Data visualization (DataViz) libraries play a crucial role in presentation, data analysis, and application development, underscoring the importance of their accuracy in transforming data into visual representations. Incorrect visualizations can adversely impact user experience, distort information conveyance, and influence user perception and decision-making processes. Visual bugs in these libraries can be particularly insidious as they may not cause obvious errors like crashes, but instead mislead users of the underlying data graphically, resulting in wrong decision making. Consequently, a good understanding of the unique characteristics of bugs in DataViz libraries is essential for researchers and developers to detect and fix bugs in DataViz libraries. This study presents the first comprehensive analysis of bugs in DataViz libraries, examining 564 bugs collected from five widely-used libraries. Our study systematically analyzes their symptoms and root causes, and provides a detailed taxonomy. We found that incorrect/inaccurate plots are pervasive in DataViz libraries and incorrect graphic computation is the major root cause, which necessitates further automated testing methods for DataViz libraries. Moreover, we identified eight key steps to trigger such bugs and two test oracles specific to DataViz libraries, which may inspire future research in designing effective automated testing techniques. Furthermore, with the recent advancements in Vision Language Models (VLMs), we explored the feasibility of applying these models to detect incorrect/inaccurate plots. The results show that the effectiveness of VLMs in bug detection varies from 29% to 57%, depending on the prompts, and adding more information in prompts does not necessarily increase the effectiveness. More findings can be found in our manuscript.
Prior natural language datasets for data visualization have focused on tasks such as visualization literacy assessment, insight generation, and visualization generation from natural language instructions. These studies often rely on controlled setups with purpose-built visualizations and artificially constructed questions. As a result, they tend to prioritize the interpretation of visualizations, focusing on decoding visualizations rather than understanding their encoding. In this paper, we present a new dataset and methodology for probing visualization design rationale through natural language. We leverage a unique source of real-world visualizations and natural language narratives: literate visualization notebooks created by students as part of a data visualization course. These notebooks combine visual artifacts with design exposition, in which students make explicit the rationale behind their design decisions. We also use large language models (LLMs) to generate and categorize question-answer-rationale triples from the narratives and articulations in the notebooks. We then carefully validate the triples and curate a dataset that captures and distills the visualization design choices and corresponding rationales of the students.
Data visualization generation using Large Language Models (LLMs) has shown promising results but often produces suboptimal visualizations that require human intervention for improvement. In this work, we introduce VIS-Shepherd, a specialized Multimodal Large Language Model (MLLM)-based critic to evaluate and provide feedback for LLM-generated data visualizations. At the core of our approach is a framework to construct a high-quality visualization critique dataset, where we collect human-created visualization instances, synthesize corresponding LLM-generated instances, and construct high-quality critiques. We conduct both model-based automatic evaluation and human preference studies to evaluate the effectiveness of our approach. Our experiments show that even small (7B parameters) open-source MLLM models achieve substantial performance gains by leveraging our high-quality visualization critique dataset, reaching levels comparable to much larger open-source or even proprietary models. Our work demonstrates significant potential for MLLM-based automated visualization critique and indicates promising directions for enhancing LLM-based data visualization generation. Our project page: https://github.com/bopan3/VIS-Shepherd.
The development of science has been transforming man's view towards nature for centuries. Observing structures and patterns in an effective approach to discover regularities from data is a key step toward theory-building. With increasingly complex data being obtained, revealing regularities systematically has become a challenge. Correlation is a most commonly-used and effective approach to describe regularities in data, yet for complex patterns, spatial inhomogeneity and complexity can often undermine the correlations. We present an algorithm to derive maps representing the type and degree of correlations, by taking the two-fold symmetry of the correlation vector into full account using the Stokes parameter. The method allows for a spatially resolved view of the nature and strength of correlations between physical quantities. In the correlation view, a region can often be separated into different subregions with different types of correlations. Subregions correspond to physical regimes for physical systems, or climate zones for climate maps. The simplicity of the method makes it widely applicable to a variety of data, where the correlation-based approach makes the map particularly useful in revealing regularities in physical systems and alike. As a new and efficient approach to represent data, the method should facilitate the development of new computational approaches to regularity discovery.
Density-equalizing map (DEM) serves as a powerful technique for creating shape deformations with the area changes reflecting an underlying density function. In recent decades, DEM has found widespread applications in fields such as data visualization, geometry processing, and medical imaging. Traditional approaches to DEM primarily rely on iterative numerical solvers for diffusion equations or optimization-based methods that minimize handcrafted energy functionals. However, these conventional techniques often face several challenges: they may suffer from limited accuracy, produce overlapping artifacts in extreme cases, and require substantial algorithmic redesign when extended from 2D to 3D, due to the derivative-dependent nature of their energy formulations. In this work, we propose a novel learning-based density-equalizing mapping framework (LDEM) using deep neural networks. Specifically, we introduce a loss function that enforces density uniformity and geometric regularity, and utilize a hierarchical approach to predict the transformations at both the coarse and dense levels. Our method demonstrates superior density-equalizing and bijectivity properties compared to prior methods for a wide range of simple and complex density distributions, and can be easily applied to surface remeshing with different effects. Also, it generalizes seamlessly from 2D to 3D domains without structural changes to the model architecture or loss formulation. Altogether, our work opens up new possibilities for scalable and robust computation of density-equalizing maps for practical applications.
Data visualizations are powerful tools for communicating patterns in quantitative data. Yet understanding any data visualization is no small feat -- succeeding requires jointly making sense of visual, numerical, and linguistic inputs arranged in a conventionalized format one has previously learned to parse. Recently developed vision-language models are, in principle, promising candidates for developing computational models of these cognitive operations. However, it is currently unclear to what degree these models emulate human behavior on tasks that involve reasoning about data visualizations. This gap reflects limitations in prior work that has evaluated data visualization understanding in artificial systems using measures that differ from those typically used to assess these abilities in humans. Here we evaluated eight vision-language models on six data visualization literacy assessments designed for humans and compared model responses to those of human participants. We found that these models performed worse than human participants on average, and this performance gap persisted even when using relatively lenient criteria to assess model performance. Moreover, while relative performance across items was somewhat correlated between models and humans, all models produced patterns of errors that were reliably distinct from those produced by human participants. Taken together, these findings suggest significant opportunities for further development of artificial systems that might serve as useful models of how humans reason about data visualizations. All code and data needed to reproduce these results are available at: https://osf.io/e25mu/?view_only=399daff5a14d4b16b09473cf19043f18.
The rapid adoption of generative AI has driven an explosion in the size of datasets consumed and produced by AI models. Traditional methods for unstructured data visualization, such as t-SNE and UMAP, have not kept up with the pace of dataset scaling. This presents a significant challenge for AI explainability, which relies on methods such as t-SNE and UMAP for exploratory data analysis. In this paper, we introduce Negative Or Mean Affinity Discrimination (NOMAD) Projection, the first method for unstructured data visualization via nonlinear dimensionality reduction that can run on multiple GPUs at train time. We provide theory that situates NOMAD Projection as an approximate upper bound on the InfoNC-t-SNE loss, and empirical results that demonstrate NOMAD Projection's superior performance and speed profile compared to existing state-of-the-art methods. We demonstrate the scalability of NOMAD Projection by computing the first complete data map of Multilingual Wikipedia.
Attribute network embedding faces significant challenges, primarily integrating heterogeneous information and managing outliers. In this paper, we introduce a novel Robust Integrating Method by High-order Proximity for Self-supervised Attribute Network Embedding (RSANE). Firstly, a novel heterogeneous topological and semantic information integration method is designed, which contains arbitrary high-order proximity and theoretically includes summation and multiplication forms. Secondly, the RSANE can adaptively reduce the influence of outliers during the embedding process. By incorporating higher-order proximity, RSANE increases the score of outliers and achieves better robustness. Finally, through a deep architecture with dual autoencoders, RSANE achieves joint embedding of network structure and node attributes. In addition, introducing end-to-end reconstruction of structure and attributes can fully extract potential information. Moreover, extensive experiments associated with statistical tests and sensitivity analysis demonstrate that RSANE outperforms state-of-the-art algorithms across various downstream tasks. The code is available at https://github.com/wuzelong/RSANE.
This paper shows a comprehensive analysis of three algorithms (Time Series, Random Forest (RF) and Deep Reinforcement Learning) into three inventory models (the Lost Sales, Dual-Sourcing and Multi-Echelon Inventory Model). These methodologies are applied in the supermarket context. The main purpose is to analyse efficient methods for the data-driven. Their possibility, potential and current challenges are taken into consideration in this report. By comparing the results in each model, the effectiveness of each algorithm is evaluated based on several key performance indicators, including forecast accuracy, adaptability to market changes, and overall impact on inventory costs and customer satisfaction levels. The data visualization tools and statistical metrics are the indicators for the comparisons and show some obvious trends and patterns that can guide decision-making in inventory management. These tools enable managers to not only track the performance of different algorithms in real-time but also to drill down into specific data points to understand the underlying causes of inventory fluctuations. This level of detail is crucial for pinpointing inefficiencies and areas for improvement within the supply chain.
Effective data visualization requires not only technical proficiency but also a deep understanding of the domain-specific context in which data exists. This context often includes tacit knowledge about data provenance, quality, and intended use, which is rarely explicit in the dataset itself. We present the Data Therapist, a web-based tool that helps domain experts externalize this implicit knowledge through a mixed-initiative process combining iterative Q&A with interactive annotation. Powered by a large language model, the system analyzes user-supplied datasets, prompts users with targeted questions, and allows annotation at varying levels of granularity. The resulting structured knowledge base can inform both human and automated visualization design. We evaluated the tool in a qualitative study involving expert pairs from Molecular Biology, Accounting, Political Science, and Usable Security. The study revealed recurring patterns in how experts reason about their data and highlights areas where AI support can improve visualization design.
For over half a century, the computer mouse has been the primary tool for interacting with digital data, yet it remains a limiting factor in exploring complex, multi-scale scientific images. Traditional 2D visualization methods hinder intuitive analysis of inherently 3D structures. Virtual Reality (VR) offers a transformative alternative, providing immersive, interactive environments that enhance data comprehension. This article introduces ASCRIBE-VR, a VR platform of Autonomous Solutions for Computational Research with Immersive Browsing \& Exploration, which integrates AI-driven algorithms with scientific images. ASCRIBE-VR enables multimodal analysis, structural assessments, and immersive visualization, supporting scientific visualization of advanced datasets such as X-ray CT, Magnetic Resonance, and synthetic 3D imaging. Our VR tools, compatible with Meta Quest, can consume the output of our AI-based segmentation and iterative feedback processes to enable seamless exploration of large-scale 3D images. By merging AI-generated results with VR visualization, ASCRIBE-VR enhances scientific discovery, bridging the gap between computational analysis and human intuition in materials research, connecting human-in-the-loop with digital twins.
Recent developments in multimodal large language models (MLLM) have equipped language models to reason about vision and language jointly. This permits MLLMs to both perceive and answer questions about data visualization across a variety of designs and tasks. Applying MLLMs to a broad range of visualization tasks requires us to properly evaluate their capabilities, and the most common way to conduct evaluation is through measuring a model's visualization reasoning capability, analogous to how we would evaluate human understanding of visualizations (e.g., visualization literacy). However, we found that in the context of visualization question answering (VisQA), how an MLLM perceives and reasons about visualizations can be fundamentally different from how humans approach the same problem. During the evaluation, even without visualization, the model could correctly answer a substantial portion of the visualization test questions, regardless of whether any selection options were provided. We hypothesize that the vast amount of knowledge encoded in the language model permits factual recall that supersedes the need to seek information from the visual signal. It raises concerns that the current VisQA evaluation may not fully capture the models' visualization reasoning capabilities. To address this, we propose a comprehensive sanity check framework that integrates a rule-based decision tree and a sanity check table to disentangle the effects of "seeing" (visual processing) and "recall" (reliance on prior knowledge). This validates VisQA datasets for evaluation, highlighting where models are truly "seeing", positively or negatively affected by the factual recall, or relying on inductive biases for question answering. Our study underscores the need for careful consideration in designing future visualization understanding studies when utilizing MLLMs.
Halide perovskites exhibit unpredictable properties in response to environmental stressors, due to several composition-dependent degradation mechanisms. In this work, we apply data visualization and machine learning (ML) techniques to reveal unexpected correlations between composition, temperature, and material properties while using high throughput, in situ environmental photoluminescence (PL) experiments. Correlation heatmaps show the strong influence of Cs content on film degradation, and dimensionality reduction visualization methods uncover clear composition-based data clusters. An extreme gradient boosting algorithm (XGBoost) effectively forecasts PL features for ten perovskite films with both composition-agnostic (>85% accuracy) and composition-dependent (>75% accuracy) model approaches, while elucidating the relative feature importance of composition (up to 99%). This model validates a previously unseen anti-correlation between Cs content and material thermal stability. Our ML-based framework can be expanded to any perovskite family, significantly reducing the analysis time currently employed to identify stable options for photovoltaics.
OLAF (Open Life Science Analysis Framework) is an open-source platform that enables researchers to perform bioinformatics analyses using natural language. By combining large language models (LLMs) with a modular agent-pipe-router architecture, OLAF generates and executes bioinformatics code on real scientific data, including formats like .h5ad. The system includes an Angular front end and a Python/Firebase backend, allowing users to run analyses such as single-cell RNA-seq workflows, gene annotation, and data visualization through a simple web interface. Unlike general-purpose AI tools, OLAF integrates code execution, data handling, and scientific libraries in a reproducible, user-friendly environment. It is designed to lower the barrier to computational biology for non-programmers and support transparent, AI-powered life science research.
In recent years, the rapid development of large reasoning models has resulted in the saturation of existing benchmarks for evaluating mathematical reasoning, highlighting the urgent need for more challenging and rigorous evaluation frameworks. To address this gap, we introduce OlymMATH, a novel Olympiad-level mathematical benchmark, designed to rigorously test the complex reasoning capabilities of LLMs. OlymMATH features 200 meticulously curated problems, each manually verified and available in parallel English and Chinese versions. The problems are systematically organized into two distinct difficulty tiers: (1) AIME-level problems (easy) that establish a baseline for mathematical reasoning assessment, and (2) significantly more challenging problems (hard) designed to push the boundaries of current state-of-the-art models. In our benchmark, these problems span four core mathematical fields, each including a verifiable numerical solution to enable objective, rule-based evaluation. Empirical results underscore the significant challenge presented by OlymMATH, with state-of-the-art models including DeepSeek-R1, OpenAI's o3-mini and Gemini 2.5 Pro Exp demonstrating notably limited accuracy on the hard subset. Furthermore, the benchmark facilitates comprehensive bilingual assessment of mathematical reasoning abilities-a critical dimension that remains largely unaddressed in mainstream mathematical reasoning benchmarks. We release the benchmark, evaluation code, detailed results and a data visualization tool at https://github.com/RUCAIBox/OlymMATH.
Generative models are popular for medical imaging tasks such as anomaly detection, feature extraction, data visualization, or image generation. Since they are parameterized by deep learning models, they are often sensitive to distribution shifts and unreliable when applied to out-of-distribution data, creating a risk of, e.g. underrepresentation bias. This behavior can be flagged using uncertainty quantification methods for generative models, but their availability remains limited. We propose SLUG: A new UQ method for VAEs that combines recent advances in Laplace approximations with stochastic trace estimators to scale gracefully with image dimensionality. We show that our UQ score -- unlike the VAE's encoder variances -- correlates strongly with reconstruction error and racial underrepresentation bias for dermatological images. We also show how pixel-wise uncertainty can detect out-of-distribution image content such as ink, rulers, and patches, which is known to induce learning shortcuts in predictive models.
To address the dual challenges of the curse of dimensionality and the difficulty in separating intra-cluster and inter-cluster structures in high-dimensional manifold embedding, we proposes an Adaptive Multi-Scale Manifold Embedding (AMSME) algorithm. By introducing ordinal distance to replace traditional Euclidean distances, we theoretically demonstrate that ordinal distance overcomes the constraints of the curse of dimensionality in high-dimensional spaces, effectively distinguishing heterogeneous samples. We design an adaptive neighborhood adjustment method to construct similarity graphs that simultaneously balance intra-cluster compactness and inter-cluster separability. Furthermore, we develop a two-stage embedding framework: the first stage achieves preliminary cluster separation while preserving connectivity between structurally similar clusters via the similarity graph, and the second stage enhances inter-cluster separation through a label-driven distance reweighting. Experimental results demonstrate that AMSME significantly preserves intra-cluster topological structures and improves inter-cluster separation on real-world datasets. Additionally, leveraging its multi-resolution analysis capability, AMSME discovers novel neuronal subtypes in the mouse lumbar dorsal root ganglion scRNA-seq dataset, with marker gene analysis revealing their distinct biological roles.
Bizard is a novel visualization code repository designed to simplify data analysis in biomedical research. It integrates diverse visualization codes, facilitating the selection and customization of optimal visualization methods for specific research needs. The platform offers a user-friendly interface with advanced browsing and filtering mechanisms, comprehensive tutorials, and interactive forums to enhance knowledge exchange and innovation. Bizard's collaborative model encourages continuous refinement and expansion of its functionalities, making it an indispensable tool for advancing biomedical data visualization and analytical methodologies. By leveraging Bizard's resources, researchers can enhance data visualization skills, drive methodological advancements, and improve data interpretation standards, ultimately fostering the development of precision medicine and personalized therapeutic interventions.Bizard can be accessed from http://genaimed.org/Bizard/.
The COVID-19 pandemic has profoundly affected the normal course of life -- from lock-downs and virtual meetings to the unprecedentedly swift creation of vaccines. To halt the COVID-19 pandemic, the world has started preparing for the global vaccine roll-out. In an effort to navigate the immense volume of information about COVID-19, the public has turned to social networks. Among them, $\mathbb{X}$ (formerly Twitter) has played a key role in distributing related information. Most people are not trained to interpret medical research and remain skeptical about the efficacy of new vaccines. Measuring their reactions and perceptions is gaining significance in the fight against COVID-19. To assess the public perception regarding the COVID-19 vaccine, our work applies a sentiment analysis approach, using natural language processing of $\mathbb{X}$ data. We show how to use textual analytics and textual data visualization to discover early insights (for example, by analyzing the most frequently used keywords and hashtags). Furthermore, we look at how people's sentiments vary across the countries. Our results indicate that although the overall reaction to the vaccine is positive, there are also negative sentiments associated with the tweets, especially when examined at the country level. Additionally, from the extracted tweets, we manually labeled 100 tweets as positive and 100 tweets as negative and trained various One-Class Classifiers (OCCs). The experimental results indicate that the S-SVDD classifiers outperform other OCCs.
Many machine learning algorithms try to visualize high dimensional metric data in 2D in such a way that the essential geometric and topological features of the data are highlighted. In this paper, we introduce a framework for aggregating dissimilarity functions that arise from locally adjusting a metric through density-aware normalization, as employed in the IsUMap method. We formalize these approaches as m-schemes, a class of methods closely related to t-norms and t-conorms in probabilistic metrics, as well as to composition laws in information theory. These m-schemes provide a flexible and theoretically grounded approach to refining distance-based embeddings.