The Effect of Edge Bundling and Seriation on Sensemaking of Biclusters in Bipartite Graphs

Biclustering data analysis: a comprehensive survey

Biclustering, the simultaneous clustering of rows and columns of a data matrix, has proved its effectiveness in bioinformatics due to its capacity to produce local instead of global models, evolving from a key technique used in gene expression data analysis into one of the most used approaches for pattern discovery and identification of biological modules, used in both descriptive and predictive learning tasks. This survey presents a comprehensive overview of biclustering. It proposes an updated taxonomy for its fundamental components (bicluster, biclustering solution, biclustering algorithms, and evaluation measures) and applications. We unify scattered concepts in the literature with new definitions to accommodate the diversity of data types (such as tabular, network, and time series data) and the specificities of biological and biomedical data domains. We further propose a pipeline for biclustering data analysis and discuss practical aspects of incorporating biclustering in real-world applications. We highlight prominent application domains, particularly in bioinformatics, and identify typical biclusters to illustrate the analysis output. Moreover, we discuss important aspects to consider when choosing, applying, and evaluating a biclustering algorithm. We also relate biclustering with other data mining tasks (clustering, pattern mining, classification, triclustering, N-way clustering, and graph mining). Thus, it provides theoretical and practical guidance on biclustering data analysis, demonstrating its potential to uncover actionable insights from complex datasets.

Towards Systematic Design Considerations for Visualizing Cross-View Data Relationships

Due to the scale of data and the complexity of analysis tasks, insight discovery often requires coordinating multiple visualizations (views), with each view displaying different parts of data or the same data from different perspectives. For example, to analyze car sales records, a marketing analyst uses a line chart to visualize the trend of car sales, a scatterplot to inspect the price and horsepower of different cars, and a matrix to compare the transaction amounts in types of deals. To explore related information across multiple views, current visual analysis tools heavily rely on brushing and linking techniques, which may require a significant amount of user effort (e.g., many trial-and-error attempts). There may be other efficient and effective ways of displaying cross-view data relationships to support data analysis with multiple views, but currently there are no guidelines to address this design challenge. In this article, we present systematic design considerations for visualizing cross-view data relationships, which leverages descriptive aspects of relationships and usable visual context of multi-view visualizations. We discuss pros and cons of different designs for showing cross-view data relationships, and provide a set of recommendations for helping practitioners make design decisions.

Understanding Missing Links in Bipartite Networks With MissBiN

The analysis of bipartite networks is critical in a variety of application domains, such as exploring entity co-occurrences in intelligence analysis and investigating gene expression in bio-informatics. One important task is missing link prediction, which infers the existence of unseen links based on currently observed ones. In this article, we propose a visual analysis system, MissBiN, to involve analysts in the loop for making sense of link prediction results. MissBiN equips a novel method for link prediction in a bipartite network by leveraging the information of bi-cliques in the network. It also provides an interactive visualization for understanding the algorithm outputs. The design of MissBiN is based on three high-level analysis questions (what, why, and how) regarding missing links, which are distilled from the literature and expert interviews. We conducted quantitative experiments to assess the performance of the proposed link prediction algorithm, and interviewed two experts from different domains to demonstrate the effectiveness of MissBiN as a whole. We also provide a comprehensive usage scenario to illustrate the usefulness of the tool in an application of intelligence analysis.

SightBi: Exploring Cross-View Data Relationships with Biclusters

Multiple-view visualization (MV) has been heavily used in visual analysis tools for sensemaking of data in various domains (e.g., bioinformatics, cybersecurity and text analytics). One common task of visual analysis with multiple views is to relate data across different views. For example, to identify threats, an intelligence analyst needs to link people from a social network graph with locations on a crime-map, and then search for and read relevant documents. Currently, exploring cross-view data relationships heavily relies on view-coordination techniques (e.g., brushing and linking), which may require significant user effort on many trial-and-error attempts, such as repetitiously selecting elements in one view, and then observing and following elements highlighted in other views. To address this, we present SightBi, a visual analytics approach for supporting cross-view data relationship explorations. We discuss the design rationale of SightBi in detail, with identified user tasks regarding the use of cross-view data relationships. SightBi formalizes cross-view data relationships as biclusters, computes them from a dataset, and uses a bi-context design that highlights creating stand-alone relationship-views. This helps preserve existing views and offers an overview of cross-view data relationships to guide user exploration. Moreover, SightBi allows users to interactively manage the layout of multiple views by using newly created relationship-views. With a usage scenario, we demonstrate the usefulness of SightBi for sensemaking of cross-view data relationships.

Auditing the Sensitivity of Graph-based Ranking with Visual Analytics

Graph mining plays a pivotal role across a number of disciplines, and a variety of algorithms have been developed to answer who/what type questions. For example, what items shall we recommend to a given user on an e-commerce platform? The answers to such questions are typically returned in the form of a ranked list, and graph-based ranking methods are widely used in industrial information retrieval settings. However, these ranking algorithms have a variety of sensitivities, and even small changes in rank can lead to vast reductions in product sales and page hits. As such, there is a need for tools and methods that can help model developers and analysts explore the sensitivities of graph ranking algorithms with respect to perturbations within the graph structure. In this paper, we present a visual analytics framework for explaining and exploring the sensitivity of any graph-based ranking algorithm by performing perturbation-based what-if analysis. We demonstrate our framework through three case studies inspecting the sensitivity of two classic graph-based ranking algorithms (PageRank and HITS) as applied to rankings in political news media and social networks.