

Multifield-graphs: an approach to visualizing correlations in multifield scalar data

We present an approach to visualizing correlations in 3D multifield scalar data. The core of our approach is the computation of correlation fields, which are scalar fields containing the local correlations of subsets of the multiple fields. While the visualization of the correlation fields can be done using standard 3D volume visualization techniques, their huge number makes selection and handling a challenge. We introduce the Multifield-Graph to give an overview of which multiple fields correlate and to show the strength of their correlation. This information guides the selection of informative correlation fields for visualization. We use our approach to visually analyze a number of real and synthetic multifield datasets.     

Coherent time-varying graph drawing with multifocus+context interaction

We present a new approach for time-varying graph drawing that achieves both spatiotemporal coherence and multifocus+context visualization in a single framework. Our approach utilizes existing graph layout algorithms to produce the initial graph layout, and formulates the problem of generating coherent time-varying graph visualization with the focus+context capability as a specially tailored deformation optimization problem. We adopt the concept of the super graph to maintain spatiotemporal coherence and further balance the needs for aesthetic quality and dynamic stability when interacting with time-varying graphs through focus+context visualization. Our method is particularly useful for multifocus+context visualization of time-varying graphs where we can preserve the mental map by preventing nodes in the focus from undergoing abrupt changes in size and location in the time sequence. Experiments demonstrate that our method strikes a good balance between maintaining spatiotemporal coherence and accentuating visual foci, thus providing a more engaging viewing experience for the users.     

A Multi‐task Comparative Study on Scatter Plots and Parallel Coordinates Plots

Previous empirical studies for comparing parallel coordinates plots and scatter plots showed some uncertainty about their relative merits. Some of these studies focused on the task of value retrieval, where visualization usually has a limited advantage over reading data directly. In this paper, we report an empirical study that compares user performance, in terms of accuracy and response time, in the context of four different visualization tasks, namely value retrieval, clustering, outlier detection, and change detection. In order to evaluate the relative merits of the two types of plots with a common base line (i.e., reading data directly), we included three forms of stimuli, data tables, scatter plots, and parallel coordinate plots. Our results show that data tables are better suited for the value retrieval task, while parallel coordinates plots generally outperform the two other visual representations in three other tasks. Subjective feedbacks from the users are also consistent with the quantitative analyses. As visualization is commonly used for aiding multiple observational and analytical tasks, our results provided new evidence to support the prevailing enthusiasm for parallel coordinates plots in the field of visualization.