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Item Sketching Vocabulary for Crowd Motion(The Eurographics Association and John Wiley & Sons Ltd., 2022) Mathew, C. D. Tharindu; Benes, Bedrich; Aliaga, Daniel; Dominik L. Michels; Soeren PirkThis paper proposes and evaluates a sketching language to author crowd motion. It focuses on the path, speed, thickness, and density parameters of crowd motion. A sketch-based vocabulary is proposed for each parameter and evaluated in a user study against complex crowd scenes. A sketch recognition pipeline converts the sketches into a crowd simulation. The user study results show that 1) participants at various skill levels and can draw accurate crowd motion through sketching, 2) certain sketch styles lead to a more accurate representation of crowd parameters, and 3) sketching allows to produce complex crowd motions in a few seconds. The results show that some styles although accurate actually are less preferred over less accurate ones.Item LineageD: An Interactive Visual System for Plant Cell Lineage Assignments based on Correctable Machine Learning(The Eurographics Association and John Wiley & Sons Ltd., 2022) Hong, Jiayi; Trubuil, Alain; Isenberg, Tobias; Borgo, Rita; Marai, G. Elisabeta; Schreck, TobiasWe describe LineageD-a hybrid web-based system to predict, visualize, and interactively adjust plant embryo cell lineages. Currently, plant biologists explore the development of an embryo and its hierarchical cell lineage manually, based on a 3D dataset that represents the embryo status at one point in time. This human decision-making process, however, is time-consuming, tedious, and error-prone due to the lack of integrated graphical support for specifying the cell lineage. To fill this gap, we developed a new system to support the biologists in their tasks using an interactive combination of 3D visualization, abstract data visualization, and correctable machine learning to modify the proposed cell lineage. We use existing manually established cell lineages to obtain a neural network model. We then allow biologists to use this model to repeatedly predict assignments of a single cell division stage. After each hierarchy level prediction, we allow them to interactively adjust the machine learning based assignment, which we then integrate into the pool of verified assignments for further predictions. In addition to building the hierarchy this way in a bottom-up fashion, we also offer users to divide the whole embryo and create the hierarchy tree in a top-down fashion for a few steps, improving the ML-based assignments by reducing the potential for wrong predictions. We visualize the continuously updated embryo and its hierarchical development using both 3D spatial and abstract tree representations, together with information about the model's confidence and spatial properties. We conducted case study validations with five expert biologists to explore the utility of our approach and to assess the potential for LineageD to be used in their daily workflow. We found that the visualizations of both 3D representations and abstract representations help with decision making and the hierarchy tree top-down building approach can reduce assignments errors in real practice.Item Neural Flow Map Reconstruction(The Eurographics Association and John Wiley & Sons Ltd., 2022) Sahoo, Saroj; Lu, Yuzhe; Berger, Matthew; Borgo, Rita; Marai, G. Elisabeta; Schreck, TobiasIn this paper we present a reconstruction technique for the reduction of unsteady flow data based on neural representations of time-varying vector fields. Our approach is motivated by the large amount of data typically generated in numerical simulations, and in turn the types of data that domain scientists can generate in situ that are compact, yet useful, for post hoc analysis. One type of data commonly acquired during simulation are samples of the flow map, where a single sample is the result of integrating the underlying vector field for a specified time duration. In our work, we treat a collection of flow map samples for a single dataset as a meaningful, compact, and yet incomplete, representation of unsteady flow, and our central objective is to find a representation that enables us to best recover arbitrary flow map samples. To this end, we introduce a technique for learning implicit neural representations of time-varying vector fields that are specifically optimized to reproduce flow map samples sparsely covering the spatiotemporal domain of the data. We show that, despite aggressive data reduction, our optimization problem - learning a function-space neural network to reproduce flow map samples under a fixed integration scheme - leads to representations that demonstrate strong generalization, both in the field itself, and using the field to approximate the flow map. Through quantitative and qualitative analysis across different datasets we show that our approach is an improvement across a variety of data reduction methods, and across a variety of measures ranging from improved vector fields, flow maps, and features derived from the flow map.Item Unfolding Edges: Adding Context to Edges in Multivariate Graph Visualization(The Eurographics Association and John Wiley & Sons Ltd., 2023) Bludau, Mark-Jan; Dörk, Marian; Tominski, Christian; Bujack, Roxana; Archambault, Daniel; Schreck, TobiasExisting work on visualizing multivariate graphs is primarily concerned with representing the attributes of nodes. Even though edges are the constitutive elements of networks, there have been only few attempts to visualize attributes of edges. In this work, we focus on the critical importance of edge attributes for interpreting network visualizations and building trust in the underlying data. We propose 'unfolding of edges' as an interactive approach to integrate multivariate edge attributes dynamically into existing node-link diagrams. Unfolding edges is an in-situ approach that gradually transforms basic links into detailed representations of the associated edge attributes. This approach extends focus+context, semantic zoom, and animated transitions for network visualizations to accommodate edge details on-demand without cluttering the overall graph layout. We explore the design space for the unfolding of edges, which covers aspects of making space for the unfolding, of actually representing the edge context, and of navigating between edges. To demonstrate the utility of our approach, we present two case studies in the context of historical network analysis and computational social science. For these, web-based prototypes were implemented based on which we conducted interviews with domain experts. The experts' feedback suggests that the proposed unfolding of edges is a useful tool for exploring rich edge information of multivariate graphs.Item SurfNet: Learning Surface Representations via Graph Convolutional Network(The Eurographics Association and John Wiley & Sons Ltd., 2022) Han, Jun; Wang, Chaoli; Borgo, Rita; Marai, G. Elisabeta; Schreck, TobiasFor scientific visualization applications, understanding the structure of a single surface (e.g., stream surface, isosurface) and selecting representative surfaces play a crucial role. In response, we propose SurfNet, a graph-based deep learning approach for representing a surface locally at the node level and globally at the surface level. By treating surfaces as graphs, we leverage a graph convolutional network to learn node embedding on a surface. To make the learned embedding effective, we consider various pieces of information (e.g., position, normal, velocity) for network input and investigate multiple losses. Furthermore, we apply dimensionality reduction to transform the learned embeddings into 2D space for understanding and exploration. To demonstrate the effectiveness of SurfNet, we evaluate the embeddings in node clustering (node-level) and surface selection (surface-level) tasks. We compare SurfNet against state-of-the-art node embedding approaches and surface selection methods. We also demonstrate the superiority of SurfNet by comparing it against a spectral-based mesh segmentation approach. The results show that SurfNet can learn better representations at the node and surface levels with less training time and fewer training samples while generating comparable or better clustering and selection results.Item 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, TobiasAnalysis 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/Item VIBE: A Design Space for VIsual Belief Elicitation in Data Journalism(The Eurographics Association and John Wiley & Sons Ltd., 2022) Mahajan, Shambhavi; Chen, Bonnie; Karduni, Alireza; Kim, Yea-Seul; Wall, Emily; Borgo, Rita; Marai, G. Elisabeta; Schreck, TobiasThe process of forming, expressing, and updating beliefs from data plays a critical role in data-driven decision making. Effectively eliciting those beliefs has potential for high impact across a broad set of applications, including increased engagement with data and visualizations, personalizing visualizations, and understanding users' visual reasoning processes, which can inform improved data analysis and decision making strategies (e.g., via bias mitigation). Recently, belief-driven visualizations have been used to elicit and visualize readers' beliefs in a visualization alongside data in narrative media and data journalism platforms such as the New York Times and FiveThirtyEight. However, there is little research on different aspects that constitute designing an effective belief-driven visualization. In this paper, we synthesize a design space for belief-driven visualizations based on formative and summative interviews with designers and visualization experts. The design space includes 7 main design considerations, beginning with an assumed data set, then structured according to: from who, why, when, what, and how the belief is elicited, and the possible feedback about the belief that may be provided to the visualization viewer. The design space covers considerations such as the type of data parameter with optional uncertainty being elicited, interaction techniques, and visual feedback, among others. Finally, we describe how more than 24 existing belief-driven visualizations from popular news media outlets span the design space and discuss trends and opportunities within this space.Item Seeing Through Sounds: Mapping Auditory Dimensions to Data and Charts for People with Visual Impairments(The Eurographics Association and John Wiley & Sons Ltd., 2022) Wang, Ruobin; Jung, Crescentia; Kim, Yea-Seul; Borgo, Rita; Marai, G. Elisabeta; Schreck, TobiasSonification can be an effective medium for people with visual impairments to understand data in visualizations. However, there are no universal design principles that apply to various charts that encode different data types. Towards generalizable principles, we conducted an exploratory experiment to assess how different auditory channels (e.g., pitch, volume) impact the data and visualization perception among people with visual impairments. In our experiment, participants evaluated the intuitiveness and accuracy of the mapping of auditory channels on different data and chart types. We found that participants rated pitch to be the most intuitive, while the number of tappings and the length of sounds yielded the most accurate perception in decoding data. We study how audio channels can intuitively represent different charts and demonstrate that data-level perception might not directly transfer to chart-level perception as participants reflect on visual aspects of the charts while listening to audio. We conclude by how future experiments can be designed to establish a robust ranking for creating audio charts.Item Teru Teru Bozu: Defensive Raincloud Plots(The Eurographics Association and John Wiley & Sons Ltd., 2023) Correll, Michael; Bujack, Roxana; Archambault, Daniel; Schreck, TobiasUnivariate visualizations like histograms, rug plots, or box plots provide concise visual summaries of distributions. However, each individual visualization may fail to robustly distinguish important features of a distribution, or provide sufficient information for all of the relevant tasks involved in summarizing univariate data. One solution is to juxtapose or superimpose multiple univariate visualizations in the same chart, as in Allen et al.'s [APW*19] ''raincloud plots.'' In this paper I examine the design space of raincloud plots, and, through a series of simulation studies, explore designs where the component visualizations mutually ''defend'' against situations where important distribution features are missed or trivial features are given undue prominence. I suggest a class of ''defensive'' raincloud plot designs that provide good mutual coverage for surfacing distributional features of interest.Item HyperNP: Interactive Visual Exploration of Multidimensional Projection Hyperparameters(The Eurographics Association and John Wiley & Sons Ltd., 2022) Appleby, Gabriel; Espadoto, Mateus; Chen, Rui; Goree, Samuel; Telea, Alexandru C.; Anderson, Erik W.; Chang, Remco; Borgo, Rita; Marai, G. Elisabeta; Schreck, TobiasProjection algorithms such as t-SNE or UMAP are useful for the visualization of high dimensional data, but depend on hyperparameters which must be tuned carefully. Unfortunately, iteratively recomputing projections to find the optimal hyperparameter values is computationally intensive and unintuitive due to the stochastic nature of such methods. In this paper we propose HyperNP, a scalable method that allows for real-time interactive hyperparameter exploration of projection methods by training neural network approximations. A HyperNP model can be trained on a fraction of the total data instances and hyperparameter configurations that one would like to investigate and can compute projections for new data and hyperparameters at interactive speeds. HyperNP models are compact in size and fast to compute, thus allowing them to be embedded in lightweight visualization systems. We evaluate the performance of HyperNP across three datasets in terms of performance and speed. The results suggest that HyperNP models are accurate, scalable, interactive, and appropriate for use in real-world settings.