Combining computational analyses and interactive visualization for document exploration and sensemaking in jigsaw

A Model for Types and Levels of Automation in Visual Analytics: A Survey, a Taxonomy, and Examples

The continuous growth in availability and access to data presents a major challenge to the human analyst. As the manual analysis of large and complex datasets is nowadays practically impossible, the need for assisting tools that can automate the analysis process while keeping the human analyst in the loop is imperative. A large and growing body of literature recognizes the crucial role of automation in Visual Analytics and suggests that automation is among the most important constituents for effective Visual Analytics systems. Today, however, there is no appropriate taxonomy nor terminology for assessing the extent of automation in a Visual Analytics system. In this article, we aim to address this gap by introducing a model of levels of automation tailored for the Visual Analytics domain. The consistent terminology of the proposed taxonomy could provide a ground for users/readers/reviewers to describe and compare automation in Visual Analytics systems. Our taxonomy is grounded on a combination of several existing and well-established taxonomies of levels of automation in the human-machine interaction domain and relevant models within the visual analytics field. To exemplify the proposed taxonomy, we selected a set of existing systems from the event-sequence analytics domain and mapped the automation of their visual analytics process stages against the automation levels in our taxonomy.

MedChemLens: An Interactive Visual Tool to Support Direction Selection in Interdisciplinary Experimental Research of Medicinal Chemistry

Interdisciplinary experimental science (e.g., medicinal chemistry) refers to the disciplines that integrate knowledge from different scientific backgrounds and involve experiments in the research process. Deciding "in what direction to proceed" is critical for the success of the research in such disciplines, since the time, money, and resource costs of the subsequent research steps depend largely on this decision. However, such a direction identification task is challenging in that researchers need to integrate information from large-scale, heterogeneous materials from all associated disciplines and summarize the related publications of which the core contributions are often showcased in diverse formats. The task also requires researchers to estimate the feasibility and potential in future experiments in the selected directions. In this work, we selected medicinal chemistry as a case and presented an interactive visual tool, MedChemLens, to assist medicinal chemists in choosing their intended directions of research. This task is also known as drug target (i.e., disease-linked proteins) selection. Given a candidate target name, MedChemLens automatically extracts the molecular features of drug compounds from chemical papers and clinical trial records, organizes them based on the drug structures, and interactively visualizes factors concerning subsequent experiments. We evaluated MedChemLens through a within-subjects study (N=16). Compared with the control condition (i.e., unrestricted online search without using our tool), participants who only used MedChemLens reported faster search, better-informed selections, higher confidence in their selections, and lower cognitive load.

A Critical Reflection on Visualization Research: Where Do Decision Making Tasks Hide?

It has been widely suggested that a key goal of visualization systems is to assist decision making, but is this true? We conduct a critical investigation on whether the activity of decision making is indeed central to the visualization domain. By approaching decision making as a user task, we explore the degree to which decision tasks are evident in visualization research and user studies. Our analysis suggests that decision tasks are not commonly found in current visualization task taxonomies and that the visualization field has yet to leverage guidance from decision theory domains on how to study such tasks. We further found that the majority of visualizations addressing decision making were not evaluated based on their ability to assist decision tasks. Finally, to help expand the impact of visual analytics in organizational as well as casual decision making activities, we initiate a research agenda on how decision making assistance could be elevated throughout visualization research.

VIStory: interactive storyboard for exploring visual information in scientific publications

Abstract

Many visual analytics have been developed for examining scientific publications comprising wealthy data such as authors and citations. The studies provide unprecedented insights on a variety of applications, e.g., literature review and collaboration analysis. However, visual information (e.g., figures) that is widely employed for storytelling and methods description are often neglected. We present VIStory, an interactive storyboard for exploring visual information in scientific publications. We harvest a new dataset of a large corpora of figures, using an automatic figure extraction method. Each figure contains various attributes such as dominant color and width/height ratio, together with faceted metadata of the publication including venues, authors, and keywords. To depict these information, we develop an intuitive interface consisting of three components: (1) Faceted View enables efficient query by publication metadata, benefiting from a nested table structure, (2) Storyboard View arranges paper rings—a well-designed glyph for depicting figure attributes, in a themeriver layout to reveal temporal trends, and (3) Endgame View presents a highlighted figure together with the publication metadata. We illustrate the applicability of VIStory with case studies on two datasets, i.e., 10-year IEEE VIS publications, and publications by a research team at CVPR, ICCV, and ECCV conferences. Quantitative and qualitative results from a formal user study demonstrate the efficiency of VIStory in exploring visual information in scientific publications.

Graphical abstract

Electronic supplementary material

The online version of this article (10.1007/s12650-020-00688-1) contains supplementary material, which is available to authorized users.

A Semantic-Based Method for Visualizing Large Image Collections

Interactive visualization of large image collections is important and useful in many applications, such as personal album management and user profiling on images. However, most prior studies focus on using low-level visual features of images, such as texture and color histogram, to create visualizations without considering the more important semantic information embedded in images. This paper proposes a novel visual analytic system to analyze images in a semantic-aware manner. The system mainly comprises two components: a semantic information extractor and a visual layout generator. The semantic information extractor employs an image captioning technique based on convolutional neural network (CNN) to produce descriptive captions for images, which can be transformed into semantic keywords. The layout generator employs a novel co-embedding model to project images and the associated semantic keywords to the same 2D space. Inspired by the galaxy metaphor, we further turn the projected 2D space to a galaxy visualization of images, in which semantic keywords and images are visually encoded as stars and planets. Our system naturally supports multi-scale visualization and navigation, in which users can immediately see a semantic overview of an image collection and drill down for detailed inspection of a certain group of images. Users can iteratively refine the visual layout by integrating their domain knowledge into the co-embedding process. Two task-based evaluations are conducted to demonstrate the effectiveness of our system.

Bridging Text Visualization and Mining: A Task-Driven Survey

Visual text analytics has recently emerged as one of the most prominent topics in both academic research and the commercial world. To provide an overview of the relevant techniques and analysis tasks, as well as the relationships between them, we comprehensively analyzed 263 visualization papers and 4,346 mining papers published between 1992-2017 in two fields: visualization and text mining. From the analysis, we derived around 300 concepts (visualization techniques, mining techniques, and analysis tasks) and built a taxonomy for each type of concept. The co-occurrence relationships between the concepts were also extracted. Our research can be used as a stepping-stone for other researchers to 1) understand a common set of concepts used in this research topic; 2) facilitate the exploration of the relationships between visualization techniques, mining techniques, and analysis tasks; 3) understand the current practice in developing visual text analytics tools; 4) seek potential research opportunities by narrowing the gulf between visualization and mining techniques based on the analysis tasks; and 5) analyze other interdisciplinary research areas in a similar way. We have also contributed a web-based visualization tool for analyzing and understanding research trends and opportunities in visual text analytics.

A Visual Approach for Interactive Keyterm-Based Clustering

The keyterm-based approach is arguably intuitive for users to direct text-clustering processes and adapt results to various applications in text analysis. Its way of markedly influencing the results, for instance, by expressing important terms in relevance order, requires little knowledge of the algorithm and has predictable effect, speeding up the task. This article first presents a text-clustering algorithm that can easily be extended into an interactive algorithm. We evaluate its performance against state-of-the-art clustering algorithms in unsupervised mode. Next, we propose three interactive versions of the algorithm based on keyterm labeling, document labeling, and hybrid labeling. We then demonstrate that keyterm labeling is more effective than document labeling in text clustering. Finally, we propose a visual approach to support the keyterm-based version of the algorithm. Visualizations are provided for the whole collection as well as for detailed views of document and cluster relationships. We show the effectiveness and flexibility of our framework, Vis-Kt , by presenting typical clustering cases on real text document collections. A user study is also reported that reveals overwhelmingly positive acceptance toward keyterm-based clustering.

A Survey on Visual Approaches for Analyzing Scientific Literature and Patents

The increasingly large number of available writings describing technical and scientific progress, calls for advanced analytic tools for their efficient analysis. This is true for many application scenarios in science and industry and for different types of writings, comprising patents and scientific articles. Despite important differences between patents and scientific articles, both have a variety of common characteristics that lead to similar search and analysis tasks. However, the analysis and visualization of these documents is not a trivial task due to the complexity of the documents as well as the large number of possible relations between their multivariate attributes. In this survey, we review interactive analysis and visualization approaches of patents and scientific articles, ranging from exploration tools to sophisticated mining methods. In a bottom-up approach, we categorize them according to two aspects: (a) data type (text, citations, authors, metadata, and combinations thereof), and (b) task (finding and comparing single entities, seeking elementary relations, finding complex patterns, and in particular temporal patterns, and investigating connections between multiple behaviours). Finally, we identify challenges and research directions in this area that ask for future investigations.

Vispubdata.org: A Metadata Collection About IEEE Visualization (VIS) Publications

We have created and made available to all a dataset with information about every paper that has appeared at the IEEE Visualization (VIS) set of conferences: InfoVis, SciVis, VAST, and Vis. The information about each paper includes its title, abstract, authors, and citations to other papers in the conference series, among many other attributes. This article describes the motivation for creating the dataset, as well as our process of coalescing and cleaning the data, and a set of three visualizations we created to facilitate exploration of the data. This data is meant to be useful to the broad data visualization community to help understand the evolution of the field and as an example document collection for text data visualization research.

Trends and challenges of visual search interfaces in digital libraries and repositories

Purpose

This paper aims to present an overview of the challenges encountered in integrating visual search interfaces into digital libraries and repositories. These challenges come in various forms, including information visualisation, the use of knowledge organisation systems and metadata quality. The main purpose of this study is the identification of criteria for the evaluation and integration of visual search interfaces, proposing guidelines and recommendations to improve information retrieval tasks with emphasis on the education-al context.

Design/methodology/approach

The information included in this study was collected based on a systematic literature review approach. The main information sources were explored in several digital libraries, including Science Direct, Scopus, ACM and IEEE, and include journal articles, conference proceedings, books, European project reports and deliverables and PhD theses published in an electronic format. A total of 142 studies comprised the review.

Findings

There are several issues that authors did not fully discuss in this literature review study; more specific, aspects associated with access of digital resources in digital libraries and repositories based on human computer interaction, i.e. usability and learnability of user interfaces; design of a suitable navigation method of search based on simple knowledge organisation schemes; and the use of usefulness of visual search interfaces to locate relevant resources.

Research limitations/implications

The main steps for carrying out a systematic review are drawn from health care; this methodology is not commonly used in fields such as digital libraries and repositories. The authors aimed to apply the fundamentals of the systematic literature review methodology considering the context of this study. Additionally, there are several aspects of accessibility that were not considered in the study, such as accessibility to content for disabled people as defined by ISO/IEC 40500:2012.

Originality/value

No other systematic literature reviews have been conducted in this field. The research presents an in-depth analysis of the criteria associated with searching and navigation methods based on the systematic literature review approach. The analysis is relevant for researchers in the field of digital library and repository creation in that it may direct them to considerations in designing and implementing visual search interfaces based on the use of information visualisation.

Visualization as Seen through its Research Paper Keywords

We present the results of a comprehensive multi-pass analysis of visualization paper keywords supplied by authors for their papers published in the IEEE Visualization conference series (now called IEEE VIS) between 1990-2015. From this analysis we derived a set of visualization topics that we discuss in the context of the current taxonomy that is used to categorize papers and assign reviewers in the IEEE VIS reviewing process. We point out missing and overemphasized topics in the current taxonomy and start a discussion on the importance of establishing common visualization terminology. Our analysis of research topics in visualization can, thus, serve as a starting point to (a) help create a common vocabulary to improve communication among different visualization sub-groups, (b) facilitate the process of understanding differences and commonalities of the various research sub-fields in visualization, (c) provide an understanding of emerging new research trends, (d) facilitate the crucial step of finding the right reviewers for research submissions, and (e) it can eventually lead to a comprehensive taxonomy of visualization research. One additional tangible outcome of our work is an online query tool (http://keyvis.org/) that allows visualization researchers to easily browse the 3952 keywords used for IEEE VIS papers since 1990 to find related work or make informed keyword choices.

cite2vec: Citation-Driven Document Exploration via Word Embeddings

Effectively exploring and browsing document collections is a fundamental problem in visualization. Traditionally, document visualization is based on a data model that represents each document as the set of its comprised words, effectively characterizing what the document is. In this paper we take an alternative perspective: motivated by the manner in which users search documents in the research process, we aim to visualize documents via their usage, or how documents tend to be used. We present a new visualization scheme - cite2vec - that allows the user to dynamically explore and browse documents via how other documents use them, information that we capture through citation contexts in a document collection. Starting from a usage-oriented word-document 2D projection, the user can dynamically steer document projections by prescribing semantic concepts, both in the form of phrase/document compositions and document:phrase analogies, enabling the exploration and comparison of documents by their use. The user interactions are enabled by a joint representation of words and documents in a common high-dimensional embedding space where user-specified concepts correspond to linear operations of word and document vectors. Our case studies, centered around a large document corpus of computer vision research papers, highlight the potential for usage-based document visualization.

Visualizing Social Media Content with SentenTree

We introduce SentenTree, a novel technique for visualizing the content of unstructured social media text. SentenTree displays frequent sentence patterns abstracted from a corpus of social media posts. The technique employs design ideas from word clouds and the Word Tree, but overcomes a number of limitations of both those visualizations. SentenTree displays a node-link diagram where nodes are words and links indicate word co-occurrence within the same sentence. The spatial arrangement of nodes gives cues to the syntactic ordering of words while the size of nodes gives cues to their frequency of occurrence. SentenTree can help people gain a rapid understanding of key concepts and opinions in a large social media text collection. It is implemented as a lightweight application that runs in the browser.

Visual analysis of online social media to open up the investigation of stance phenomena

Online social media are a perfect text source for stance analysis. Stance in human communication is concerned with speaker attitudes, beliefs, feelings and opinions. Expressions of stance are associated with the speakers' view of what they are talking about and what is up for discussion and negotiation in the intersubjective exchange. Taking stance is thus crucial for the social construction of meaning. Increased knowledge of stance can be useful for many application fields such as business intelligence, security analytics, or social media monitoring. In order to process large amounts of text data for stance analyses, linguists need interactive tools to explore the textual sources as well as the processed data based on computational linguistics techniques. Both original texts and derived data are important for refining the analyses iteratively. In this work, we present a visual analytics tool for online social media text data that can be used to open up the investigation of stance phenomena. Our approach complements traditional linguistic analysis techniques and is based on the analysis of utterances associated with two stance categories: sentiment and certainty. Our contributions include (1) the description of a novel web-based solution for analyzing the use and patterns of stance meanings and expressions in human communication over time; and (2) specialized techniques used for visualizing analysis provenance and corpus overview/navigation. We demonstrate our approach by means of text media on a highly controversial scandal with regard to expressions of anger and provide an expert review from linguists who have been using our tool.

TelCoVis: Visual Exploration of Co-occurrence in Urban Human Mobility Based on Telco Data

Understanding co-occurrence in urban human mobility (i.e. people from two regions visit an urban place during the same time span) is of great value in a variety of applications, such as urban planning, business intelligence, social behavior analysis, as well as containing contagious diseases. In recent years, the widespread use of mobile phones brings an unprecedented opportunity to capture large-scale and fine-grained data to study co-occurrence in human mobility. However, due to the lack of systematic and efficient methods, it is challenging for analysts to carry out in-depth analyses and extract valuable information. In this paper, we present TelCoVis, an interactive visual analytics system, which helps analysts leverage their domain knowledge to gain insight into the co-occurrence in urban human mobility based on telco data. Our system integrates visualization techniques with new designs and combines them in a novel way to enhance analysts' perception for a comprehensive exploration. In addition, we propose to study the correlations in co-occurrence (i.e. people from multiple regions visit different places during the same time span) by means of biclustering techniques that allow analysts to better explore coordinated relationships among different regions and identify interesting patterns. The case studies based on a real-world dataset and interviews with domain experts have demonstrated the effectiveness of our system in gaining insights into co-occurrence and facilitating various analytical tasks.

TimeLineCurator: Interactive Authoring of Visual Timelines from Unstructured Text

We present TimeLineCurator, a browser-based authoring tool that automatically extracts event data from temporal references in unstructured text documents using natural language processing and encodes them along a visual timeline. Our goal is to facilitate the timeline creation process for journalists and others who tell temporal stories online. Current solutions involve manually extracting and formatting event data from source documents, a process that tends to be tedious and error prone. With TimeLineCurator, a prospective timeline author can quickly identify the extent of time encompassed by a document, as well as the distribution of events occurring along this timeline. Authors can speculatively browse possible documents to quickly determine whether they are appropriate sources of timeline material. TimeLineCurator provides controls for curating and editing events on a timeline, the ability to combine timelines from multiple source documents, and export curated timelines for online deployment. We evaluate TimeLineCurator through a benchmark comparison of entity extraction error against a manual timeline curation process, a preliminary evaluation of the user experience of timeline authoring, a brief qualitative analysis of its visual output, and a discussion of prospective use cases suggested by members of the target author communities following its deployment.

CiteRivers: Visual Analytics of Citation Patterns

The exploration and analysis of scientific literature collections is an important task for effective knowledge management. Past interest in such document sets has spurred the development of numerous visualization approaches for their interactive analysis. They either focus on the textual content of publications, or on document metadata including authors and citations. Previously presented approaches for citation analysis aim primarily at the visualization of the structure of citation networks and their exploration. We extend the state-of-the-art by presenting an approach for the interactive visual analysis of the contents of scientific documents, and combine it with a new and flexible technique to analyze their citations. This technique facilitates user-steered aggregation of citations which are linked to the content of the citing publications using a highly interactive visualization approach. Through enriching the approach with additional interactive views of other important aspects of the data, we support the exploration of the dataset over time and enable users to analyze citation patterns, spot trends, and track long-term developments. We demonstrate the strengths of our approach through a use case and discuss it based on expert user feedback.

BiSet: Semantic Edge Bundling with Biclusters for Sensemaking

Identifying coordinated relationships is an important task in data analytics. For example, an intelligence analyst might want to discover three suspicious people who all visited the same four cities. Existing techniques that display individual relationships, such as between lists of entities, require repetitious manual selection and significant mental aggregation in cluttered visualizations to find coordinated relationships. In this paper, we present BiSet, a visual analytics technique to support interactive exploration of coordinated relationships. In BiSet, we model coordinated relationships as biclusters and algorithmically mine them from a dataset. Then, we visualize the biclusters in context as bundled edges between sets of related entities. Thus, bundles enable analysts to infer task-oriented semantic insights about potentially coordinated activities. We make bundles as first class objects and add a new layer, "in-between", to contain these bundle objects. Based on this, bundles serve to organize entities represented in lists and visually reveal their membership. Users can interact with edge bundles to organize related entities, and vice versa, for sensemaking purposes. With a usage scenario, we demonstrate how BiSet supports the exploration of coordinated relationships in text analytics.

Guidelines for Effective Usage of Text Highlighting Techniques

Semi-automatic text analysis involves manual inspection of text. Often, different text annotations (like part-of-speech or named entities) are indicated by using distinctive text highlighting techniques. In typesetting there exist well-known formatting conventions, such as bold typeface, italics, or background coloring, that are useful for highlighting certain parts of a given text. Also, many advanced techniques for visualization and highlighting of text exist; yet, standard typesetting is common, and the effects of standard typesetting on the perception of text are not fully understood. As such, we surveyed and tested the effectiveness of common text highlighting techniques, both individually and in combination, to discover how to maximize pop-out effects while minimizing visual interference between techniques. To validate our findings, we conducted a series of crowdsourced experiments to determine: i) a ranking of nine commonly-used text highlighting techniques; ii) the degree of visual interference between pairs of text highlighting techniques; iii) the effectiveness of techniques for visual conjunctive search. Our results show that increasing font size works best as a single highlighting technique, and that there are significant visual interferences between some pairs of highlighting techniques. We discuss the pros and cons of different combinations as a design guideline to choose text highlighting techniques for text viewers.

Exploratory Visual Analysis and Interactive Pattern Extraction from Semi-Structured Data

Semi-structured documents are a common type of data containing free text in natural language (unstructured data) as well as additional information about the document, or meta-data, typically following a schema or controlled vocabulary (structured data). Simultaneous analysis of unstructured and structured data enables the discovery of hidden relationships that cannot be identified from either of these sources when analyzed independently of each other. In this work, we present a visual text analytics tool for semi-structured documents (ViTA-SSD), that aims to support the user in the exploration and finding of insightful patterns in a visual and interactive manner in a semi-structured collection of documents. It achieves this goal by presenting to the user a set of coordinated visualizations that allows the linking of the metadata with interactively generated clusters of documents in such a way that relevant patterns can be easily spotted. The system contains two novel approaches in its back end: a feature-learning method to learn a compact representation of the corpus and a fast-clustering approach that has been redesigned to allow user supervision. These novel contributions make it possible for the user to interact with a large and dynamic document collection and to perform several text analytical tasks more efficiently. Finally, we present two use cases that illustrate the suitability of the system for in-depth interactive exploration of semi-structured document collections, two user studies, and results of several evaluations of our text-mining components.

Knowledge Generation Model for Visual Analytics

Visual analytics enables us to analyze huge information spaces in order to support complex decision making and data exploration. Humans play a central role in generating knowledge from the snippets of evidence emerging from visual data analysis. Although prior research provides frameworks that generalize this process, their scope is often narrowly focused so they do not encompass different perspectives at different levels. This paper proposes a knowledge generation model for visual analytics that ties together these diverse frameworks, yet retains previously developed models (e.g., KDD process) to describe individual segments of the overall visual analytic processes. To test its utility, a real world visual analytics system is compared against the model, demonstrating that the knowledge generation process model provides a useful guideline when developing and evaluating such systems. The model is used to effectively compare different data analysis systems. Furthermore, the model provides a common language and description of visual analytic processes, which can be used for communication between researchers. At the end, our model reflects areas of research that future researchers can embark on.

A Five-Level Design Framework for Bicluster Visualizations

Analysts often need to explore and identify coordinated relationships (e.g., four people who visited the same five cities on the same set of days) within some large datasets for sensemaking. Biclusters provide a potential solution to ease this process, because each computed bicluster bundles individual relationships into coordinated sets. By understanding such computed, structural, relations within biclusters, analysts can leverage their domain knowledge and intuition to determine the importance and relevance of the extracted relationships for making hypotheses. However, due to the lack of systematic design guidelines, it is still a challenge to design effective and usable visualizations of biclusters to enhance their perceptibility and interactivity for exploring coordinated relationships. In this paper, we present a five-level design framework for bicluster visualizations, with a survey of the state-of-the-art design considerations and applications that are related or that can be applied to bicluster visualizations. We summarize pros and cons of these design options to support user tasks at each of the five-level relationships. Finally, we discuss future research challenges for bicluster visualizations and their incorporation into visual analytics tools.

Overview: The Design, Adoption, and Analysis of a Visual Document Mining Tool for Investigative Journalists

For an investigative journalist, a large collection of documents obtained from a Freedom of Information Act request or a leak is both a blessing and a curse: such material may contain multiple newsworthy stories, but it can be difficult and time consuming to find relevant documents. Standard text search is useful, but even if the search target is known it may not be possible to formulate an effective query. In addition, summarization is an important non-search task. We present Overview, an application for the systematic analysis of large document collections based on document clustering, visualization, and tagging. This work contributes to the small set of design studies which evaluate a visualization system "in the wild", and we report on six case studies where Overview was voluntarily used by self-initiated journalists to produce published stories. We find that the frequently-used language of "exploring" a document collection is both too vague and too narrow to capture how journalists actually used our application. Our iterative process, including multiple rounds of deployment and observations of real world usage, led to a much more specific characterization of tasks. We analyze and justify the visual encoding and interaction techniques used in Overview's design with respect to our final task abstractions, and propose generalizable lessons for visualization design methodology.