The Role of Text in Visualizations: How Annotations Shape Perceptions of Bias and Influence Predictions.

This paper investigates the role of text in visualizations, specifically the impact of text position, semantic content, and biased wording. Two empirical studies were conducted based on two tasks (predicting data trends and appraising bias) using two visualization types (bar and line charts). While the addition of text had a minimal effect on how people perceive data trends, there was a significant impact on how biased they perceive the authors to be. This finding revealed a relationship between the degree of bias in textual information and the perception of the authors' bias. Exploratory analyses support an interaction between a person's prediction and the degree of bias they perceived. This paper also develops a crowdsourced method for creating chart annotations that range from neutral to highly biased. This research highlights the need for designers to mitigate potential polarization of readers' opinions based on how authors' ideas are expressed.

Striking a Balance: Reader Takeaways and Preferences when Integrating Text and Charts.

While visualizations are an effective way to represent insights about information, they rarely stand alone. When designing a visualization, text is often added to provide additional context and guidance for the reader. However, there is little experimental evidence to guide designers as to what is the right amount of text to show within a chart, what its qualitative properties should be, and where it should be placed. Prior work also shows variation in personal preferences for charts versus textual representations. In this paper, we explore several research questions about the relative value of textual components of visualizations. 302 participants ranked univariate line charts containing varying amounts of text, ranging from no text (except for the axes) to a written paragraph with no visuals. Participants also described what information they could take away from line charts containing text with varying semantic content. We find that heavily annotated charts were not penalized. In fact, participants preferred the charts with the largest number of textual annotations over charts with fewer annotations or text alone. We also find effects of semantic content. For instance, the text that describes statistical or relational components of a chart leads to more takeaways referring to statistics or relational comparisons than text describing elemental or encoded components. Finally, we find different effects for the semantic levels based on the placement of the text on the chart; some kinds of information are best placed in the title, while others should be placed closer to the data. We compile these results into four chart design guidelines and discuss future implications for the combination of text and charts.

An Evaluation of Semantically Grouped Word Cloud Designs.

Word clouds continue to be a popular tool for summarizing textual information, despite their well-documented deficiencies for analytic tasks. Much of their popularity rests on their playful visual appeal. In this paper, we present the results of a series of controlled experiments that show that layouts in which words are arranged into semantically and visually distinct zones are more effective for understanding the underlying topics than standard word cloud layouts. White space separators and/or spatially grouped color coding led to significantly stronger understanding of the underlying topics compared to a standard Wordle layout, while simultaneously scoring higher on measures of aesthetic appeal. This work is an advance on prior research on semantic layouts for word clouds because that prior work has either not ensured that the different semantic groupings are visually or semantically distinct, or has not performed usability studies. An additional contribution of this work is the development of a dataset for a semantic category identification task that can be used for replication of these results or future evaluations of word cloud designs.

Futzing and Moseying: Interviews with Professional Data Analysts on Exploration Practices.

We report the results of interviewing thirty professional data analysts working in a range of industrial, academic, and regulatory environments. This study focuses on participants' descriptions of exploratory activities and tool usage in these activities. Highlights of the findings include: distinctions between exploration as a precursor to more directed analysis versus truly open-ended exploration; confirmation that some analysts see "finding something interesting" as a valid goal of data exploration while others explicitly disavow this goal; conflicting views about the role of intelligent tools in data exploration; and pervasive use of visualization for exploration, but with only a subset using direct manipulation interfaces. These findings provide guidelines for future tool development, as well as a better understanding of the meaning of the term "data exploration" based on the words of practitioners "in the wild."

Do peers see more in a paper than its authors?

Recent years have shown a gradual shift in the content of biomedical publications that is freely accessible, from titles and abstracts to full text. This has enabled new forms of automatic text analysis and has given rise to some interesting questions: How informative is the abstract compared to the full-text? What important information in the full-text is not present in the abstract? What should a good summary contain that is not already in the abstract? Do authors and peers see an article differently? We answer these questions by comparing the information content of the abstract to that in citances-sentences containing citations to that article. We contrast the important points of an article as judged by its authors versus as seen by peers. Focusing on the area of molecular interactions, we perform manual and automatic analysis, and we find that the set of all citances to a target article not only covers most information (entities, functions, experimental methods, and other biological concepts) found in its abstract, but also contains 20% more concepts. We further present a detailed summary of the differences across information types, and we examine the effects other citations and time have on the content of citances.

Full text and figure display improves bioscience literature search.

When reading bioscience journal articles, many researchers focus attention on the figures and their captions. This observation led to the development of the BioText literature search engine, a freely available Web-based application that allows biologists to search over the contents of Open Access Journals, and see figures from the articles displayed directly in the search results. This article presents a qualitative assessment of this system in the form of a usability study with 20 biologist participants using and commenting on the system. 19 out of 20 participants expressed a desire to use a bioscience literature search engine that displays articles' figures alongside the full text search results. 15 out of 20 participants said they would use a caption search and figure display interface either frequently or sometimes, while 4 said rarely and 1 said undecided. 10 out of 20 participants said they would use a tool for searching the text of tables and their captions either frequently or sometimes, while 7 said they would use it rarely if at all, 2 said they would never use it, and 1 was undecided. This study found evidence, supporting results of an earlier study, that bioscience literature search systems such as PubMed should show figures from articles alongside search results. It also found evidence that full text and captions should be searched along with the article title, metadata, and abstract. Finally, for a subset of users and information needs, allowing for explicit search within captions for figures and tables is a useful function, but it is not entirely clear how to cleanly integrate this within a more general literature search interface. Such a facility supports Open Access publishing efforts, as it requires access to full text of documents and the lifting of restrictions in order to show figures in the search interface.

Evidence for showing gene/protein name suggestions in bioscience literature search interfaces.

This paper reports on the results of two questionnaires asking biologists about the incorporation of text-extracted entity information, specifically gene and protein names, into bioscience literature search user interfaces. Among the findings are that study participants want to see gene/protein metadata in combination with organism information; that a significant proportion would like to see gene names grouped by type (synonym, homolog, etc.), and that most participants want to see information that the system is confident about immediately, and see less certain information after taking additional action. These results inform future interface designs.

BioText Search Engine: beyond abstract search.

UNLABELLED: The BioText Search Engine is a freely available Web-based application that provides biologists with new ways to access the scientific literature. One novel feature is the ability to search and browse article figures and their captions. A grid view juxtaposes many different figures associated with the same keywords, providing new insight into the literature. An abstract/title search and list view shows at a glance many of the figures associated with each article. The interface is carefully designed according to usability principles and techniques. The search engine is a work in progress, and more functionality will be added over time. AVAILABILITY: http://biosearch.berkeley.edu.

Tools for loading MEDLINE into a local relational database.

BACKGROUND: Researchers who use MEDLINE for text mining, information extraction, or natural language processing may benefit from having a copy of MEDLINE that they can manage locally. The National Library of Medicine (NLM) distributes MEDLINE in eXtensible Markup Language (XML)-formatted text files, but it is difficult to query MEDLINE in that format. We have developed software tools to parse the MEDLINE data files and load their contents into a relational database. Although the task is conceptually straightforward, the size and scope of MEDLINE make the task nontrivial. Given the increasing importance of text analysis in biology and medicine, we believe a local installation of MEDLINE will provide helpful computing infrastructure for researchers. RESULTS: We developed three software packages that parse and load MEDLINE, and ran each package to install separate instances of the MEDLINE database. For each installation, we collected data on loading time and disk-space utilization to provide examples of the process in different settings. Settings differed in terms of commercial database-management system (IBM DB2 or Oracle 9i), processor (Intel or Sun), programming language of installation software (Java or Perl), and methods employed in different versions of the software. The loading times for the three installations were 76 hours, 196 hours, and 132 hours, and disk-space utilization was 46.3 GB, 37.7 GB, and 31.6 GB, respectively. Loading times varied due to a variety of differences among the systems. Loading time also depended on whether data were written to intermediate files or not, and on whether input files were processed in sequence or in parallel. Disk-space utilization depended on the number of MEDLINE files processed, amount of indexing, and whether abstracts were stored as character large objects or truncated. CONCLUSIONS: Relational database (RDBMS) technology supports indexing and querying of very large datasets, and can accommodate a locally stored version of MEDLINE. RDBMS systems support a wide range of queries and facilitate certain tasks that are not directly supported by the application programming interface to PubMed. Because there is variation in hardware, software, and network infrastructures across sites, we cannot predict the exact time required for a user to load MEDLINE, but our results suggest that performance of the software is reasonable. Our database schemas and conversion software are publicly available at http://biotext.berkeley.edu.

A simple algorithm for identifying abbreviation definitions in biomedical text.

The volume of biomedical text is growing at a fast rate, creating challenges for humans and computer systems alike. One of these challenges arises from the frequent use of novel abbreviations in these texts, thus requiring that biomedical lexical ontologies be continually updated. In this paper we show that the problem of identifying abbreviations' definitions can be solved with a much simpler algorithm than that proposed by other research efforts. The algorithm achieves 96% precision and 82% recall on a standard test collection, which is at least as good as existing approaches. It also achieves 95% precision and 82% recall on another, larger test set. A notable advantage of the algorithm is that, unlike other approaches, it does not require any training data.