Sebastian Bremm

Space-in-time and time-in-space self-organizing maps for exploring spatiotemporal patterns

Spatiotemporal data pose serious challenges to analysts in geographic and other domains. Owing to the complexity of the geospatial and temporal components, this kind of data cannot be analyzed by fully automatic methods but require the involvement of the human analysts expertise. For a comprehensive analysis, the data need to be considered from two complementary perspectives: (1) as spatial distributions (situations) changing over time and (2) as profiles of local temporal variation distributed over space. In order to support the visual analysis of spatiotemporal data, we suggest a framework based on the “Self‐Organizing Map” (SOM) method combined with a set of interactive visual tools supporting both analytic perspectives. SOM can be considered as a combination of clustering and dimensionality reduction. In the first perspective, SOM is applied to the spatial situations at different time moments or intervals. In the other perspective, SOM is applied to the local temporal evolution profiles. The integrated visual analytics environment includes interactive coordinated displays enabling various transformations of spatiotemporal data and post‐processing of SOM results. The SOM matrix display offers an overview of the groupings of data objects and their two‐dimensional arrangement by similarity. This view is linked to a cartographic map display, a time series graph, and a periodic pattern view. The linkage of these views supports the analysis of SOM results in both the spatial and temporal contexts. The variable SOM grid coloring serves as an instrument for linking the SOM with the corresponding items in the other displays. The framework has been validated on a large dataset with real city traffic data, where expected spatiotemporal patterns have been successfully uncovered. We also describe the use of the framework for discovery of previously unknown patterns in 41‐years time series of 7 crime rate attributes in the states of the USA.

Interactive visual comparison of multiple trees

Traditionally, the visual analysis of hierarchies, respectively, trees, is conducted by focusing on one given hierarchy. However, in many research areas multiple, differing hierarchies need to be analyzed simultaneously in a comparative way - in particular to highlight differences between them, which sometimes can be subtle. A prominent example is the analysis of so-called phylogenetic trees in biology, reflecting hierarchical evolutionary relationships among a set of organisms. Typically, the analysis considers multiple phylogenetic trees, either to account for statistical significance or for differences in derivation of such evolutionary hierarchies; for example, based on different input data, such as the 16S ribosomal RNA and protein sequences of highly conserved enzymes. The simultaneous analysis of a collection of such trees leads to more insight into the evolutionary process. We introduce a novel visual analytics approach for the comparison of multiple hierarchies focusing on both global and local structures. A new tree comparison score has been elaborated for the identification of interesting patterns. We developed a set of linked hierarchy views showing the results of automatic tree comparison on various levels of details. This combined approach offers detailed assessment of local and global tree similarities. The approach was developed in close cooperation with experts from the evolutionary biology domain. We apply it to a phylogenetic data set on bacterial ancestry, demonstrating its application benefit.

Techniques for precision-based visual analysis of projected data

The analysis of high-dimensional data is an important, yet inherently difficult problem. Projection techniques such as Principal Component Analysis, Multi-dimensional Scaling and Self-Organizing Map can be used to map high-dimensional data to 2D display space. However, projections typically incur a loss in information. Often, uncertainty exists regarding the precision of the projection as compared with its original data characteristics. While the output quality of these projection techniques can be discussed in terms of aggregate numeric error values, visualization is often helpful for better understanding the projection results. We address the visual assessment of projection precision by an approach integrating an appropriately designed projection precision measure directly into the projection visualization. To this end, a flexible projection precision measure is defined that allows the user to balance the degree of locality at which the measure is evaluated. Several visual mappings are designed for integrating the precision measure into the projection visualization at various levels of abstraction. The techniques are implemented in an interactive system, including methods supporting the user in finding appropriate settings of relevant parameters. We demonstrate the usefulness of the approach for visual analysis of classified and unclassified high-dimensional data sets. We show how our interactive precision quality visualization system helps to examine the preservation of original data properties in projected space.

Visual analytics methods for categoric spatio-temporal data

We focus on visual analysis of space- and time-referenced categorical data, which describe possible states of spatial (geographical) objects or locations and their changes over time. The analysis of these data is difficult as there are only limited possibilities to analyze the three aspects (location, time and category) simultaneously. We present a new approach which interactively combines (a) visualization of categorical changes over time; (b) various spatial data displays; (c) computational techniques for task-oriented selection of time steps. They provide an expressive visualization with regard to either the overall evolution over time or unusual changes. We apply our approach on two use cases demonstrating its usefulness for a wide variety of tasks. We analyze data from movement tracking and meteorologic areas. Using our approach, expected events could be detected and new insights were gained.

Assisted descriptor selection based on visual comparative data analysis

Exploration and selection of data descriptors representing objects using a set of features are important components in many data analysis tasks. Usually, for a given dataset, an optimal data description does not exist, as the suitable data representation is strongly use case dependent. Many solutions for selecting a suitable data description have been proposed. In most instances, they require data labels and often are black box approaches. Non‐expert users have difficulties to comprehend the coherency of input, parameters, and output of these algorithms. Alternative approaches, interactive systems for visual feature selection, overburden the user with an overwhelming set of options and data views. Therefore, it is essential to offer the users a guidance in this analytical process. In this paper, we present a novel system for data description selection, which facilitates the users access to the data analysis process. As finding of suitable data description consists of several steps, we support the user with guidance. Our system combines automatic data analysis with interactive visualizations. By this, the system provides a recommendation for suitable data descriptor selections. It supports the comparison of data descriptors with differing dimensionality for unlabeled data. We propose specialized scores and interactive views for descriptor comparison. The visualization techniques are scatterplot‐based and grid‐based. For the latter case, we apply Self‐Organizing Maps as adaptive grids which are well suited for large multi‐dimensional data sets. As an example, we demonstrate the usability of our system on a real‐world biochemical application.

A framework for using self-organising maps to analyse spatio-temporal patterns, exemplified by analysis of mobile phone usage

We suggest a visual analytics framework for the exploration and analysis of spatially and temporally referenced values of numeric attributes. The framework supports two complementary perspectives on spatio-temporal data: as a temporal sequence of spatial distributions of attribute values (called spatial situations) and as a set of spatially referenced time series of attribute values representing local temporal variations. To handle a large amount of data, we use the self-organising map (SOM) method, which groups objects and arranges them according to similarity of relevant data features. We apply the SOM approach to spatial situations and to local temporal variations and obtain two types of SOM outcomes, called space-in-time SOM and time-in-space SOM, respectively. The examination and interpretation of both types of SOM outcomes are supported by appropriate visualisation and interaction techniques. This article describes the use of the framework by an example scenario of data analysis. We also discuss how the framework can be extended from supporting explorative analysis to building predictive models of the spatio-temporal variation of attribute values. We apply our approach to phone call data showing its usefulness in real-world analytic scenarios.

Visual Analytics for model-based medical image segmentation: Opportunities and challenges

Segmentation of medical images is a prerequisite in clinical practice. Many segmentation algorithms use statistical shape models. Due to the lack of tools providing prior information on the data, standard models are frequently used. However, they do not necessarily describe the data in an optimal way. Model-based segmentation can be supported by Visual Analytics tools, which give the user a deeper insight into the correspondence between data and model result. Combining both approaches, better models for segmentation of organs in medical images are created. In this work, we identify the main tasks and problems in model-based image segmentation. As a proof of concept, we show that already small visual-interactive extensions can be very beneficial. Based on these results, we present research challenges for Visual Analytics in this area.

Computing and visually analyzing mutual information in molecular co-evolution

BackgroundSelective pressure in molecular evolution leads to uneven distributions of amino acids and nucleotides. In fact one observes correlations among such constituents due to a large number of biophysical mechanisms (folding properties, electrostatics, ...). To quantify these correlations the mutual information -after proper normalization - has proven most effective. The challenge is to navigate the large amount of data, which in a study for a typical protein cannot simply be plotted.ResultsTo visually analyze mutual information we developed a matrix visualization tool that allows different views on the mutual information matrix: filtering, sorting, and weighting are among them. The user can interactively navigate a huge matrix in real-time and search e.g., for patterns and unusual high or low values. A computation of the mutual information matrix for a sequence alignment in FASTA-format is possible. The respective stand-alone program computes in addition proper normalizations for a null model of neutral evolution and maps the mutual information to Z-scores with respect to the null model.ConclusionsThe new tool allows to compute and visually analyze sequence data for possible co-evolutionary signals. The tool has already been successfully employed in evolutionary studies on HIV1 protease and acetylcholinesterase. The functionality of the tool was defined by users using the tool in real-world research. The software can also be used for visual analysis of other matrix-like data, such as information obtained by DNA microarray experiments. The package is platform-independently implemented in Java and free for academic use under a GPL license.

ClustNails: Visual analysis of subspace clusters

Subspace clustering addresses an important problem in clustering multi-dimensional data. In sparse multi-dimensional data, many dimensions are irrelevant and obscure the cluster boundaries. Subspace clustering helps by mining the clusters present in only locally relevant subsets of dimensions. However, understanding the result of subspace clustering by analysts is not trivial. In addition to the grouping information, relevant sets of dimensions and overlaps between groups, both in terms of dimensions and records, need to be analyzed. We introduce a visual subspace cluster analysis system called ClustNails. It integrates several novel visualization techniques with various user interaction facilities to support navigating and interpreting the result of subspace clustering. We demonstrate the effectiveness of the proposed system by applying it to the analysis of real world data and comparing it with existing visual subspace cluster analysis systems.

Visual analysis of contagion in networks

Contagion is a process whereby the collapse of a node in a network leads to the collapse of neighboring nodes and thereby sets off a chain reaction in the network. It thus creates a special type of time-dependent network. Such processes are studied in various applications, for example, in financial network analysis, infection diffusion prediction, supply-chain management, or gene regulation. Visual analytics methods can help analysts examine contagion effects. For this purpose, network visualizations need to be complemented with specific features to illustrate the contagion process. Moreover, new visual analysis techniques for comparison of contagion need to be developed. In this paper, we propose a system geared to the visual analysis of contagion. It includes the simulation of contagion effects as well as their visual exploration. We present new tools able to compare the evolution of the different contagion processes. In this way, propagation of disturbances can be effectively analyzed. We focus on financial networks; however, our system can be applied to other use cases as well.