Formal representations of the visualization design space, such as knowledge bases and graphs, consolidate design practices into a shared resource and enable automated reasoning and interpretable design recommendations. However, prior approaches typically depend on fixed, manually authored rules, making it difficult to build novel representations or extend them for different visualization domains. Instead, we propose data-driven methods that automatically synthesize visualization design knowledge bases. Specifically, our methods (1) extract candidate design features from a visualization corpus, (2) select features forward and backward, and (3) render the final knowledge base. In our benchmark evaluation compared to Draco 2, our synthesized knowledge base offers general and interpretable design features and improves the accuracy of predicting effective designs by 1–15% in varied training and test sets. When we apply our approach to genomics visualization, the synthesized knowledge base includes sensible features with accuracy up to 97%, demonstrating the applicability of our approach to other visualization domains.

Various computational approaches predict chromatin structure, yielding concrete models that position genomic loci in physical space and help reveal genome organization and function. While prior visualization research has explored data and task abstractions for genomics, the design space for depicting these three-dimensional (3D) genome models-and associated genome-mapped data-remains unclear. In this paper, we investigate the visualization of genomic data with a spatial component. First, we systematically survey how 3D genome models are used and depicted in computational biology. We analyze over 300 papers with figures that visualize 3D genomic data and categorize the methods for visual representation. From this survey, we derive a design space for visualizing 3D genome data, identifying common patterns and key properties such as representation, visual channels, and composition. We position these findings within an existing genomics visualization taxonomy, refining and extending existing classifications. Second, we augment Gosling, a declarative visualization grammar for genomics, to support 3D genomic data. Our integration enables expressive authoring of visualizations that connect traditional genome-mapped information with 3D genome models, emphasizing their spatial characteristics. To demonstrate its utility, we employ our extended grammar to recreate interactive examples, showcasing its ability to represent complex visual designs. Comprehensive examples and an interactive editor are available at 3d.gosling-lang.org.

Effective visualization is essential for interpreting genomics data, yet researchers often face challenges in finding relevant, reusable examples. Existing tools offer limited support for searching the vast landscape of genomics visualizations, making the process of authoring new visualizations time-consuming and inefficient. To address this gap, we introduce Geranium, a data visualization retrieval system for searching and authoring genomics visualizations. Geranium supports multimodal retrieval, enabling users to query with images, text, or grammar-based specifications. Retrieved examples serve as scaffolds for authoring, providing templates that researchers can adapt with their own data, thereby streamlining the mechanics of visualization construction. Geranium integrates three embedding methods to combine specialized and general knowledge: grammar-based embeddings tailored to genomics visualizations, multimodal embeddings from a biomedical vision-language foundation model, and text embeddings from a fine-tuned large language model. For each visualization, we construct a multimodal representation that includes a Gosling specification, a pixel-based rendering, and natural language descriptions. We evaluate embedding strategies to maximize top-$k$k retrieval accuracy and conduct user studies with domain collaborators to gather feedback on usability. Our collection comprises 3,200 visualizations across 50 categories, ranging from single-view to coordinated multi-view designs and supporting applications from single-cell epigenomics to structural variation analysis.

Genomics experts rely on visualization to extract and share insights from complex and large-scale datasets. Beyond off-the-shelf tools for data exploration, there is an increasing need for platforms that aid experts in authoring customized visualizations for both exploration and communication of insights. A variety of interactive techniques have been proposed for authoring data visualizations, such as template editing, shelf configuration, natural language input, and code editors. However, it remains unclear how genomics experts create visualizations and which techniques best support their visualization tasks and needs. To address this gap, we conducted two user studies with genomics researchers: (1) semi-structured interviews (n=20) to identify the tasks, user contexts, and current visualization authoring techniques and (2) an exploratory study (n=13) using visual probes to elicit users' intents and desired techniques when creating visualizations. Our contributions include (1) a characterization of how visualization authoring is currently utilized in genomics visualization, identifying limitations and benefits in light of common criteria for authoring tools, and (2) generalizable design implications for genomics visualization authoring tools based on our findings on task- and user-specific usefulness of authoring techniques. All supplemental materials are available at https://osf.io/bdj4v/.

A wide range of visualization authoring interfaces enable the creation of highly customized visualizations. However, prioritizing expressiveness often impedes the learnability of the authoring interface. The diversity of users, such as varying computational skills and prior experiences in user interfaces, makes it even more challenging for a single authoring interface to satisfy the needs of a broad audience. In this paper, we introduce a framework to balance learnability and expressivity in a visualization authoring system. Adopting insights from learnability studies, such as multimodal interaction and visualization literacy, we explore the design space of blending multiple visualization authoring interfaces for supporting authoring tasks in a complementary and flexible manner. To evaluate the effectiveness of blending interfaces, we implemented a proof-of-concept system, Blace, that combines four common visualization authoring interfaces-template-based, shelf configuration, natural language, and code editor-that are tightly linked to one another to help users easily relate unfamiliar interfaces to more familiar ones. Using the system, we conducted a user study with 12 domain experts who regularly visualize genomics data as part of their analysis workflow. Participants with varied visualization and programming backgrounds were able to successfully reproduce unfamiliar visualization examples without a guided tutorial in the study. Feedback from a post-study qualitative questionnaire further suggests that blending interfaces enabled participants to learn the system easily and assisted them in confidently editing unfamiliar visualization grammar in the code editor, enabling expressive customization. Reflecting on our study results and the design of our system, we discuss the different interaction patterns that we identified and design implications for blending visualization authoring interfaces.

MOTIVATION: Biomedical visualizations are key to accessing biomedical knowledge and detecting new patterns in large datasets. Interactive visualizations are essential for biomedical data scientists and are omnipresent in data analysis software and data portals. Without appropriate descriptions, these visualizations are not accessible to all people with blindness and low vision, who often rely on screen reader accessibility technologies to access visual information on digital devices. Screen readers require descriptions to convey image content. However, many images lack informative descriptions due to unawareness and difficulty writing such descriptions. Describing complex and interactive visualizations, like genomics data visualizations, is even more challenging. Automatic generation of descriptions could be beneficial, yet current alt text generating models are limited to basic visualizations and cannot be used for genomics. RESULTS: We present AltGosling, an automated description generation tool focused on interactive data visualizations of genome-mapped data, created with the grammar-based genomics toolkit Gosling. The logic-based algorithm of AltGosling creates various descriptions including a tree-structured navigable panel. We co-designed AltGosling with a blind screen reader user (co-author). We show that AltGosling outperforms state-of-the-art large language models and common image-based neural networks for alt text generation of genomics data visualizations. As a first of its kind in genomic research, we lay the groundwork to increase accessibility in the field. AVAILABILITY AND IMPLEMENTATION: The source code, examples, and interactive demo are accessible under the MIT License at https://github.com/gosling-lang/altgosling. The package is available at https://www.npmjs.com/package/altgosling.

., t-SNE) but suffer from a lack of interpretability. While previous studies employed disentangled representation learning (DRL) to enable more interpretable exploration, they often overlooked the potential mismatches between the concepts of humans and the semantic dimensions learned by DRL. To address this issue, we propose Drava, a visual analytics system that supports users in 1) relating the concepts of humans with the semantic dimensions of DRL and identifying mismatches, 2) providing feedback to minimize the mismatches, and 3) obtaining data insights from concept-driven exploration. Drava provides a set of visualizations and interactions based on visual piles to help users understand and refine concepts and conduct concept-driven exploration. Meanwhile, Drava employs a concept adaptor model to fine-tune the semantic dimensions of DRL based on user refinement. The usefulness of Drava is demonstrated through application scenarios and experimental validation.

SUMMARY: The regulation of genes by cis-regulatory elements (CREs) is complex and differs between cell types. Visual analysis of large collections of chromatin profiles across diverse cell types, integrated with computational methods, can reveal meaningful biological insights. We developed Cistrome Explorer, a web-based interactive visual analytics tool for exploring thousands of chromatin profiles in diverse cell types. Integrated with the Cistrome Data Browser database which contains thousands of ChIP-seq, DNase-seq and ATAC-seq samples, Cistrome Explorer enables the discovery of patterns of CREs across cell types and the identification of transcription factor binding underlying these patterns. AVAILABILITY AND IMPLEMENTATION: Cistrome Explorer and its source code are available at http://cisvis.gehlenborglab.org/ and released under the MIT License. Documentation can be accessed via http://cisvis.gehlenborglab.org/docs/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: Gos is a declarative Python library designed to create interactive multiscale visualizations of genomics and epigenomics data. It provides a consistent and simple interface to the flexible Gosling visualization grammar. Gos hides technical complexities involved with configuring web-based genome browsers and integrates seamlessly within computational notebooks environments to enable new interactive analysis workflows. AVAILABILITY AND IMPLEMENTATION: Gos is released under the MIT License and available on the Python Package Index (PyPI). The source code is publicly available on GitHub (https://github.com/gosling-lang/gos), and documentation with examples can be found at https://gosling-lang.github.io/gos.

A series of recent studies has focused on designing cross-resolution and cross-device visualizations, i.e., responsive visualization, a concept adopted from responsive web design. However, these studies mainly focused on visualizations with a single view to a small number of views, and there are still unresolved questions about how to design responsive multi-view visualizations. In this paper, we present a reusable and generalizable framework for designing responsive multi-view visualizations focused on genomics data. To gain a better understanding of existing design challenges, we review web-based genomics visualization tools in the wild. By characterizing tools based on a taxonomy of responsive designs, we find that responsiveness is rarely supported in existing tools. To distill insights from the survey results in a systematic way, we classify typical view composition patterns, such as "vertically long," "horizontally wide," "circular," and "cross-shaped" compositions. We then identify their usability issues in different resolutions that stem from the composition patterns, as well as discussing approaches to address the issues and to make genomics visualizations responsive. By extending the Gosling visualization grammar to support responsive constructs, we show how these approaches can be supported. A valuable follow-up study would be taking different input modalities into account, such as mouse and touch interactions, which was not considered in our study.

Interpretation of genomics data is critically reliant on the application of a wide range of visualization tools. A large number of visualization techniques for genomics data and different analysis tasks pose a significant challenge for analysts: which visualization technique is most likely to help them generate insights into their data? Since genomics analysts typically have limited training in data visualization, their choices are often based on trial and error or guided by technical details, such as data formats that a specific tool can load. This approach prevents them from making effective visualization choices for the many combinations of data types and analysis questions they encounter in their work. Visualization recommendation systems assist non-experts in creating data visualization by recommending appropriate visualizations based on the data and task characteristics. However, existing visualization recommendation systems are not designed to handle domain-specific problems. To address these challenges, we designed GenoREC, a novel visualization recommendation system for genomics. GenoREC enables genomics analysts to select effective visualizations based on a description of their data and analysis tasks. Here, we present the recommendation model that uses a knowledge-based method for choosing appropriate visualizations and a web application that enables analysts to input their requirements, explore recommended visualizations, and export them for their usage. Furthermore, we present the results of two user studies demonstrating that GenoREC recommends visualizations that are both accepted by domain experts and suited to address the given genomics analysis problem. All supplemental materials are available at https://osf.io/y73pt/.

The combination of diverse data types and analysis tasks in genomics has resulted in the development of a wide range of visualization techniques and tools. However, most existing tools are tailored to a specific problem or data type and offer limited customization, making it challenging to optimize visualizations for new analysis tasks or datasets. To address this challenge, we designed Gosling-a grammar for interactive and scalable genomics data visualization. Gosling balances expressiveness for comprehensive multi-scale genomics data visualizations with accessibility for domain scientists. Our accompanying JavaScript toolkit called Gosling.js provides scalable and interactive rendering. Gosling.js is built on top of an existing platform for web-based genomics data visualization to further simplify the visualization of common genomics data formats. We demonstrate the expressiveness of the grammar through a variety of real-world examples. Furthermore, we show how Gosling supports the design of novel genomics visualizations. An online editor and examples of Gosling.js, its source code, and documentation are available at https://gosling.js.org.

We present a new visual exploration concept-Progressive Visual Analytics with Safeguards-that helps people manage the uncertainty arising from progressive data exploration. Despite its potential benefits, intermediate knowledge from progressive analytics can be incorrect due to various machine and human factors, such as a sampling bias or misinterpretation of uncertainty. To alleviate this problem, we introduce PVA-Guards, safeguards people can leave on uncertain intermediate knowledge that needs to be verified, and derive seven PVA-Guards based on previous visualization task taxonomies. PVA-Guards provide a means of ensuring the correctness of the conclusion and understanding the reason when intermediate knowledge becomes invalid. We also present ProReveal, a proof-of-concept system designed and developed to integrate the seven safeguards into progressive data exploration. Finally, we report a user study with 14 participants, which shows people voluntarily employed PVA-Guards to safeguard their findings and ProReveal's PVA-Guard view provides an overview of uncertain intermediate knowledge. We believe our new concept can also offer better consistency in progressive data exploration, alleviating people's heterogeneous interpretation of uncertainty.

We present a systematic review on three comparative layouts-juxtaposition, superposition, and explicit-encoding-which are information visualization (InfoVis) layouts designed to support comparison tasks. For the last decade, these layouts have served as fundamental idioms in designing many visualization systems. However, we found that the layouts have been used with inconsistent terms and confusion, and the lessons from previous studies are fragmented. The goal of our research is to distill the results from previous studies into a consistent and reusable framework. We review 127 research papers, including 15 papers with quantitative user studies, which employed comparative layouts. We first alleviate the ambiguous boundaries in the design space of comparative layouts by suggesting lucid terminology (e.g., chart-wise and item-wise juxtaposition). We then identify the diverse aspects of comparative layouts, such as the advantages and concerns of using each layout in the real-world scenarios and researchers' approaches to overcome the concerns. Building our knowledge on top of the initial insights gained from the Gleicher et al.'s survey [19], we elaborate on relevant empirical evidence that we distilled from our survey (e.g., the actual effectiveness of the layouts in different study settings) and identify novel facets that the original work did not cover (e.g., the familiarity of the layouts to people). Finally, we show the consistent and contradictory results on the performance of comparative layouts and offer practical implications for using the layouts by suggesting trade-offs and seven actionable guidelines.

Abstract Most visualization recommendation systems predominantly rely on graphical previews to describe alternative visual encodings. However, since InfoVis novices are not familiar with visual representations (e.g., interpretation barriers [GTS10]), novices might have difficulty understanding and choosing recommended visual encodings. As an initial step toward understanding effective representation methods for visualization recommendations, we investigate the effectiveness of three representation methods (i.e., previews, animated transitions, and textual descriptions) under scatterplot construction tasks. Our results show how different representations individually and cooperatively help users understand and choose recommended visualizations, for example, by supporting their expect‐and‐confirm process. Based on our study results, we discuss design implications for visualization recommendation interfaces.

Recent advancements in tablet technology pose a great opportunity for information visualization to expand its horizons beyond desktops. In this paper, we present TouchPivot, a novel interface that assists visual data exploration on tablet devices. With novices in mind, TouchPivot supports data transformations, such as pivoting and filtering, with simple pen and touch interactions, and facilitates understanding of the transformations through tight coupling between a data table and visualization. We bring in WIMP interfaces to TouchPivot, leveraging their familiarity and accessibility to novices. We report on a user study conducted to compare TouchPivot with two commercial interfaces, Tableau and Microsoft Excel's PivotTable. Our results show that novices not only answered data-driven questions faster, but also created a larger number of meaningful charts during freeform exploration with TouchPivot than others. Finally, we discuss the main hurdles novices encountered during our study and possible remedies for them.

We present CloakingNote, a novel desktop interface for subtle writing. The main idea of CloakingNote is to misdirect observers' attention away from a real text by using a prominent decoy text. To assess the subtlety of CloakingNote, we conducted a subtlety test while varying the contrast ratio between the real text and its background. Our results demonstrated that the real text as well as the interface itself were subtle even when participants were aware that a writer might be engaged in suspicious activities. We also evaluated the feasibility of CloakingNote through a performance test and categorized the users' layout strategies.

As large-screen smartphones are trending, they bring a new set of challenges such as acquiring unreachable screen targets using one hand. To understand users' touch behavior on large mobile touchscreens, we conducted an empirical experiment to discover their usage patterns of tilting devices toward their thumbs to touch screen regions. Exploiting this natural tilting behavior, we designed three novel mobile interaction techniques: TiltSlide, TiltReduction, and TiltCursor. We conducted a controlled experiment to compare our methods with other existing methods, and then evaluated them in real mobile phone scenarios such as sending an e-mail and web surfing. We constructed a design space for one-hand targeting interactions and proposed design considerations for one-hand targeting in real mobile phone circumstances.

BACKGROUND: Though cluster analysis has become a routine analytic task for bioinformatics research, it is still arduous for researchers to assess the quality of a clustering result. To select the best clustering method and its parameters for a dataset, researchers have to run multiple clustering algorithms and compare them. However, such a comparison task with multiple clustering results is cognitively demanding and laborious. RESULTS: In this paper, we present XCluSim, a visual analytics tool that enables users to interactively compare multiple clustering results based on the Visual Information Seeking Mantra. We build a taxonomy for categorizing existing techniques of clustering results visualization in terms of the Gestalt principles of grouping. Using the taxonomy, we choose the most appropriate interactive visualizations for presenting individual clustering results from different types of clustering algorithms. The efficacy of XCluSim is shown through case studies with a bioinformatician. CONCLUSIONS: Compared to other relevant tools, XCluSim enables users to compare multiple clustering results in a more scalable manner. Moreover, XCluSim supports diverse clustering algorithms and dedicated visualizations and interactions for different types of clustering results, allowing more effective exploration of details on demand. Through case studies with a bioinformatics researcher, we received positive feedback on the functionalities of XCluSim, including its ability to help identify stably clustered items across multiple clustering results.