Chaoli Wang

Kuangshi Ai, Haichao Miao, Kaiyuan Tang et al.

Recent advances in agentic visualization have enabled the translation of natural language into executable scientific visualization (SciVis) workflows. While general-purpose coding agents show strong capabilities, they often lack the tool-specific expertise required for SciVis tasks. In this work, we present SciVisAgentSkills, a collection of reusable agent skills that augment coding agents for scientific data analysis and visualization by encoding environment assumptions, tool usage patterns, and domain heuristics across scientific tools such as ParaView, napari, VMD, and TTK. We evaluate these skills on Codex and Claude Code using SciVisAgentBench, a benchmark of 108 expert-designed multi-step tasks. Results show that agent skills improve mean task scores across the evaluated suites, with token-efficiency benefits that depend on the agent harness and tool setting. These findings highlight the importance of structured procedural knowledge for enabling reliable, long-horizon SciVis workflows, while also showing that skills should be studied alongside the execution harness that loads and applies them. The skills are available at https://github.com/KuangshiAi/SciVisAgentSkills.

Yunfei Lu, Pengfei Gu, Chaoli Wang

We present FCNR, a fast compressive neural representation for tens of thousands of visualization images under varying viewpoints and timesteps. The existing NeRVI solution, albeit enjoying a high compression ratio, incurs slow speeds in encoding and decoding. Built on the recent advances in stereo image compression, FCNR assimilates stereo context modules and joint context transfer modules to compress image pairs. Our solution significantly improves encoding and decoding speed while maintaining high reconstruction quality and satisfying compression ratio. To demonstrate its effectiveness, we compare FCNR with state-of-the-art neural compression methods, including E-NeRV, HNeRV, NeRVI, and ECSIC. The source code can be found at https://github.com/YunfeiLu0112/FCNR.

Delin An, Chaoli Wang

Diffusion probabilistic models have demonstrated significant potential in generating high-quality, realistic medical images, providing a promising solution to the persistent challenge of data scarcity in the medical field. Nevertheless, producing 3D medical volumes with anatomically consistent structures under multimodal conditions remains a complex and unresolved problem. We introduce Sketch2CT, a multimodal diffusion framework for structure-aware 3D medical volume generation, jointly guided by a user-provided 2D sketch and a textual description that captures 3D geometric semantics. The framework initially generates 3D segmentation masks of the target organ from random noise, conditioned on both modalities. To effectively align and fuse these inputs, we propose two key modules that refine sketch features with localized textual cues and integrate global sketch-text representations. Built upon a capsule-attention backbone, these modules leverage the complementary strengths of sketches and text to produce anatomically accurate organ shapes. The synthesized segmentation masks subsequently guide a latent diffusion model for 3D CT volume synthesis, enabling realistic reconstruction of organ appearances that are consistent with user-defined sketches and descriptions. Extensive experiments on public CT datasets demonstrate that Sketch2CT achieves superior performance in generating multimodal medical volumes. Its controllable, low-cost generation pipeline enables principled, efficient augmentation of medical datasets. Code is available at https://github.com/adlsn/Sketch2CT.

Chaoli Wang, Jun Han

Since 2016, we have witnessed the tremendous growth of artificial intelligence+visualization (AI+VIS) research. However, existing survey papers on AI+VIS focus on visual analytics and information visualization, not scientific visualization (SciVis). In this paper, we survey related deep learning (DL) works in SciVis, specifically in the direction of DL4SciVis: designing DL solutions for solving SciVis problems. To stay focused, we primarily consider works that handle scalar and vector field data but exclude mesh data. We classify and discuss these works along six dimensions: domain setting, research task, learning type, network architecture, loss function, and evaluation metric. The paper concludes with a discussion of the remaining gaps to fill along the discussed dimensions and the grand challenges we need to tackle as a community. This state-of-the-art survey guides SciVis researchers in gaining an overview of this emerging topic and points out future directions to grow this research.

Pengfei Gu, Yejia Zhang, Chaoli Wang et al.

Convolutional neural network (CNN) based methods have achieved great successes in medical image segmentation, but their capability to learn global representations is still limited due to using small effective receptive fields of convolution operations. Transformer based methods are capable of modelling long-range dependencies of information for capturing global representations, yet their ability to model local context is lacking. Integrating CNN and Transformer to learn both local and global representations while exploring multi-scale features is instrumental in further improving medical image segmentation. In this paper, we propose a hierarchical CNN and Transformer hybrid architecture, called ConvFormer, for medical image segmentation. ConvFormer is based on several simple yet effective designs. (1) A feed forward module of Deformable Transformer (DeTrans) is re-designed to introduce local information, called Enhanced DeTrans. (2) A residual-shaped hybrid stem based on a combination of convolutions and Enhanced DeTrans is developed to capture both local and global representations to enhance representation ability. (3) Our encoder utilizes the residual-shaped hybrid stem in a hierarchical manner to generate feature maps in different scales, and an additional Enhanced DeTrans encoder with residual connections is built to exploit multi-scale features with feature maps of different scales as input. Experiments on several datasets show that our ConvFormer, trained from scratch, outperforms various CNN- or Transformer-based architectures, achieving state-of-the-art performance.

Kuangshi Ai, Haichao Miao, Kaiyuan Tang et al.

Recent advances in large language models (LLMs) have enabled agentic systems that 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/.

Kaiyuan Tang, Chaoli Wang

Due to its conceptual simplicity and generality, compressive neural representation has emerged as a promising alternative to traditional compression methods for managing massive volumetric datasets. The current practice of neural compression utilizes a single large multilayer perceptron (MLP) to encode the global volume, incurring slow training and inference. This paper presents an efficient compressive neural representation (ECNR) solution for time-varying data compression, utilizing the Laplacian pyramid for adaptive signal fitting. Following a multiscale structure, we leverage multiple small MLPs at each scale for fitting local content or residual blocks. By assigning similar blocks to the same MLP via size uniformization, we enable balanced parallelization among MLPs to significantly speed up training and inference. Working in concert with the multiscale structure, we tailor a deep compression strategy to compact the resulting model. We show the effectiveness of ECNR with multiple datasets and compare it with state-of-the-art compression methods (mainly SZ3, TTHRESH, and neurcomp). The results position ECNR as a promising solution for volumetric data compression.

Kaiyuan Tang, Chaoli Wang

In volume visualization, visualization synthesis has attracted much attention due to its ability to generate novel visualizations without following the conventional rendering pipeline. However, existing solutions based on generative adversarial networks often require many training images and take significant training time. Still, issues such as low quality, consistency, and flexibility persist. This paper introduces StyleRF-VolVis, an innovative style transfer framework for expressive volume visualization (VolVis) via neural radiance field (NeRF). The expressiveness of StyleRF-VolVis is upheld by its ability to accurately separate the underlying scene geometry (i.e., content) and color appearance (i.e., style), conveniently modify color, opacity, and lighting of the original rendering while maintaining visual content consistency across the views, and effectively transfer arbitrary styles from reference images to the reconstructed 3D scene. To achieve these, we design a base NeRF model for scene geometry extraction, a palette color network to classify regions of the radiance field for photorealistic editing, and an unrestricted color network to lift the color palette constraint via knowledge distillation for non-photorealistic editing. We demonstrate the superior quality, consistency, and flexibility of StyleRF-VolVis by experimenting with various volume rendering scenes and reference images and comparing StyleRF-VolVis against other image-based (AdaIN), video-based (ReReVST), and NeRF-based (ARF and SNeRF) style rendering solutions.

Patrick Phuoc Do, Kaiyuan Tang, Kuangshi Ai et al.

Scientific visualization (SciVis) has become an essential means for exploring, understanding, and communicating complex scientific phenomena. However, the field still lacks a validated instrument assessing how well people read, understand, and interpret them. We present a scientific visualization literacy assessment test (SVLAT) that measures the general public's SciVis literacy. Covering a range of visualization forms and interpretation demands, SVLAT comprises 49 items grounded in 18 scientific visualizations and illustrations spanning eight visualization techniques and 11 tasks. Instrument development followed a staged, psychometrically grounded pipeline. We defined the construct and blueprint, followed by item generation, and expert review with five SciVis experts using the content validity ratio (mean CVR = 0.79). We subsequently administered a pilot test (30 participants) and a large-scale test tryout (485 participants) to evaluate the instrument's psychometric properties. For validation, we performed item analysis and refinement using both classical test theory (CTT) and item response theory (IRT) to examine item functioning and overall test quality. SVLAT demonstrates high reliability in the tryout sample (McDonald's omega_t = 0.82, Cronbach's alpha = 0.81). The assessment materials are available at https://osf.io/hr3nw/.

Siyuan Yao, Weixi Song, Chaoli Wang

This comparative study evaluates various neural surface reconstruction methods, particularly focusing on their implications for scientific visualization through reconstructing 3D surfaces via multi-view rendering images. We categorize ten methods into neural radiance fields and neural implicit surfaces, uncovering the benefits of leveraging distance functions (i.e., SDFs and UDFs) to enhance the accuracy and smoothness of the reconstructed surfaces. Our findings highlight the efficiency and quality of NeuS2 for reconstructing closed surfaces and identify NeUDF as a promising candidate for reconstructing open surfaces despite some limitations. By sharing our benchmark dataset, we invite researchers to test the performance of their methods, contributing to the advancement of surface reconstruction solutions for scientific visualization.

Haichao Miao, Zhimin Li, Kuangshi Ai et al.

The ability to inspect, interpret, and communicate complex data is crucial for virtually any scientific endeavor, but often requires significant expertise outside the core domain ranging from data management and analysis to visualization design and implementation. We present an end-to-end agentic harness that, based on only the data and a high level description of the tasks, independently designs custom visual analysis applications (VIS apps). This represents an important step towards a general AI co-scientist envisioned by many as an autonomous system that can autonomously execute long horizon tasks based on high-level directions. Our proposed VIS co-scientist is an essential component of this broader AI co-scientist vision: a harness that can autonomously analyze data and design visualization solutions using a collection of agents and specialized skills that coordinate exploratory analysis, plan, configure the environment, implement, validate the interface, and most importantly evaluate the overall task completion. Each stage produces document and instruction artifacts that guide downstream work and enable iterative refinement. We validate this approach on IEEE SciVis Contests spanning multiple science and engineering fields. These contests serve as ideal proving grounds because they encode real-world complexity: ambiguous requirements, diverse data modalities, design trade-offs, and task-driven validation. Given only the data and target tasks, our system autonomously produces functional single-page VIS Apps with verified linked-view behavior, highly customized to domain experts' specified tasks and needs.

Siyuan Yao, Siavash Ghorbany, Kuangshi Ai et al.

We present a novel framework for automatically evaluating building conditions nationwide in the United States by leveraging large language models (LLMs) and Google Street View (GSV) imagery. By fine-tuning Gemma 3 27B on a modest human-labeled dataset, our approach achieves strong alignment with human mean opinion scores (MOS), outperforming even individual raters on SRCC and PLCC relative to the MOS benchmark. To enhance efficiency, we apply knowledge distillation, transferring the capabilities of Gemma 3 27B to a smaller Gemma 3 4B model that achieves comparable performance with a 3x speedup. Further, we distill the knowledge into a CNN-based model (EfficientNetV2-M) and a transformer (SwinV2-B), delivering close performance while achieving a 30x speed gain. Furthermore, we investigate LLMs' capabilities for assessing an extensive list of built environment and housing attributes through a human-AI alignment study and develop a visualization dashboard that integrates LLM assessment outcomes for downstream analysis by homeowners. Our framework offers a flexible and efficient solution for large-scale building condition assessment, enabling high accuracy with minimal human labeling effort.

Kaiyuan Tang, Siyuan Yao, Chaoli Wang

In volume visualization, users can interactively explore the three-dimensional data by specifying color and opacity mappings in the transfer function (TF) or adjusting lighting parameters, facilitating meaningful interpretation of the underlying structure. However, rendering large-scale volumes demands powerful GPUs and high-speed memory access for real-time performance. While existing novel view synthesis (NVS) methods offer faster rendering speeds with lower hardware requirements, the visible parts of a reconstructed scene are fixed and constrained by preset TF settings, significantly limiting user exploration. This paper introduces inverse volume rendering via Gaussian splatting (iVR-GS), an innovative NVS method that reduces the rendering cost while enabling scene editing for interactive volume exploration. Specifically, we compose multiple iVR-GS models associated with basic TFs covering disjoint visible parts to make the entire volumetric scene visible. Each basic model contains a collection of 3D editable Gaussians, where each Gaussian is a 3D spatial point that supports real-time scene rendering and editing. We demonstrate the superior reconstruction quality and composability of iVR-GS against other NVS solutions (Plenoxels, CCNeRF, and base 3DGS) on various volume datasets. The code is available at https://github.com/TouKaienn/iVR-GS.

Maizhe Yang, Kaiyuan Tang, Chaoli Wang

Implicit neural representation (INR) has emerged as a promising solution for encoding volumetric data, offering continuous representations and seamless compatibility with the volume rendering pipeline. However, optimizing an INR network from randomly initialized parameters for each new volume is computationally inefficient, especially for large-scale time-varying or ensemble volumetric datasets where volumes share similar structural patterns but require independent training. To close this gap, we propose Meta-INR, a pretraining strategy adapted from meta-learning algorithms to learn initial INR parameters from partial observation of a volumetric dataset. Compared to training an INR from scratch, the learned initial parameters provide a strong prior that enhances INR generalizability, allowing significantly faster convergence with just a few gradient updates when adapting to a new volume and better interpretability when analyzing the parameters of the adapted INRs. We demonstrate that Meta-INR can effectively extract high-quality generalizable features that help encode unseen similar volume data across diverse datasets. Furthermore, we highlight its utility in tasks such as simulation parameter analysis and representative timestep selection. The code is available at https://github.com/spacefarers/MetaINR.

Delin An, Pan Du, Pengfei Gu et al.

Accurate segmentation of the aorta and its associated arch branches is crucial for diagnosing aortic diseases. While deep learning techniques have significantly improved aorta segmentation, they remain challenging due to the intricate multiscale structure and the complexity of the surrounding tissues. This paper presents a novel approach for enhancing aorta segmentation using a Bayesian neural network-based hierarchical Laplacian of Gaussian (LoG) model. Our model consists of a 3D U-Net stream and a hierarchical LoG stream: the former provides an initial aorta segmentation, and the latter enhances blood vessel detection across varying scales by learning suitable LoG kernels, enabling self-adaptive handling of different parts of the aorta vessels with significant scale differences. We employ a Bayesian method to parameterize the LoG stream and provide confidence intervals for the segmentation results, ensuring robustness and reliability of the prediction for vascular medical image analysts. Experimental results show that our model can accurately segment main and supra-aortic vessels, yielding at least a 3% gain in the Dice coefficient over state-of-the-art methods across multiple volumes drawn from two aorta datasets, and can provide reliable confidence intervals for different parts of the aorta. The code is available at https://github.com/adlsn/LoGBNet.

Delin An, Pengfei Gu, Milan Sonka et al.

Deep learning (DL) methods have shown remarkable successes in medical image segmentation, often using large amounts of annotated data for model training. However, acquiring a large number of diverse labeled 3D medical image datasets is highly difficult and expensive. Recently, mask propagation DL methods were developed to reduce the annotation burden on 3D medical images. For example, Sli2Vol~\cite{yeung2021sli2vol} proposed a self-supervised framework (SSF) to learn correspondences by matching neighboring slices via slice reconstruction in the training stage; the learned correspondences were then used to propagate a labeled slice to other slices in the test stage. But, these methods are still prone to error accumulation due to the inter-slice propagation of reconstruction errors. Also, they do not handle discontinuities well, which can occur between consecutive slices in 3D images, as they emphasize exploiting object continuity. To address these challenges, in this work, we propose a new SSF, called \proposed, {for segmenting any anatomical structures in 3D medical images using only a single annotated slice per training and testing volume.} Specifically, in the training stage, we first propagate an annotated 2D slice of a training volume to the other slices, generating pseudo-labels (PLs). Then, we develop a novel Object Estimation Guided Correspondence Flow Network to learn reliable correspondences between consecutive slices and corresponding PLs in a self-supervised manner. In the test stage, such correspondences are utilized to propagate a single annotated slice to the other slices of a test volume. We demonstrate the effectiveness of our method on various medical image segmentation tasks with different datasets, showing better generalizability across different organs, modalities, and modals. Code is available at \url{https://github.com/adlsn/Sli2Volplus}

Zixuan Pan, Kaiyuan Tang, Jun Xia et al.

2D Gaussian Splatting has emerged as a novel image representation technique that can support efficient rendering on low-end devices. However, scaling to high-resolution images requires optimizing and storing millions of unstructured Gaussian primitives independently, leading to slow convergence and redundant parameters. To address this, we propose Structured Gaussian Image (SGI), a compact and efficient framework for representing high-resolution images. SGI decomposes a complex image into multi-scale local spaces defined by a set of seeds. Each seed corresponds to a spatially coherent region and, together with lightweight multi-layer perceptrons (MLPs), generates structured implicit 2D neural Gaussians. This seed-based formulation imposes structural regularity on otherwise unstructured Gaussian primitives, which facilitates entropy-based compression at the seed level to reduce the total storage. However, optimizing seed parameters directly on high-resolution images is a challenging and non-trivial task. Therefore, we designed a multi-scale fitting strategy that refines the seed representation in a coarse-to-fine manner, substantially accelerating convergence. Quantitative and qualitative evaluations demonstrate that SGI achieves up to 7.5x compression over prior non-quantized 2D Gaussian methods and 1.6x over quantized ones, while also delivering 1.6x and 6.5x faster optimization, respectively, without degrading, and often improving, image fidelity. Code is available at https://github.com/zx-pan/SGI.

Xiaojing Duan, Frederick Nwanganga, Chaoli Wang

We present CODE-GEN, a human-in-the-Loop, retrieval-augmented generation (RAG)-based agentic AI system for generating context-aligned multiple-choice questions to develop student code reasoning and comprehension abilities. CODE-GEN employs an agentic AI architecture in which a Generator agent produces multiple-choice coding comprehension questions aligned with course-specific learning objectives, while a Validator agent independently assesses content quality across seven pedagogical dimensions. Both agents are augmented with specialized tools that enhance computational accuracy and verify code outputs. To evaluate the effectiveness of CODE-GEN, we conducted an evaluation study involving six human subject-matter experts (SMEs) who judged 288 AI-generated questions. The SMEs produced a total of 2,016 human-AI rating pairs, indicating agreement or disagreement with the assessments of Validator, along with 131 instances of qualitative feedback. Analyses of SME judgments show strong system performance, with human-validated success rates ranging from 79.9% to 98.6% across the seven pedagogical dimensions. The analysis of qualitative feedback reveals that CODE-GEN achieves high reliability on dimensions well suited to computational verification and explicit criteria matching, including question clarity, code validity, concept alignment, and correct answer validity. In contrast, human expertise remains essential for dimensions requiring deeper instructional judgment, such as designing pedagogically meaningful distractors and providing high-quality feedback that reinforces understanding. These findings inform the strategic allocation of human and AI effort in AI-assisted educational content generation.

Delin An, Chaoli Wang

Unlike their line-based counterparts, surface-based techniques have yet to be thoroughly investigated in flow visualization due to their significant placement, speed, perception, and evaluation challenges. This paper presents SurfPatch, a novel framework supporting exploratory stream surface visualization. To begin with, we translate the issue of surface placement to surface selection and trace a large number of stream surfaces from a given flow field dataset. Then, we introduce a three-stage process: vertex-level classification, patch-level matching, and surface-level clustering that hierarchically builds the connection between vertices and patches and between patches and surfaces. This bottom-up approach enables fine-grained, multiscale patch-level matching, sharply contrasts surface-level matching offered by existing works, and provides previously unavailable flexibility during querying. We design an intuitive visual interface for users to conveniently visualize and analyze the underlying collection of stream surfaces in an exploratory manner. SurfPatch is not limited to stream surfaces traced from steady flow datasets. We demonstrate its effectiveness through experiments on stream surfaces produced from steady and unsteady flows as well as isosurfaces extracted from scalar fields. The code is available at https://github.com/adlsn/SurfPatch.

Jackson Vonderhorst, Kuangshi Ai, Haichao Miao et al.

This paper examines how different types of large language model (LLM) agents perform on scientific visualization (SciVis) tasks, where users generate visualization workflows from natural-language instructions. We compare three primary interaction paradigms, including domain-specific agents with structured tool use, computer-use agents, and general-purpose coding agents, by evaluating eight representative agents across 15 benchmark tasks and measuring visualization quality, efficiency, robustness, and computational cost. We further analyze interaction modalities, including code scripts and model context protocol (MCP) or API calls for structured tool use, as well as command-line interfaces (CLI) and graphical user interfaces (GUI) for more general interaction, while additionally studying the effect of persistent memory in selected agents. The results reveal clear tradeoffs across paradigms and modalities. General-purpose coding agents achieve the highest task success rates but are computationally expensive, while domain-specific agents are more efficient and stable but less flexible. Computer-use agents perform well on individual steps but struggle with longer multi-step workflows, indicating that long-horizon planning is their primary limitation. Across both CLI- and GUI-based settings, persistent memory improves performance over repeated trials, although its benefits depend on the underlying interaction mode and the quality of feedback. These findings suggest that no single approach is sufficient, and future SciVis systems should combine structured tool use, interactive capabilities, and adaptive memory mechanisms to balance performance, robustness, and flexibility.

Kaiyuan Tang, Kuangshi Ai, Jun Han et al.

Advancements in volume visualization (VolVis) focus on extracting insights from 3D volumetric data by generating visually compelling renderings that reveal complex internal structures. Existing VolVis approaches have explored non-photorealistic rendering techniques to enhance the clarity, expressiveness, and informativeness of visual communication. While effective, these methods often rely on complex predefined rules and are limited to transferring a single style, restricting their flexibility. To overcome these limitations, we advocate the representation of VolVis scenes using differentiable Gaussian primitives combined with pretrained large models to enable arbitrary style transfer and real-time rendering. However, conventional 3D Gaussian primitives tightly couple geometry and appearance, leading to suboptimal stylization results. To address this, we introduce TexGS-VolVis, a textured Gaussian splatting framework for VolVis. TexGS-VolVis employs 2D Gaussian primitives, extending each Gaussian with additional texture and shading attributes, resulting in higher-quality, geometry-consistent stylization and enhanced lighting control during inference. Despite these improvements, achieving flexible and controllable scene editing remains challenging. To further enhance stylization, we develop image- and text-driven non-photorealistic scene editing tailored for TexGS-VolVis and 2D-lift-3D segmentation to enable partial editing with fine-grained control. We evaluate TexGS-VolVis both qualitatively and quantitatively across various volume rendering scenes, demonstrating its superiority over existing methods in terms of efficiency, visual quality, and editing flexibility.

Hyunsoo Son, Jeonghyun Noh, Suemin Jeon et al.

Implicit Neural Representations (INRs) are widely used to encode data as continuous functions, enabling the visualization of large-scale multivariate scientific simulation data with reduced memory usage. However, existing INR-based methods face three main limitations: (1) inflexible representation of complex structures, (2) primarily focusing on single-variable data, and (3) dependence on structured grids. Thus, their performance degrades when applied to complex real-world datasets. To address these limitations, we propose a novel neural network-based framework, MC-INR, which handles multivariate data on unstructured grids. It combines meta-learning and clustering to enable flexible encoding of complex structures. To further improve performance, we introduce a residual-based dynamic re-clustering mechanism that adaptively partitions clusters based on local error. We also propose a branched layer to leverage multivariate data through independent branches simultaneously. Experimental results demonstrate that MC-INR outperforms existing methods on scientific data encoding tasks.

Pan Du, Delin An, Chaoli Wang et al.

Image-based modeling is essential for understanding cardiovascular hemodynamics and advancing the diagnosis and treatment of cardiovascular diseases. Constructing patient-specific vascular models remains labor-intensive, error-prone, and time-consuming, limiting their clinical applications. This study introduces a deep-learning framework that automates the creation of simulation-ready vascular models from medical images. The framework integrates a segmentation module for accurate voxel-based vessel delineation with a surface deformation module that performs anatomically consistent and unsupervised surface refinements guided by medical image data. By unifying voxel segmentation and surface deformation into a single cohesive pipeline, the framework addresses key limitations of existing methods, enhancing geometric accuracy and computational efficiency. Evaluated on publicly available datasets, the proposed approach demonstrates state-of-the-art performance in segmentation and mesh quality while significantly reducing manual effort and processing time. This work advances the scalability and reliability of image-based computational modeling, facilitating broader applications in clinical and research settings.

Pengfei Gu, Hongxiao Wang, Yejia Zhang et al.

Topological structures in image data, such as connected components and loops, play a crucial role in understanding image content (e.g., biomedical objects). % Despite remarkable successes of numerous image processing methods that rely on appearance information, these methods often lack sensitivity to topological structures when used in general deep learning (DL) frameworks. % In this paper, we introduce a new general approach, called TopoImages (for Topology Images), which computes a new representation of input images by encoding local topology of patches. % In TopoImages, we leverage persistent homology (PH) to encode geometric and topological features inherent in image patches. % Our main objective is to capture topological information in local patches of an input image into a vectorized form. % Specifically, we first compute persistence diagrams (PDs) of the patches, % and then vectorize and arrange these PDs into long vectors for pixels of the patches. % The resulting multi-channel image-form representation is called a TopoImage. % TopoImages offers a new perspective for data analysis. % To garner diverse and significant topological features in image data and ensure a more comprehensive and enriched representation, we further generate multiple TopoImages of the input image using various filtration functions, which we call multi-view TopoImages. % The multi-view TopoImages are fused with the input image for DL-based classification, with considerable improvement. % Our TopoImages approach is highly versatile and can be seamlessly integrated into common DL frameworks. Experiments on three public medical image classification datasets demonstrate noticeably improved accuracy over state-of-the-art methods.

Kuangshi Ai, Jonathan A. Karr, Meng Jiang et al.

We present Knowledge Extraction on OMIn (KEO), a domain-specific knowledge extraction and reasoning framework with large language models (LLMs) in safety-critical contexts. Using the Operations and Maintenance Intelligence (OMIn) dataset, we construct a QA benchmark spanning global sensemaking and actionable maintenance tasks. KEO builds a structured Knowledge Graph (KG) and integrates it into a retrieval-augmented generation (RAG) pipeline, enabling more coherent, dataset-wide reasoning than traditional text-chunk RAG. We evaluate locally deployable LLMs (Gemma-3, Phi-4, Mistral-Nemo) and employ stronger models (GPT-4o, Llama-3.3) as judges. Experiments show that KEO markedly improves global sensemaking by revealing patterns and system-level insights, while text-chunk RAG remains effective for fine-grained procedural tasks requiring localized retrieval. These findings underscore the promise of KG-augmented LLMs for secure, domain-specific QA and their potential in high-stakes reasoning.

Kuangshi Ai, Haichao Miao, Zhimin Li et al.

Recent advances in multi-modal large language models (MLLMs) have enabled increasingly sophisticated autonomous visualization agents capable of translating user intentions into data visualizations. However, measuring progress and comparing different agents remains challenging, particularly in scientific visualization (SciVis), due to the absence of comprehensive, large-scale benchmarks for evaluating real-world capabilities. This position paper examines the various types of evaluation required for SciVis agents, outlines the associated challenges, provides a simple proof-of-concept evaluation example, and discusses how evaluation benchmarks can facilitate agent self-improvement. We advocate for a broader collaboration to develop a SciVis agentic evaluation benchmark that would not only assess existing capabilities but also drive innovation and stimulate future development in the field.

Delin An, Pan Du, Jian-Xun Wang et al.

Accurate 3D aortic construction is crucial for clinical diagnosis, preoperative planning, and computational fluid dynamics (CFD) simulations, as it enables the estimation of critical hemodynamic parameters such as blood flow velocity, pressure distribution, and wall shear stress. Existing construction methods often rely on large annotated training datasets and extensive manual intervention. While the resulting meshes can serve for visualization purposes, they struggle to produce geometrically consistent, well-constructed surfaces suitable for downstream CFD analysis. To address these challenges, we introduce AortaDiff, a diffusion-based framework that generates smooth aortic surfaces directly from CT/MRI volumes. AortaDiff first employs a volume-guided conditional diffusion model (CDM) to iteratively generate aortic centerlines conditioned on volumetric medical images. Each centerline point is then automatically used as a prompt to extract the corresponding vessel contour, ensuring accurate boundary delineation. Finally, the extracted contours are fitted into a smooth 3D surface, yielding a continuous, CFD-compatible mesh representation. AortaDiff offers distinct advantages over existing methods, including an end-to-end workflow, minimal dependency on large labeled datasets, and the ability to generate CFD-compatible aorta meshes with high geometric fidelity. Experimental results demonstrate that AortaDiff performs effectively even with limited training data, successfully constructing both normal and pathologically altered aorta meshes, including cases with aneurysms or coarctation. This capability enables the generation of high-quality visualizations and positions AortaDiff as a practical solution for cardiovascular research.

Pengfei Gu, Zihan Zhao, Hongxiao Wang et al.

The Segment Anything Model (SAM) exhibits impressive capabilities in zero-shot segmentation for natural images. Recently, SAM has gained a great deal of attention for its applications in medical image segmentation. However, to our best knowledge, no studies have shown how to harness the power of SAM for medical image classification. To fill this gap and make SAM a true ``foundation model'' for medical image analysis, it is highly desirable to customize SAM specifically for medical image classification. In this paper, we introduce SAMAug-C, an innovative augmentation method based on SAM for augmenting classification datasets by generating variants of the original images. The augmented datasets can be used to train a deep learning classification model, thereby boosting the classification performance. Furthermore, we propose a novel framework that simultaneously processes raw and SAMAug-C augmented image input, capitalizing on the complementary information that is offered by both. Experiments on three public datasets validate the effectiveness of our new approach.

Pengfei Gu, Huimin Li, Yejia Zhang et al.

Masked Autoencoders (MAEs) have been shown to be effective in pre-training Vision Transformers (ViTs) for natural and medical image analysis problems. By reconstructing missing pixel/voxel information in visible patches, a ViT encoder can aggregate contextual information for downstream tasks. But, existing MAE pre-training methods, which were specifically developed with the ViT architecture, lack the ability to capture geometric shape and spatial information, which is critical for medical image segmentation tasks. In this paper, we propose a novel extension of known MAEs for self pre-training (i.e., models pre-trained on the same target dataset) for 3D medical image segmentation. (1) We propose a new topological loss to preserve geometric shape information by computing topological signatures of both the input and reconstructed volumes, learning geometric shape information. (2) We introduce a pre-text task that predicts the positions of the centers and eight corners of 3D crops, enabling the MAE to aggregate spatial information. (3) We extend the MAE pre-training strategy to a hybrid state-of-the-art (SOTA) medical image segmentation architecture and co-pretrain it alongside the ViT. (4) We develop a fine-tuned model for downstream segmentation tasks by complementing the pre-trained ViT encoder with our pre-trained SOTA model. Extensive experiments on five public 3D segmentation datasets show the effectiveness of our new approach.

Hao Zheng, Jun Han, Hongxiao Wang et al.

A large labeled dataset is a key to the success of supervised deep learning, but for medical image segmentation, it is highly challenging to obtain sufficient annotated images for model training. In many scenarios, unannotated images are abundant and easy to acquire. Self-supervised learning (SSL) has shown great potentials in exploiting raw data information and representation learning. In this paper, we propose Hierarchical Self-Supervised Learning (HSSL), a new self-supervised framework that boosts medical image segmentation by making good use of unannotated data. Unlike the current literature on task-specific self-supervised pretraining followed by supervised fine-tuning, we utilize SSL to learn task-agnostic knowledge from heterogeneous data for various medical image segmentation tasks. Specifically, we first aggregate a dataset from several medical challenges, then pre-train the network in a self-supervised manner, and finally fine-tune on labeled data. We develop a new loss function by combining contrastive loss and classification loss and pretrain an encoder-decoder architecture for segmentation tasks. Our extensive experiments show that multi-domain joint pre-training benefits downstream segmentation tasks and outperforms single-domain pre-training significantly. Compared to learning from scratch, our new method yields better performance on various tasks (e.g., +0.69% to +18.60% in Dice scores with 5% of annotated data). With limited amounts of training data, our method can substantially bridge the performance gap w.r.t. denser annotations (e.g., 10% vs.~100% of annotated data).

Hao Zheng, Yizhe Zhang, Lin Yang et al.

3D image segmentation plays an important role in biomedical image analysis. Many 2D and 3D deep learning models have achieved state-of-the-art segmentation performance on 3D biomedical image datasets. Yet, 2D and 3D models have their own strengths and weaknesses, and by unifying them together, one may be able to achieve more accurate results. In this paper, we propose a new ensemble learning framework for 3D biomedical image segmentation that combines the merits of 2D and 3D models. First, we develop a fully convolutional network based meta-learner to learn how to improve the results from 2D and 3D models (base-learners). Then, to minimize over-fitting for our sophisticated meta-learner, we devise a new training method that uses the results of the base-learners as multiple versions of "ground truths". Furthermore, since our new meta-learner training scheme does not depend on manual annotation, it can utilize abundant unlabeled 3D image data to further improve the model. Extensive experiments on two public datasets (the HVSMR 2016 Challenge dataset and the mouse piriform cortex dataset) show that our approach is effective under fully-supervised, semi-supervised, and transductive settings, and attains superior performance over state-of-the-art image segmentation methods.