While clustering is one of the most popular methods for data mining, analysts lack adequate tools for quick, iterative clustering analysis, which is essential for hypothesis generation and data reasoning. We introduce Clustrophile, an interactive tool for iteratively computing discrete and continuous data clusters, rapidly exploring different choices of clustering parameters, and reasoning about clustering instances in relation to data dimensions. Clustrophile combines three basic visualizations -- a table of raw datasets, a scatter plot of planar projections, and a matrix diagram (heatmap) of discrete clusterings -- through interaction and intermediate visual encoding. Clustrophile also contributes two spatial interaction techniques, @math and @math , and a visualization method, @math , for reasoning about two-dimensional projections obtained through dimensionality reductions.
When analyzing multidimensional, quantitative data, the comparison of two or more groups of dimensions is a common task. Typical sources of such data are experiments in biology, physics or engineering, which are conducted in different configurations and use replicates to ensure statistically significant results. One common way to analyze this data is to filter it using statistical methods and then run clustering algorithms to group similar values. The clustering results can be visualized using heat maps, which show differences between groups as changes in color. However, in cases where groups of dimensions have an a priori meaning, it is not desirable to cluster all dimensions combined, since a clustering algorithm can fragment continuous blocks of records. Furthermore, identifying relevant elements in heat maps becomes more difficult as the number of dimensions increases. To aid in such situations, we have developed Matchmaker, a visualization technique that allows researchers to arbitrarily arrange and compare multiple groups of dimensions at the same time. We create separate groups of dimensions which can be clustered individually, and place them in an arrangement of heat maps reminiscent of parallel coordinates. To identify relations, we render bundled curves and ribbons between related records in different groups. We then allow interactive drill-downs using enlarged detail views of the data, which enable in-depth comparisons of clusters between groups. To reduce visual clutter, we minimize crossings between the views. This paper concludes with two case studies. The first demonstrates the value of our technique for the comparison of clustering algorithms. In the second, biologists use our system to investigate why certain strains of mice develop liver disease while others remain healthy, informally showing the efficacy of our system when analyzing multidimensional data containing distinct groups of dimensions. Abstract This paper describes Cluster Sculptor, a novel interactive clustering system that allows a user to iteratively update the cluster labels of a data set, and an associated low-dimensional projection. The system is fed by clustering results computed in a high-dimensional space, and uses a two-dimensional (2D) projection, both as support for overlaying the cluster labels, and engaging user interaction. By easily interacting with elements directly in the visualization, the user can inject his or her domain knowledge progressively. Via interactive controls, the distribution of the data in the 2D space can be used to amend the cluster labels. Reciprocally, the 2D projection can be updated so as to emphasize the current clusters. The 2D projection updates follow a smooth physical metaphor that gives insight of the process to the user. Updates can be interrupted any time, for further data inspection, or modifying the input preferences. The interest of the system is demonstrated by detailed experimental scenarios on three real data sets. To date, work in microarrays, sequenced genomes and bioinformatics has focused largely on algorithmic methods for processing and manipulating vast biological data sets. Future improvements will likely provide users with guidance in selecting the most appropriate algorithms and metrics for identifying meaningful clusters-interesting patterns in large data sets, such as groups of genes with similar profiles. Hierarchical clustering has been shown to be effective in microarray data analysis for identifying genes with similar profiles and thus possibly with similar functions. Users also need an efficient visualization tool, however, to facilitate pattern extraction from microarray data sets. The Hierarchical Clustering Explorer integrates four interactive features to provide information visualization techniques that allow users to control the processes and interact with the results. Thus, hybrid approaches that combine powerful algorithms with interactive visualization tools will join the strengths of fast processors with the detailed understanding of domain experts. Visual-interactive cluster analysis provides valuable tools for effectively analyzing large and complex data sets. Due to desirable properties and an inherent predisposition for visualization, the Kohonen Feature Map (or self-organizing map, or SOM) algorithm is among the most popular and widely used visual clustering techniques. However, the unsupervised nature of the algorithm may be disadvantageous in certain applications. Depending on initialization and data characteristics, cluster maps (cluster layouts) may emerge that do not comply with user preferences, expectations, or the application context. Considering SOM-based analysis of trajectory data, we propose a comprehensive visual-interactive monitoring and control framework extending the basic SOM algorithm. The framework implements the general Visual Analytics idea to effectively combine automatic data analysis with human expert supervision. It provides simple, yet effective facilities for visually monitoring and interactively controlling the trajectory clustering process at arbitrary levels of detail. The approach allows the user to leverage existing domain knowledge and user preferences, arriving at improved cluster maps. We apply the framework on a trajectory clustering problem, demonstrating its potential in combining both unsupervised (machine) and supervised (human expert) processing, in producing appropriate cluster results. Cluster analysis (CA) is a powerful strategy for the exploration of high-dimensional data in the absence of a-priori hypotheses or data classification models, and the results of CA can then be used to form such models. But even though formal models and classification rules may not exist in these data exploration scenarios, domain scientists and experts generally have a vast amount of non-compiled knowledge and intuition that they can bring to bear in this effort. In CA, there are various popular mechanisms to generate the clusters, however, the results from their non- supervised deployment rarely fully agree with this expert knowledge and intuition. To this end, our paper describes a comprehensive and intuitive framework to aid scientists in the derivation of classification hierarchies in CA, using k-means as the overall clustering engine, but allowing them to tune its parameters interactively based on a non-distorted compact visual presentation of the inherent characteristics of the data in high- dimensional space. These include cluster geometry, composition, spatial relations to neighbors, and others. In essence, we provide all the tools necessary for a high-dimensional activity we call cluster sculpting, and the evolving hierarchy can then be viewed in a space-efficient radial dendrogram. We demonstrate our system in the context of the mining and classification of a large collection of millions of data items of aerosol mass spectra, but our framework readily applies to any high-dimensional CA scenario.