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arXiv subjects

Angus G. Forbes

Publications and source records attributed to Angus G. Forbes.

At least 19 recordsLinked to original sources

DiffUNet^2: Bidirectional Prediction, Probabilistic Generation and Collaborative Visual Discovery for Scientific Data

Modeling temporal evolution is important to analyzing and reasoning about scientific phenomena, yet most machine learning methods provide deterministic forward predictions that overlook multiple plausible outcomes and rarely support backward reasoning, limiting their usefulness in practical scientific workflows. We present a framework that integrates diffusion-based generative modeling with interactive visual analytics for scientific exploration. We introduce DiffUNet^2, a conditional diffusion model that enables bidirectional, any-to-any generation across time and captures distributions of plausible system evolutions. Built upon the model, our interactive system supports branching timeline exploration, user-guided state editing, and probability-space navigation, enabling scientists to actively explore alternative hypotheses rather than passively observe predictions. We evaluate the model on 5 datasets across different scientific domains to validate its predictive accuracy and probability-space ensemble quality. In collaboration with domain experts, we demonstrate the effectiveness of our approach in supporting practical scientific temporal data analysis workflows. By integrating modeling and visual interaction, our approach enables scientists to interactively explore system dynamics, transforming generative models into tools for hypothesis-driven scientific analysis.

cs.HC

A11yShape: AI-Assisted 3-D Modeling for Blind and Low-Vision Programmers

Building 3-D models is challenging for blind and low-vision (BLV) users due to the inherent complexity of 3-D models and the lack of support for non-visual interaction in existing tools. To address this issue, we introduce A11yShape, a novel system designed to help BLV users who possess basic programming skills understand, modify, and iterate on 3-D models. A11yShape leverages LLMs and integrates with OpenSCAD, a popular open-source editor that generates 3-D models from code. Key functionalities of A11yShape include accessible descriptions of 3-D models, version control to track changes in models and code, and a hierarchical representation of model components. Most importantly, A11yShape employs a cross-representation highlighting mechanism to synchronize semantic selections across all model representations -- code, semantic hierarchy, AI description, and 3-D rendering. We conducted a multi-session user study with four BLV programmers, where, after an initial tutorial session, participants independently completed 12 distinct models across two testing sessions, achieving results that aligned with their own satisfaction. The result demonstrates that participants were able to comprehend provided 3-D models, as well as independently create and modify 3-D models -- tasks that were previously impossible without assistance from sighted individuals.

cs.HC

FathomGPT: A Natural Language Interface for Interactively Exploring Ocean Science Data

We introduce FathomGPT, an open source system for the interactive investigation of ocean science data via a natural language interface. FathomGPT was developed in close collaboration with marine scientists to enable researchers to explore and analyze the FathomNet image database. FathomGPT provides a custom information retrieval pipeline that leverages OpenAI's large language models to enable: the creation of complex queries to retrieve images, taxonomic information, and scientific measurements; mapping common names and morphological features to scientific names; generating interactive charts on demand; and searching by image or specified patterns within an image. In designing FathomGPT, particular emphasis was placed on enhancing the user's experience by facilitating free-form exploration and optimizing response times. We present an architectural overview and implementation details of FathomGPT, along with a series of ablation studies that demonstrate the effectiveness of our approach to name resolution, fine tuning, and prompt modification. We also present usage scenarios of interactive data exploration sessions and document feedback from ocean scientists and machine learning experts.

cs.HC

Designing Ocean Vision AI: An Investigation of Community Needs for Imaging-based Ocean Conservation

Ocean scientists studying diverse organisms and phenomena increasingly rely on imaging devices for their research. These scientists have many tools to collect their data, but few resources for automated analysis. In this paper, we report on discussions with diverse stakeholders to identify community needs and develop a set of functional requirements for the ongoing development of ocean science-specific analysis tools. We conducted 36 in-depth interviews with individuals working in the Blue Economy space, revealing four central issues inhibiting the development of effective imaging analysis monitoring tools for marine science. We also identified twelve user archetypes that will engage with these services. Additionally, we held a workshop with 246 participants from 35 countries centered around FathomNet, a web-based open-source annotated image database for marine research. Findings from these discussions are being used to define the feature set and interface design of Ocean Vision AI, a suite of tools and services to advance observational capabilities of life in the ocean.

cs.HC

SDSS DR17: The Cosmic Slime Value Added Catalog

The "cosmic web", the filamentary large-scale structure in a cold dark matter Universe, is readily apparent via galaxy tracers in spectroscopic surveys. However, the underlying dark matter structure is as of yet unobservable and mapping the diffuse gas permeating it lies beyond practical observational capabilities. A recently developed technique, inspired by the growth and movement of Physarum polycephalum "slime mold", has been used to map the cosmic web of a low redshift sub-sample of the SDSS spectroscopic galaxy catalog. This model, the Monte Carlo Physarum Machine (MCPM) was shown to promisingly reconstruct the cosmic web. Here, we improve the formalism used in calibrating the MCPM to better recreate the Bolshoi-Planck cosmological simulation's density distributions and apply them to a significantly larger cosmological volume than previous works using the Sloan Digital Sky Survey (SDSS, $z < 0.1$) and the Extended Baryon Oscillation Spectroscopic Survey (eBOSS) Luminous Red Galaxy (LRG, $z \lesssim 0.5$) spectroscopic catalogs. We present the "Cosmic Slime Value Added Catalog" which provides estimates for the cosmic overdensity for the sample of galaxies probed spectroscopically by the above SDSS surveys. In addition, we provide the fully reconstructed 3D density cubes of these volumes. These data products were released as part of Sloan Digital Sky Survey Data Release 17 and are publicly available. We present the input catalogs and the methodology for constructing these data products. We also highlight exciting potential applications to galaxy evolution, cosmology, the intergalactic and circumgalactic medium, and transient phenomenon localization.

astro-ph.CO

Data Feel: Exploring Visual Effects in Video Games to Support Sensemaking Tasks

This paper explores the use of visual effects common in video games that support a range of tasks that are similar in many ways to analysis tasks supported in visual analytics tools. While some visual effects are meant to increase engagement or to support a game's overall visual design, we find that in many games visual effects are used throughout gameplay in order to assist a player in reasoning about the game world. In this work, we survey popular games across a range of categories (from casual games to "Triple A" games), focusing specifically on visual effects that support a player's sensemaking within the game world. Based on our analysis of these games, we identify a range of tasks that could benefit from the use of "data feel," and advocate for the continued investigation of visual effects and their application in data visualization software tools.

cs.HC

Monte Carlo Physarum Machine: Characteristics of Pattern Formation in Continuous Stochastic Transport Networks

We present Monte Carlo Physarum Machine: a computational model suitable for reconstructing continuous transport networks from sparse 2D and 3D data. MCPM is a probabilistic generalization of Jones's 2010 agent-based model for simulating the growth of Physarum polycephalum slime mold. We compare MCPM to Jones's work on theoretical grounds, and describe a task-specific variant designed for reconstructing the large-scale distribution of gas and dark matter in the Universe known as the Cosmic web. To analyze the new model, we first explore MCPM's self-patterning behavior, showing a wide range of continuous network-like morphologies -- called "polyphorms" -- that the model produces from geometrically intuitive parameters. Applying MCPM to both simulated and observational cosmological datasets, we then evaluate its ability to produce consistent 3D density maps of the Cosmic web. Finally, we examine other possible tasks where MCPM could be useful, along with several examples of fitting to domain-specific data as proofs of concept.

astro-ph.CO

Visualization in Astrophysics: Developing New Methods, Discovering Our Universe, and Educating the Earth

We present a state-of-the-art report on visualization in astrophysics. We survey representative papers from both astrophysics and visualization and provide a taxonomy of existing approaches based on data analysis tasks. The approaches are classified based on five categories: data wrangling, data exploration, feature identification, object reconstruction, as well as education and outreach. Our unique contribution is to combine the diverse viewpoints from both astronomers and visualization experts to identify challenges and opportunities for visualization in astrophysics. The main goal is to provide a reference point to bring modern data analysis and visualization techniques to the rich datasets in astrophysics.

astro-ph.IM

Disentangling the Cosmic Web Towards FRB 190608

FRB 190608 was detected by ASKAP and localized to a spiral galaxy at $z_{host}=0.11778$ in the SDSS footprint. The burst has a large dispersion measure ($DM_{FRB}=339.8$ $pc/cm^3$) compared to the expected cosmic average at its redshift. It also has a large rotation measure ($RM_{FRB}=353$ $rad/m^2$) and scattering timescale ($τ=3.3$ $ms$ at $1.28$ $GHz$). Chittidi et al (2020) perform a detailed analysis of the ultraviolet and optical emission of the host galaxy and estimate the host DM contribution to be $110\pm 37$ $pc/cm^3$. This work complements theirs and reports the analysis of the optical data of galaxies in the foreground of FRB 190608 to explore their contributions to the FRB signal. Together, the two manuscripts delineate an observationally driven, end-to-end study of matter distribution along an FRB sightline; the first study of its kind. Combining KCWI observations and public SDSS data, we estimate the expected cosmic dispersion measure $DM_{cosmic}$ along the sightline to FRB 190608. We first estimate the contribution of hot, ionized gas in intervening virialized halos ($DM_{halos} \approx 7-28$ $pc/cm^3$). Then, using the Monte Carlo Physarum Machine (MCPM) methodology, we produce a 3D map of ionized gas in cosmic web filaments and compute the DM contribution from matter outside halos ($DM_{IGM} \approx 91-126$ $pc/cm^3$). This implies a greater fraction of ionized gas along this sightline is extant outside virialized halos. We also investigate whether the intervening halos can account for the large FRB rotation measure and pulse width and conclude that it is implausible. Both the pulse broadening and the large Faraday rotation likely arise from the progenitor environment or the host galaxy.

astro-ph.GA

Bio-inspired Structure Identification in Language Embeddings

Word embeddings are a popular way to improve downstream performances in contemporary language modeling. However, the underlying geometric structure of the embedding space is not well understood. We present a series of explorations using bio-inspired methodology to traverse and visualize word embeddings, demonstrating evidence of discernible structure. Moreover, our model also produces word similarity rankings that are plausible yet very different from common similarity metrics, mainly cosine similarity and Euclidean distance. We show that our bio-inspired model can be used to investigate how different word embedding techniques result in different semantic outputs, which can emphasize or obscure particular interpretations in textual data.

cs.CL

Polyphorm: Structural Analysis of Cosmological Datasets via Interactive Physarum Polycephalum Visualization

This paper introduces Polyphorm, an interactive visualization and model fitting tool that provides a novel approach for investigating cosmological datasets. Through a fast computational simulation method inspired by the behavior of Physarum polycephalum, an unicellular slime mold organism that efficiently forages for nutrients, astrophysicists are able to extrapolate from sparse datasets, such as galaxy maps archived in the Sloan Digital Sky Survey, and then use these extrapolations to inform analyses of a wide range of other data, such as spectroscopic observations captured by the Hubble Space Telescope. Researchers can interactively update the simulation by adjusting model parameters, and then investigate the resulting visual output to form hypotheses about the data. We describe details of Polyphorm's simulation model and its interaction and visualization modalities, and we evaluate Polyphorm through three scientific use cases that demonstrate the effectiveness of our approach.

astro-ph.IM

Revealing the Dark Threads of the Cosmic Web

Modern cosmology predicts that matter in our Universe has assembled today into a vast network of filamentary structures colloquially termed the Cosmic Web. Because this matter is either electromagnetically invisible (i.e., dark) or too diffuse to image in emission, tests of this cosmic web paradigm are limited. Wide-field surveys do reveal web-like structures in the galaxy distribution, but these luminous galaxies represent less than 10% of baryonic matter. Statistics of absorption by the intergalactic medium (IGM) via spectroscopy of distant quasars support the model yet have not conclusively tied the diffuse IGM to the web. Here, we report on a new method inspired by the Physarum polycephalum slime mold that is able to infer the density field of the Cosmic Web from galaxy surveys. Applying our technique to galaxy and absorption-line surveys of the local Universe, we demonstrate that the bulk of the IGM indeed resides in the Cosmic Web. From the outskirts of Cosmic Web filaments, at approximately the cosmic mean matter density (rho_m) and approx. 5 virial radii from nearby galaxies, we detect an increasing H I absorption signature towards higher densities and the circumgalactic medium, to approx. 200 rho_m. However, the absorption is suppressed within the densest environments, suggesting shock-heating and ionization deep within filaments and/or feedback processes within galaxies.

astro-ph.GA

RuleVis: Constructing Patterns and Rules for Rule-Based Models

We introduce RuleVis, a web-based application for defining and editing "correct-by-construction" executable rules that model biochemical functionality, which can be used to simulate the behavior of protein-protein interaction networks and other complex systems. Rule-based models involve emergent effects based on the interactions between rules, which can vary considerably with regard to the scale of a model, requiring the user to inspect and edit individual rules. RuleVis bridges the graph rewriting and systems biology research communities by providing an external visual representation of salient patterns that experts can use to determine the appropriate level of detail for a particular modeling context. We describe the visualization and interaction features available in RuleVisand provide a detailed example demonstrating how RuleVis can be used to reason about intracellular interactions.

q-bio.QM

TempoCave: Visualizing Dynamic Connectome Datasets to Support Cognitive Behavioral Therapy

We introduce TempoCave, a novel visualization application for analyzing dynamic brain networks, or connectomes. TempoCave provides a range of functionality to explore metrics related to the activity patterns and modular affiliations of different regions in the brain. These patterns are calculated by processing raw data retrieved functional magnetic resonance imaging (fMRI) scans, which creates a network of weighted edges between each brain region, where the weight indicates how likely these regions are to activate synchronously. In particular, we support the analysis needs of clinical psychologists, who examine these modular affiliations and weighted edges and their temporal dynamics, utilizing them to understand relationships between neurological disorders and brain activity, which could have a significant impact on the way in which patients are diagnosed and treated. We summarize the core functionality of TempoCave, which supports a range of comparative tasks, and runs both in a desktop mode and in an immersive mode. Furthermore, we present a real-world use case that analyzes pre- and post-treatment connectome datasets from 27 subjects in a clinical study investigating the use of cognitive behavior therapy to treat major depression disorder, indicating that TempoCave can provide new insight into the dynamic behavior of the human brain.

cs.HC

IGM-Vis: Analyzing Intergalactic and Circumgalactic Medium Absorption Using Quasar Sightlines in a Cosmic Web Context

We introduce IGM-Vis, a novel astrophysics visualization and data analysis application for investigating galaxies and the gas that surrounds them in context with their larger scale environment, the Cosmic Web. Environment is an important factor in the evolution of galaxies from actively forming stars to quiescent states with little, if any, discernible star formation activity. The gaseous halos of galaxies (the circumgalactic medium, or CGM) play a critical role in their evolution, because the gas necessary to fuel star formation and any gas expelled from widely observed galactic winds must encounter this interface region between galaxies and the intergalactic medium (IGM). We present a taxonomy of tasks typically employed in IGM/CGM studies informed by a survey of astrophysicists at various career levels, and demonstrate how these tasks are facilitated via the use of our visualization software. Finally, we evaluate the effectiveness of IGM-Vis through two in-depth use cases that depict real-world analysis sessions that use IGM/CGM data.

astro-ph.IM

CAVE-AR: A VR Authoring System to Interactively Design, Simulate, and Debug Multi-user AR Experiences

Despite advances in augmented reality (AR), the process of creating meaningful experiences with this technology is still extremely challenging. Due to different tracking implementations and hardware constraints, developing AR applications either requires low-level programming skills, or is done through specific authoring tools that largely sacrifice the possibility of customizing the AR experience. Existing development workflows also do not support previewing or simulating the AR experience, requiring a lengthy process of trial and error by which content creators deploy and physically test applications in each iteration. To mitigate these limitations, we propose CAVE-AR, a novel virtual reality system for authoring, simulating and debugging custom AR experiences. Available both as a standalone or a plug-in tool, CAVE-AR is based on the concept of representing in the same global reference system both in AR content and tracking information, mixing geographical information, architectural features, and sensor data to simulate the context of an AR experience. Thanks to its novel abstraction of existing tracking technologies, CAVE-AR operates independently of users' devices, and integrates with existing programming tools to provide maximum flexibility. Our VR application provides designers with ways to create and modify an AR application, even while others are in the midst of using it. CAVE-AR further allows the designer to track how users are behaving, preview what they are currently seeing, and interact with them through several different channels. To illustrate our proposed development workflow and demonstrate the advantages of our authoring system, we introduce two CAVEAR use cases in which an augmented reality application is created and tested. We compare the CAVE-AR workflow to traditional development methods and demonstrate the importance of simulation and live application debugging.

cs.HC

Deep Illumination: Approximating Dynamic Global Illumination with Generative Adversarial Network

We present Deep Illumination, a novel machine learning technique for approximating global illumination (GI) in real-time applications using a Conditional Generative Adversarial Network. Our primary focus is on generating indirect illumination and soft shadows with offline rendering quality at interactive rates. Inspired from recent advancement in image-to-image translation problems using deep generative convolutional networks, we introduce a variant of this network that learns a mapping from Gbuffers (depth map, normal map, and diffuse map) and direct illumination to any global illumination solution. Our primary contribution is showing that a generative model can be used to learn a density estimation from screen space buffers to an advanced illumination model for a 3D environment. Once trained, our network can approximate global illumination for scene configurations it has never encountered before within the environment it was trained on. We evaluate Deep Illumination through a comparison with both a state of the art real-time GI technique (VXGI) and an offline rendering GI technique (path tracing). We show that our method produces effective GI approximations and is also computationally cheaper than existing GI techniques. Our technique has the potential to replace existing precomputed and screen-space techniques for producing global illumination effects in dynamic scenes with physically-based rendering quality.

cs.GR

Text Annotation Graphs: Annotating Complex Natural Language Phenomena

This paper introduces a new web-based software tool for annotating text, Text Annotation Graphs, or TAG. It provides functionality for representing complex relationships between words and word phrases that are not available in other software tools, including the ability to define and visualize relationships between the relationships themselves (semantic hypergraphs). Additionally, we include an approach to representing text annotations in which annotation subgraphs, or semantic summaries, are used to show relationships outside of the sequential context of the text itself. Users can use these subgraphs to quickly find similar structures within the current document or external annotated documents. Initially, TAG was developed to support information extraction tasks on a large database of biomedical articles. However, our software is flexible enough to support a wide range of annotation tasks for any domain. Examples are provided that showcase TAG's capabilities on morphological parsing and event extraction tasks. The TAG software is available at: https://github.com/ CreativeCodingLab/TextAnnotationGraphs.

cs.CL