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        "title": "Wiggle! Wiggle! Wiggle! Visualizing uncertainty in node attributes in straight-line node-link diagrams using animated wiggliness",
        "date": "2025-10",
        "abstract": "Uncertainty is common to most types of data, from meteorology to the biomedical sciences. Here, we are interested in the visualization of uncertainty within the context of multivariate graphs, specifically the visualization of uncertainty attached to node attributes. Many visual channels offer themselves up for the visualization of node attributes and their uncertainty. One controversial and relatively under-explored channel, however, is animation, despite its conceptual advantages. In this paper, we investigate node “wiggliness”, i.e. uncertainty-dependent pseudo-random motion of nodes, as a potential new visual channel with which to communicate node attribute uncertainty. To study wiggliness’ effectiveness, we compare it against three other visual channels identified from a thorough review of uncertainty visualization literature—namely node enclosure, node fuzziness, and node color saturation. In a larger-scale, mixed method, Prolific-crowd-sourced, online user study of 160 participants, we quantitatively and qualitatively compare these four uncertainty encodings across eight low-level graph analysis tasks that probe participants’ abilities to parse the presented networks both on an attribute and topological level. We ultimately conclude that all four uncertainty encodings appear comparably useful—as opposed to previous findings. Wiggliness may be a suitable and effective visual channel with which to communicate node attribute uncertainty, at least for the kinds of data and tasks considered in our study.",
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        "doi": "10.1016/j.cag.2025.104290",
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        "journal": "COMPUTERS & GRAPHICS-UK",
        "publisher": "PERGAMON-ELSEVIER SCIENCE LTD",
        "volume": "131",
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        "keywords": [
            "Network Visualization",
            "Uncertainty Visualization",
            "Animation",
            "Fuzziness",
            "Enclosure",
            "Saturation"
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        "tu_id": null,
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        "title": "An introduction to and survey of biological network visualization",
        "date": "2025-02",
        "abstract": "Biological networks describe complex relationships in biological systems, which represent biological entities as vertices and their underlying connectivity as edges. Ideally, for a complete analysis of such systems, domain experts need to visually integrate multiple sources of heterogeneous data, and visually, as well as numerically, probe said data in order to explore or validate (mechanistic) hypotheses. Such visual analyses require the coming together of biological domain experts, bioinformaticians, as well as network scientists to create useful visualization tools. Owing to the underlying graph data becoming ever larger and more complex, the visual representation of such biological networks has become challenging in its own right. This introduction and survey aims to describe the current state of biological network visualization in order to identify scientific gaps for visualization experts, network scientists, bioinformaticians, and domain experts, such as biologists, or biochemists, alike. Specifically, we revisit the classic visualization pipeline, upon which we base this paper’s taxonomy and structure, which in turn forms the basis of our literature classification. This pipeline describes the process of visualizing data, starting with the raw data itself, through the construction of data tables, to the actual creation of visual structures and views, as a function of task-driven user interaction. Literature was systematically surveyed using API-driven querying where possible, and the collected papers were manually read and categorized based on the identified sub-components of this visualization pipeline’s individual steps. From this survey, we highlight a number of exemplary visualization tools from multiple biological sub-domains in order to explore how they adapt these discussed techniques and why. Additionally, this taxonomic classification of the collected set of papers allows us to identify existing gaps in biological network visualization practices. We finally conclude this report with a list of open challenges and potential research directions. Examples of such gaps include (i) the overabundance of visualization tools using schematic or straight-line node-link diagrams, despite the availability of powerful alternatives, or (ii) the lack of visualization tools that also integrate more advanced network analysis techniques beyond basic graph descriptive statistics.",
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        "articleno": "104115",
        "doi": "10.1016/j.cag.2024.104115",
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        "pages": "31",
        "publisher": "PERGAMON-ELSEVIER SCIENCE LTD",
        "volume": "126",
        "research_areas": [
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            "Network visualization",
            "Visualization pipeline",
            "Sensemaking loop",
            "Visual analytics",
            "Network analysis",
            "Biological networks",
            "State-of-the-art-report"
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        "id": "pahr-2025-nodkant",
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        "title": "NODKANT: exploring constructive network physicalization",
        "date": "2025",
        "abstract": "Physicalizations, which combine perceptual and sensorimotor interactions, offer an immersive way to comprehend complex data visualizations by stimulating active construction and manipulation. This study investigates the impact of personal construction on the comprehension of physicalized networks. We propose a physicalization toolkit—NODKANT—for constructing modular node-link diagrams consisting of a magnetic surface, 3D printable and stackable node labels, and edges of adjustable length. In a mixed-methods between-subject lab study with 27 participants, three groups of people used NODKANT to complete a series of low-level analysis tasks in the context of an animal contact network. The first group was tasked with freely constructing their network using a sorted edge list, the second group received step-by-step instructions to create a predefined layout, and the third group received a pre-constructed representation. While free construction proved on average more time-consuming, we show that users extract more insights from the data during construction and interact with their representation more frequently, compared to those presented with step-by-step instructions. Interestingly, the increased time demand cannot be measured in users' subjective task load. Finally, our findings indicate that participants who constructed their own representations were able to recall more detailed insights after a period of 10–14 days compared to those who were given a pre-constructed network physicalization. All materials, data, code for generating instructions, and 3D printable meshes are available on https://osf.io/tk3g5/.",
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        "id": "pahr-2024-squishicalization",
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        "tu_id": null,
        "repositum_id": "20.500.12708/208691",
        "title": "Squishicalization: Exploring Elastic Volume Physicalization",
        "date": "2024-12",
        "abstract": "We introduce Squishicalization , a pipeline for generating physicalizations of volumetric data that encode scalar information through their physical characteristics—specifically, by varying their “squishiness” or local elasticity. Data physicalization research is increasingly exploring multisensory information encoding, with a particular focus on enhancing direct interactivity. With Squishicalization , we leverage the tactile dimension of physicalization as a means of direct interactivity. Inspired by conventional volume rendering, we adapt the concept of transfer functions to encode scalar values from volumetric data into local elasticity levels. In this way, volumetric scalar data are transformed into sculptures, where the elasticity represents physical properties such as the material's density distribution within the volume. In our pipeline, scalar values guide the weighted sampling of the scalar field. The sampled data is then processed through Voronoi tessellation to create a sponge-like structure, which can be printed with consumer-grade 3D printers and readily available filament. To validate our pipeline, we conduct a computational and mechanical evaluation, as well as a two-stage perceptual study of the capabilities of our generated squishicalizations. To further investigate potential application scenarios, we interview experts across several domains. Finally, we summarize actionable insights and future avenues for the application of our All supplemental materials are available at https://osf.io/35gnv/?view_only=605e5085061f40439a98545f0c447cf3 .",
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        "journal": "IEEE Transactions on Visualization and Computer Graphics",
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        "tu_id": null,
        "repositum_id": "20.500.12708/205726",
        "title": "Me! Me! Me! Me! A study and comparison of ego network representations",
        "date": "2024-12",
        "abstract": "From social networks to brain connectivity, ego networks are a simple yet powerful approach to visualizing parts of a larger graph, i.e. those related to a selected focal node — the so-called “ego”. While surveys and comparisons of general graph visualization approaches exist in the literature, we note (i) the many conflicting results of comparisons of adjacency matrices and node-link diagrams, thus motivating further study, as well as (ii) the absence of such systematic comparisons for ego networks specifically. In this paper, we propose the development of empirical recommendations for ego network visualization strategies. First, we survey the literature across application domains and collect examples of network visualizations to identify the most common visual encodings, namely straight-line, radial, and layered node-link diagrams, as well as adjacency matrices. These representations are then applied to a representative, intermediate-sized network and subsequently compared in a large-scale, crowd-sourced user study in a mixed-methods analysis setup to investigate their impact on both user experience and performance. Within the limits of this study, and contrary to previous comparative investigations of adjacency matrices and node-link diagrams (outside of ego networks specifically), participants performed systematically worse when using adjacency matrices than those using node-link diagrammatic representations. Similar to previous comparisons of different node-link diagrams, we do not detect any notable differences in participant performance between the three node-link diagrams. Lastly, our quantitative and qualitative results indicate that participants found adjacency matrices harder to learn, use, and understand than node-link diagrams. We conclude that in terms of both participant experience and performance, a layered node-link diagrammatic representation appears to be the most preferable for ego network visualization purposes.",
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        "articleno": "104123",
        "doi": "10.1016/j.cag.2024.104123",
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        "open_access": "yes",
        "pages": "15",
        "pages_from": "1",
        "pages_to": "15",
        "publisher": "PERGAMON-ELSEVIER SCIENCE LTD",
        "volume": "125",
        "research_areas": [
            "NetVis"
        ],
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            "Adjacency matrix",
            "Ego network visualization",
            "Layered node-link diagram",
            "Radial node-link diagram",
            "Straight-line node-link diagram",
            "User study"
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        "repositum_id": "20.500.12708/199161",
        "title": "Investigating the Effect of Operation Mode and Manifestation on Physicalizations of Dynamic Processes",
        "date": "2024-06",
        "abstract": "We conducted a study to systematically investigate the communication of complex dynamic processes along a two-dimensional design space, where the axes represent a representation's manifestation (physical or virtual) and operation (manual or automatic). We exemplify the design space on a model embodying cardiovascular pathologies, represented by a mechanism where a liquid is pumped into a draining vessel, with complications illustrated through modifications to the model. The results of a mixed-methods lab study with 28 participants show that both physical manifestation and manual operation have a strong positive impact on the audience's engagement. The study does not show a measurable knowledge increase with respect to cardiovascular pathologies using manually operated physical representations. However, subjectively, participants report a better understanding of the process—mainly through non-visual cues like haptics, but also auditory cues. The study also indicates an increased task load when interacting with the process, which, however, seems to play a minor role for the participants. Overall, the study shows a clear potential of physicalization for the communication of complex dynamic processes, which only fully unfold if observers have to chance to interact with the process.",
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        "research_areas": [
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        "id": "ehlers-2024-vgs",
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        "repositum_id": "20.500.12708/196069",
        "title": "Visualizing Group Structure in Compound Graphs: The Current State, Lessons Learned, and Outstanding Opportunities",
        "date": "2024-03-11",
        "abstract": "Compound graphs are common across domains, from social science to biochemical pathway studies, and their visualization is important to both their exploration and analysis. However, effectively visualizing a compound graph's topology and group structure requires careful consideration, as evident by the many different approaches to this particular problem. To better understand the current advancements in compound graph visualization, we have consolidated and streamlined existing surveys' taxonomies. More specifically, we aim to disentangle the visual relationship between graph topology and group structure from the visual encoding used to visualize its group structure in order to identify interesting gaps in the literature. In so doing, we are able to enumerate a number of lessons learned and gain a better understanding of the outstanding research opportunities and practical implications across domains.",
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        "booktitle": "Proceedings of the 19th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications - Volume 1, HUCAPP and IVAPP",
        "date_from": "2024-02-27",
        "date_to": "2024-02-29",
        "doi": "10.5220/0012431200003660",
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        "abstract": "We present a novel vertex-splitting approach to iteratively resolve edge crossings in order to improve the readability of graph drawings. Dense graphs, even when small in size (10 to 15 nodes in size) quickly become difficult to read with increasing numbers of edges, and form so-called “hairballs”. The readability of a graph drawing is measured using many different quantitative aesthetic metrics. One such metric of particular importance is the number of edge crossings. Classical approaches to improving readability, such as the minimization of the number of edge crossings, focus on providing overviews of the input graph by aggregating or sampling vertices and/or edges. However, this simplification of the graph drawing does not allow for detailed views into the data, as not all vertices or edges are rendered, and also requires sophisticated interaction approaches to perform well. To avoid this, our locally optimal vertex splitting approach aims to minimize the number of remaining edge crossings while also minimizing the number of vertices that need to be split. In each iteration, we identify the vertex contributing the largest number of edge crossings, remove it, locate the embedding locations of said vertex's two split copies, and determine each copy's unique adjacency. We conduct a user study with 52 participants to evaluate whether vertex splitting affects users’ abilities to conduct a set of graph analytical tasks on graphs 12 nodes in size. Users were tasked with identifying a vertex's adjacency, determining the shared neighbors of two vertices, and checking the validity of a set of paths. We ultimately conclude that within the context of small, dense graphs, systematic vertex splitting is preferred by participants and even positively impacts user performance, though at the cost of the time taken per task.",
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        "title": "Untangling circular drawings: Algorithms and complexity",
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        "abstract": "We consider the problem of untangling a given (non-planar) straight-line circular drawing δG of an outerplanar graph G=(V,E) into a planar straight-line circular drawing of G by shifting a minimum number of vertices to a new position on the circle. For an outerplanar graph G, it is obvious that such a crossing-free circular drawing always exists and we define the circular shifting number shift∘(δG) as the minimum number of vertices that are required to be shifted in order to resolve all crossings of δG. We show that the problem CIRCULAR UNTANGLING, asking whether shift∘(δG)≤K for a given integer K, is NP-complete. For n-vertex outerplanar graphs, we obtain a tight upper bound of shift∘(δG)≤n−⌊n−2⌋−2. Moreover, we study the CIRCULAR UNTANGLING for almost-planar circular drawings, in which a single edge is involved in all of the crossings. For this problem, we provide a tight upper bound [Formula presented] and present an O(n2)-time algorithm to compute the circular shifting number of almost-planar drawings.",
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        "abstract": "The splitting number of a graph G= (V, E) is the minimum number of vertex splits required to turn G into a planar graph, where a vertex split removes a vertex v∈ V, introduces two new vertices v1, v2, and distributes the edges formerly incident to v among v1, v2. The splitting number problem is known to be NP-complete for abstract graphs and we provide a non-uniform fixed-parameter tractable (FPT) algorithm for this problem. We then shift focus to the splitting number of a given topological graph drawing in R2, where the new vertices resulting from vertex splits must be re-embedded into the existing drawing of the remaining graph. We show NP-completeness of this embedded splitting number problem, even for its two subproblems of (1) selecting a minimum subset of vertices to split and (2) for re-embedding a minimum number of copies of a given set of vertices. For the latter problem we present an FPT algorithm parameterized by the number of vertex splits. This algorithm reduces to a bounded outerplanarity case and uses an intricate dynamic program on a sphere-cut decomposition.",
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        "title": "Spatial-Data-Driven Layouting for Brain Network Visualization",
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        "abstract": "Recent advances in neuro-imaging enable scientists to create brain network data that can lead to novel insights into neurocircuitry, and a better understanding of the brain’s organization. These networks inherently involve a spatial component, depicting which brain regions are structurally, functionally or genetically related. Their visualization in 3D suffers from occlusion and clutter, especially with increasing number of nodes and connections, while 2D representations such as connectograms, connectivity matrices, and node-link diagrams neglect the spatio-anatomical context. Approaches to arrange 2D-graphs manually are tedious, species-dependent, and require the knowledge of domain experts.\r\nIn this paper, we present a spatial-data-driven approach for layouting 3D brain networks in 2D node-link diagrams, while maintaining their spatial organization. The produced graphs do not need manual positioning of nodes, are consistent (even for sub-graphs), and provide a perspective-dependent arrangement for orientation. Furthermore, we provide a visual design for highlighting anatomical context, including the shape of the brain, and the size of brain regions. We present in several case-studies the applicability of our approach for different neuroscience-relevant species, including the mouse, human, and Drosophila larvae. In a user study conducted with several domain experts, we demonstrate its relevance and validity, as well as its potential for neuroscientific publications, presentations, and education.",
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        "id": "batik-2022-smm",
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        "title": "Shape-Guided Mixed Metro Map Layout",
        "date": "2022",
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        "booktitle": "Pacific Graphics 2022",
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        "location": "Kyoto",
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        "publisher": "The Eurographics Association and John Wiley & Sons Ltd.",
        "volume": "41",
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        "title": "Untangling Circular Drawings: Algorithms and Complexity",
        "date": "2021-12",
        "abstract": "We consider the problem of untangling a given (non-planar) straight-line circular drawing δG of an\r\nouterplanar graph G = (V,E) into a planar straight-line circular drawing by shifting a minimum\r\nnumber of vertices to a new position on the circle. For an outerplanar graph G, it is clear that such\r\na crossing-free circular drawing always exists and we define the circular shifting number shift◦(δG)\r\nas the minimum number of vertices that need to be shifted to resolve all crossings of δG. We show\r\nthat the problem Circular Untangling, asking whether shift◦(δG) ≤ K for a given integer K,\r\nis NP-complete. Based on this result we study Circular Untangling for almost-planar circular\r\ndrawings, in which a single edge is involved in all the crossings. In this case we provide a tight upper\r\nbound shift◦(δG) ≤ ⌊n2\r\n⌋ − 1, where n is the number of vertices in G, and present a polynomial-time\r\nalgorithm to compute the circular shifting number of almost-planar drawings.",
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        "booktitle": "Proceedings of the 32nd International Symposium on Algorithms and Computation",
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        "title": "The Anatomical Edutainer",
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        "abstract": "Physical visualizations (i.e., data representations by means of physical objects) have been used for many centuries in medical and anatomical education. Recently, 3D printing techniques started also to emerge. Still, other medical physicalizations that rely on affordable and easy-to-find materials are limited, while smart strategies that take advantage of the optical properties of our physical world have not been thoroughly investigated. We propose the Anatomical Edutainer, a workflow to guide the easy, accessible, and affordable generation of physicalizations for tangible, interactive anatomical edutainment. The Anatomical Edutainer supports 2D printable and 3D foldable physicalizations that change their visual properties (i.e., hues of the visible spectrum) under colored lenses or colored lights, to reveal distinct anatomical structures through user interaction.",
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        "title": "Mixed Labeling: Integrating Internal and External Labels",
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        "title": "Mental Map Preservation for Progressively Labeling Railway Networks",
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        "repositum_id": null,
        "title": "Metabopolis: Scalable Network Layout for Biological Pathway Diagrams in Urban Map Style",
        "date": "2019-05-15",
        "abstract": "Background\nBiological pathways represent chains of molecular interactions in biological systems that jointly form complex dynamic networks. The network structure changes from the significance of biological experiments and layout algorithms often sacrifice low-level details to maintain high-level information, which complicates the entire image to large biochemical systems such as human metabolic pathways.\n\nResults\nOur work is inspired by concepts from urban planning since we create a visual hierarchy of biological pathways, which is analogous to city blocks and grid-like road networks in an urban area. We automatize the manual drawing process of biologists by first partitioning the map domain into multiple sub-blocks, and then building the corresponding pathways by routing edges schematically, to maintain the global and local context simultaneously. Our system incorporates constrained floor-planning and network-flow algorithms to optimize the layout of sub-blocks and to distribute the edge density along the map domain. We have developed the approach in close collaboration with domain experts and present their feedback on the pathway diagrams based on selected use cases.\n\nConclusions\nWe present a new approach for computing biological pathway maps that untangles visual clutter by decomposing large networks into semantic sub-networks and bundling long edges to create space for presenting relationships systematically.",
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        "title": "OptiRoute: Interactive Maps for Wayfinding in a Complex Environment",
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        "abstract": "Visitors to amusement parks use mobile map appli- cations to decide where to go and to plan efficient routes. Such applications are especially helpful when visitors wish to avoid re-tracking their steps or visiting regions in the park several times. Visitors have limited time in the park, which typically covers a very large area, and the attractions have waiting times of varying duration. Time management is therefore important. In this paper, we propose a new visualization technique to support such route decision making, using an interactive environment. The main contribution of our system, OptiRoute, is the automatic computation of an optimal route between selected attractions as well as its effective visualization, which focuses on reducing visual clutter. This is achieved by improving the branch and bound route-finding algorithm, and introducing an intersection minimization algorithm for route representation. We demonstrate the feasibility of our approach through a case study of Tokyo Disneyland, in addition to a user study.",
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        "title": "Aspect-Ratio-Preserved Labeling on Metro Maps",
        "date": "2019-04-11",
        "abstract": "For better readability, metro lines are often aligned along the octilinear directions. Predefined layouts, however, limit the feasibility of placing station name labels. In this paper, we present a novel approach to automating the placement of station names around a schematic network while maximally respecting its original layout as the mental map. The idea behind the proposed approach is to progressively annotate stations from congested central downtown areas to sparse rural areas by intro- ducing the sum of geodesic distances over the network to identify the proper order of stations to be annotated. Our approach elongates line segments of the network without changing their directions to spare labeling space around the station. Additional constraints are introduced to restrict the aspect ratios of the region confined by the metro network for better preservation of the mental map in the original schematic layout.",
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    {
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        "tu_id": null,
        "repositum_id": null,
        "title": " A Survey on Computing Schematic Network Maps: The Challenge to Interactivity",
        "date": "2019-04-11",
        "abstract": "Schematic maps are in daily use to show the connec- tivity of subway systems and to facilitate travellers to plan their journeys effectively. This study surveys up-to-date algorithmic approaches in order to give an overview of the state of the art in schematic network mapping. The study investigates the hypothesis that the choice of algorithmic approach is often guided by the requirements of the mapping application. For example, an algorithm that computes globally optimal solutions for schematic maps is capable of producing results for printing, while it is not suitable for computing instant layouts due to its long running time. Our analysis and discussion, therefore, focus on the compu- tational complexity of the problem formulation and the running times of the schematic map algorithms, including algorithmic network layout techniques and station labeling techniques. The correlation between problem complexity and running time is then visually depicted using scatter plot diagrams. Moreover, since metro maps are common metaphors for data visualization, we also investigate online tools and application domains using metro map representations for analytics purposes, and finally summarize the potential future opportunities for schematic maps.",
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