Scientific Visualization

Both Dimensionality Reduction (DR) and Graph Drawing (GD) aim to visualize abstract, non-linear structures, yet rely on different optimization paradigms. This contrast is evident in Multidimensional Scaling (MDS), which typically depends on the SMACOF algorithm despite graph drawing results showing that simpler stochastic optimization schemes can be more effective for the same objective. We bridge these domains by adapting Stochastic Gradient Descent (SGD) techniques from graph drawing to vector data embedding. We present a scikit-learn compatible estimator that minimizes global stress through local pairwise updates, improving upon the existing implementation. Experiments on standard high-dimensional benchmarks show that our stochastic solver converges substantially faster than SMACOF while achieving comparable or lower stress.

This paper examines how large language model (LLM) agents perform on scientific visualization (SciVis) tasks that require generating visualization workflows from natural-language instructions. We compare three representative agent designs: domain-specific agents with structured tool use, computer-use agents, and general-purpose coding agents, across 15 benchmark tasks, evaluating visualization quality, efficiency, robustness, computational cost, and the impact of persistent memory. We further study interaction modalities, including code scripts, model context protocol (MCP) or API calls, command-line interfaces (CLI), and graphical user interfaces (GUI). Our goal is to characterize the tradeoffs among representative SciVis agent configurations used in practice. The results reveal clear tradeoffs across agent designs and interaction modalities. General-purpose coding agents achieve the highest task success rates but incur greater computational cost, whereas domain-specific agents are more efficient and stable but less flexible. Computer-use agents perform well on individual operations but struggle with multi-step workflows. Across both CLI- and GUI-based settings, persistent memory improves performance over repeated trials, but its effectiveness depends on the interaction mode and the quality of feedback. These findings suggest that future SciVis systems should combine structured tool use, interactive capabilities, and adaptive memory mechanisms to balance performance, robustness, and flexibility.

Thematic maps play a central role in academic communication, yet their large-scale design evolution has rarely been examined empirically. This study presents a longitudinal and multilingual analysis of thematic map design practices in academic cartography from 1990 to 2020. We compile a corpus of 45,732 research articles from sixteen authoritative Chinese- and English-language journals and extract 23,928 maps using computer vision and large-model-based document parsing to build a structured dataset. Map design characteristics are quantified across three dimensions: map elements, color design, and layout structure. Results show that Chinese- and Englishlanguage academic maps share highly similar structural conventions, typically employing restrained color palettes with neutral dominant hues, low saturation, high brightness, and limited hue diversity, as well as centered layouts with high main-map occupation ratios. Differences exist in that English-language maps show slightly greater hue richness and compactness, whereas Chinese-language maps historically rely more on neutral hues and integrated layouts. Temporal analysis reveals parallel evolutionary trends in both groups, including increasing element richness, legend usage, and hue diversity, alongside stable layout structures. Overall, the findings suggest that academic map design evolution is characterized more by institutional convergence than cultural divergence.

Mapping large origin-destination (OD) datasets remains challenging because flow maps become cluttered, meaningful patterns occur at multiple spatial scales, and existing flow-mapping approaches frequently rely on predefined aggregation units or manual generalization. This paper presents XFlowMap, a framework for the cross-scale generalization and mapping of massive OD data. Specifically, the framework integrates cross-scale flow pattern (cluster) detection, automated flow map generalization, and a new cartographic representation for analyzing and visualizing complex origin-destination flow structures. The approach detects salient flow patterns at their appropriate origin and destination scales, extracts high-level structures, and generates a new flow map representation that supports holistic interpretation of complex origin-destination flow patterns. A scan-statistic-based procedure is developed to evaluate and generalize cross-scale flow clusters. The detected clusters are then visualized using a novel flow symbol that integrates location, direction, strength, and OD scales in a single representation. The framework supports both area-based and point-based OD data, is robust to sparse and noisy datasets, and enables comparative mapping of stratified flow data. Experiments with synthetic data and U.S. migration data demonstrate that the method effectively extracts meaningful cross-scale flow patterns and produces clear, information-rich flow maps for large mobility datasets, supporting both static presentation and interactive exploration.

Vision-Language Models (VLMs) frequently misread values, hallucinate details, and confuse overlapping elements in charts. Current approaches rely solely on pixel interpretation, creating a Pixel-Only Bottleneck: agents treat interactive charts as static images, losing access to the structured specification that encodes exact values. We introduce Introspective and Interactive Visual Grounding (IVG), a framework that combines (1) spec-grounded introspection, which queries the underlying specification for deterministic evidence, with (2) view-grounded interaction, which manipulates the view to resolve visual ambiguity. To enable evaluation without VLM bias, we present iPlotBench, a benchmark of 500 interactive Plotly figures with 6,706 binary questions and ground-truth specifications. Experiments show that introspection improves data reconstruction fidelity, while the combination with interaction achieves the highest QA accuracy (0.81), with +6.7 % gains on overlapping geometries. We further demonstrate IVG in deployed agents that explore data autonomously and collaborate with human users in real time.

We present SciDraw-6K, a curated dataset of 6,291 scientific illustrations synthesized by Google Gemini image-generation models, each paired with prompts in eleven languages (English, Simplified Chinese, Traditional Chinese, Japanese, Korean, German, French, Spanish, Brazilian Portuguese, Italian, and Russian). Images span eight broad scientific categories -- biomedical, chemistry, materials, electronics, environment, AI systems, physics, and a long "other" tail -- and are produced primarily by the gemini-2.5-flash-image and gemini-3-pro-image-preview model families. In contrast to general-purpose text-to-image corpora that dominate the literature, SciDraw-6K is purpose-built for the scientific illustration genre: schematic diagrams, mechanism figures, table-of-contents graphics, and conceptual posters. We describe the construction pipeline, report dataset statistics, and document its use as the substrate of sci-draw.com, a public scientific drawing service. The dataset is released to support multilingual text-to-image research, domain-adapted diffusion fine-tuning, and prompt-engineering studies for scientific visualization. Dataset: https://huggingface.co/datasets/SciDrawAI/SciDraw-6K Code: https://github.com/SciDrawAI/scidraw-6k

The choice of visualisation in empirical performance analysis is not a neutral presentation decision but an analytical one: different graphical forms reveal different features of the same dataset, and reliance on any single type systematically conceals what the others expose. This paper presents and argues for a suite of five complementary visualisation tools; tempographs, histograms with spline-smoothed probability density functions, ridgeline plots, stacked bar charts, and combination charts. These are applied to bar-level beats-per-minute data from recordings of Beethoven's five piano and cello sonatas (Op.~5 Nos.1 and2; Op.~69; Op.~102 Nos.1 and2) spanning 1930--2012. Each tool is described formally, its analytical properties characterised, its implementation detailed in working Python and MATLAB code, and its specific contribution demonstrated on a worked example using two recordings of Op.~5 No.~1 (Casals/Horszowski 1930--39 and Isserlis/Levin 2012) separated by eight decades. A five-panel composite figure applies all five tools to the same two recordings simultaneously, making the complementarity argument concrete: the tempograph reveals moment-to-moment structural parallels invisible in aggregate statistics; the spline-smoothed histogram exposes bimodality and secondary peaks suppressed by binning artefacts; the ridgeline plot positions both recordings within the full distributional space; the stacked bar chart shows divergent sectional pacing concealed by identical movement means; and the combination chart integrates mean tempo, variability, and historical reference marks in a single view. The spline-CDF smoothing method, applied to histogram data via cubic spline interpolation with zero-slope boundary conditions, is presented as a novel contribution to the performance analysis toolkit. Full implementation code is publicly available.

Recent advances in large language models (LLMs) have enabled agentic systems to translate natural-language intent into executable scientific visualization (SciVis) tasks. Despite rapid progress, the community lacks a principled and reproducible benchmark for evaluating these emerging SciVis agents in realistic, multi-step analysis settings. We present SciVisAgentBench, a comprehensive and extensible benchmark for evaluating scientific data analysis and visualization agents. Our benchmark is grounded in a structured taxonomy spanning four dimensions: application domain, data type, complexity level, and visualization operation. It currently comprises 108 expert-crafted cases covering diverse SciVis scenarios. To enable reliable assessment, we introduce a multimodal outcome-centric evaluation pipeline that combines LLM-based judging with deterministic evaluators, including image-based metrics, code checkers, rule-based verifiers, and case-specific evaluators. We also conduct a validity study with 12 SciVis experts to examine the agreement between human and LLM judges. Using this framework, we evaluate representative SciVis agents and general-purpose coding agents to establish initial baselines and reveal capability gaps. SciVisAgentBench is designed as a living benchmark to support systematic comparison, diagnose failure modes, and drive progress in agentic SciVis. The benchmark is available at https://scivisagentbench.github.io/.

Scientists face significant visualization challenges as time-varying datasets grow in speed and volume, often requiring specialized infrastructure and expertise to handle massive datasets. Petascale climate models generated in NASA laboratories require a dedicated group of graphics and media experts and access to high-performance computing resources. Scientists may need to share scientific results with the community iteratively and quickly. However, the time-consuming trial-and-error process incurs significant data transfer overhead and far exceeds the time and resources allocated for typical post-analysis visualization tasks, disrupting the production workflow. Our paper introduces a user-friendly framework for creating 3D animations of petascale, time-varying data on a commodity workstation. Our contributions: (i) Generalized Animation Descriptor (GAD) with a keyframe-based adaptable abstraction for animation, (ii) efficient data access from cloud-hosted repositories to reduce data management overhead, (iii) tailored rendering system, and (iv) an LLM-assisted conversational interface as a scripting module to allow domain scientists with no visualization expertise to create animations of their region of interest. We demonstrate the framework's effectiveness with two case studies: first, by generating animations in which sampling criteria are specified based on prior knowledge, and second, by generating AI-assisted animations in which sampling parameters are derived from natural-language user prompts. In all cases, we use large-scale NASA climate-oceanographic datasets that exceed 1PB in size yet achieve a fast turnaround time of 1 minute to 2 hours. Users can generate a rough draft of the animation within minutes, then seamlessly incorporate as much high-resolution data as needed for the final version.

We present a general approach to visualizing uncertainty in static 2-D statistical graphics. If we treat a visualization as a function of its underlying quantities, uncertainty in those quantities induces a distribution over images. We show how to aggregate these images into a single visualization that represents the uncertainty. The approach can be viewed as a generalization of sample-based approaches that use overlay. Notably, standard representations, such as confidence intervals and bands, emerge with their usual coverage guarantees without being explicitly quantified or visualized. As a proof of concept, we implement our approach in the IID setting using resampling, provided as an open-source Python library. Because the approach operates directly on images, the user needs only to supply the data and the code for visualizing the quantities of interest without uncertainty. Through several examples, we show how both familiar and novel forms of uncertainty visualization can be created. The implementation is not only a practical validation of the underlying theory but also an immediately usable tool that can complement existing uncertainty-visualization libraries.