Volume 42 (2023)

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ChemoGraph: Interactive Visual Exploration of the Chemical Space
(The Eurographics Association and John Wiley & Sons Ltd., 2023) Kale, Bharat; Clyde, Austin; Sun, Maoyuan; Ramanathan, Arvind; Stevens, Rick; Papka, Michael E.; Bujack, Roxana; Archambault, Daniel; Schreck, Tobias
Exploratory analysis of the chemical space is an important task in the field of cheminformatics. For example, in drug discovery research, chemists investigate sets of thousands of chemical compounds in order to identify novel yet structurally similar synthetic compounds to replace natural products. Manually exploring the chemical space inhabited by all possible molecules and chemical compounds is impractical, and therefore presents a challenge. To fill this gap, we present ChemoGraph, a novel visual analytics technique for interactively exploring related chemicals. In ChemoGraph, we formalize a chemical space as a hypergraph and apply novel machine learning models to compute related chemical compounds. It uses a database to find related compounds from a known space and a machine learning model to generate new ones, which helps enlarge the known space. Moreover, ChemoGraph highlights interactive features that support users in viewing, comparing, and organizing computationally identified related chemicals. With a drug discovery usage scenario and initial expert feedback from a case study, we demonstrate the usefulness of ChemoGraph.
DASS Good: Explainable Data Mining of Spatial Cohort Data
(The Eurographics Association and John Wiley & Sons Ltd., 2023) Wentzel, Andrew; Floricel, Carla; Canahuate, Guadalupe; Naser, Mohamed A.; Mohamed, Abdallah S.; Fuller, Clifton David; Dijk, Lisanne van; Marai, G. Elisabeta; Bujack, Roxana; Archambault, Daniel; Schreck, Tobias
Developing applicable clinical machine learning models is a difficult task when the data includes spatial information, for example, radiation dose distributions across adjacent organs at risk. We describe the co-design of a modeling system, DASS, to support the hybrid human-machine development and validation of predictive models for estimating long-term toxicities related to radiotherapy doses in head and neck cancer patients. Developed in collaboration with domain experts in oncology and data mining, DASS incorporates human-in-the-loop visual steering, spatial data, and explainable AI to augment domain knowledge with automatic data mining. We demonstrate DASS with the development of two practical clinical stratification models and report feedback from domain experts. Finally, we describe the design lessons learned from this collaborative experience.
An Efficient Self-supporting Infill Structure for Computational Fabrication
(The Eurographics Association and John Wiley & Sons Ltd., 2023) Wang, Shengfa; Liu, Zheng; Hu, Jiangbei; Lei, Na; Luo, Zhongxuan; Chaine, Raphaëlle; Deng, Zhigang; Kim, Min H.
Efficiently optimizing the internal structure of 3D printing models is a critical focus in the field of industrial manufacturing, particularly when designing self-supporting structures that offer high stiffness and lightweight characteristics. To tackle this challenge, this research introduces a novel approach featuring a self-supporting polyhedral structure and an efficient optimization algorithm. Specifically, the internal space of the model is filled with a combination of self-supporting octahedrons and tetrahedrons, strategically arranged to maximize structural integrity. Our algorithm optimizes the wall thickness of the polyhedron elements to satisfy specific stiffness requirements, while ensuring efficient alignment of the filled structures in finite element calculations. Our approach results in a considerable decrease in optimization time. The optimization process is stable, converges rapidly, and consistently delivers effective results. Through a series of experiments, we have demonstrated the effectiveness and efficiency of our method in achieving the desired design objectives
Fabricatable 90° Pop-ups: Interactive Transformation of a 3D Model into a Pop-up Structure
(The Eurographics Association and John Wiley & Sons Ltd., 2023) Fujikawa, Junpei; Ijiri, Takashi; Chaine, Raphaëlle; Deng, Zhigang; Kim, Min H.
Ninety-degree pop-ups are a type of papercraft on which a three-dimensional (3D) structure pops up when the angle of the base fold is 90°. They are fabricated by cutting and creasing a single sheet of paper. Traditional 90° pop-ups are limited to 3D shapes only comprising planar shapes because they are made of paper. In this paper, we present novel pop-ups, fabricatable 90° pop-ups that employ the 90° pop-up mechanism, consist of components with curved shapes, and can be fabricatable using a 3D printer. We propose a method for converting a 3D model into a fabricatable 90° pop-up. The user first interactively designs a layout of pop-up components, and the system automatically deforms the components using the 3D model. Because the generated pop-ups contain necessary cuts and folds, no additional assembly process is required. To demonstrate the feasibility of the proposed method, we designed and fabricated various 90° pop-ups using a 3D printer.
A Fully Integrated Pipeline for Visual Carotid Morphology Analysis
(The Eurographics Association and John Wiley & Sons Ltd., 2023) Eulzer, Pepe; Deylen, Fabienne von; Hsu, Wei-Chan; Wickenhöfer, Ralph; Klingner, Carsten M.; Lawonn, Kai; Bujack, Roxana; Archambault, Daniel; Schreck, Tobias
Analyzing stenoses of the internal carotids - local constrictions of the artery - is a critical clinical task in cardiovascular disease treatment and prevention. For this purpose, we propose a self-contained pipeline for the visual analysis of carotid artery geometries. The only inputs are computed tomography angiography (CTA) scans, which are already recorded in clinical routine. We show how integrated model extraction and visualization can help to efficiently detect stenoses and we provide means for automatic, highly accurate stenosis degree computation. We directly connect multiple sophisticated processing stages, including a neural prediction network for lumen and plaque segmentation and automatic global diameter computation. We enable interactive and retrospective user control over the processing stages. Our aims are to increase user trust by making the underlying data validatable on the fly, to decrease adoption costs by minimizing external dependencies, and to optimize scalability by streamlining the data processing. We use interactive visualizations for data inspection and adaption to guide the user through the processing stages. The framework was developed and evaluated in close collaboration with radiologists and neurologists. It has been used to extract and analyze over 100 carotid bifurcation geometries and is built with a modular architecture, available as an extendable open-source platform.
GO-Compass: Visual Navigation of Multiple Lists of GO terms
(The Eurographics Association and John Wiley & Sons Ltd., 2023) Harbig, Theresa; Witte Paz, Mathias; Nieselt, Kay; Bujack, Roxana; Archambault, Daniel; Schreck, Tobias
Analysis pipelines in genomics, transcriptomics, and proteomics commonly produce lists of genes, e.g., differentially expressed genes. Often these lists overlap only partly or not at all and contain too many genes for manual comparison. However, using background knowledge, such as the functional annotations of the genes, the lists can be abstracted to functional terms. One approach is to run Gene Ontology (GO) enrichment analyses to determine over- and/or underrepresented functions for every list of genes. Due to the hierarchical structure of the Gene Ontology, lists of enriched GO terms can contain many closely related terms, rendering the lists still long, redundant, and difficult to interpret for researchers. In this paper, we present GO-Compass (Gene Ontology list comparison using Semantic Similarity), a visual analytics tool for the dispensability reduction and visual comparison of lists of GO terms. For dispensability reduction, we adapted the REVIGO algorithm, a summarization method based on the semantic similarity of GO terms, to perform hierarchical dispensability clustering on multiple lists. In an interactive dashboard, GO-Compass offers several visualizations for the comparison and improved interpretability of GO terms lists. The hierarchical dispensability clustering is visualized as a tree, where users can interactively filter out dispensable GO terms and create flat clusters by cutting the tree at a chosen dispensability. The flat clusters are visualized in animated treemaps and are compared using a correlation heatmap, UpSet plots, and bar charts. With two use cases on published datasets from different omics domains, we demonstrate the general applicability and effectiveness of our approach. In the first use case, we show how the tool can be used to compare lists of differentially expressed genes from a transcriptomics pipeline and incorporate gene information into the analysis. In the second use case using genomics data, we show how GO-Compass facilitates the analysis of many hundreds of GO terms. For qualitative evaluation of the tool, we conducted feedback sessions with five domain experts and received positive comments. GO-Compass is part of the Tue- Vis Visualization Server as a web application available at https://go-compass-tuevis.cs.uni-tuebingen.de/
Interactive Depixelization of Pixel Art through Spring Simulation
(The Eurographics Association and John Wiley & Sons Ltd., 2023) Matusovic, Marko; Parakkat, Amal Dev; Eisemann, Elmar; Myszkowski, Karol; Niessner, Matthias
We introduce an approach for converting pixel art into high-quality vector images. While much progress has been made on automatic conversion, there is an inherent ambiguity in pixel art, which can lead to a mismatch with the artist's original intent. Further, there is room for incorporating aesthetic preferences during the conversion. In consequence, this work introduces an interactive framework to enable users to guide the conversion process towards high-quality vector illustrations. A key idea of the method is to cast the conversion process into a spring-system optimization that can be influenced by the user. Hereby, it is possible to resolve various ambiguities that cannot be handled by an automatic algorithm.
Precomputed Radiative Heat Transport for Efficient Thermal Simulation
(The Eurographics Association and John Wiley & Sons Ltd., 2023) Freude, Christian; Hahn, David; Rist, Florian; Lipp, Lukas; Wimmer, Michael; Chaine, Raphaëlle; Deng, Zhigang; Kim, Min H.
Architectural design and urban planning are complex design tasks. Predicting the thermal impact of design choices at interactive rates enhances the ability of designers to improve energy efficiency and avoid problematic heat islands while maintaining design quality. We show how to use and adapt methods from computer graphics to efficiently simulate heat transfer via thermal radiation, thereby improving user guidance in the early design phase of large-scale construction projects and helping to increase energy efficiency and outdoor comfort. Our method combines a hardware-accelerated photon tracing approach with a carefully selected finite element discretization, inspired by precomputed radiance transfer. This combination allows us to precompute a radiative transport operator, which we then use to rapidly solve either steady-state or transient heat transport throughout the entire scene. Our formulation integrates time-dependent solar irradiation data without requiring changes in the transport operator, allowing us to quickly analyze many different scenarios such as common weather patterns, monthly or yearly averages, or transient simulations spanning multiple days or weeks. We show how our approach can be used for interactive design workflows such as city planning via fast feedback in the early design phase.
visMOP - A Visual Analytics Approach for Multi-omics Pathways
(The Eurographics Association and John Wiley & Sons Ltd., 2023) Brich, Nicolas; Schacherer, Nadine; Hoene, Miriam; Weigert, Cora; Lehmann, Rainer; Krone, Michael; Bujack, Roxana; Archambault, Daniel; Schreck, Tobias
We present an approach for the visual analysis of multi-omics data obtained using high-throughput methods. The term ''omics'' denotes measurements of different types of biologically relevant molecules, like the products of gene transcription (transcriptomics) or the abundance of proteins (proteomics). Current popular visualization approaches often only support analyzing each of these omics separately. This, however, disregards the interconnectedness of different biologically relevant molecules and processes. Consequently, it describes the actual events in the organism suboptimally or only partially. Our visual analytics approach for multi-omics data provides a comprehensive overview and details-on-demand by integrating the different omics types in multiple linked views. To give an overview, we map the measurements to known biological pathways and use a combination of a clustered network visualization, glyphs, and interactive filtering. To ensure the effectiveness and utility of our approach, we designed it in close collaboration with domain experts and assessed it using an exemplary workflow with real-world transcriptomics, proteomics, and lipidomics measurements from mice.

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Browsing Volume 42 (2023) by Subject "Applied computing"

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