@article{simkin2002read,
  title={Read before you cite!},
  author={Simkin, Mikhail V and Roychowdhury, Vwani P},
  journal={arXiv preprint cond-mat/0212043},
  year={2002},
  url={https://arxiv.org/pdf/cond-mat/0212043}
}

@article{leskovec2016snap,
  title={SNAP: A General-Purpose Network Analysis and Graph-Mining Library},
  author={Leskovec, Jure and Sosi{\v{c}}, Rok},
  journal={ACM Transactions on Intelligent Systems and Technology (TIST)},
  pages={1},
  year={2016},
  publisher={ACM},
  doi={10.1145/2898361}
}

@article{Hachul2006,
doi = {10.1007/11618058_22},
year = {2006},
publisher = {Springer Berlin Heidelberg},
pages = {235-250},
author = {Hachul, Stefan and J{\"u}nger, Mıchael},
title = {An Experimental Comparison of Fast Algorithms for Drawing General Large Graphs},
booktitle = {Graph Drawing}
}

@InProceedings{bachmaier2012,
author="Bachmaier, Christian
and Brandenburg, Franz Josef
and Effinger, Philip
and Gutwenger, Carsten
and Katajainen, Jyrki
and Klein, Karsten
and Sp{\"o}nemann, Miro
and Stegmaier, Matthias
and Wybrow, Michael",
editor="van Kreveld, Marc
and Speckmann, Bettina",
title="The Open Graph Archive: A Community-Driven Effort",
booktitle="Graph Drawing",
year="2012",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="435--440",
abstract="A graphbase, a term coined by Knuth [7], is a database of graphs and computer programs that generate, analyze, manipulate, and visualize graphs. The terms graphlibrary and grapharchive are often used as synonyms for this term. Our vision is to provide an infrastructure and quality standards for a public graphbase, named the Open Graph Archive, that is accessible to researchers and other interested parties around the world via the worldwide web. This paper describes the current work undertaken towards this goal; the paper is also intended to be a call for participation since this will be a community-driven effort where most of the content will be provided by users of the system.",
isbn="978-3-642-25878-7"
}



@article{dibartolomeo2024evaluating,
author = {Di~Bartolomeo, Sara and Crnovrsanin, Tarik and Saffo, David and Puerta, Eduardo and Wilson, Connor and Dunne, Cody},
title = {Evaluating Graph Layout Algorithms: A Systematic Review of Methods and Best Practices},
journal = {Computer Graphics Forum},
volume = {n/a},
number = {n/a},
pages = {e15073},
year = {2024},
keywords = {visualization, graph drawing, graph layout algorithms, evaluation},
doi = {10.1111/cgf.15073},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.15073},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.15073},
abstract = {Abstract Evaluations—encompassing computational evaluations, benchmarks and user studies—are essential tools for validating the performance and applicability of graph and network layout algorithms (also known as graph drawing). These evaluations not only offer significant insights into an algorithm's performance and capabilities, but also assist the reader in determining if the algorithm is suitable for a specific purpose, such as handling graphs with a high volume of nodes or dense graphs. Unfortunately, there is no standard approach for evaluating layout algorithms. Prior work holds a ‘Wild West’ of diverse benchmark datasets and data characteristics, as well as varied evaluation metrics and ways to report results. It is often difficult to compare layout algorithms without first implementing them and then running your own evaluation. In this systematic review, we delve into the myriad of methodologies employed to conduct evaluations—the utilized techniques, reported outcomes and the pros and cons of choosing one approach over another. Our examination extends beyond computational evaluations, encompassing user-centric evaluations, thus presenting a comprehensive understanding of algorithm validation. This systematic review—and its accompanying website—guides readers through evaluation types, the types of results reported, and the available benchmark datasets and their data characteristics. Our objective is to provide a valuable resource for readers to understand and effectively apply various evaluation methods for graph layout algorithms. A free copy of this paper and all supplemental material is available at osf.io, and the categorized papers are accessible on our website at https://visdunneright.github.io/gd-comp-eval/.}
}

@misc{graphvizExamples,
  author = {Graphviz},
  title = {{Graphviz Gallery}},
  howpublished = "\url{https://graphviz.org/gallery/}",
  year = {2008}, 
  note = "[Online; accessed 20 Jan 2023]"
}

@misc{knowncrossings,
  author = {Markus Chimani and Max Ilsen and Tilo Wiedera},
  title = {{Crossing Number}},
  howpublished = "\url{https://tcs.uos.de/doku.php?id=research/cr}",
  year = {2021}, 
  note = "[Online; accessed 20 Jan 2023]"
}

@misc{walshawcollection,
  author = {Chris Walshaw},
  title = {C. Walshaw's graph collection},
  howpublished = "\url{https://chriswalshaw.co.uk/partition/}",
  year = {2001}, 
  note = "[Online; accessed 20 Jan 2023]"
}

@misc{graphreplicabilitystamp,
  title = {Graphics Replicability Stamp},
  author = {Graphics Replicability Stamp},
  howpublished = "\url{https://www.replicabilitystamp.org/}",
}

@misc{acmreplicability,
  title = {ACM Replicability Badges},
  author = {ACM},
  howpublished = "\url{https://www.acm.org/publications/policies/artifact-review-and-badging-current}",
}

@misc{sigmodreplicability,
  title = {SIGMOD availability and reproducibility initiative},
  author = {SIGMOD},
  howpublished = "\url{https://reproducibility.sigmod.org/}",
}

@misc{ournotion,
  author = {Di~Bartolomeo, Sara and Crnovrsanin, Tarik and Saffo, David and Dunne, Cody},
  title = {Interactive list of surveyed papers on notion},
  howpublished = "\url{\notionurl}",
  year = {2023}, 
  note = "[Online; accessed 20 Jan 2023]"
}

@misc{ourosf,
  author = {Di~Bartolomeo, Sara and Crnovrsanin, Tarik and Saffo, David and Dunne, Cody},
  title = {Supplemental material location},
  howpublished = "\url{\osfurl}",
  year = {2023}, 
  note = "[Online; accessed 20 Jan 2023]"
}

@misc{graphdrawingwebsite,
  author = {Graph Drawing},
  title = {{Graph Drawing Website}},
  howpublished = "\url{http://www.graphdrawing.org/data.html}",
  year = {2022}, 
  note = "[Online; accessed 20 Jan 2023]"
}

@misc{matrixmarket,
  author = {NIST},
  title = {Matrix Market},
  howpublished = "\url{https://math.nist.gov/MatrixMarket/}",
  year = {2007}, 
  note = "[Online; accessed 20 Jan 2023]"
}


@misc{pajekdatasets,
  author = {Vladimir Batagelj and Andrej Mrvar},
  title = {Pajek datasets},
  howpublished = "\url{http://vlado.fmf.uni-lj.si/pub/networks/data/}",
  year = {2006}, 
  note = "[Online; accessed 20 Jan 2023]"
}

@inproceedings{konect,
	title = {{KONECT} -- {The} {Koblenz} {Network} {Collection}},
	author = {J\'{e}r\^{o}me Kunegis},
	year = {2013},
	booktitle = {Proc. Int. Conf. on World Wide Web Companion},
	pages = {1343--1350},
	url = {http://dl.acm.org/citation.cfm?id=2488173},
}

@misc{di_bartolomeo_puerta_wilson_crnovrsanin_dunne_2023,
 title={A collection of benchmark datasets for evaluating graph layout algorithms},
 url={osf.io/yftju},
 DOI={10.31219/osf.io/yftju},
 publisher={OSF Preprints},
 author={Di~Bartolomeo, Sara and Puerta, Eduardo and Wilson, Connor and Crnovrsanin, Tarik and Dunne, Cody},
 year={2023},
 month={Sep}
}

@InProceedings{Forster2002,
author="Forster, Michael",
editor="Goodrich, Michael T.
and Kobourov, Stephen G.",
title="Applying Crossing Reduction Strategies to Layered Compound Graphs",
booktitle="Graph Drawing",
year="2002",
doi={10.1007/3-540-36151-0_26},
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="276--284",
abstract="We present a new method for the application of 2-layer crossing reduction algorithms to layered compound graphs.It is based on an algorithm by Sander [9], [7], [8] and improves it with fewer crossings.Our method is optimal in the sense that it does not introduce unnecessary crossings by itself.If used with an optimal 2-layer crossing reduction algorithm, the crossing reduction for 2-layer compound graphs is optimal, too.",
isbn="978-3-540-36151-0"
}

@article{bekos2022,
author = {Bekos, M.A. and Dekker, D.J.C. and Frank, F. and Meulemans, W. and Rodgers, P. and Schulz, A. and Wessel, S.},
title = {Computing Schematic Layouts for Spatial Hypergraphs on Concentric Circles and Grids},
journal = {Computer Graphics Forum},
volume = {41},
number = {6},
pages = {316-335},
keywords = {information visualization, hypergraph drawing, visualization, computational geometry, modelling},
doi = {10.1111/cgf.14497},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.14497},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.14497},
abstract = {Abstract Set systems can be visualized in various ways. An important distinction between techniques is whether the elements have a spatial location that is to be used for the visualization; for example, the elements are cities on a map. Strictly adhering to such location may severely limit the visualization and force overlay, intersections and other forms of clutter. On the other hand, completely ignoring the spatial dimension omits information and may hide spatial patterns in the data. We study layouts for set systems (or hypergraphs) in which spatial locations are displaced onto concentric circles or a grid, to obtain schematic set visualizations. We investigate the tractability of the underlying algorithmic problems adopting different optimization criteria (e.g. crossings or bends) for the layout structure, also known as the support of the hypergraph. Furthermore, we describe a simulated-annealing approach to heuristically optimize a combination of such criteria. Using this method in computational experiments, we explore the trade-offs and dependencies between criteria for computing high-quality schematic set visualizations.},
year = {2022}
}

@InProceedings{binucci2023,
author="Binucci, Carla
and Didimo, Walter
and Patrignani, Maurizio",
editor="Angelini, Patrizio
and von Hanxleden, Reinhard",
title="st-Orientations with Few Transitive Edges",
booktitle="Graph Drawing and Network Visualization",
year="2023",
publisher="Springer International Publishing",
address="Cham",
pages="201--216",
doi={10.1007/978-3-031-22203-0_15},
abstract="The problem of orienting the edges of an undirected graph such that the resulting digraph is acyclic and has a single source s and a single sink t has a long tradition in graph theory and is central to many graph drawing algorithms. Such an orientation is called an st-orientation. We address the problem of computing st-orientations of undirected graphs with the minimum number of transitive edges. We prove that the problem is NP-hard in the general case. For planar graphs we describe an ILP model that is fast in practice. We experimentally show that optimum solutions dramatically reduce the number of transitive edges with respect to unconstrained st-orientations computed via classical st-numbering algorithms. Moreover, focusing on popular graph drawing algorithms that apply an st-orientation as a preliminary step, we show that reducing the number of transitive edges leads to drawings that are much more compact.",
isbn="978-3-031-22203-0"
}

@article{burch2017,
author = {Burch, M. and Hlawatsch, M. and Weiskopf, D.},
title = {Visualizing a Sequence of a Thousand Graphs (or Even More)},
journal = {Computer Graphics Forum},
volume = {36},
number = {3},
pages = {261-271},
keywords = {Categories and Subject Descriptors (according to ACM CCS), Data Structures E.1: Graphs and Networks—},
doi = {10.1111/cgf.13185},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13185},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13185},
abstract = {Abstract The visualization of dynamic graphs demands visually encoding at least three major data dimensions: vertices, edges, and time steps. Many of the state-of-the-art techniques can show an overview of vertices and edges but lack a data-scalable visual representation of the time aspect. In this paper, we address the problem of displaying dynamic graphs with a thousand or more time steps. Our proposed interleaved parallel edge splatting technique uses a time-to-space mapping and shows the complete dynamic graph in a static visualization. It provides an overview of all data dimensions, allowing for visually detecting time-varying data patterns; hence, it serves as a starting point for further data exploration. By applying clustering and ordering techniques on the vertices, edge splatting on the links, and a dense time-to-space mapping, our approach becomes visually scalable in all three dynamic graph data dimensions. We illustrate the usefulness of our technique by applying it to call graphs and US domestic flight data with several hundred vertices, several thousand edges, and more than a thousand time steps.},
year = {2017}
}

@article{eades1984,
author="Eades, P.",
title="A heuristic for graph drawing",
journal="Congressus Numerantium",
year="1984",
volume="42",
pages="149-160",
URL={https://cir.nii.ac.jp/crid/1573387448853684864}
}

@article{DIDIMO201871,
title = {A visual analytics system to support tax evasion discovery},
journal = {Decision Support Systems},
volume = {110},
pages = {71-83},
year = {2018},
issn = {0167-9236},
doi = {10.1016/j.dss.2018.03.008},
url = {https://www.sciencedirect.com/science/article/pii/S0167923618300563},
author = {Walter Didimo and Luca Giamminonni and Giuseppe Liotta and Fabrizio Montecchiani and Daniele Pagliuca},
keywords = {Tax evasion, Network analysis, Graph visualization, Visual analytics, Graph pattern matching, Graph database},
abstract = {This paper describes TaxNet, a decision support system for tax evasion discovery, based on a powerful visual language and on advanced network visualization techniques. It has been developed in cooperation with the Italian Revenue Agency, where it is currently used. TaxNet allows users to visually define classes of suspicious patterns, it exploits effective graph pattern matching technologies to rapidly extract subgraphs that correspond to one or more patterns, it provides facilities to conveniently merge the results, and it implements new ad-hoc centrality indexes to rank taxpayers based on their fiscal risk. Moreover, it offers a visual interface to analyze and interact with those networks that match a desired pattern. The paper discusses the results of an experimental study and some use cases conducted with expert officers on real data and in a real working environment. The experiments give evidence of the effectiveness of our system.}
}

@ARTICLE{burch1999,
author={Burch, H. and Cheswick, B.},
journal={Computer},
title={Mapping the Internet},
year={1999},
volume={32},
number={4},
pages={97-98},
doi={10.1109/2.755008}}

@misc{math2006-mw,
author= "North Dakota State University, and American Mathematical Society",
title= "The Mathematics Genealogy Project",
publisher = "American Mathematical Society",
year = 2006,
address = "United States", 
url = {https://genealogy.math.ndsu.nodak.edu/index.php}
}

@InProceedings{felice2017,
author="De Luca, Felice
and Di Giacomo, Emilio
and Didimo, Walter
and Kobourov, Stephen
and Liotta, Giuseppe",
editor="Poon, Sheung-Hung
and Rahman, Md. Saidur
and Yen, Hsu-Chun",
title="An Experimental Study on the Ply Number of Straight-Line Drawings",
booktitle="WALCOM: Algorithms and Computation",
year="2017",
publisher="Springer International Publishing",
address="Cham",
pages="135--148",
abstract="The ply number of a drawing is a new criterion of interest for graph drawing. Informally, the ply number of a straight-line drawing of a graph is defined as the maximum number of overlapping disks, where each disk is associated with a vertex and has a radius that is half the length of the longest edge incident to that vertex. This paper reports the results of an extensive experimental study that attempts to estimate correlations between the ply numbers and other aesthetic quality metrics for a graph layout, such as stress, edge-length uniformity, and edge crossings. We also investigate the performances of several graph drawing algorithms in terms of ply number, and provides new insights on the theoretical gap between lower and upper bounds on the ply number of k-ary trees.",
isbn="978-3-319-53925-6"
}



@InProceedings{felice2019,
author="De Luca, Felice
and Hossain, Md. Iqbal
and Kobourov, Stephen",
editor="Archambault, Daniel
and T{\'o}th, Csaba D.",
title="Symmetry Detection and Classification in Drawings of Graphs",
booktitle="Graph Drawing and Network Visualization",
year="2019",
publisher="Springer International Publishing",
address="Cham",
pages="499--513",
doi={10.1007/978-3-030-35802-0_38},
abstract="Symmetry is a key feature observed in nature (from flowers and leaves, to butterflies and birds) and in human-made objects (from paintings and sculptures, to manufactured objects and architectural design). Rotational, translational, and especially reflectional symmetries, are also important in drawings of graphs. Detecting and classifying symmetries can be very useful in algorithms that aim to create symmetric graph drawings and in this paper we present a machine learning approach for these tasks. Specifically, we show that deep neural networks can be used to detect reflectional symmetries with 92{\%} accuracy. We also build a multi-class classifier to distinguish between reflectional horizontal, reflectional vertical, rotational, and translational symmetries. Finally, we make available a collection of images of graph drawings with specific symmetric features that can be used in machine learning systems for training, testing and validation purposes. Our datasets, best trained ML models, source code are available online.",
isbn="978-3-030-35802-0"
}

@article{hofmann2017,
author = {Hofmann, J. and Größler, M. and Rubio-Sánchez, M. and Pichler, P.-P. and Lehmann, D. J.},
title = {Visual Exploration of Global Trade Networks with Time-Dependent and Weighted Hierarchical Edge Bundles on GPU},
journal = {Computer Graphics Forum},
volume = {36},
number = {3},
pages = {273-282},
keywords = {Categories and Subject Descriptors (according to ACM CCS), I.3.3 Computer Graphics: Picture/Image Generation—Graphs and Networks, Hierarchy Data, Time Series Data, GPUs and Multi-core Architectures},
doi = {10.1111/cgf.13186},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13186},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13186},
abstract = {Abstract The UN Comtrade database is the world's largest repository of bilateral trade data. Their complexity poses a challenge to visualization systems, leading to issues such as scalability and visual clutter. Thus, we propose a radial layout-based visual exploration system to enable the user to smoothly explore the change over time and to explore different commodity classes at once by using a novel edge bundling concept. We evaluated our system with the aid of a group of domain experts.},
year = {2017}
}

@article{kamada19897,
title = {An algorithm for drawing general undirected graphs},
journal = {Information Processing Letters},
volume = {31},
number = {1},
pages = {7-15},
year = {1989},
issn = {0020-0190},
doi = {10.1016/0020-0190(89)90102-6},
url = {https://www.sciencedirect.com/science/article/pii/0020019089901026},
author = {Tomihisa Kamada and Satoru Kawai},
keywords = {Graph, network structure, layout, drawing algorithm}
}

@article{davidson1996,
author = {Davidson, Ron and Harel, David},
title = {Drawing Graphs Nicely Using Simulated Annealing},
year = {1996},
issue_date = {Oct. 1996},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
volume = {15},
number = {4},
issn = {0730-0301},
url = {10.1145/234535.234538},
doi = {10.1145/234535.234538},
abstract = {The paradigm of simulated annealing is applied to the problem of drawing graphs “nicely.” Our algorithm deals with general undirected graphs with straight-line edges, and employs several simple criteria for the aesthetic quality of the result. The algorithm is flexible, in that the relative weights of the criteria can be changed. For graphs of modest size it produces good results, competitive with those produced by other methods, notably, the “spring method” and its variants.},
journal = {ACM Trans. Graph.},
month = {oct},
pages = {301–331},
numpages = {31},
keywords = {graph drawing, aesthetics, simulated annealing}
}

@incollection{Marner2014,
doi = {10.1007/978-3-662-45803-7_10},
url = {10.1007/978-3-662-45803-7_10},
year = {2014},
publisher = {Springer International Publishing},
pages = {113--124},
author = {Michael R. Marner and Ross T. Smith and Bruce H. Thomas and Karsten Klein and Peter Eades and Seok-Hee Hong},
title = {{GION}: Interactively Untangling Large Graphs on Wall-Sized Displays},
booktitle = {Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications}
}

@article{novak_graph-based_2010,
title = {Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data},
volume = {11},
issn = {1471-2105},
url = {10.1186/1471-2105-11-378},
doi = {10.1186/1471-2105-11-378},
abstract = {The investigation of plant genome structure and evolution requires comprehensive characterization of repetitive sequences that make up the majority of higher plant nuclear DNA. Since genome-wide characterization of repetitive elements is complicated by their high abundance and diversity, novel approaches based on massively-parallel sequencing are being adapted to facilitate the analysis. It has recently been demonstrated that the low-pass genome sequencing provided by a single 454 sequencing reaction is sufficient to capture information about all major repeat families, thus providing the opportunity for efficient repeat investigation in a wide range of species. However, the development of appropriate data mining tools is required in order to fully utilize this sequencing data for repeat characterization.},
number = {1},
journal = {BMC Bioinformatics},
author = {Novák, Petr and Neumann, Pavel and Macas, Jiří},
month = jul,
year = {2010},
pages = {378},
}

@article{cypko2017,
author = {Cypko, M.A. and Wojdziak, J. and Stoehr, M. and Kirchner, B. and Preim, B. and Dietz, A. and Lemke, H. U. and Oeltze-Jafra, S.},
title = {Visual Verification of Cancer Staging for Therapy Decision Support},
journal = {Computer Graphics Forum},
volume = {36},
number = {3},
pages = {109-120},
keywords = {Categories and Subject Descriptors (according to ACM CCS), I.3.8 Computer Graphics: Applications—Applications, J.3 Computer Applications: Life and Medical Sciences—Life and Medical Sciences},
doi = {10.1111/cgf.13172},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13172},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13172},
abstract = {Abstract It is generally accepted practice that each cancer patient case should be discussed in a clinical expert meeting, the so-called tumor board. A central role in finding the best therapy options for patients with solid tumors plays the Tumor, lymph Node, and Metastasis staging (TNM staging). Correctness of TNM staging has a significant impact on the therapy choice and hence on the patient's post-therapeutic quality of life or even survival. If inconsistencies in the TNM staging occur, possible explanations and solutions must be found based on the complex patient records, which takes the costly time of (multiple) physicians. We propose a more efficient visual analysis component, which supports a physician in verifying the given TNM staging before forwarding it to the tumor board. Our component comprises a Bayesian network model of the TNM staging process. Using information from the patient records and Bayesian inference, the models computes a patient-specific TNM staging, which is then explored and compared to the given staging by means of a graph-based visualization. Our component is implemented in a research prototype that supports an understanding of the model computations, allows for a fast identification of important influencing factors, and facilitates a quick detection of differences between two TNM stagings. We evaluated our component with five physicians, each studying 20 cases of laryngeal cancer.},
year = {2017}
}

@article{mennens2019,
author = {Mennens, Robin J.P. and Scheepens, Roeland and Westenberg, Michel A.},
title = {A stable graph layout algorithm for processes},
journal = {Computer Graphics Forum},
volume = {38},
number = {3},
pages = {725-737},
keywords = {CCS Concepts, • Human-centered computing → Graph drawings, • Applied computing → Business process monitoring},
doi = {10.1111/cgf.13723},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13723},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13723},
abstract = {Abstract Process mining enables organizations to analyze data about their (business) processes. Visualization is key to gaining insight into these processes and the associated data. Process visualization requires a high-quality graph layout that intuitively represents the semantics of the process. Process analysis additionally requires interactive filtering to explore the process data and process graph. The ideal process visualization therefore provides a high-quality, intuitive layout and preserves the mental map of the user during the visual exploration. The current industry standard used for process visualization does not satisfy either of these requirements. In this paper, we propose a novel layout algorithm for processes based on the Sugiyama framework. Our approach consists of novel ranking and order constraint algorithms and a novel crossing minimization algorithm. These algorithms make use of the process data to compute stable, high-quality layouts. In addition, we use phased animation to further improve mental map preservation. Quantitative and qualitative evaluations show that our approach computes layouts of higher quality and preserves the mental map better than the industry standard. Additionally, our approach is substantially faster, especially for graphs with more than 250 edges.},
year = {2019}
}

@article{lukasczyk2017,
author = {Lukasczyk, Jonas and Weber, Gunther and Maciejewski, Ross and Garth, Christoph and Leitte, Heike},
title = {Nested Tracking Graphs},
journal = {Computer Graphics Forum},
volume = {36},
number = {3},
pages = {12-22},
keywords = {Categories and Subject Descriptors (according to ACM CCS), Data Computer Graphics: Data Structures—Graphs and Networks},
doi = {10.1111/cgf.13164},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13164},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13164},
abstract = {Abstract Tracking graphs are a well established tool in topological analysis to visualize the evolution of components and their properties over time, i.e., when components appear, disappear, merge, and split. However, tracking graphs are limited to a single level threshold and the graphs may vary substantially even under small changes to the threshold. To examine the evolution of features for varying levels, users have to compare multiple tracking graphs without a direct visual link between them. We propose a novel, interactive, nested graph visualization based on the fact that the tracked superlevel set components for different levels are related to each other through their nesting hierarchy. This approach allows us to set multiple tracking graphs in context to each other and enables users to effectively follow the evolution of components for different levels simultaneously. We demonstrate the effectiveness of our approach on datasets from finite pointset methods, computational fluid dynamics, and cosmology simulations.},
year = {2017}
}

@article{filipov2023,
author = {Filipov, Velitchko and Arleo, Alessio and Miksch, Silvia},
title = {Are We There Yet? A Roadmap of Network Visualization from Surveys to Task Taxonomies},
journal = {Computer Graphics Forum},
volume = {42},
number = {6},
pages = {e14794},
keywords = {information visualization, network visualization, visual analytics},
doi = {10.1111/cgf.14794},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.14794},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.14794},
abstract = {Abstract Networks are abstract and ubiquitous data structures, defined as a set of data points and relationships between them. Network visualization provides meaningful representations of these data, supporting researchers in understanding the connections, gathering insights, and detecting and identifying unexpected patterns. Research in this field is focusing on increasingly challenging problems, such as visualizing dynamic, complex, multivariate, and geospatial networked data. This ever-growing, and widely varied, body of research led to several surveys being published, each covering one or more disciplines of network visualization. Despite this effort, the variety and complexity of this research represents an obstacle when surveying the domain and building a comprehensive overview of the literature. Furthermore, there exists a lack of clarification and uniformity between the terminology used in each of the surveys, which requires further effort when mapping and categorizing the plethora of different visualization techniques and approaches. In this paper, we aim at providing researchers and practitioners alike with a “roadmap” detailing the current research trends in the field of network visualization. We design our contribution as a meta-survey where we discuss, summarize, and categorize recent surveys and task taxonomies published in the context of network visualization. We identify more and less saturated disciplines of research and consolidate the terminology used in the surveyed literature. We also survey the available task taxonomies, providing a comprehensive analysis of their varying support to each network visualization discipline and by establishing and discussing a classification for the individual tasks. With this combined analysis of surveys and task taxonomies, we provide an overarching structure of the field, from which we extrapolate the current state of research and promising directions for future work.},
year = {2023}
}



@article{Frishman2008,
doi = {10.1109/tvcg.2008.11},
year = {2008},
month = jul,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {14},
number = {4},
pages = {727--740},
author = {Y. Frishman and A. Tal},
title = {Online Dynamic Graph Drawing},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{davis2011,
author = {Davis, Timothy A. and Hu, Yifan},
title = {The University of Florida Sparse Matrix Collection},
year = {2011},
issue_date = {November 2011},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
volume = {38},
number = {1},
issn = {0098-3500},
doi = {10.1145/2049662.2049663},
abstract = {We describe the University of Florida Sparse Matrix Collection, a large and actively growing set of sparse matrices that arise in real applications. The Collection is widely used by the numerical linear algebra community for the development and performance evaluation of sparse matrix algorithms. It allows for robust and repeatable experiments: robust because performance results with artificially generated matrices can be misleading, and repeatable because matrices are curated and made publicly available in many formats. Its matrices cover a wide spectrum of domains, include those arising from problems with underlying 2D or 3D geometry (as structural engineering, computational fluid dynamics, model reduction, electromagnetics, semiconductor devices, thermodynamics, materials, acoustics, computer graphics/vision, robotics/kinematics, and other discretizations) and those that typically do not have such geometry (optimization, circuit simulation, economic and financial modeling, theoretical and quantum chemistry, chemical process simulation, mathematics and statistics, power networks, and other networks and graphs). We provide software for accessing and managing the Collection, from MATLAB™, Mathematica™, Fortran, and C, as well as an online search capability. Graph visualization of the matrices is provided, and a new multilevel coarsening scheme is proposed to facilitate this task.},
journal = {ACM Transactions on Mathematical Software},
month = {dec},
articleno = {1},
numpages = {25},
keywords = {sparse matrices, Graph drawing, multilevel algorithms, performance evaluation}
}

@misc{enrondataset,
  author = {W. W. Cohen},
  title = {{Enron email dataset}},
  url = "https://
www.cs.cmu.edu/~enron/",
  year = {2022}, 
  note = "[Online; accessed 20 Jan 2023]"
}

@article{Buhmann:1998:DCQ,
	AUTHOR = {J. M. Buhmann and D. W. Fellner and M. Held and J.
		Ketterer and J. Puzicha},
	TITLE = {Dithered Color Quantization},
	JOURNAL = cgforum,
	EDITOR = {N. Ferreira and M. G\"{o}bel},
	VOLUME = {17},	NUMBER = {3},
	MONTH = Sep,	YEAR = {1998},	PAGES = {C219-C231},
	DOI = {10.1111/1467-8659.00269},
  NOTE = {(Proc. Eurographics'98)
	       \httpsAddr{//diglib.eg.org/handle/10.2312/8491}} }

@inproceedings{pawel2000,
author = {Gajer, Pawel and Kobourov, Stephen G.},
title = {GRIP: Graph DRawing with Intelligent Placement},
year = {2000},
isbn = {3540415548},
publisher = {Springer-Verlag},
address = {Berlin, Heidelberg},
doi={10.5555/647552.729406},
abstract = {This paper describes a system for Graph dRawing with Intelligent Placement, GRIP. The system is designed for drawing large graphs and uses a novel multi-dimensional force-directed method together with fast energy function minimization. The system allows for drawing graphs with tens of thousands of vertices in under a minute on a mid-range PC. To the best of the authors' knowledge GRIP surpasses the fastest previous algorithms. However, speed is not achieved at the expense of quality as the resulting drawings are quite aesthetically pleasing.},
booktitle = {Proceedings of the 8th International Symposium on Graph Drawing},
pages = {222–228},
numpages = {7},
series = {GD '00}
}

@ARTICLE{Fellner-Helmberg93,
	AUTHOR = {Fellner, Dieter W. and Helmberg, Christoph},
	TITLE = {Robust Rendering of General Ellipses and Elliptical Arcs},
	JOURNAL = tog,
	VOLUME = {12},	NUMBER = {3},
	MONTH = Jul,	YEAR = {1993},	PAGES = {251-276},
  DOI= {10.1145/169711.169704}
  }

  @ARTICLE{wook2018,
  author={Kim, Nam Wook and Bach, Benjamin and Im, Hyejin and Schriber, Sasha and Gross, Markus and Pfister, Hanspeter},
  journal={IEEE Transactions on Visualization and Computer Graphics}, 
  title={Visualizing Nonlinear Narratives with Story Curves}, 
  year={2018},
  volume={24},
  number={1},
  pages={595-604},
  doi={10.1109/TVCG.2017.2744118}}

@InProceedings{brandes2000,
author="Brandes, Ulrik
and Shubina, Galina
and Tamassia, Roberto",
editor="de Leeuw, Willem Cornelis
and van~Liere, Robert",
title="Improving Angular Resolution in Visualizations of Geographic Networks",
booktitle="Data Visualization 2000",
year="2000",
publisher="Springer Vienna",
address="Vienna",
pages="23--32",
abstract="In visualizations of large-scale transportation and communications networks, node coordinates are usually fixed to preserve the underlying geography, while links are represented as geodesics for simplicity. This often leads to severe readability problems due to poor angular resolution, i.e. small angles formed by lines converging in a node. We present a new method using automatically routed eubie curves that both preserves node coordinates and eliminates the resolution problem. The approach is applied to representations in the plane and on the sphere, showing European train connections and Internet traffic, respectively.",
isbn="978-3-7091-6783-0",
doi={10.1007/978-3-7091-6783-0_3}
}



@article{
girvan2002,
author = {M. Girvan  and M. E. J. Newman },
title = {Community structure in social and biological networks},
journal = {Proceedings of the National Academy of Sciences},
volume = {99},
number = {12},
pages = {7821-7826},
year = {2002},
doi = {10.1073/pnas.122653799},
abstract = {A number of recent studies have focused on the statistical properties of networked systems such as social networks and the Worldwide Web. Researchers have concentrated particularly on a few properties that seem to be common to many networks: the small-world property, power-law degree distributions, and network transitivity. In this article, we highlight another property that is found in many networks, the property of community structure, in which network nodes are joined together in tightly knit groups, between which there are only looser connections. We propose a method for detecting such communities, built around the idea of using centrality indices to find community boundaries. We test our method on computer-generated and real-world graphs whose community structure is already known and find that the method detects this known structure with high sensitivity and reliability. We also apply the method to two networks whose community structure is not well known—a collaboration network and a food web—and find that it detects significant and informative community divisions in both cases.}}

@article{formann1993,
author = {Formann, M. and Hagerup, T. and Haralambides, J. and Kaufmann, M. and Leighton, F. T. and Symvonis, A. and Welzl, E. and Woeginger, G.},
title = {Drawing Graphs in the Plane with High Resolution},
journal = {SIAM Journal on Computing},
volume = {22},
number = {5},
pages = {1035-1052},
year = {1993},
doi = {10.1137/0222063},
}

@Inbook{Didimo2013,
author="Didimo, Walter
and Liotta, Giuseppe",
title="The Crossing-Angle Resolution in Graph Drawing",
bookTitle="Thirty Essays on Geometric Graph Theory",
year="2013",
publisher="Springer New York",
address="New York, NY",
pages="167--184",
abstract="The crossing-angle resolution of a drawing of a graph measures the smallest angle formed by any pair of crossing edges. In this chapter, we survey some of the most recent results and discuss the current research agenda on drawings of graphs with good crossing-angle resolution.",
isbn="978-1-4614-0110-0",
doi="10.1007/978-1-4614-0110-0_10",
}



@article{Isenberg:2017:VMC,
  author      = {Petra Isenberg and Florian Heimerl and Steffen Koch and Tobias Isenberg and Panpan Xu and Chad Stolper and Michael Sedlmair and Jian Chen and Torsten M{\"o}ller and John Stasko},
  title       = {vispubdata.org: A Metadata Collection about {IEEE} Visualization ({VIS}) Publications},
  journal     = {IEEE Transactions on Visualization and Computer Graphics},
  year        = {2017},
  volume      = {23},
  number      = {9},
  month       = sep,
  pages       = {2199--2206},
  doi         = {10.1109/TVCG.2016.2615308},
  doi_url     = {10.1109/TVCG.2016.2615308},
  url         = {https://tobias.isenberg.cc/VideosAndDemos/Isenberg2017VMC},
  url2        = {http://www.vispubdata.org/site/vispubdata/},
  pdf         = {https://petra.isenberg.cc/publications/papers/Isenberg_2017_VMC.pdf},
}

@BOOK{FolDamFeiHug.etal93,
	AUTHOR = {Foley, James D. and van~Dam, Andries and
		Feiner, Stephen K. and Hughes, John F. and Phillips, R.},
	TITLE = {Introduction to Computer Graphics},
	PUBLISHER = {Addison-Wesley},
	YEAR = {1993} }

@ARTICLE{Kobbelt97-USHDR,
	author = {L. Kobbelt and M. Stamminger and H.-P. Seidel},
	title = {Using Subdivision on Hierarchical Data to Reconstruct Radiosity
		Distribution},
	JOURNAL = cgforum,
	volume = 16,	number = 3,	pages = {C347-C355},
	year = 1997,
	DOI = {10.1111/1467-8659.16.3conferenceissue.36},
	note = {(Proc. Eurographics'97)
	       \httpsAddr{//diglib.eg.org/handle/10.2312/8393}} }

@INPROCEEDINGS{huang2008,
  author={Huang, Weidong and Hong, Seok-Hee and Eades, Peter},
  booktitle={2008 IEEE Pacific Visualization Symposium}, 
  title={Effects of Crossing Angles}, 
  year={2008},
  volume={},
  number={},
  pages={41-46},
  doi={10.1109/PACIFICVIS.2008.4475457}}


@INPROCEEDINGS{Lafortune97-NARF,
	author = {Eric P. Lafortune and Sing-Choong Foo and Kenneth E. Torrance and
		Donald P. Greenberg},
	title = {Non-Linear Approximation of Reflectance Functions},
	booktitle = {Proc. SIGGRAPH '97},
	volume = 31,	pages = {117-126},
	year = 1997,
	DOI = {10.1145/258734.258801}
  }

@ARTICLE{Lous90,
	AUTHOR = {Y. Le Lous},
	TITLE = {Report on the {F}irst {E}urographics {W}orkshop on {V}isualization in
		{S}cientific {C}omputing},
	JOURNAL = cgforum,
	VOLUME = {9},	NUMBER = {4},
	MONTH = dec,	YEAR = {1990},	PAGES = {371-372},
  DOI= {10.1111/j.1467-8659.1990.tb00430.x}
  }

  @InProceedings{gutwenger2014,
author="Gutwenger, Carsten
and L{\"o}ffler, Maarten
and Nachmanson, Lev
and Rutter, Ignaz",
editor="Duncan, Christian
and Symvonis, Antonios",
title="Graph Drawing Contest Report",
booktitle="Graph Drawing",
year="2014",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="501--506",
doi={10.1007/978-3-662-45803-7_42},
abstract="This report describes the 21st Annual Graph Drawing Contest, held in conjunction with the 2014 Graph Drawing Symposium in W{\"u}rzburg, Germany. The purpose of the contest is to monitor and challenge the current state of graph-drawing technology.",
isbn="978-3-662-45803-7"
}

@inproceedings{li2005,
author = {Li, Wanchun and Eades, Peter and Nikolov, Nikola},
title = {Using Spring Algorithms to Remove Node Overlapping},
year = {2005},
isbn = {1920682279},
publisher = {Australian Computer Society, Inc.},
address = {AUS},
doi = {10.5555/1082315.1082334},
abstract = {Cluttered drawings of graphs cannot effectively convey the information of graphs. Two issues might cause node overlapping when one draws a picture of a graph. The first issue occurs when applying a layout algorithm for an abstract graph to a practical application in which nodes are labeled. The second is the changing of a node's size in a dynamic drawing system. This paper presents two algorithms, DNLS and ODNLS, for removing the two kinds of overlapping. The algorithms are based on the well-known spring embedder model. The outputs of the algorithms provide the features of spring algorithms. Experiments are carried out to compare DNLS and ODNLS to the Force Scan(FS) algorithm and its variants. The results demonstrate the advantages of DNLS and ODNLS in terms of some aesthetic criteria.},
booktitle = {Proceedings of the 2005 Asia-Pacific Symposium on Information Visualisation - Volume 45},
pages = {131–140},
numpages = {10},
keywords = {node overlapping, graph drawing, spring algorithm},
location = {Sydney, Australia},
series = {APVis '05}
}

@article{strobelt2012,
author = {Strobelt, H. and Spicker, M. and Stoffel, A. and Keim, D. and Deussen, O.},
title = {Rolled-out Wordles: A Heuristic Method for Overlap Removal of 2D Data Representatives},
year = {2012},
issue_date = {June 2012},
publisher = {The Eurographs Association \& John Wiley \& Sons, Ltd.},
address = {Chichester, GBR},
volume = {31},
number = {3pt3},
issn = {0167-7055},
doi = {10.1111/j.1467-8659.2012.03106.x},
abstract = {When representing 2D data points with spacious objects such as labels, overlap can occur. We present a simple algorithm which modifies the (Mani-) Wordle idea with scan-line based techniques to allow a better placement. We give an introduction to common placement techniques from different fields and compare our method to these techniques w.r.t. euclidean displacement, changes in orthogonal ordering as well as shape and size preservation. Especially in dense scenarios our method preserves the overall shape better than known techniques and allows a good trade-off between the other measures. Applications on real world data are given and discussed. © 2012 Wiley Periodicals, Inc.},
journal = {Comput. Graph. Forum},
month = {jun},
pages = {1135–1144},
numpages = {10},
keywords = {I.3.3 [Computer Graphics]: Picture/Image Generation—Line and curve generation}
}

  @InProceedings{duncan2013,
author="Duncan, Christian A.
and Gutwenger, Carsten
and Nachmanson, Lev
and Sander, Georg",
editor="Didimo, Walter
and Patrignani, Maurizio",
title="Graph Drawing Contest Report",
booktitle="Graph Drawing",
year="2013",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="575--579",
doi={10.1007/978-3-642-36763-2_58},
abstract="This report describes the 19th Annual Graph Drawing Contest, held in conjunction with the 2012 Graph Drawing Symposium in Redmond, USA. The purpose of the contest is to monitor and challenge the current state of graph-drawing technology. For the first time, we introduced a graph drawing game contest and asked conference attendees to judge the games.",
isbn="978-3-642-36763-2"
}

@article{palmer2022,
author = {Glenn Palmer and Roseanne W McManus and Vito D’Orazio and Michael R Kenwick and Mikaela Karstens and Chase Bloch and Nick Dietrich and Kayla Kahn and Kellan Ritter and Michael J Soules},
title ={The MID5 Dataset, 2011–2014: Procedures, coding rules, and description},
journal = {Conflict Management and Peace Science},
volume = {39},
number = {4},
pages = {470-482},
year = {2022},
doi = {10.1177/0738894221995743},
URL = {
10.1177/0738894221995743
},
eprint = {
10.1177/0738894221995743
}
,
abstract = { This article introduces the latest iteration of the most widely used dataset on interstate conflicts, the Militarized Interstate Dispute (MID) 5 dataset. We begin by outlining the data collection process used in the MID5 project. Next, we discuss some of the most challenging cases that we coded and some updates to the coding manual that resulted. Finally, we provide descriptive statistics for the new years of the MID data. }
}
  
  @article{Tanahashi2012,
doi = {10.1109/tvcg.2012.212},
year = {2012},
month = dec,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {18},
number = {12},
pages = {2679--2688},
author = {Y. Tanahashi and Kwan-Liu Ma},
title = {Design Considerations for Optimizing Storyline Visualizations},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{leskovec2016snap,
  title={SNAP: A General-Purpose Network Analysis and Graph-Mining Library},
  author={Leskovec, Jure and Sosi{\v{c}}, Rok},
  journal={ACM Transactions on Intelligent Systems and Technology (TIST)},
  volume={8},
  number={1},
  pages={1},
  year={2016},
  publisher={ACM},
  doi={10.1145/2898361}
}

@article{Tanahashi2015,
doi = {10.1109/tvcg.2015.2392771},
year = {2015},
month = jun,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {21},
number = {6},
pages = {730--742},
author = {Yuzuru Tanahashi and Chien-Hsin Hsueh and Kwan-Liu Ma},
title = {An Efficient Framework for Generating Storyline Visualizations from Streaming Data},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{Bartolomeo2021,
doi = {10.1109/tvcg.2020.3030442},
year = {2021},
month = feb,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {27},
number = {2},
pages = {1353--1363},
author = {Di~Bartolomeo, Sara and Yixuan Zhang and Fangfang Sheng and Cody Dunne},
title = {{Sequence Braiding}: Visual Overviews of Temporal Event Sequences and Attributes},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@incollection{vanDijk2018,
doi = {10.1007/978-3-319-73915-1_29},
year = {2018},
publisher = {Springer International Publishing},
pages = {365--378},
author = {Thomas C. van~Dijk and Fabian Lipp and Peter Markfelder and Alexander Wolff},
title = {Computing Storyline Visualizations with Few Block Crossings},
booktitle = {Lecture Notes in Computer Science}
}

@InProceedings{junger1997,
author="J{\"u}nger, Michael
and Mutzel, Petra",
editor="Brandenburg, Franz J.",
title="Exact and heuristic algorithms for 2-layer straightline crossing minimization",
booktitle="Graph Drawing",
year="1996",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="337--348",
doi={10.1007/BFb0021817},
abstract="We present algorithms for the two layer straightline crossing minimization problem that are able to compute exact optima. Our computational results lead us to the conclusion that there is no need for heuristics if one layer is fixed, even though the problem is NP-hard, and that for the general problem with two variable layers, true optima can be computed for sparse instances in which the smaller layer contains up to 15 nodes. For bigger instances, the iterated barycenter method turns out to be the method of choice among several popular heuristics whose performance we could assess by comparing the results to optimum solutions.",
isbn="978-3-540-49351-8"
}

@inproceedings{hu2020,
author = {Hu, Weihua and Fey, Matthias and Zitnik, Marinka and Dong, Yuxiao and Ren, Hongyu and Liu, Bowen and Catasta, Michele and Leskovec, Jure},
title = {Open graph benchmark: datasets for machine learning on graphs},
year = {2020},
isbn = {9781713829546},
publisher = {Curran Associates Inc.},
address = {Red Hook, NY, USA},
abstract = {We present the OPEN GRAPH BENCHMARK (OGB), a diverse set of challenging and realistic benchmark datasets to facilitate scalable, robust, and reproducible graph machine learning (ML) research. OGB datasets are large-scale, encompass multiple important graph ML tasks, and cover a diverse range of domains, ranging from social and information networks to biological networks, molecular graphs, source code ASTs, and knowledge graphs. For each dataset, we provide a unified evaluation protocol using meaningful application-specific data splits and evaluation metrics. In addition to building the datasets, we also perform extensive benchmark experiments for each dataset. Our experiments suggest that OGB datasets present significant challenges of scalability to large-scale graphs and out-of-distribution generalization under realistic data splits, indicating fruitful opportunities for future research. Finally, OGB provides an automated end-to-end graph ML pipeline that simplifies and standardizes the process of graph data loading, experimental setup, and model evaluation. OGB will be regularly updated and welcomes inputs from the community.},
booktitle = {Proceedings of the 34th International Conference on Neural Information Processing Systems},
articleno = {1855},
numpages = {16},
location = {Vancouver, BC, Canada},
series = {NIPS '20}
}


@incollection{Gronemann2016b,
doi = {10.1007/978-3-319-50106-2_29},
year = {2016},
publisher = {Springer International Publishing},
pages = {367--381},
author = {Martin Gronemann and Michael J\"{u}nger and Frauke Liers and Francesco Mambelli},
title = {Crossing Minimization in Storyline Visualization},
booktitle = {Lecture Notes in Computer Science}
}

@article{ShixiaLiu2013,
doi = {10.1109/tvcg.2013.196},
year = {2013},
month = dec,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {19},
number = {12},
pages = {2436--2445},
author = {Shixia Liu and Yingcai Wu and Enxun Wei and Mengchen Liu and Yang Liu},
title = {{StoryFlow}: Tracking the Evolution of Stories},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@incollection{Klawitter2021,
doi = {10.1007/978-3-030-92931-2_11},
url = {10.1007/978-3-030-92931-2_11},
year = {2021},
publisher = {Springer International Publishing},
pages = {149--165},
author = {Jonathan Klawitter and Johannes Zink},
title = {Upward Planar Drawings with~Three and~More Slopes},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Nllenburg2021,
doi = {10.1007/978-3-030-92931-2_23},
url = {10.1007/978-3-030-92931-2_23},
year = {2021},
publisher = {Springer International Publishing},
pages = {318--326},
author = {Martin N\"{o}llenburg and Anaïs Villedieu and Jules Wulms},
title = {Layered Area-Proportional Rectangle Contact Representations},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Nllenburg2010,
doi = {10.1007/978-3-642-11805-0_36},
url = {10.1007/978-3-642-11805-0_36},
year = {2010},
publisher = {Springer Berlin Heidelberg},
pages = {381--392},
author = {Martin N\"{o}llenburg},
title = {An Improved Algorithm for the Metro-line Crossing Minimization Problem},
booktitle = {Graph Drawing}
}

@incollection{Oikonomou2018,
doi = {10.1007/978-3-030-04414-5_24},
url = {10.1007/978-3-030-04414-5_24},
year = {2018},
publisher = {Springer International Publishing},
pages = {347--353},
author = {Anargyros Oikonomou and Antonios Symvonis},
title = {Monotone Drawings of k-Inner Planar Graphs},
booktitle = {Lecture Notes in Computer Science}
}

@TECHREPORT{Sander1996,
    author = {Georg Sander},
    title = {Layout of Compound Directed Graphs},
    institution = {FB INFORMATIK, UNIVERSITAT DES SAARLANDES},
    year = {1996}
}

@incollection{Skambath2016,
doi = {10.1007/978-3-319-50106-2_44},
url = {10.1007/978-3-319-50106-2_44},
year = {2016},
publisher = {Springer International Publishing},
pages = {572--586},
author = {Malte Skambath and Till Tantau},
title = {Offline Drawing of Dynamic Trees: Algorithmics and Document Integration},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{vanDijk2016,
doi = {10.1007/978-3-319-50106-2_30},
url = {10.1007/978-3-319-50106-2_30},
year = {2016},
publisher = {Springer International Publishing},
pages = {382--398},
author = {Thomas C. van Dijk and Martin Fink and Norbert Fischer and Fabian Lipp and Peter Markfelder and Alexander Ravsky and Subhash Suri and Alexander Wolff},
title = {Block Crossings in Storyline Visualizations},
booktitle = {Lecture Notes in Computer Science}
}

@ARTICLE{Taurus2023,
author={Xue, Mingliang and Wang, Zhi and Zhong, Fahai and Wang, Yong and Xu, Mingliang and Deussen, Oliver and Wang, Yunhai},
journal={IEEE Transactions on Visualization and Computer Graphics},
title={Taurus: Towards a Unified Force Representation and Universal Solver for Graph Layout},
year={2023},
volume={29},
number={1},
pages={886-895},
doi={10.1109/TVCG.2022.3209371}}

@InProceedings{barth2002,
author="Barth, Wilhelm
and J{\"u}nger, Michael
and Mutzel, Petra",
editor="Goodrich, Michael T.
and Kobourov, Stephen G.",
title="Simple and Efficient Bilayer Cross Counting",
booktitle="Graph Drawing",
year="2002",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="130--141",
doi= {10.1007/3-540-36151-0_13},
abstract="We consider the problem of counting the interior edge crossings when a bipartite graph G = (V,E) with node set V and edge set E is drawn such that the nodes of the two shores of the bipartition are drawn as distinct points on two parallel lines and the edges as straight line segments. The efficient solution of this problem is important in layered graph drawing. Our main observation is that it can be reduced to counting the inversions of a certain sequence. This leads to an O(∣E∣+∣C∣) algorithm, where C denotes the set of pairwise interior edge crossings, as well as to a simple O(∣E∣ log ∣Vsmall∣) algorithm, where Vsmall is the smaller cardinality node set in the bipartition of the node set V of the graph. We present the algorithms and the results of computational experiments with these and other algorithms on a large collection of instances.",
isbn="978-3-540-36151-0"
}

@InProceedings{chimani2016,
author="Chimani, Markus
and Klein, Karsten
and Wiedera, Tilo",
editor="Hu, Yifan
and N{\"o}llenburg, Martin",
title="A Note on the Practicality of Maximal Planar Subgraph Algorithms",
booktitle="Graph Drawing and Network Visualization",
year="2016",
publisher="Springer International Publishing",
address="Cham",
pages="357--364",
abstract="Given a graph G, the NP-hard Maximum Planar Subgraph problem (MPS) asks for a planar subgraph of G with the maximum number of edges. There are several heuristic, approximative, and exact algorithms to tackle the problem, but---to the best of our knowledge---they have never been compared competitively in practice.",
isbn="978-3-319-50106-2"
}

@incollection{Castermans2018,
doi = {10.1007/978-3-030-04414-5_4},
year = {2018},
publisher = {Springer International Publishing},
pages = {53--66},
author = {Thom Castermans and Mereke van~Garderen and Wouter Meulemans and Martin N\"{o}llenburg and Xiaoru Yuan},
title = {Short Plane Supports for Spatial Hypergraphs},
booktitle = {Lecture Notes in Computer Science}
}

@InProceedings{Forster2005,
doi = {10.1007/978-3-540-31843-9_22},
year = {2005},
publisher = {Springer Berlin Heidelberg},
pages = {206--216},
author = {Mıchael Forster},
title = {A Fast and Simple Heuristic for Constrained Two-Level Crossing Reduction},
booktitle = {Graph Drawing}
}

@InProceedings{Buchheim2006,
author="Buchheim, Christoph
and Ebner, Dietmar
and J{\"u}nger, Michael
and Klau, Gunnar W.
and Mutzel, Petra
and Weiskircher, Ren{\'e}",
editor="Healy, Patrick
and Nikolov, Nikola S.",
title="Exact Crossing Minimization",
booktitle="Graph Drawing",
year="2006",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="37--48",
doi={10.1007/11618058_4},
abstract="The crossing number of a graph is the minimum number of edge crossings in any drawing of the graph into the plane. This very basic property has been studied extensively in the literature from a theoretic point of view and many bounds exist for a variety of graph classes. In this paper, we present the first algorithm able to compute the crossing number of general sparse graphs of moderate size and present computational results on a popular benchmark set of graphs. The approach uses a new integer linear programming formulation of the problem combined with strong heuristics and problem reduction techniques. This enables us to compute the crossing number for 91 percent of all graphs on up to 40 nodes in the benchmark set within a time limit of five minutes per graph.",
isbn="978-3-540-31667-1"
}

@article{Meulemans2013,
doi = {10.1109/tvcg.2013.76},
year = {2013},
month = nov,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {19},
number = {11},
pages = {1846--1858},
author = {Wouter Meulemans and Nathalie Henry Riche and Bettina Speckmann and Basak Alper and Tim Dwyer},
title = {{KelpFusion}: A Hybrid Set Visualization Technique},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{NanCao2011,
doi = {10.1109/tvcg.2011.188},
year = {2011},
month = dec,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {17},
number = {12},
pages = {2581--2590},
author = {Nan Cao and D. Gotz and J. Sun and Huamin Qu},
title = {{DICON}: Interactive Visual Analysis of Multidimensional Clusters},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{Nollenburg2011,
doi = {10.1109/tvcg.2010.81},
year = {2011},
month = may,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {17},
number = {5},
pages = {626--641},
author = {M Nollenburg and A Wolff},
title = {Drawing and Labeling High-Quality Metro Maps by Mixed-Integer Programming},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{Huang2016,
doi = {10.1109/tvcg.2015.2467771},
year = {2016},
month = jan,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {22},
number = {1},
pages = {160--169},
author = {Xiaoke Huang and Ye Zhao and Chao Ma and Jing Yang and Xinyue Ye and Chong Zhang},
title = {{TrajGraph}: A Graph-Based Visual Analytics Approach to Studying Urban Network Centralities Using Taxi Trajectory Data},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{Bach2014,
doi = {10.1109/tvcg.2013.254},
year = {2014},
month = may,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {20},
number = {5},
pages = {740--754},
author = {Benjamin Bach and Emmanuel Pietriga and Jean-Daniel Fekete},
title = {{GraphDiaries}: Animated Transitions {andTemporal} Navigation for Dynamic Networks},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{Ballweg2018,
author = {{Kathrin}  {Ballweg} and {Margit}  {Pohl} and {Günter}  {Wallner} and {Tatiana}  {von~Landesberger}},
title = {Visual Similarity Perception of Directed Acyclic 
Graphs: A Study on Influencing Factors and Similarity Judgment 
Strategies},
journal = {Journal of Graph Algorithms and Applications},
year = {2018},
volume = {22},
number = {3},
pages = {519--553},
doi = {10.7155/jgaa.00467}
}

@article{padia2018,
doi = {10.20380/GI2018.05},
author = {Padia, Kalpesh and Bandara, Kaveen and Healey, Christopher},
keywords = {000 computer science, HTN Planning, Narratives, Storyline Visualization},
language = {en},
title = {Yarn: Generating Storyline Visualizations Using HTN Planning},
journal = {Proceedings of Graphics Interface 2018},
volume = {Toronto},
pages = {26--33},
publisher = {Canadian Human-Computer Communications Society / Société canadienne du dialogue humain-machine},
year = {2018},
copyright = {Permission is granted to quote short excerpts and to reproduce figures and tables from these proceed­ings, provided that the source of such material is fully acknowledged.}
}

@article{padia2019,
doi = {10.1016/j.cag.2018.11.004},
year = {2019},
month = feb,
publisher = {Elsevier {BV}},
volume = {78},
pages = {64--75},
author = {Kalpesh Padia and Kaveen Herath Bandara and Christopher G. Healey},
title = {A system for generating storyline visualizations using hierarchical task network planning},
journal = {Computers \& Graphics}
}

@incollection{Perri2020,
doi = {10.1007/978-3-030-68766-3_8},
year = {2020},
publisher = {Springer International Publishing},
pages = {99--114},
author = {Vincenzo Perri and Ingo Scholtes},
title = {{HOTVis}: Higher-Order Time-Aware Visualisation of Dynamic Graphs},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Klawitter2018,
  doi = {10.1007/978-3-319-73915-1_19},
  year = {2018},
  publisher = {Springer International Publishing},
  pages = {224--238},
  author = {Jonathan Klawitter and Tamara Mchedlidze and Martin N\"{o}llenburg},
  title = {Experimental Evaluation of Book Drawing Algorithms},
  booktitle = {Lecture Notes in Computer Science}
}

@incollection{Lim2021,
doi = {10.1007/978-3-030-92931-2_10},
year = {2021},
publisher = {Springer International Publishing},
pages = {138--146},
author = {HeuiChan Lim and Stephen Kobourov},
title = {Visualizing {JIT} Compiler Graphs},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Firman2019,
doi = {10.1007/978-3-030-35802-0_16},
year = {2019},
publisher = {Springer International Publishing},
pages = {203--215},
author = {Oksana Firman and Philipp Kindermann and Alexander Ravsky and Alexander Wolff and Johannes Zink},
title = {Computing Height-Optimal Tangles~Faster},
booktitle = {Lecture Notes in Computer Science}
}



@incollection{Olszewski2018,
doi = {10.1007/978-3-030-04414-5_8},
year = {2018},
publisher = {Springer International Publishing},
pages = {106--119},
author = {Maya Olszewski and Jeff Meder and Emmanuel Kieffer and Raphaël Bleuse and Martin Rosalie and Gr{\'{e}}goire Danoy and Pascal Bouvry},
title = {Visualizing the Template of a Chaotic Attractor},
booktitle = {Lecture Notes in Computer Science}
}

@article{Holten2006,
doi = {10.1109/tvcg.2006.147},
year = {2006},
month = sep,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {12},
number = {5},
pages = {741--748},
author = {D. Holten},
title = {Hierarchical Edge Bundles: Visualization of Adjacency Relations in Hierarchical Data},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{burch2011,
doi = {10.1109/tvcg.2011.226},
year = {2011},
month = dec,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {17},
number = {12},
pages = {2344--2353},
author = {M. Burch and C. Vehlow and F. Beck and S. Diehl and D. Weiskopf},
title = {Parallel Edge Splatting for Scalable Dynamic Graph Visualization},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{Fruchterman1991,
doi = {10.1002/spe.4380211102},
year = {1991},
month = nov,
publisher = {Wiley},
volume = {21},
number = {11},
pages = {1129--1164},
author = {Thomas M. J. Fruchterman and Edward M. Reingold},
title = {Graph drawing by force-directed placement},
journal = {Software: Practice and Experience}
}

@incollection{Ni2018,
doi = {10.1007/978-3-030-04414-5_32},
year = {2018},
publisher = {Springer International Publishing},
pages = {447--462},
author = {Chien-Chun Ni and Yu-Yao Lin and Jie Gao and Xianfeng Gu},
title = {Network Alignment by Discrete Ollivier-Ricci Flow},
booktitle = {Lecture Notes in Computer Science}
}

@article{holten2009,
author = {Holten, Danny and Van Wijk, Jarke J.},
title = {Force-Directed Edge Bundling for Graph Visualization},
journal = {Computer Graphics Forum},
volume = {28},
number = {3},
pages = {983-990},
keywords = {I.3.3 Computer Graphics: Picture/Image Generation—Line and Curve Generation, I.3.5 Computer Graphics: Computational Geometry and Object Modeling—Physically Based Modeling},
doi = {10.1111/j.1467-8659.2009.01450.x},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1467-8659.2009.01450.x},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1467-8659.2009.01450.x},
abstract = {Abstract Graphs depicted as node-link diagrams are widely used to show relationships between entities. However, node-link diagrams comprised of a large number of nodes and edges often suffer from visual clutter. The use of edge bundling remedies this and reveals high-level edge patterns. Previous methods require the graph to contain a hierarchy for this, or they construct a control mesh to guide the edge bundling process, which often results in bundles that show considerable variation in curvature along the overall bundle direction. We present a new edge bundling method that uses a self-organizing approach to bundling in which edges are modeled as flexible springs that can attract each other. In contrast to previous methods, no hierarchy is used and no control mesh. The resulting bundled graphs show significant clutter reduction and clearly visible high-level edge patterns. Curvature variation is furthermore minimized, resulting in smooth bundles that are easy to follow. Finally, we present a rendering technique that can be used to emphasize the bundling.},
year = {2009}
}

@ARTICLE{cui2008,
author={Cui, Weiwei and Zhou, Hong and Qu, Huamin and Wong, Pak Chung and Li, Xiaoming},
journal={IEEE Transactions on Visualization and Computer Graphics},
title={Geometry-Based Edge Clustering for Graph Visualization},
year={2008},
volume={14},
number={6},
pages={1277-1284},
abstract={Graphs have been widely used to model relationships among data. For large graphs, excessive edge crossings make the display visually cluttered and thus difﬁcult to explore. In this paper, we propose a novel geometry-based edge-clustering framework that can group edges into bundles to reduce the overall edge crossings. Our method uses a control mesh to guide the edge-clustering process; edge bundles can be formed by forcing all edges to pass through some control points on the mesh. The control mesh can be generated at different levels of detail either manually or automatically based on underlying graph patterns. Users can further interact with the edge-clustering results through several advanced visualization techniques such as color and opacity enhancement. Compared with other edge-clustering methods, our approach is intuitive, ﬂexible, and efﬁcient. The experiments on some large graphs demonstrate the effectiveness of our method.},
keywords={},
doi={10.1109/TVCG.2008.135},
ISSN={1941-0506},
month={Nov},}

@article{zachary1977,
ISSN = {00917710},
URL = {http://www.jstor.org/stable/3629752},
abstract = {Data from a voluntary association are used to construct a new formal model for a traditional anthropological problem, fission in small groups. The process leading to fission is viewed as an unequal flow of sentiments and information across the ties in a social network. This flow is unequal because it is uniquely constrained by the contextual range and sensitivity of each relationship in the network. The subsequent differential sharing of sentiments leads to the formation of subgroups with more internal stability than the group as a whole, and results in fission. The Ford-Fulkerson labeling algorithm allows an accurate prediction of membership in the subgroups and of the locus of the fission to be made from measurements of the potential for information flow across each edge in the network. Methods for measurement of potential information flow are discussed, and it is shown that all appropriate techniques will generate the same predictions.},
author = {Wayne W. Zachary},
journal = {Journal of Anthropological Research},
number = {4},
pages = {452--473},
publisher = {[University of New Mexico, University of Chicago Press]},
title = {An Information Flow Model for Conflict and Fission in Small Groups},
urldate = {2023-05-26},
volume = {33},
year = {1977}
}

@article{Grabowicz2014,
doi = {10.1140/epjds/s13688-014-0027-8},
url = {10.1140/epjds/s13688-014-0027-8},
year = {2014},
month = oct,
publisher = {Springer Science and Business Media {LLC}},
volume = {3},
number = {1},
author = {Przemyslaw A Grabowicz and Luca Maria Aiello and Filippo Menczer},
title = {Fast filtering and animation of large dynamic networks},
journal = {{EPJ} Data Science}
}

@article{dang2016,
author = {Dang, T. N. and Pendar, N. and Forbes, A. G.},
title = {TimeArcs: Visualizing Fluctuations in Dynamic Networks},
journal = {Computer Graphics Forum},
volume = {35},
number = {3},
pages = {61-69},
keywords = {Categories and Subject Descriptors (according to ACM CCS):, H.5.2 Information Interfaces and Presentation: User Interfaces—Graphical user interfaces},
doi = {10.1111/cgf.12882},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.12882},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.12882},
abstract = {Abstract In this paper we introduce TimeArcs, a novel visualization technique for representing dynamic relationships between entities in a network. Force-directed layouts provide a way to highlight related entities by positioning them near to each other Entities are brought closer to each other (forming clusters) by forces applied on nodes and connections between nodes. In many application domains, relationships between entities are not temporally stable, which means that cluster structures and cluster memberships also may vary across time. Our approach merges multiple force-directed layouts at different time points into a single comprehensive visualization that provides a big picture overview of the most significant clusters within a user-defined period of time. TimeArcs also supports a range of interactive features, such as allowing users to drill-down in order to see details about a particular cluster. To highlight the benefits of this technique, we demonstrate its application to various datasets, including the IMDB co-star network, a dataset showing conflicting evidences within biomedical literature of protein interactions, and collocated popular phrases obtained from political blogs.},
year = {2016}
}

@inproceedings{feng2019dropout,
title={Understanding Dropouts in MOOCs},
author={Wenzheng Feng and Jie Tang and Tracy Xiao Liu and Shuhuai Zhang and Jian Guan},
booktitle={Proceedings of the 33rd AAAI Conference on Artificial Intelligence},
year={2019}, 
doi = {10.1609/aaai.v33i01.3301517}
}

@article{red2011,
author = {Red, Veronica and Kelsic, Eric D. and Mucha, Peter J. and Porter, Mason A.},
title = {Comparing Community Structure to Characteristics in Online Collegiate Social Networks},
journal = {SIAM Review},
volume = {53},
number = {3},
pages = {526-543},
year = {2011},
doi = {10.1137/080734315},
URL = {
10.1137/080734315
},
eprint = {
10.1137/080734315
}
,
abstract = { We study the structure of social networks of students by examining the graphs of Facebook “friendships” at five U.S. universities at a single point in time. We investigate the community structure of each single-institution network and employ visual and quantitative tools, including standardized pair-counting methods, to measure the correlations between the network communities and a set of self-identified user characteristics (residence, class year, major, and high school). We review the basic properties and statistics of the employed pair-counting indices and recall, in simplified notation, a useful formula for the z-score of the Rand coefficient. Our study illustrates how to examine different instances of social networks constructed in similar environments, emphasizes the array of social forces that combine to form “communities,” and leads to comparative observations about online social structures, which reflect offline social structures. We calculate the relative contributions of different characteristics to the community structure of individual universities and compare these relative contributions at different universities. For example, we examine the importance of common high school affiliation at large state universities and the varying degrees of influence that common major can have on the social structure at different universities. The heterogeneity of the communities that we observe indicates that university networks typically have multiple organizing factors rather than a single dominant one. }
}

@article{facebooklong,
author = {Traud, Amanda L. and Mucha, Peter J. and Porter, Mason A.},
title = {Social Structure of Facebook Networks},
note = {ar{X}iv:1102.2166},
year = {2011}, 
url = {http://arxiv.org/abs/1102.2116}
}

@article{van_de_bunt_friendship_1999,
title = {Friendship {Networks} {Through} {Time}: {An} {Actor}-{Oriented} {Dynamic} {Statistical} {Network} {Model}},
volume = {5},
issn = {1572-9346},
url = {10.1023/A:1009683123448},
doi = {10.1023/A:1009683123448},
abstract = {We propose a class of actor-oriented statistical models for closed social networks in general, and friendship networks in particular. The models are random utility models developed within a rational choice framework. Based on social psychological and sociological theories about friendship, mathematical functions capturing expected utility of individual actors with respect to friendship are constructed. Expected utility also contains a random (unexplained) component. We assume that, given their restrictions and contact opportunities, individuals evaluate their utility functions and behave such that they maximize the expected amount of utility. The behavior under consideration is the expression of like and dislike (choice of friends). Theoretical mechanisms that are modelled are, e.g., the principle of diminishing returns, the tendency towards reciprocated choices, and the preference for friendship relations with similar others. Constraints imposed on individuals are, e.g., the structure of the existing network, and the distribution of personal characteristics over the respondents. The models are illustrated by means of a data-set collected among university freshmen at 7 points in time during 1994 and 1995.},
number = {2},
journal = {Computational \& Mathematical Organization Theory},
author = {Van De Bunt, Gerhard G. and Van Duijn, Marijtje A.J. and Snijders, Tom A.B.},
month = jul,
year = {1999},
pages = {167--192},
}

@article{ISELLA2011166,
title = {What's in a crowd? Analysis of face-to-face behavioral networks},
journal = {Journal of Theoretical Biology},
volume = {271},
number = {1},
pages = {166-180},
year = {2011},
issn = {0022-5193},
doi = {10.1016/j.jtbi.2010.11.033},
url = {https://www.sciencedirect.com/science/article/pii/S0022519310006284},
author = {Lorenzo Isella and Juliette Stehlé and Alain Barrat and Ciro Cattuto and Jean-François Pinton and Wouter {Van den Broeck}},
keywords = {Dynamic networks, Face-to-face proximity, Information spreading, Behavioral social networks, Complex networks},
abstract = {The availability of new data sources on human mobility is opening new avenues for investigating the interplay of social networks, human mobility and dynamical processes such as epidemic spreading. Here we analyze data on the time-resolved face-to-face proximity of individuals in large-scale real-world scenarios. We compare two settings with very different properties, a scientific conference and a long-running museum exhibition. We track the behavioral networks of face-to-face proximity, and characterize them from both a static and a dynamic point of view, exposing differences and similarities. We use our data to investigate the dynamics of a susceptible–infected model for epidemic spreading that unfolds on the dynamical networks of human proximity. The spreading patterns are markedly different for the conference and the museum case, and they are strongly impacted by the causal structure of the network data. A deeper study of the spreading paths shows that the mere knowledge of static aggregated networks would lead to erroneous conclusions about the transmission paths on the dynamical networks.}
}

@inproceedings{mcauley2012,
author = {McAuley, Julian and Leskovec, Jure},
title = {Learning to Discover Social Circles in Ego Networks},
year = {2012},
publisher = {Curran Associates Inc.},
address = {Red Hook, NY, USA},
abstract = {Our personal social networks are big and cluttered, and currently there is no good way to organize them. Social networking sites allow users to manually categorize their friends into social circles (e.g. 'circles' on Google+, and 'lists' on Facebook and Twitter), however they are laborious to construct and must be updated whenever a user's network grows. We define a novel machine learning task of identifying users' social circles. We pose the problem as a node clustering problem on a user's ego-network, a network of connections between her friends. We develop a model for detecting circles that combines network structure as well as user profile information. For each circle we learn its members and the circle-specific user profile similarity metric. Modeling node membership to multiple circles allows us to detect overlapping as well as hierarchically nested circles. Experiments show that our model accurately identifies circles on a diverse set of data from Facebook, Google+, and Twitter for all of which we obtain hand-labeled ground-truth.},
booktitle = {Proceedings of the 25th International Conference on Neural Information Processing Systems - Volume 1},
pages = {539–547},
numpages = {9},
location = {Lake Tahoe, Nevada},
series = {NIPS'12}
}

@incollection{pellegrini:hal-00770422,
TITLE = {{Scotch and PT-Scotch Graph Partitioning Software: An Overview}},
AUTHOR = {Pellegrini, Fran{\c c}ois},
URL = {https://inria.hal.science/hal-00770422},
BOOKTITLE = {{Combinatorial Scientific Computing}},
EDITOR = {Uwe Naumann, Olaf Schenk},
PUBLISHER = {{Chapman and Hall/CRC}},
PAGES = {373-406},
YEAR = {2012},
DOI = {10.1201/b11644-15},
HAL_ID = {hal-00770422},
HAL_VERSION = {v1},
}

@article{chevalier:hal-00402893,
TITLE = {{PT-Scotch: A tool for efficient parallel graph ordering}},
AUTHOR = {Chevalier, C{\'e}dric and Pellegrini, Fran{\c c}ois},
URL = {https://hal.science/hal-00402893},
JOURNAL = {{Parallel Computing}},
PUBLISHER = {{Elsevier}},
VOLUME = {34},
NUMBER = {6-8},
PAGES = {318-331},
YEAR = {2008},
MONTH = Jul,
DOI = {10.1016/j.parco.2007.12.001},
KEYWORDS = {Parallel graph ordering ; Nested dissection ; Distributed memory computer ; Multi-threading},
PDF = {https://hal.science/hal-00402893/file/article_full.pdf},
HAL_ID = {hal-00402893},
HAL_VERSION = {v1},
}

@online{kegg,
author = {{Kanehisa Laboratories}},
title = {{KEGG} Pathway Database},
year = {2023},
url = {https://www.kegg.jp},
organization = {{Kyoto University}},
}

@article{gove2019,
author = {Gove, R.},
title = {A Random Sampling O(n) Force-calculation Algorithm for Graph Layouts},
journal = {Computer Graphics Forum},
volume = {38},
number = {3},
pages = {739-751},
keywords = {CCS Concepts, • Human-centered computing → Graph drawings; Empirical studies in visualization},
doi = {10.1111/cgf.13724},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13724},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13724},
abstract = {Abstract This paper proposes a linear-time repulsive-force-calculation algorithm with sub-linear auxiliary space requirements, achieving an asymptotic improvement over the Barnes-Hut and Fast Multipole Method force-calculation algorithms. The algorithm, named random vertex sampling (RVS), achieves its speed by updating a random sample of vertices at each iteration, each with a random sample of repulsive forces. This paper also proposes a combination algorithm that uses RVS to derive an initial layout and then applies Barnes-Hut to refine the layout. An evaluation of RVS and the combination algorithm compares their speed and quality on 109 graphs against a Barnes-Hut layout algorithm. The RVS algorithm performs up to 6.1 times faster on the tested graphs while maintaining comparable layout quality. The combination algorithm also performs faster than Barnes-Hut, but produces layouts that are more symmetric than using RVS alone. Data and code: https://osf.io/nb7m8/},
year = {2019}
}

@article{Zhao2021,
doi = {10.1109/tvcg.2020.3030428},
year = {2021},
month = feb,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {27},
number = {2},
pages = {1698--1708},
author = {Ying Zhao and Haojin Jiang and Qi{\textquotesingle}an Chen and Yaqi Qin and Huixuan Xie and Yitao Wu and Shixia Liu and Zhiguang Zhou and Jiazhi Xia and Fangfang Zhou},
title = {Preserving Minority Structures in Graph Sampling},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{Ersoy2011,
doi = {10.1109/tvcg.2011.233},
year = {2011},
month = dec,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {17},
number = {12},
pages = {2364--2373},
author = {O. Ersoy and C. Hurter and Fernando V. Paulovich and G. Cantareiro and A. Telea},
title = {Skeleton-Based Edge Bundling for Graph Visualization},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{vonLandesberger2016,
doi = {10.1109/tvcg.2015.2468111},
year = {2016},
month = jan,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {22},
number = {1},
pages = {11--20},
author = {Tatiana von~Landesberger and Felix Brodkorb and Philipp Roskosch and Natalia Andrienko and Gennady Andrienko and Andreas Kerren},
title = {{MobilityGraphs}: Visual Analysis of Mass Mobility Dynamics via Spatio-Temporal Graphs and Clustering},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{Buchin2011,
doi = {10.1109/tvcg.2011.202},
year = {2011},
month = dec,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {17},
number = {12},
pages = {2536--2544},
author = {K. Buchin and B. Speckmann and K. Verbeek},
title = {Flow Map Layout via Spiral Trees},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@incollection{Heinsohn2018,
  doi = {10.1007/978-3-319-73915-1_4},

  year = {2018},
  publisher = {Springer International Publishing},
  pages = {38--51},
  author = {Niklas Heinsohn and Michael Kaufmann},
  title = {An Interactive Tool to Explore and Improve the Ply Number of Drawings},
  booktitle = {Lecture Notes in Computer Science}
}

@InProceedings{frick1995,
author="Frick, Arne
and Ludwig, Andreas
and Mehldau, Heiko",
editor="Tamassia, Roberto
and Tollis, Ioannis G.",
title="A fast adaptive layout algorithm for undirected graphs (extended abstract and system demonstration)",
booktitle="Graph Drawing",
year="1995",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="388--403",
doi={10.1007/3-540-58950-3_393},
abstract="We present a randomized adaptive layout algorithm for nicely drawing undirected graphs that is based on the spring-embedder paradigm and contains several new heuristics to improve the convergence, including local temperatures, gravitational forces and the detection of rotations and oscillations. The proposed algorithm achieves drawings of high quality on a wide range of graphs with standard settings. Moreover, the algorithm is fast, being thus applicable on general undirected graphs of substantially larger size and complexity than before [9, 6, 3]. Aesthetically pleasing solutions are found in most cases. We give empirical data for the running time of the algorithm and the quality of the computed layouts.",
isbn="978-3-540-49155-2"
}

@article{Gansner2005b,
doi = {10.1109/tvcg.2005.66},
year = {2005},
month = jul,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {11},
number = {4},
pages = {457--468},
author = {E.R. Gansner and Y. Koren and S.C. North},
title = {Topological Fisheye Views for Visualizing Large Graphs},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{barabasi1999,
author = {Albert-László Barabási  and Réka Albert },
title = {Emergence of Scaling in Random Networks},
journal = {Science},
volume = {286},
number = {5439},
pages = {509-512},
year = {1999},
doi = {10.1126/science.286.5439.509},
abstract = {Systems as diverse as genetic networks or the World Wide Web are best described as networks with complex topology. A common property of many large networks is that the vertex connectivities follow a scale-free power-law distribution. This feature was found to be a consequence of two generic mechanisms: (i) networks expand continuously by the addition of new vertices, and (ii) new vertices attach preferentially to sites that are already well connected. A model based on these two ingredients reproduces the observed stationary scale-free distributions, which indicates that the development of large networks is governed by robust self-organizing phenomena that go beyond the particulars of the individual systems.}}

@article{Grabowicz2014,
doi = {10.1140/epjds/s13688-014-0027-8},
year = {2014},
month = oct,
publisher = {Springer Science and Business Media {LLC}},
volume = {3},
number = {1},
author = {Przemyslaw A Grabowicz and Luca Maria Aiello and Filippo Menczer},
title = {Fast filtering and animation of large dynamic networks},
journal = {{EPJ} Data Science}
}

@article{erdHos1960evolution,
  title={On the evolution of random graphs},
  author={Erd{\H{o}}s, Paul and R{\'e}nyi, Alfr{\'e}d and others},
  journal={Publ. Math. Inst. Hung. Acad. Sci},
  volume={5},
  number={1},
  pages={17--60},
  year={1960}
}

@article{sugiyama1981,
  author={Sugiyama, Kozo and Tagawa, Shojiro and Toda, Mitsuhiko},
  journal={IEEE Transactions on Systems, Man, and Cybernetics}, 
  title={Methods for Visual Understanding of Hierarchical System Structures}, 
  year={1981},
  volume={11},
  number={2},
  pages={109-125},
  doi={10.1109/TSMC.1981.4308636}
}

@article{Wongsuphasawat2018,
doi = {10.1109/tvcg.2017.2744878},
year = {2018},
month = jan,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {24},
number = {1},
pages = {1--12},
author = {Kanit Wongsuphasawat and Daniel Smilkov and James Wexler and Jimbo Wilson and Dandelion Mane and Doug Fritz and Dilip Krishnan and Fernanda B. Viegas and Martin Wattenberg},
title = {Visualizing Dataflow Graphs of Deep Learning Models in {TensorFlow}},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{cohen1997,
author = {Cohen, Jonathan D.},
title = {Drawing Graphs to Convey Proximity: An Incremental Arrangement Method},
year = {1997},
issue_date = {Sept. 1997},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
volume = {4},
number = {3},
issn = {1073-0516},
doi = {10.1145/264645.264657},
abstract = {Graph drawings are increasingly finding their way into user interfaces to convey a variety of relationships. This article deals with rendering graphs to show proximity between vertices by making their configuration (screen) distances reflect their distances in the graph. An arrangement method is described that achieves good drawings at speeds suitable for user interaction on a desktop computer. The method is “incremental” in that it first arranges a small portion of the graph, then arranges successively larger fractions of the graph until a suitable arrangement for the entirety is achieved. The incremental approach not only offers speed improvements, but avoids many of the suboptimal solutions reached with other iterative approaches. Algorithms are described in pseudocode, and results are presented.},
journal = {ACM Transactions on Computer-Human Interaction},
month = {sep},
pages = {197–229},
numpages = {33},
keywords = {force-directed, graph drawing, graph layout, multidimensional scaling, MDS}
}

        @article{Kindermann2018,
  doi = {10.7155/jgaa.00474},

  year = {2018},
  publisher = {Journal of Graph Algorithms and Applications},
  volume = {22},
  number = {3},
  pages = {501--518},
  author = {Philipp Kindermann and Wouter Meulemans and Andr{\'{e}} Schulz},
  title = {Experimental Analysis of the Accessibility of Drawings with Few Segments},
  journal = {Journal of Graph Algorithms and Applications}
}

@incollection{Misue2019,
doi = {10.1007/978-3-030-35802-0_26},
year = {2019},
publisher = {Springer International Publishing},
pages = {337--349},
author = {Kazuo Misue and Katsuya Akasaka},
title = {Graph Drawing with Morphing Partial Edges},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Purchase2020,
doi = {10.1007/978-3-030-68766-3_36},
year = {2020},
publisher = {Springer International Publishing},
pages = {466--481},
author = {Helen C. Purchase and Daniel Archambault and Stephen Kobourov and Martin N\"{o}llenburg and Sergey Pupyrev and Hsiang-Yun Wu},
title = {The Turing Test for Graph Drawing Algorithms},
booktitle = {Lecture Notes in Computer Science}
}

@article{Dwyer2013,
doi = {10.1109/tvcg.2013.151},
year = {2013},
month = dec,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {19},
number = {12},
pages = {2596--2605},
author = {Tim Dwyer and Nathalie Henry Riche and Kim Marriott and Christopher Mears},
title = {Edge Compression Techniques for Visualization of Dense Directed Graphs},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{Qu2022,
doi = {10.1109/tvcg.2021.3114759},
year = {2022},
month = jan,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {28},
number = {1},
pages = {633--642},
author = {Botong Qu and Eugene Zhang and Yue Zhang},
title = {Automatic Polygon Layout for Primal-Dual Visualization of Hypergraphs},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{pach2000,
author = {Pach, J\'{a}nos and T\'{o}th, G\'{e}za},
title = {Which Crossing Number Is It Anyway?},
year = {2000},
issue_date = {Nov. 2000},
publisher = {Academic Press, Inc.},
address = {USA},
volume = {80},
number = {2},
issn = {0095-8956},
doi = {10.1006/jctb.2000.1978},
abstract = {A drawing of a graph G is a mapping which assigns to each vertex a point of the plane and to each edge a simple continuous arc connecting the corresponding two points. The crossing number of G is the minimum number of crossing points in any drawing of G. We define two new parameters, as follows. The pairwise crossing number (resp. the odd-crossing number) of G is the minimum number of pairs of edges that cross (resp. cross an odd number of times) over all drawings of G. We prove that the largest of these numbers (the crossing number) cannot exceed, twice the square of the smallest (the odd-crossing number). Our proof is based on the following generalization of an old result of Hanani, which is of independent interest. Let G be a graph and let E0 be a subset of its edges such that there is a drawing of G, in which every edge belonging to E0 crosses any other edge an even number of times. Then g can be redrawn so that the elements of E0 are not involved in any crossing. Finally, we show that the determination of each of these parameters is an NP-hard problem and it is NP-complete in the case of the crossing number and the odd-crossing number.},
journal = {J. Comb. Theory Ser. B},
month = {nov},
pages = {225–246},
numpages = {22}
}
  
  @article{VINES201494,
title = {The Availability of Research Data Declines Rapidly with Article Age},
journal = {Current Biology},
volume = {24},
number = {1},
pages = {94-97},
year = {2014},
issn = {0960-9822},
doi = {10.1016/j.cub.2013.11.014},
author = {Timothy H. Vines and Arianne Y.K. Albert and Rose L. Andrew and Florence Débarre and Dan G. Bock and Michelle T. Franklin and Kimberly J. Gilbert and Jean-Sébastien Moore and Sébastien Renaut and Diana J. Rennison},
abstract = {Summary
Policies ensuring that research data are available on public archives are increasingly being implemented at the government [1], funding agency [2, 3, 4], and journal [5, 6] level. These policies are predicated on the idea that authors are poor stewards of their data, particularly over the long term [7], and indeed many studies have found that authors are often unable or unwilling to share their data [8, 9, 10, 11]. However, there are no systematic estimates of how the availability of research data changes with time since publication. We therefore requested data sets from a relatively homogenous set of 516 articles published between 2 and 22 years ago, and found that availability of the data was strongly affected by article age. For papers where the authors gave the status of their data, the odds of a data set being extant fell by 17\% per year. In addition, the odds that we could find a working e-mail address for the first, last, or corresponding author fell by 7\% per year. Our results reinforce the notion that, in the long term, research data cannot be reliably preserved by individual researchers, and further demonstrate the urgent need for policies mandating data sharing via public archives.}
}

@incollection{Gange2011,
doi = {10.1007/978-3-642-18469-7_22},
year = {2011},
publisher = {Springer Berlin Heidelberg},
pages = {238--249},
author = {Graeme Gange and Peter J. Stuckey and Kim Marriott},
title = {Optimal k-Level Planarization and Crossing Minimization},
booktitle = {Graph Drawing}
}

@INPROCEEDINGS{haroz2018,  author={Haroz, Steve},  booktitle={2018 IEEE Evaluation and Beyond - Methodological Approaches for Visualization (BELIV)},   title={Open Practices in Visualization Research : Opinion Paper},   year={2018},  volume={},  number={},  pages={46-52},  doi={10.1109/BELIV.2018.8634427}}

@article{Henry2007,
doi = {10.1109/tvcg.2007.70582},
year = {2007},
month = nov,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {13},
number = {6},
pages = {1302--1309},
author = {Nathalie Henry and Jean-Daniel Fekete and Michael J. McGuffin},
title = {{NodeTrix}: a Hybrid Visualization of Social Networks},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@ARTICLE{Seidel93,
	AUTHOR = {Seidel, Hans-Peter},
	TITLE = {Polar Forms for Geometrically Continuous Spline Curves of
		Arbitrary Degree},
	JOURNAL = tog,
	VOLUME = {12},	NUMBER = {1},
	MONTH = Jan,	YEAR = {1993},	PAGES = {1-34},
  DOI= {10.1145/169728.169726}
}
  
  @inproceedings{wohlin2014,
author = {Wohlin, Claes},
title = {Guidelines for Snowballing in Systematic Literature Studies and a Replication in Software Engineering},
year = {2014},
isbn = {9781450324762},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
doi = {10.1145/2601248.2601268},
abstract = {Background: Systematic literature studies have become common in software engineering, and hence it is important to understand how to conduct them efficiently and reliably.Objective: This paper presents guidelines for conducting literature reviews using a snowballing approach, and they are illustrated and evaluated by replicating a published systematic literature review.Method: The guidelines are based on the experience from conducting several systematic literature reviews and experimenting with different approaches.Results: The guidelines for using snowballing as a way to search for relevant literature was successfully applied to a systematic literature review.Conclusions: It is concluded that using snowballing, as a first search strategy, may very well be a good alternative to the use of database searches.},
booktitle = {Proceedings of the 18th International Conference on Evaluation and Assessment in Software Engineering},
articleno = {38},
numpages = {10},
keywords = {systematic mapping studies, systematic literature review, snowballing, snowball search, replication},
location = {London, England, United Kingdom},
series = {EASE '14}
}

@InProceedings{brandes1998,
author="Brandes, Ulrik
and Wagner, Dorothea",
editor="Whitesides, Sue H.",
title="Using Graph Layout to Visualize Train Interconnection Data",
booktitle="Graph Drawing",
year="1998",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="44--56",
doi={10.1007/3-540-37623-2_4},
abstract="We are concerned with the problem of visualizing interconnections in railroad systems. The real-world systems we have to deal with contain connections of thousands of trains. To visualize such a system from a given set of time tables a so-called train graph is used. It contains a vertex for each station met by any train, and one edge between every pair of vertices connected by some train running from one station to the other without halting in between.",
isbn="978-3-540-37623-1"
}

@article {Pagen71,
	author = {Page, Matthew J and McKenzie, Joanne E and Bossuyt, Patrick M and Boutron, Isabelle and Hoffmann, Tammy C and Mulrow, Cynthia D and Shamseer, Larissa and Tetzlaff, Jennifer M and Akl, Elie A and Brennan, Sue E and Chou, Roger and Glanville, Julie and Grimshaw, Jeremy M and Hr{\'o}bjartsson, Asbj{\o}rn and Lalu, Manoj M and Li, Tianjing and Loder, Elizabeth W and Mayo-Wilson, Evan and McDonald, Steve and McGuinness, Luke A and Stewart, Lesley A and Thomas, James and Tricco, Andrea C and Welch, Vivian A and Whiting, Penny and Moher, David},
	title = {The {PRISMA} 2020 statement: an updated guideline for reporting systematic reviews},
	volume = {372},
	elocation-id = {n71},
	year = {2021},
	doi = {10.1136/bmj.n71},
	publisher = {BMJ Publishing Group Ltd},
	journal = {BMJ}
}

@article{diBartolomeo2022b,
doi = {10.1109/tvcg.2021.3114756},
year = {2022},
month = jan,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {28},
number = {1},
pages = {324--334},
author = {Di~Bartolomeo, Sara and Mirek Riedewald and Wolfgang Gatterbauer and Cody Dunne},
title = {{STRATISFIMAL} {LAYOUT}: A modular optimization model for laying out layered node-link network visualizations},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@article{nocaj2015,
title={Untangling the Hairballs of Multi-Centered, Small-World Online Social Media Networks},
year={2015},
doi={10.7155/jgaa.00370},
number={2},
volume={19},
journal={Journal of Graph Algorithms and Applications : JGAA},
pages={595--618},
author={Nocaj, Arlind and Ortmann, Mark and Brandes, Ulrik}
}

@incollection{Mallach2019,
doi = {10.1007/978-3-030-35802-0_40},
year = {2019},
publisher = {Springer International Publishing},
pages = {532--544},
author = {Sven Mallach},
title = {A Natural Quadratic Approach to the Generalized Graph Layering Problem},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Regg2016,
doi = {10.1007/978-3-319-50106-2_16},
year = {2016},
publisher = {Springer International Publishing},
pages = {196--208},
author = {Ulf R\"{u}egg and Thorsten Ehlers and Miro Sp\"{o}nemann and Reinhard von~Hanxleden},
title = {A Generalization of the Directed Graph Layering Problem},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Jnger2018,
doi = {10.1007/978-3-030-04414-5_13},
year = {2018},
publisher = {Springer International Publishing},
pages = {187--199},
author = {Michael J\"{u}nger and Petra Mutzel and Christiane Spisla},
title = {A Flow Formulation for Horizontal Coordinate Assignment with Prescribed Width},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{DiGiacomo2020,
doi = {10.1007/978-3-030-68766-3_25},
year = {2020},
publisher = {Springer International Publishing},
pages = {324--332},
author = {Emilio Di Giacomo and Walter Didimo and Giuseppe Liotta and Fabrizio Montecchiani and Alessandra Tappini},
title = {Storyline Visualizations with Ubiquitous Actors},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Niedermann2020,
doi = {10.1007/978-3-030-68766-3_19},
year = {2020},
publisher = {Springer International Publishing},
pages = {235--249},
author = {Benjamin Niedermann and Ignaz Rutter},
title = {An Integer-Linear Program for Bend-Minimization in Ortho-Radial Drawings},
booktitle = {Lecture Notes in Computer Science}
}

@inproceedings{Ogawa2010,
doi = {10.1145/1879211.1879219},
year = {2010},
publisher = {{ACM} Press},
author = {Michael Ogawa and Kwan-Liu Ma},
title = {Software evolution storylines},
booktitle = {Proceedings of the 5th international symposium on Software visualization - {SOFTVIS} {\textquotesingle}10}
}

@incollection{Raj2018,
doi = {10.1007/978-3-319-73915-1_28},
year = {2018},
publisher = {Springer International Publishing},
pages = {351--364},
author = {Mukund Raj and Ross T. Whitaker},
title = {Anisotropic Radial Layout for Visualizing Centrality and Structure in Graphs},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{deCol2019,
doi = {10.1007/978-3-030-35802-0_35},
year = {2019},
publisher = {Springer International Publishing},
pages = {460--467},
author = {Philipp de Col and Fabian Klute and Martin N\"{o}llenburg},
title = {Mixed Linear Layouts: Complexity, Heuristics, and Experiments},
booktitle = {Lecture Notes in Computer Science}
}

@article{saket2016,
author = {Saket, Bahador and Scheidegger, Carlos and Kobourov, Stephen},
title = {Comparing Node-Link and Node-Link-Group Visualizations From An Enjoyment Perspective},
journal = {Computer Graphics Forum},
volume = {35},
number = {3},
pages = {41-50},
doi = {10.1111/cgf.12880},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.12880},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.12880},
year = {2016}
}

@article{arleo2022,
author = {Arleo, A. and Miksch, S. and Archambault, D.},
title = {Event-based Dynamic Graph Drawing without the Agonizing Pain},
journal = {Computer Graphics Forum},
volume = {41},
number = {6},
pages = {226-244},
keywords = {Visualization, Graph Drawing, Temporal Networks},
doi = {10.1111/cgf.14615},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.14615},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.14615},
year = {2022}
}

@ARTICLE{DRGraph21,
author={Zhu, Minfeng and Chen, Wei and Hu, Yuanzhe and Hou, Yuxuan and Liu, Liangjun and Zhang, Kaiyuan},
journal={IEEE Transactions on Visualization and Computer Graphics},
title={DRGraph: An Efficient Graph Layout Algorithm for Large-scale Graphs by Dimensionality Reduction},
year={2021},
volume={27},
number={2},
pages={1666-1676},
doi={10.1109/TVCG.2020.3030447}}

@ARTICLE{zhong2023,
  author={Zhong, Fahai and Xue, Mingliang and Zhang, Jian and Zhang, Fan and Ban, Rui and Deussen, Oliver and Wang, Yunhai},
  journal={IEEE Transactions on Visualization and Computer Graphics}, 
  title={Force-Directed Graph Layouts Revisited: A New Force Based on the T-Distribution}, 
  year={2023},
  volume={},
  number={},
  pages={1-14},
  doi={10.1109/TVCG.2023.3238821}}

  @InProceedings{miller2023,
author="Miller, Jacob
and Huroyan, Vahan
and Kobourov, Stephen",
editor="Angelini, Patrizio
and von Hanxleden, Reinhard",
title="Spherical Graph Drawing by Multi-dimensional Scaling",
booktitle="Graph Drawing and Network Visualization",
year="2023",
publisher="Springer International Publishing",
address="Cham",
pages="77--92",
doi={10.1007/978-3-031-22203-0_7},
abstract="We describe an efficient and scalable spherical graph embedding method. The method uses a generalization of the Euclidean stress function for Multi-Dimensional Scaling adapted to spherical space, where geodesic pairwise distances are employed instead of Euclidean distances. The resulting spherical stress function is optimized by means of stochastic gradient descent. Quantitative and qualitative evaluations demonstrate the scalability and effectiveness of the proposed method. We also show that some graph families can be embedded with lower distortion on the sphere, than in Euclidean and hyperbolic spaces.",
isbn="978-3-031-22203-0"
}

@InProceedings{meidiana2023,
author={Meidıana, Amyra
and Hong, Seok-Hee
and Eades, Peter},
editor="Angelini, Patrizio
and von Hanxleden, Reinhard",
title={Shape-Faithful Graph Drawings},
booktitle="Graph Drawing and Network Visualization",
year="2023",
publisher="Springer International Publishing",
address="Cham",
pages="93--108",
doi={10.1007/978-3-031-22203-0_8},
abstract="Shape-based metrics measure how faithfully a drawing D represents the structure of a graph G, using the proximity graph S of D. While some limited graph classes admit proximity drawings (i.e., optimally shape-faithful drawings, where {\$}{\$}S = G{\$}{\$}S=G), algorithms for shape-faithful drawings of general graphs have not been investigated.",
isbn="978-3-031-22203-0"
}

@article{batik2022,
author = {Batik, T. and Terziadis, S. and Wang, Y.-S. and Nöllenburg, M. and Wu, H.-Y.},
title = {Shape-Guided Mixed Metro Map Layout},
journal = {Computer Graphics Forum},
volume = {41},
number = {7},
pages = {495-506},
keywords = {CCS Concepts, • Human-centered computing → Visualization techniques, Interactive systems and tools},
doi = {10.1111/cgf.14695},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.14695},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.14695},
abstract = {Abstract Metro or transit maps, are schematic representations of transit networks to facilitate effective route-finding. These maps are often advertised on a web page or pamphlet highlighting routes from source to destination stations. To visually support such route-finding, designers often distort the layout by embedding symbolic shapes (e.g., circular routes) in order to guide readers' attention (e.g., Moscow map and Japan railway map). However, manually producing such maps is labor-intensive and the effect of shapes remains unclear. In this paper, we propose an approach to generalize such mixed metro maps that take user-defined shapes as an input. In this mixed design, lines that are used to approximate the shapes are arranged symbolically, while the remaining lines follow classical layout convention. A three-step algorithm, including (1) detecting and selecting routes for shape approximation, (2) shape and layout deformation, and (3) aligning lines on a grid, is integrated to guarantee good visual quality. Our contribution lies in the definition of the mixed metro map problem and the formulation of design criteria so that the problem can be resolved systematically using the optimization paradigm. Finally, we evaluate the performance of our approach and perform a user study to test if the embedded shapes are recognizable or reduce the map quality.},
year = {2022}
}

@article{preiner2020,
author = {Preiner, R. and Schmidt, J. and Krösl, K. and Schreck, T. and Mistelbauer, G.},
title = {Augmenting Node-Link Diagrams with Topographic Attribute Maps},
journal = {Computer Graphics Forum},
volume = {39},
number = {3},
pages = {369-381},
keywords = {CCS Concepts, • Human-centered computing → Graph drawings; Social networks; Information visualization},
doi = {10.1111/cgf.13987},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13987},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13987},
abstract = {Abstract We propose a novel visualization technique for graphs that are attributed with scalar data. In many scenarios, these attributes (e.g., birth date in a family network) provide ambient context information for the graph structure, whose consideration is important for different visual graph analysis tasks. Graph attributes are usually conveyed using different visual representations (e.g., color, size, shape) or by reordering the graph structure according to the attribute domain (e.g., timelines). While visual encodings allow graphs to be arranged in a readable layout, assessing contextual information such as the relative similarities of attributes across the graph is often cumbersome. In contrast, attribute-based graph reordering serves the comparison task of attributes, but typically strongly impairs the readability of the structural information given by the graph's topology. In this work, we augment force-directed node-link diagrams with a continuous ambient representation of the attribute context. This way, we provide a consistent overview of the graph's topological structure as well as its attributes, supporting a wide range of graph-related analysis tasks. We resort to an intuitive height field metaphor, illustrated by a topographic map rendering using contour lines and suitable color maps. Contour lines visually connect nodes of similar attribute values, and depict their relative arrangement within the global context. Moreover, our contextual representation supports visualizing attribute value ranges associated with graph nodes (e.g., lifespans in a family network) as trajectories routed through this height field. We discuss how user interaction with both the structural and the contextual information fosters exploratory graph analysis tasks. The effectiveness and versatility of our technique is confirmed in a user study and case studies from various application domains.},
year = {2020}
}

@article{bast2020,
author = {Bast, Hannah and Brosi, Patrick and Storandt, Sabine},
title = {Metro Maps on Octilinear Grid Graphs},
journal = {Computer Graphics Forum},
volume = {39},
number = {3},
pages = {357-367},
keywords = {CCS Concepts, • Human-centered computing → Graph drawings; • Theory of computation → Integer programming; • Mathematics of computing → Approximation algorithms},
doi = {10.1111/cgf.13986},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13986},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13986},
abstract = {Abstract Schematic transit maps (often called “metro maps” in the literature) are important to produce comprehensible visualizations of complex public transit networks. In this work, we investigate the problem of automatically drawing such maps on an octilinear grid with an arbitrary (but optimal) number of edge bends. Our approach can naturally deal with obstacles that should be respected in the final drawing (points of interest, rivers, coastlines) and can prefer grid edges near the real-world course of a line. This allows our drawings to be combined with existing maps, for example as overlays in map services. We formulate an integer linear program which can be used to solve the problem exactly. We also provide a fast approximation algorithm which greedily calculates shortest paths between node candidates on the underlying octilinear grid graph. Previous work used local search techniques to update node positions until a local optimum was found, but without guaranteeing octilinearity. We can thus calculate nearly optimal metro maps in a fraction of a second even for complex networks, enabling the interactive use of our method in map editors.},
year = {2020}
}

@ARTICLE{fisheye2019,
author={Wang, Yunhai and Wang, Yanyan and Zhang, Haifeng and Sun, Yinqi and Fu, Chi-Wing and Sedlmair, Michael and Chen, Baoquan and Deussen, Oliver},
journal={IEEE Transactions on Visualization and Computer Graphics},
title={Structure-aware Fisheye Views for Efficient Large Graph Exploration},
year={2019},
volume={25},
number={1},
pages={566-575},
doi={10.1109/TVCG.2018.2864911}}

@article{wallinger2023,
author = {Wallinger, Markus and Archambault, Daniel and Auber, David and Nöllenburg, Martin and Peltonen, Jaakko},
title = {Faster Edge-Path Bundling through Graph Spanners},
journal = {Computer Graphics Forum},
volume = {n/a},
number = {n/a},
pages = {},
keywords = {computational geometry, information visualization, visualization},
doi = {10.1111/cgf.14789},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.14789},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.14789},
year={2023},
abstract = {Abstract Edge-Path bundling is a recent edge bundling approach that does not incur ambiguities caused by bundling disconnected edges together. Although the approach produces less ambiguous bundlings, it suffers from high computational cost. In this paper, we present a new Edge-Path bundling approach that increases the computational speed of the algorithm without reducing the quality of the bundling. First, we demonstrate that biconnected components can be processed separately in an Edge-Path bundling of a graph without changing the result. Then, we present a new edge bundling algorithm that is based on observing and exploiting a strong relationship between Edge-Path bundling and graph spanners. Although the worst case complexity of the approach is the same as of the original Edge-Path bundling algorithm, we conduct experiments to demonstrate that the new approach is 5–256 times faster than Edge-Path bundling depending on the dataset, which brings its practical running time more in line with traditional edge bundling algorithms.}
}

@article{meidiana2020,
author = {Meidiana, Amyra and Hong, Seok-Hee and Torkel, Marnijati and Cai, Shijun and Eades, Peter},
title = {Sublinear Time Force Computation for Big Complex Network Visualization},
journal = {Computer Graphics Forum},
volume = {39},
number = {3},
pages = {579-591},
doi = {10.1111/cgf.14003},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.14003},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.14003},
abstract = {Abstract In this paper, we present a new framework for sublinear time force computation for visualization of big complex graphs. Our algorithm is based on the sampling of vertices for computing repulsion forces and edge sparsification for attraction force computation. More specifically, for vertex sampling, we present three types of sampling algorithms, including random sampling, geometric sampling, and combinatorial sampling, to reduce the repulsion force computation to sublinear in the number of vertices. We utilize a spectral sparsification approach to reduce the number of attraction force computations to sublinear in the number of edges for dense graphs. We also present a smart initialization method based on radial tree drawing of the BFS spanning tree rooted at the center. Experiments show that our new sublinear time force computation algorithms run quite fast, while producing good visualization of large and complex networks, with significant improvements in quality metrics such as shape-based and edge crossing metrics.},
year = {2020}
}

@incollection{Hachul2005,
doi = {10.1007/978-3-540-31843-9_29},
url = {10.1007/978-3-540-31843-9_29},
year = {2005},
publisher = {Springer Berlin Heidelberg},
pages = {285--295},
author = {Stefan Hachul and Michael J\"{u}nger},
title = {Drawing Large Graphs with a Potential-Field-Based Multilevel Algorithm},
booktitle = {Graph Drawing}
}

@article{welch2017,
author = {Welch, E. and Kobourov, S.},
title = {Measuring Symmetry in Drawings of Graphs},
journal = {Computer Graphics Forum},
volume = {36},
number = {3},
pages = {341-351},
doi = {10.1111/cgf.13192},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13192},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13192},
abstract = {Abstract Layout symmetry is an important and desired feature in graph drawing. While there is a substantial body of work in computer vision around the detection and measurement of symmetry in images, there has been little effort to define and validate meaningful measures of the symmetry of graph drawings. In this paper, we evaluate two algorithms that have been proposed for measuring graph drawing symmetry, comparing their judgments to those of human subjects, and investigating the use of stress as an alternative measure of symmetry. We discuss advantages and disadvantages of these measures, possible ways to improve them, and implications for the design of algorithms that optimize the symmetry in the layout.},
year = {2017}
}

@article{binucci2022,
author = {Binucci, Carla and Didimo, Walter and Kaufmann, Michael and Liotta, Giuseppe and Montecchiani, Fabrizio},
title = {Placing Arrows in Directed Graph Layouts: Algorithms and Experiments},
journal = {Computer Graphics Forum},
volume = {41},
number = {1},
pages = {364-376},
keywords = {user studies, interaction, information visualization, visualization},
doi = {10.1111/cgf.14440},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.14440},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.14440},
abstract = {Abstract We study how to place arrow heads in directed graph drawings aiming at minimizing their overlaps and avoiding intersections between arrow heads and edges. The objective is to support users to correctly and quickly recognize edge orientations, i.e. to deduce unambiguously the edge orientations. Our contribution is two-fold: (i) We present exact and heuristic algorithms for this arrow placement problem, along with an extensive experimental analysis of these techniques; and (ii) we report on a user study aimed to understand the impact of different arrow placement strategies on performing global and local analysis tasks on directed graph layouts.},
year = {2022}
}

@incollection{Alegra2021,
doi = {10.1007/978-3-030-92931-2_12},
url = {10.1007/978-3-030-92931-2_12},
year = {2021},
publisher = {Springer International Publishing},
pages = {166--183},
author = {Carlos Alegr{\'{\i}}a and Manuel Borrazzo and Giordano Da Lozzo and Giuseppe Di Battista and Fabrizio Frati and Maurizio Patrignani},
title = {Planar Straight-Line Realizations of~2-Trees with~Prescribed Edge Lengths},
booktitle = {Lecture Notes in Computer Science}
}

@article{Barnes1986,
doi = {10.1038/324446a0},
url = {10.1038/324446a0},
year = {1986},
month = dec,
publisher = {Springer Science and Business Media {LLC}},
volume = {324},
number = {6096},
pages = {446--449},
author = {Josh Barnes and Piet Hut},
title = {A hierarchical O(N log N) force-calculation algorithm},
journal = {Nature}
}

@incollection{Bekos2007,
doi = {10.1007/978-3-540-77537-9_24},
url = {10.1007/978-3-540-77537-9_24},
publisher = {Springer Berlin Heidelberg},
pages = {231--242},
year = {2007},
author = {Michael A. Bekos and Michael Kaufmann and Katerina Potika and Antonios Symvonis},
title = {Line Crossing Minimization on Metro Maps},
booktitle = {Graph Drawing}
}

@article{Bhatt1984,
doi = {10.1016/0022-0000(84)90071-0},
url = {10.1016/0022-0000(84)90071-0},
year = {1984},
month = apr,
publisher = {Elsevier {BV}},
volume = {28},
number = {2},
pages = {300--343},
author = {Sandeep N. Bhatt and Frank Thomson Leighton},
title = {A framework for solving {VLSI} graph layout problems},
journal = {Journal of Computer and System Sciences}
}

@incollection{Biedl2018,
doi = {10.1007/978-3-319-73915-1_12},
url = {10.1007/978-3-319-73915-1_12},
year = {2018},
publisher = {Springer International Publishing},
pages = {140--152},
author = {Therese Biedl and Veronika Irvine},
title = {Drawing Bobbin Lace Graphs, or, Fundamental Cycles for a Subclass of Periodic Graphs},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Binucci2021,
doi = {10.1007/978-3-030-92931-2_14},
url = {10.1007/978-3-030-92931-2_14},
year = {2021},
publisher = {Springer International Publishing},
pages = {195--209},
author = {Carla Binucci and Emilio Di Giacomo and Giuseppe Liotta and Alessandra Tappini},
title = {Quasi-upward Planar Drawings with~Minimum Curve Complexity},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Didimo2018,
doi = {10.1007/978-3-030-04414-5_34},
url = {10.1007/978-3-030-04414-5_34},
year = {2018},
publisher = {Springer International Publishing},
pages = {481--494},
author = {Walter Didimo and Giuseppe Liotta and Maurizio Patrignani},
title = {Bend-Minimum Orthogonal Drawings in Quadratic Time},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Fulek2018,
doi = {10.1007/978-3-030-04414-5_16},
url = {10.1007/978-3-030-04414-5_16},
year = {2018},
publisher = {Springer International Publishing},
pages = {229--241},
author = {Radoslav Fulek and Csaba D. T{\'{o}}th},
title = {Crossing Minimization in Perturbed Drawings},
booktitle = {Lecture Notes in Computer Science}
}

@ARTICLE{Gansner1993,
  author={Gansner, E.R. and Koutsofios, E. and North, S.C. and Vo, K.-P.},
  journal={IEEE Transactions on Software Engineering}, 
  title={A technique for drawing directed graphs}, 
  year={1993},
  volume={19},
  number={3},
  pages={214-230},
  doi={10.1109/32.221135}}

@article{Gibson2012,
doi = {10.1177/1473871612455749},
url = {10.1177/1473871612455749},
year = {2012},
month = sep,
publisher = {{SAGE} Publications},
volume = {12},
number = {3-4},
pages = {324--357},
author = {Helen Gibson and Joe Faith and Paul Vickers},
title = {A survey of two-dimensional graph layout techniques for information visualisation},
journal = {Information Visualization}
}

@incollection{Gronemann2016,
doi = {10.1007/978-3-319-50106-2_18},
url = {10.1007/978-3-319-50106-2_18},
year = {2016},
publisher = {Springer International Publishing},
pages = {222--235},
author = {Martin Gronemann},
title = {Bitonic st-orderings for Upward Planar Graphs},
booktitle = {Lecture Notes in Computer Science}
}

@article{Didimo2019,
doi = {10.1145/3301281},
url = {10.1145/3301281},
year = {2019},
month = feb,
publisher = {Association for Computing Machinery ({ACM})},
volume = {52},
number = {1},
pages = {1--37},
author = {Walter Didimo and Giuseppe Liotta and Fabrizio Montecchiani},
title = {A Survey on Graph Drawing Beyond Planarity},
journal = {{ACM} Computing Surveys}
}

@InProceedings{giovannangeli2023,
author="Giovannangeli, Loann
and Lalanne, Frederic
and Giot, Romain
and Bourqui, Romain",
editor="Angelini, Patrizio
and von Hanxleden, Reinhard",
title="FORBID: Fast Overlap Removal by Stochastic GradIent Descent for Graph Drawing",
booktitle="Graph Drawing and Network Visualization",
year="2023",
publisher="Springer International Publishing",
address="Cham",
pages="61--76",
doi={10.1007/978-3-031-22203-0_6},
abstract="While many graph drawing algorithms consider nodes as points, graph visualization tools often represent them as shapes. These shapes support the display of information such as labels or encode various data with size or color. However, they can create overlaps between nodes which hinder the exploration process by hiding parts of the information. It is therefore of utmost importance to remove these overlaps to improve graph visualization readability. If not handled by the layout process, Overlap Removal (OR) algorithms have been proposed as layout post-processing. As graph layouts usually convey information about their topology, it is important that OR algorithms preserve them as much as possible. We propose a novel algorithm that models OR as a joint stress and scaling optimization problem, and leverages efficient stochastic gradient descent. This approach is compared with state-of-the-art algorithms, and several quality metrics demonstrate its efficiency to quickly remove overlaps while retaining the initial layout structures.",
isbn="978-3-031-22203-0"
}

@ARTICLE{zheng2019,
author={Zheng, Jonathan X. and Pawar, Samraat and Goodman, Dan F. M.},
journal={IEEE Transactions on Visualization and Computer Graphics},
title={Graph Drawing by Stochastic Gradient Descent},
year={2019},
volume={25},
number={9},
pages={2738-2748},
doi={10.1109/TVCG.2018.2859997}}

@article{mizuno2019,
author = {Mizuno, Kazuyo and Wu, Hsiang-Yun and Takahashi, Shigeo and Igarashi, Takeo},
title = {Optimizing Stepwise Animation in Dynamic Set Diagrams},
journal = {Computer Graphics Forum},
volume = {38},
number = {3},
pages = {13-24},
keywords = {CCS Concepts, • Human-centered computing → Information visualization, Graph drawings, • Computing methodologies → Perception},
doi = {10.1111/cgf.13668},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13668},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13668},
abstract = {Abstract A set diagram represents the membership relation among data elements. It is often visualized as secondary information on top of primary information, such as the spatial positions of elements on maps and charts. Visualizing the temporal evolution of such set diagrams as well as their primary features is quite important; however, conventional approaches have only focused on the temporal behavior of the primary features and do not provide an effective means to highlight notable transitions within the set relationships. This paper presents an approach for generating a stepwise animation between set diagrams by decomposing the entire transition into atomic changes associated with individual data elements. The key idea behind our approach is to optimize the ordering of the atomic changes such that the synthesized animation minimizes unwanted set occlusions by considering their depth ordering and reduces the gaze shift between two consecutive stepwise changes. Experimental results and a user study demonstrate that the proposed approach effectively facilitates the visual identification of the detailed transitions inherent in dynamic set diagrams.},
year = {2019}
}

@article{gove2019,
author = {Gove, R.},
title = {A Random Sampling O(n) Force-calculation Algorithm for Graph Layouts},
journal = {Computer Graphics Forum},
volume = {38},
number = {3},
pages = {739-751},
keywords = {CCS Concepts, • Human-centered computing → Graph drawings; Empirical studies in visualization},
doi = {10.1111/cgf.13724},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13724},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13724},
abstract = {Abstract This paper proposes a linear-time repulsive-force-calculation algorithm with sub-linear auxiliary space requirements, achieving an asymptotic improvement over the Barnes-Hut and Fast Multipole Method force-calculation algorithms. The algorithm, named random vertex sampling (RVS), achieves its speed by updating a random sample of vertices at each iteration, each with a random sample of repulsive forces. This paper also proposes a combination algorithm that uses RVS to derive an initial layout and then applies Barnes-Hut to refine the layout. An evaluation of RVS and the combination algorithm compares their speed and quality on 109 graphs against a Barnes-Hut layout algorithm. The RVS algorithm performs up to 6.1 times faster on the tested graphs while maintaining comparable layout quality. The combination algorithm also performs faster than Barnes-Hut, but produces layouts that are more symmetric than using RVS alone. Data and code: https://osf.io/nb7m8/},
year = {2019}
}

@article{Liu2017,
doi = {10.1109/tvcg.2016.2598831},
year = {2017},
month = jan,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {23},
number = {1},
pages = {91--100},
author = {Mengchen Liu and Jiaxin Shi and Zhen Li and Chongxuan Li and Jun Zhu and Shixia Liu},
title = {Towards Better Analysis of Deep Convolutional Neural Networks},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@incollection{Devkota2019,
  doi = {10.1007/978-3-030-35802-0_23},
  year = {2019},
  publisher = {Springer International Publishing},
  pages = {291--304},
  author = {Sabin Devkota and Reyan Ahmed and Felice De Luca and Katherine E. Isaacs and Stephen Kobourov},
  title = {Stress-Plus-X ({SPX}) Graph Layout},
  booktitle = {Lecture Notes in Computer Science}
}

@ARTICLE{muelder2008, 
author={Chris Muelder and Kwan Liu Ma}, 
journal={IEEE Transactions on Visualization and Computer Graphics}, 
title={Rapid Graph Layout Using Space Filling Curves}, 
year={2008}, 
volume={14}, 
number={6}, 
pages={1301-1308}, 
doi={10.1109/TVCG.2008.158}
}

@INPROCEEDINGS{muelder2008b, author={Muelder, Chris and Ma, Kwan-Liu}, booktitle={2008 IEEE Pacific Visualization Symposium}, title={A Treemap Based Method for Rapid Layout of Large Graphs}, year={2008}, volume={}, number={}, pages={231-238}, doi={10.1109/PACIFICVIS.2008.4475481}}

@incollection{Chimani2012,
doi = {10.1007/978-3-642-25878-7_10},
year = {2012},
publisher = {Springer Berlin Heidelberg},
pages = {87--98},
author = {Markus Chimani and Carsten Gutwenger},
title = {Advances in the Planarization Method: Effective Multiple Edge Insertions},
booktitle = {Graph Drawing}
}

@inproceedings{brandes2006,
author = {Brandes, Ulrik and Pich, Christian},
title = {Eigensolver Methods for Progressive Multidimensional Scaling of Large Data},
year = {2006},
isbn = {9783540709039},
publisher = {Springer-Verlag},
address = {Berlin, Heidelberg},
doi={10.5555/1758612.1758620},
abstract = {We present a novel sampling-based approximation technique for classical multidimensional scaling that yields an extremely fast layout algorithm suitable even for very large graphs. It produces layouts that compare favorably with other methods for drawing large graphs, and it is among the fastest methods available. In addition, our approach allows for progressive computation, i.e. a rough approximation of the layout can be produced even faster, and then be refined until satisfaction.},
booktitle = {Proceedings of the 14th International Conference on Graph Drawing},
pages = {42–53},
numpages = {12},
location = {Karlsruhe, Germany},
series = {GD'06}
}

@incollection{Eades2018,
doi = {10.1007/978-3-319-73915-1_22},
year = {2018},
publisher = {Springer International Publishing},
pages = {272--286},
author = {Peter Eades and Quan Nguyen and Seok-Hee Hong},
title = {Drawing Big Graphs Using Spectral Sparsification},
booktitle = {Lecture Notes in Computer Science}
}

@article{Ortmann2017,
doi = {10.7155/jgaa.00440},
year = {2017},
publisher = {Journal of Graph Algorithms and Applications},
volume = {21},
number = {5},
pages = {791--821},
author = {Mark Ortmann and Mirza Klimenta and Ulrik Brandes},
title = {A Sparse Stress Model},
journal = {Journal of Graph Algorithms and Applications}
}

@InProceedings{civril2006,
author="Civril, Ali
and Magdon-Ismail, Malik
and Bocek-Rivele, Eli",
editor="Healy, Patrick
and Nikolov, Nikola S.",
title="SDE: Graph Drawing Using Spectral Distance Embedding",
booktitle="Graph Drawing",
year="2006",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="512--513",
doi={10.1007/11618058_48},
abstract="We present a novel graph drawing algorithm which uses a spectral decomposition of the distance matrix to approximate the graph theoretical distances. The algorithm preserves symmetry and node densities, i.e., the drawings are aesthetically pleasing. The runtime for typical 20,000 node graphs ranges from 100 to 150 seconds.",
isbn="978-3-540-31667-1"
}

@techreport{hacul2005,
author = "Stefan Hachul and Michael Juenger",
year = {2005},
title = {Large-Graph Layout with the Fast Multipole Multilevel Method},
type = {Working Paper},
institution = {Universit{\"a}t zu K{\"o}ln},
abstract = {The visualization of of large and complex networks or graphs is an indispensable instrument for getting deeper insight into their structure. Force-directed graph-drawing algorithms are widely used to draw such graphs. However, these methods do not guarantee a sub-quadratic running time in general. We present a new force-directed method that is based on a combination of an efficient multilevel scheme and a strategy for approximating the repulsive forces in the system by rapidly evaluating potential fields. Given a graph G=(V,E), the asymptotic worst-case running time of this method is O({\ensuremath{|}}V{\ensuremath{|}}log{\ensuremath{|}}V{\ensuremath{|}}+{\ensuremath{|}}E{\ensuremath{|}}) with linear memory requirements. In practice, the algorithm generates nice drawings of graphs with 100000 nodes in less than 5 minutes. Furthermore, it clearly visualizes even the structures of those graphs that turned out to be challenging for other methods.},
url = {https://kups.ub.uni-koeln.de/54892/}
}

@article{chimani2010,
author = {Chimani, Markus and Gutwenger, Carsten and Mutzel, Petra and Wong, Hoi-Ming},
title = {Layer-Free Upward Crossing Minimization},
year = {2010},
issue_date = {2010},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
volume = {15},
issn = {1084-6654},
doi = {10.1145/1671970.1671975},
abstract = {An upward drawing of a DAG G is a drawing of G in which all arcs are drawn as curves increasing monotonically in the vertical direction. In this article, we present a new approach for upward crossing minimization, that is, finding an upward drawing of a DAG G with as few crossings as possible. Our algorithm is based on a two-stage upward planarization approach, which computes a feasible upward planar subgraph in the first step and reinserts the remaining arcs by computing constraint-feasible upward insertion paths. An experimental study shows that the new algorithm leads to much better results than existing algorithms for upward crossing minimization, including the classical Sugiyama approach.},
journal = {ACM J. Exp. Algorithmics},
month = {mar},
articleno = {2.2},
numpages = {27},
keywords = {planarization approach, Crossing number, upward drawing, upward planarization}
}

@article{diBartolomeo2022,
author = {Di~Bartolomeo, Sara and Pister, Alexis and Buono, Paolo and Plaisant, Catherine and Dunne, Cody and Fekete, Jean-Daniel},
title = {Six methods for transforming layered hypergraphs to apply layered graph layout algorithms},
journal = {Computer Graphics Forum},
volume = {41},
number = {3},
pages = {259-270},
keywords = {CCS Concepts, • Human-centered computing → Graph drawings, Visualization theory, concepts and paradigms},
doi = {10.1111/cgf.14538},
abstract = {Abstract Hypergraphs are a generalization of graphs in which edges (hyperedges) can connect more than two vertices—as opposed to ordinary graphs where edges involve only two vertices. Hypergraphs are a fairly common data structure but there is little consensus on how to visualize them. To optimize a hypergraph drawing for readability, we need a layout algorithm. Common graph layout algorithms only consider ordinary graphs and do not take hyperedges into account. We focus on layered hypergraphs, a particular class of hypergraphs that, like layered graphs, assigns every vertex to a layer, and the vertices in a layer are drawn aligned on a linear axis with the axes arranged in parallel. In this paper, we propose a general method to apply layered graph layout algorithms to layered hypergraphs. We introduce six different transformations for layered hypergraphs. The choice of transformation affects the subsequent graph layout algorithm in terms of computational performance and readability of the results. Thus, we perform a comparative evaluation of these transformations in terms of number of crossings, edge length, and impact on performance. We also provide two case studies showing how our transformations can be applied to real-life use cases. A copy of this paper with all appendices and supplemental material is available at osf.io/grvwu.},
year = {2022}
}

@InProceedings{meidiana2022,
author={Meidiana, Amyra
and Hong, Seok-Hee
and Eades, Peter},
editor="Auber, David
and Valtr, Pavel",
title="New Quality Metrics for Dynamic Graph Drawing",
booktitle="Graph Drawing and Network Visualization",
year="2020",
publisher="Springer International Publishing",
address="Cham",
doi={10.1007/978-3-030-68766-3_35},
pages="450--465",
abstract="In this paper, we present new quality metrics for dynamic graph drawings. Namely, we present a new framework for change faithfulness metrics for dynamic graph drawings, which compare the ground truth change in dynamic graphs and the geometric change in drawings.",
isbn="978-3-030-68766-3"
}

@article{greilich2009,
author = {Greilich, Martin and Burch, Michael and Diehl, Stephan},
title = {Visualizing the Evolution of Compound Digraphs with TimeArcTrees},
journal = {Computer Graphics Forum},
volume = {28},
number = {3},
pages = {975-982},
keywords = {Data Structures E.1: Graphs and Networks},
doi = {10.1111/j.1467-8659.2009.01451.x},
abstract = {Abstract Compound digraphs are a widely used model in computer science. In many application domains these models evolve over time. Only few approaches to visualize such dynamic compound digraphs exist and mostly use animation to show the dynamics. In this paper we present a new visualization tool called TimeArcTrees that visualizes weighted, dynamic compound digraphs by drawing a sequence of node-link diagrams in a single view. Compactness is achieved by aligning the nodes of a graph vertically. Edge crossings are reduced by drawing upward and downward edges separately as colored arcs. Horizontal alignment of the instances of the same node in different graphs facilitates comparison of the graphs in the sequence. Many interaction techniques allow to explore the given graphs. Smooth animation supports the user to better track the transitions between views and to preserve his or her mental map. We illustrate the usefulness of the tool by looking at the particular problem of how shortest paths evolve over time. To this end, we applied the system to an evolving graph representing the German Autobahn and its traffic jams.},
year = {2009}
}



@INPROCEEDINGS{zarate2018, author={Zarate, David Cheng and Bodic, Pierre Le and Dwyer, Tim and Gange, Graeme and Stuckey, Peter}, booktitle={2018 IEEE Pacific Visualization Symposium (PacificVis)}, title={Optimal Sankey Diagrams Via Integer Programming}, year={2018}, volume={}, number={}, pages={135-139}, doi={10.1109/PacificVis.2018.00025}}

@INPROCEEDINGS{frishman2004, author={Frishman, Y. and Ayellet Tal}, booktitle={IEEE Symposium on Information Visualization}, title={Dynamic Drawing of Clustered Graphs}, year={2004}, volume={}, number={}, pages={191-198}, doi={10.1109/INFVIS.2004.18}}



@InProceedings{noack2004,
author="Noack, Andreas",
editor="Liotta, Giuseppe",
title="An Energy Model for Visual Graph Clustering",
booktitle="Graph Drawing",
year="2004",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="425--436",
doi={10.1007/978-3-540-24595-7_40},
abstract="We introduce an energy model whose minimum energy drawings reveal the clusters of the drawn graph. Here a cluster is a set of nodes with many internal edges and few edges to nodes outside the set. The drawings of the best-known force and energy models do not clearly show clusters for graphs whose diameter is small relative to the number of nodes. We formally characterize the minimum energy drawings of our energy model. This characterization shows in what sense the drawings separate clusters, and how the distance of separated clusters to the other nodes can be interpreted.",
isbn="978-3-540-24595-7"
}



@incollection{Gansner2006,
doi = {10.1007/978-3-540-70904-6_37},
year={2006},
publisher = {Springer Berlin Heidelberg},
pages = {386--398},
author = {Emden R. Gansner and Yehuda Koren},
title = {Improved Circular Layouts},
booktitle = {Graph Drawing}
}

@INPROCEEDINGS{koren2002, author={Yehuda Koren and Carmel, L. and Harel, D.}, booktitle={IEEE Symposium on Information Visualization, 2002. INFOVIS 2002.}, title={ACE: a fast multiscale eigenvectors computation for drawing huge graphs}, year={2002}, volume={}, number={}, pages={137-144}, doi={10.1109/INFVIS.2002.1173159}}

@incollection{Ortali2018,
doi = {10.1007/978-3-030-04414-5_41},
url = {10.1007/978-3-030-04414-5_41},
year = {2018},
publisher = {Springer International Publishing},
pages = {579--592},
author = {Giacomo Ortali and Ioannis G. Tollis},
title = {Algorithms and Bounds for Drawing Directed Graphs},
booktitle = {Lecture Notes in Computer Science}
}

@article{cornel2016,
author = {Cornel, D. and Konev, A. and Sadransky, B. and Horváth, Z. and Brambilla, A. and Viola, I. and Waser, J.},
title = {Composite Flow Maps},
journal = {Computer Graphics Forum},
volume = {35},
number = {3},
pages = {461-470},
doi = {10.1111/cgf.12922},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.12922},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.12922},
abstract = {Abstract Flow maps are widely used to provide an overview of geospatial transportation data. Existing solutions lack the support for the interactive exploration of multiple flow components at once. Flow components are given by different materials being transported, different flow directions, or by the need for comparing alternative scenarios. In this paper, we combine flows as individual ribbons in one composite flow map. The presented approach can handle an arbitrary number of sources and sinks. To avoid visual clutter, we simplify our flow maps based on a force-driven algorithm, accounting for restrictions with respect to application semantics. The goal is to preserve important characteristics of the geospatial context. This feature also enables us to highlight relevant spatial information on top of the flow map such as traffic conditions or accessibility. The flow map is computed on the basis of flows between zones. We describe a method for auto-deriving zones from geospatial data according to application requirements. We demonstrate the method in real-world applications, including transportation logistics, evacuation procedures, and water simulation. Our results are evaluated with experts from corresponding fields.},
year = {2016}
}

@article{devkota2018,
author = {Devkota, Sabin and Isaacs, Katherine E.},
title = {CFGExplorer: Designing a Visual Control Flow Analytics System around Basic Program Analysis Operations},
journal = {Computer Graphics Forum},
volume = {37},
number = {3},
pages = {453-464},
doi = {10.1111/cgf.13433},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13433},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13433},
year = {2018}
}

@article{elassady2017,
author = {El-Assady, Mennatallah and Sevastjanova, Rita and Gipp, Bela and Keim, Daniel and Collins, Christopher},
title = {NEREx: Named-Entity Relationship Exploration in Multi-Party Conversations},
journal = {Computer Graphics Forum},
volume = {36},
number = {3},
pages = {213-225},
doi = {10.1111/cgf.13181},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13181},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13181},
year = {2017}
}

@incollection{Bhore2021,
doi = {10.1007/978-3-030-92931-2_22},
url = {10.1007/978-3-030-92931-2_22},
year = {2021},
publisher = {Springer International Publishing},
pages = {304--317},
author = {Sujoy Bhore and Maarten L\"{o}ffler and Soeren Nickel and Martin N\"{o}llenburg},
title = {Unit Disk Representations of~Embedded Trees, Outerplanar and~Multi-legged Graphs},
booktitle = {Lecture Notes in Computer Science}
}

@article{zeng2019,
author = {Zeng, W. and Shen, Q. and Jiang, Y. and Telea, A.},
title = {Route-Aware Edge Bundling for Visualizing Origin-Destination Trails in Urban Traffic},
journal = {Computer Graphics Forum},
volume = {38},
number = {3},
pages = {581-593},
keywords = {CCS Concepts, •Human-centered computing → Graph drawings, Geographic visualization},
doi = {10.1111/cgf.13712},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13712},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13712},
abstract = {Abstract Origin-destination (OD) trails describe movements across space. Typical visualizations thereof use either straight lines or plot the actual trajectories. To reduce clutter inherent to visualizing large OD datasets, bundling methods can be used. Yet, bundling OD trails in urban traffic data remains challenging. Two specific reasons hereof are the constraints implied by the underlying road network and the difficulty of finding good bundling settings. To cope with these issues, we propose a new approach called Route Aware Edge Bundling (RAEB). To handle road constraints, we first generate a hierarchical model of the road-and-trajectory data. Next, we derive optimal bundling parameters, including kernel size and number of iterations, for a user-selected level of detail of this model, thereby allowing users to explicitly trade off simplification vs accuracy. We demonstrate the added value of RAEB compared to state-of-the-art trail bundling methods on both synthetic and real-world traffic data for tasks that include the preservation of road network topology and the support of multiscale exploration.},
year = {2019}
}

@ARTICLE{wang2020,
author={Wang, Yunhai and Xue, Mingliang and Wang, Yanyan and Yan, Xinyuan and Chen, Baoquan and Fu, Chi-Wing and Hurter, Christophe},
journal={IEEE Transactions on Visualization and Computer Graphics},
title={Interactive Structure-aware Blending of Diverse Edge Bundling Visualizations},
year={2020},
volume={26},
number={1},
pages={687-696},
doi={10.1109/TVCG.2019.2934805}}

@incollection{Klemz2021,
doi = {10.1007/978-3-030-92931-2_4},
url = {10.1007/978-3-030-92931-2_4},
year = {2021},
publisher = {Springer International Publishing},
pages = {57--71},
author = {Boris Klemz and Kristin Knorr and Meghana M. Reddy and Felix Schr\"{o}der},
title = {Simplifying Non-simple Fan-Planar Drawings},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Frster2021,
doi = {10.1007/978-3-030-92931-2_6},
url = {10.1007/978-3-030-92931-2_6},
year = {2021},
publisher = {Springer International Publishing},
pages = {87--100},
author = {Henry F\"{o}rster and Michael Kaufmann and Chrysanthi N. Raftopoulou},
title = {Recognizing and Embedding Simple Optimal 2-Planar Graphs},
booktitle = {Lecture Notes in Computer Science}
}

@InProceedings{brandes2002,
author="Brandes, Ulrik
and K{\"o}pf, Boris",
editor="Mutzel, Petra
and J{\"u}nger, Michael
and Leipert, Sebastian",
title="Fast and Simple Horizontal Coordinate Assignment",
booktitle="Graph Drawing",
year="2002",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="31--44",
abstract="We present a simple, linear-time algorithm to determine horizontal coordinates in layered layouts subject to a given ordering within each layer. The algorithm is easy to implement and compares well with existing approaches in terms of assignment quality.",
isbn="978-3-540-45848-7"
}

@article{Bertault2000,
doi = {10.1016/s0020-0190(00)00042-9},
url = {10.1016/s0020-0190(00)00042-9},
year = {2000},
month = apr,
publisher = {Elsevier {BV}},
volume = {74},
number = {1-2},
pages = {7--13},
author = {Fran{\c{c}}ois Bertault},
title = {A force-directed algorithm that preserves edge-crossing properties},
journal = {Information Processing Letters}
}

@incollection{Hong2019,
doi = {10.1007/978-3-030-35802-0_11},
year = {2019},
publisher = {Springer International Publishing},
pages = {139--146},
author = {Seok-Hee Hong and Peter Eades and Marnijati Torkel and Ziyang Wang and David Chae and Sungpack Hong and Daniel Langerenken and Hassan Chafi},
title = {Multi-level Graph Drawing Using Infomap Clustering},
booktitle = {Lecture Notes in Computer Science}
}

@article{hoffswell2018,
author = {Hoffswell, Jane and Borning, Alan and Heer, Jeffrey},
title = {SetCoLa: High-Level Constraints for Graph Layout},
journal = {Computer Graphics Forum},
volume = {37},
number = {3},
pages = {537-548},
keywords = {CCS Concepts, •Human-centered computing → Graph drawings},
doi = {10.1111/cgf.13440},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.13440},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.13440},
abstract = {Abstract Constraints enable flexible graph layout by combining the ease of automatic layout with customizations for a particular domain. However, constraint-based layout often requires many individual constraints defined over specific nodes and node pairs. In addition to the effort of writing and maintaining a large number of similar constraints, such constraints are specific to the particular graph and thus cannot generalize to other graphs in the same domain. To facilitate the specification of customized and generalizable constraint layouts, we contribute SetCoLa: a domain-specific language for specifying high-level constraints relative to properties of the backing data. Users identify node sets based on data or graph properties and apply high-level constraints within each set. Applying constraints to node sets rather than individual nodes reduces specification effort and facilitates reapplication of customized layouts across distinct graphs. We demonstrate the conciseness, generalizability, and expressiveness of SetCoLa on a series of real-world examples from ecological networks, biological systems, and social networks.},
year = {2018}
}

@ARTICLE{wang2018,
author={Wang, Yunhai and Wang, Yanyan and Sun, Yinqi and Zhu, Lifeng and Lu, Kecheng and Fu, Chi-Wing and Sedlmair, Michael and Deussen, Oliver and Chen, Baoquan},
journal={IEEE Transactions on Visualization and Computer Graphics},
title={Revisiting Stress Majorization as a Unified Framework for Interactive Constrained Graph Visualization},
year={2018},
volume={24},
number={1},
pages={489-499},
doi={10.1109/TVCG.2017.2745919}}

@incollection{Gansner2005,
doi = {10.1007/978-3-540-31843-9_25},
year = {2005},
publisher = {Springer Berlin Heidelberg},
pages = {239--250},
author = {Emden R. Gansner and Yehuda Koren and Stephen North},
title = {Graph Drawing by Stress Majorization},
booktitle = {Graph Drawing}
}

@article{Arleo2019,
doi = {10.1109/tpds.2018.2869805},
year = {2019},
month = apr,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {30},
number = {4},
pages = {754--765},
author = {Alessio Arleo and Walter Didimo and Giuseppe Liotta and Fabrizio Montecchiani},
title = {A Distributed Multilevel Force-Directed Algorithm},
journal = {{IEEE} Transactions on Parallel and Distributed Systems}
}

@InProceedings{klammler2018,
author="Klammler, Moritz
and Mchedlidze, Tamara
and Pak, Alexey",
editor="Biedl, Therese
and Kerren, Andreas",
title="Aesthetic Discrimination of Graph Layouts",
booktitle="Graph Drawing and Network Visualization",
year="2018",
publisher="Springer International Publishing",
address="Cham",
pages="169--184",
doi={10.1007/978-3-030-04414-5_12},
abstract="This paper addresses the following basic question: given two layouts of the same graph, which one is more aesthetically pleasing? We propose a neural network-based discriminator model trained on a labeled dataset that decides which of two layouts has a higher aesthetic quality. The feature vectors used as inputs to the model are based on known graph drawing quality metrics, classical statistics, information-theoretical quantities, and two-point statistics inspired by methods of condensed matter physics. The large corpus of layout pairs used for training and testing is constructed using force-directed drawing algorithms and the layouts that naturally stem from the process of graph generation. It is further extended using data augmentation techniques. Our model demonstrates a mean prediction accuracy of 96.48{\%}, outperforming discriminators based on stress and on the linear combination of popular quality metrics by a small but statistically significant margin.",
isbn="978-3-030-04414-5"
}

@article{Jacomy2014,
doi = {10.1371/journal.pone.0098679},
year = {2014},
month = jun,
publisher = {Public Library of Science ({PLoS})},
volume = {9},
number = {6},
pages = {e98679},
author = {Mathieu Jacomy and Tommaso Venturini and Sebastien Heymann and Mathieu Bastian},
editor = {Mark R. Muldoon},
title = {{ForceAtlas}2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software},
journal = {{PLoS} {ONE}}
}

@article{Nachmanson2017,
  doi = {10.7155/jgaa.00442},
  year = {2017},
  publisher = {Journal of Graph Algorithms and Applications},
  volume = {21},
  number = {5},
  pages = {857--872},
  author = {Lev Nachmanson and Arlind Nocaj and Sergey Bereg and Leishi Zhang and Alexander Holroyd},
  title = {Node Overlap Removal by Growing a Tree},
  journal = {Journal of Graph Algorithms and Applications}
}

@inproceedings{Zhang2010,
doi = {10.1109/cise.2010.5677225},
year = {2010},
month = dec,
publisher = {{IEEE}},
author = {Yonghe Zhang and Yanyan Li},
title = {{BaryLayout}: A Simple Algorithm for Fast Drawing Large Graphs},
booktitle = {2010 International Conference on Computational Intelligence and Software Engineering}
}

@incollection{Chimani2021,
doi = {10.1007/978-3-030-92931-2_3},
year = {2021},
publisher = {Springer International Publishing},
pages = {41--56},
author = {Markus Chimani and Max Ilsen and Tilo Wiedera},
title = {Star-Struck by Fixed Embeddings: Modern Crossing Number Heuristics},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Marner2014,
doi = {10.1007/978-3-662-45803-7_10},
year = {2014},
publisher = {Springer International Publishing},
pages = {113--124},
author = {Michael R. Marner and Ross T. Smith and Bruce H. Thomas and Karsten Klein and Peter Eades and Seok-Hee Hong},
title = {{GION}: Interactively Untangling Large Graphs on Wall-Sized Displays},
booktitle = {Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications}
}

@InProceedings{harel2001,
author="Harel, David
and Koren, Yehuda",
editor="Marks, Joe",
title="A Fast Multi-scale Method for Drawing Large Graphs",
booktitle="Graph Drawing",
year="2001",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="183--196",
doi={10.1007/3-540-44541-2_18},
abstract="We present a multi-scale layout algorithm for the aesthetic drawing of undirected graphs with straight-line edges. The algorithm is extremely fast, and is capable of drawing graphs of substantially larger size than any other algorithm we are aware of. For example, the algorithm achieves optimal drawings of 1000 vertex graphs in about 2 seconds. The paper contains graphs with over 6000 nodes. The proposed algorithm embodies a new multi-scale scheme for drawing graphs, which was motivated by the recently published multi-scale algorithm of Hadany and Harel [7]. It can significantly improve the speed of essentially any force-directed method (regardless of that method's ability of drawing weighted graphs or the continuity of its cost-function).",
isbn="978-3-540-44541-8"
}

@incollection{Chen2019,
doi = {10.1007/978-3-030-35802-0_14},
year = {2019},
publisher = {Springer International Publishing},
pages = {179--192},
author = {Fati Chen and Laurent Piccinini and Pascal Poncelet and Arnaud Sallaberry},
title = {Node Overlap Removal Algorithms: A Comparative Study},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Meidiana2019,
doi = {10.1007/978-3-030-35802-0_10},
year = {2019},
publisher = {Springer International Publishing},
pages = {125--138},
author = {Amyra Meidiana and Seok-Hee Hong and Peter Eades and Daniel Keim},
title = {A Quality Metric for Visualization of Clusters in Graphs},
booktitle = {Lecture Notes in Computer Science}
}

@article{Donati2015,
author = {Donati, Beatrice and Baudet, Christian and Sinaimeri, Blerina and Crescenzi, Pierluigi and Sagot, Marie-France},
title = {EUCALYPT: efficient tree reconciliation enumerator},
journal = {Algorithms for Molecular Biology},
year = {2015},
volume = {10},
issue = {1},
pages = {3},
url = {10.1186/s13015-014-0031-3},
doi = {10.1186/s13015-014-0031-3},
abstract = {Phylogenetic tree reconciliation is the approach of choice for investigating the coevolution of sets of organisms such as hosts and parasites. It consists in a mapping between the parasite tree and the host tree using event-based maximum parsimony. Given a cost model for the events, many optimal reconciliations are however possible. Any further biological interpretation of them must therefore take this into account, making the capacity to enumerate all optimal solutions a crucial point. Only two algorithms currently exist that attempt such enumeration; in one case not all possible solutions are produced while in the other not all cost vectors are currently handled. The objective of this paper is two-fold. The first is to fill this gap, and the second is to test whether the number of solutions generally observed can be an issue in terms of interpretation.},
issn = {1748-7188},
}

@Inbook{Koch2001,
author="Koch, Thorsten
and Martin, Alexander
and Vo{\ss}, Stefan",
editor="Cheng, Xiu Zhen
and Du, Ding-Zhu",
title="SteinLib: An Updated Library on Steiner Tree Problems in Graphs",
bookTitle="Steiner Trees in Industry",
year="2001",
publisher="Springer US",
address="Boston, MA",
pages="285--325",
abstract="In this paper we present the SteinLib, a library of data sets for the Steiner tree problem in graphs. This library extends former libraries on Steiner tree problems by many new interesting and difficult instances, most of them arising from real-world applications. We give a survey on the difficulty of these problem instances by stating references to state-of-the-art software packages that were the first or are currently among the best to solve these instances.",
isbn="978-1-4613-0255-1",
doi="10.1007/978-1-4613-0255-1_9",
url="10.1007/978-1-4613-0255-1_9"
}

@article{soper_combined_2004,
title = {A {Combined} {Evolutionary} {Search} and {Multilevel} {Optimisation} {Approach} to {Graph}-{Partitioning}},
volume = {29},
issn = {1573-2916},
url = {10.1023/B:JOGO.0000042115.44455.f3},
doi = {10.1023/B:JOGO.0000042115.44455.f3},
abstract = {The graph-partitioning problem is to divide a graph into several pieces so that the number of vertices in each piece is the same within some defined tolerance and the number of cut edges is minimised. Important applications of the problem arise, for example, in parallel processing where data sets need to be distributed across the memory of a parallel machine. Very effective heuristic algorithms have been developed for this problem which run in real-time, but it is not known how good the partitions are since the problem is, in general, NP-complete. This paper reports an evolutionary search algorithm for finding benchmark partitions. A distinctive feature is the use of a multilevel heuristic algorithm to provide an effective crossover. The technique is tested on several example graphs and it is demonstrated that our method can achieve extremely high quality partitions significantly better than those found by the state-of-the-art graph-partitioning packages.},
number = {2},
journal = {Journal of Global Optimization},
author = {Soper, A.J. and Walshaw, C. and Cross, M.},
month = jun,
year = {2004},
pages = {225--241},
}

@article{walshaw2000,
author = {Walshaw, C. and Cross, M.},
title = {Mesh Partitioning: A Multilevel Balancing and Refinement Algorithm},
year = {2000},
issue_date = {2000},
publisher = {Society for Industrial and Applied Mathematics},
address = {USA},
volume = {22},
number = {1},
issn = {1064-8275},
url = {10.1137/S1064827598337373},
doi = {10.1137/S1064827598337373},
abstract = {Multilevel algorithms are a successful class of optimization techniques which addresses the mesh partitioning problem. They usually combine a graph contraction algorithm together with a local optimization method which refines the partition at each graph level. In this paper we present an enhancement of the technique which uses imbalance to achieve higher quality partitions. We also present a formulation of the Kernighan--Lin partition optimization algorithm which incorporates load-balancing. The resulting algorithm is tested against a different but related state-of-the-art partitioner and shown to provide improved results.},
journal = {SIAM J. Sci. Comput.},
month = {jan},
pages = {63–80},
numpages = {18},
keywords = {graph-partitioning, 05C85, multilevel algorithms, load-balancing, 65Y05, mesh partitioning}
}

@misc{Bachmaier_Gleißner_Hofmeier_2012,
 title={DAGmar: Library for DAGs},
author={Bachmaier, Christian and Gleißner, Andreas and Hofmeier, Andreas}, 
url = {https://www.infosun.fim.uni-passau.de/~chris/down/MIP-1202.pdf},
year={2012}}

@phdthesis{gutwenger_phd,
author = "Carsten Gutwenger",
title = "Application of SPQR-Trees in the Planarization Approach for Drawing Graphs",
school = "Technische Universität Dortmund",
year = "2010",
url = "https://eldorado.tu-dortmund.de/handle/2003/27430",
}

@InProceedings{chimani2016c,
author =	{Markus Chimani and Tilo Wiedera},
title =	{{An ILP-based Proof System for the Crossing Number Problem}},
booktitle =	{24th Annual European Symposium on Algorithms (ESA 2016)},
pages =	{29:1--29:13},
series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN =	{978-3-95977-015-6},
ISSN =	{1868-8969},
year =	{2016},
volume =	{57},
editor =	{Piotr Sankowski and Christos Zaroliagis},
publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
address =	{Dagstuhl, Germany},
URL =	{http://drops.dagstuhl.de/opus/volltexte/2016/6380},
URN =	{urn:nbn:de:0030-drops-63803},
doi =	{10.4230/LIPIcs.ESA.2016.29},
annote =	{Keywords: automatic formal proof, crossing number, integer linear programming}
}

@article{gansner2000, author = {Gansner, Emden R. and North, Stephen C.}, title = {An Open Graph Visualization System and Its Applications to Software Engineering}, year = {2000}, issue_date = {Sept. 2000}, publisher = {John Wiley & Sons, Inc.}, address = {USA}, volume = {30}, number = {11}, issn = {0038-0644}, journal = {Softw. Pract. Exper.}, month = {sep}, pages = {1203–1233}, numpages = {31}, keywords = {graph visualization, open systems, software engineering} }

@article{DIBATTISTA2000,
doi = {10.1142/s0218195900000358},
year = {2000},
month = dec,
publisher = {World Scientific Pub Co Pte Lt},
volume = {10},
number = {06},
pages = {623--648},
author = {Giuseppe Di~Battista and Ashim Garg and Giuseppe Liotta and Armando Parise and Roberto Tamassia and Emanuele Tassinari and Francesco Vargiu and Luca Vismara},
title = {Drawing Directed Acyclic Graphs: An Experimental Study},
journal = {International Journal of Computational Geometry {\&} Applications}
}

@inproceedings{vandenElzen2013,
doi = {10.1109/pacificvis.2013.6596125},
year = {2013},
month = feb,
publisher = {{IEEE}},
author = {Stef van~den~Elzen and Danny Holten and Jorik Blaas and Jarke J. van~Wijk},
title = {Reordering Massive Sequence Views: Enabling temporal and structural analysis of dynamic networks},
booktitle = {2013 {IEEE} Pacific Visualization Symposium ({PacificVis})}
}

@inproceedings{Lin2010,
doi = {10.1137/1.9781611972801.37},
year = {2010},
month = apr,
publisher = {Society for Industrial and Applied Mathematics},
author = {Yu-Ru Lin and Jimeng Sun and Nan Cao and Shixia Liu},
title = {{ContexTour}: Contextual Contour Visual Analysis on Dynamic Multi-Relational Clustering},
booktitle = {Proceedings of the 2010 {SIAM} International Conference on Data Mining}
}

@incollection{Jabrayilov2016,
  doi = {10.1007/978-3-319-50106-2_17},
  year = {2016},
  publisher = {Springer International Publishing},
  pages = {209--221},
  author = {Adalat Jabrayilov and Sven Mallach and Petra Mutzel and Ulf R\"{u}egg and Reinhard von~Hanxleden},
  title = {Compact Layered Drawings of General Directed Graphs},
  booktitle = {Lecture Notes in Computer Science}
}

@article{Holten2009,
doi = {10.1111/j.1467-8659.2009.01450.x},
year = {2009},
month = jun,
publisher = {Wiley},
volume = {28},
number = {3},
pages = {983--990},
author = {Danny Holten and Jarke J. van~Wijk},
title = {Force-Directed Edge Bundling for Graph Visualization},
journal = {Computer Graphics Forum}
}

@article{Wu2020,
doi = {10.1109/tvcg.2020.3038154},
year = {2020},
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
pages = {1--1},
author = {Hsiang-Yun Wu and Martin Nollenburg and Ivan Viola},
title = {Multi-level Area Balancing of Clustered Graphs},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@incollection{Wu2018,
doi = {10.1007/978-3-319-73915-1_30},
year = {2018},
publisher = {Springer International Publishing},
pages = {379--393},
author = {Jieting Wu and Jianping Zeng and Feiyu Zhu and Hongfeng Yu},
title = {{MLSEB}: Edge Bundling Using Moving Least Squares Approximation},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Binucci2016,
  doi = {10.1007/978-3-319-50106-2_4},
  year = {2016},
  publisher = {Springer International Publishing},
  pages = {44--51},
  author = {Carla Binucci and Markus Chimani and Walter Didimo and Giuseppe Liotta and Fabrizio Montecchiani},
  title = {Placing Arrows in Directed Graph Drawings},
  booktitle = {Lecture Notes in Computer Science}
}

@incollection{Angori2019,
doi = {10.1007/978-3-030-35802-0_22},
year = {2019},
publisher = {Springer International Publishing},
pages = {276--290},
author = {Lorenzo Angori and Walter Didimo and Fabrizio Montecchiani and Daniele Pagliuca and Alessandra Tappini},
title = {{ChordLink}: A New Hybrid Visualization Model},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Calamoneri2018,
doi = {10.1007/978-3-319-73915-1_27},
year = {2018},
publisher = {Springer International Publishing},
pages = {334--347},
author = {Tiziana Calamoneri and Valentino Di Donato and Diego Mariottini and Maurizio Patrignani},
title = {Visualizing Co-phylogenetic Reconciliations},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Simonetto2018,
  doi = {10.1007/978-3-319-73915-1_31},
  year = {2018},
  publisher = {Springer International Publishing},
  pages = {394--409},
  author = {Paolo Simonetto and Daniel Archambault and Stephen Kobourov},
  title = {Drawing Dynamic Graphs Without Timeslices},
  booktitle = {Lecture Notes in Computer Science}
}



@incollection{Nickel2019,
doi = {10.1007/978-3-030-35802-0_4},
year = {2019},
publisher = {Springer International Publishing},
pages = {46--60},
author = {Soeren Nickel and Max Sondag and Wouter Meulemans and Markus Chimani and Stephen Kobourov and Jaakko Peltonen and Martin N\"{o}llenburg},
title = {Computing Stable Demers Cartograms},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Walter2020,
doi = {10.1007/978-3-030-68766-3_18},
year = {2020},
publisher = {Springer International Publishing},
pages = {220--234},
author = {Julian Walter and Johannes Zink and Joachim Baumeister and Alexander Wolff},
title = {Layered Drawing of Undirected Graphs with Generalized Port Constraints},
booktitle = {Lecture Notes in Computer Science}
}

@article{Wallinger2022,
doi = {10.1109/tvcg.2021.3114795},
year = {2022},
month = jan,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {28},
number = {1},
pages = {313--323},
author = {Markus Wallinger and Daniel Archambault and David Auber and Martin Nollenburg and Jaakko Peltonen},
title = {Edge-Path Bundling: A Less Ambiguous Edge Bundling Approach},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}

@InProceedings{brandes2009,
author="Brandes, Ulrik
and Pich, Christıan",
editor="Tollis, Ioannis G.
and Patrignani, Maurizio",
title="An Experimental Study on Distance-Based Graph Drawing",
booktitle="Graph Drawing",
year="2009",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="218--229",
doi={10.1007/978-3-642-00219-9_21},
abstract="In numerous application areas, general undirected graphs need to be drawn, and force-directed layout appears to be the most frequent choice. We present an extensive experimental study showing that, if the goal is to represent the distances in a graph well, a combination of two simple algorithms based on variants of multidimensional scaling is to be preferred because of their efficiency, reliability, and even simplicity. We also hope that details in the design of our study help advance experimental methodology in algorithm engineering and graph drawing, independent of the case at hand.",
isbn="978-3-642-00219-9"
}

@article{kruiger2017,
author = {Kruiger, J. F. and Rauber, P. E. and Martins, R. M. and Kerren, A. and Kobourov, S. and Telea, A. C.},
title = {Graph Layouts by t-SNE},
journal = {Computer Graphics Forum},
volume = {36},
number = {3},
pages = {283-294},
doi = {10.1111/cgf.13187},
abstract = {Abstract We propose a new graph layout method based on a modification of the t-distributed Stochastic Neighbor Embedding (t-SNE) dimensionality reduction technique. Although t-SNE is one of the best techniques for visualizing high-dimensional data as 2D scatterplots, t-SNE has not been used in the context of classical graph layout. We propose a new graph layout method, tsNET, based on representing a graph with a distance matrix, which together with a modified t-SNE cost function results in desirable layouts. We evaluate our method by a formal comparison with state-of-the-art methods, both visually and via established quality metrics on a comprehensive benchmark, containing real-world and synthetic graphs. As evidenced by the quality metrics and visual inspection, tsNET produces excellent layouts.},
year = {2017}
}

@article{Gansner2013,
doi = {10.1109/tvcg.2012.299},
year = {2013},
month = jun,
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {19},
number = {6},
pages = {927--940},
author = {E. R. Gansner and Yifan Hu and S. North},
title = {A Maxent-Stress Model for Graph Layout},
journal = {{IEEE} Transactions on Visualization and Computer Graphics}
}



@article{fruc,
author = {Fruchterman, Thomas M. J. and Reingold, Edward M.},
title = {Graph drawing by force-directed placement},
journal = {Software: Practice and Experience},
volume = {21},
number = {11},
pages = {1129-1164},
keywords = {Graph drawing, Force-directed placement, Multi-level techniques, Simulated annealing},
doi = {10.1002/spe.4380211102},
abstract = {Abstract We present a modification of the spring-embedder model of Eades [Congressus Numerantium, 42, 149–160, (1984)] for drawing undirected graphs with straight edges. Our heuristic strives for uniform edge lengths, and we develop it in analogy to forces in natural systems, for a simple, elegant, conceptually-intuitive, and efficient algorithm.},
year = {1991}
}

@INPROCEEDINGS{vanderkouwe2019,  author={van~der~Kouwe, Erik and Heiser, Gernot and Andriesse, Dennis and Bos, Herbert and Giuffrida, Cristiano},  booktitle={2019 IEEE European Symposium on Security and Privacy (EuroS\&P)},   title={SoK: Benchmarking Flaws in Systems Security},   year={2019},  volume={},  number={},  pages={310-325},  doi={10.1109/EuroSP.2019.00031}}

@incollection{Chimani2008,
doi = {10.1007/978-3-540-87744-8_24},
publisher = {Springer Berlin Heidelberg},
pages = {284--296},
year= {2008},
author = {Markus Chimani and Petra Mutzel and Immanuel Bomze},
title = {A New Approach to Exact Crossing Minimization},
booktitle = {Algorithms - {ESA} 2008}
}

@incollection{Hummel2019,
doi = {10.1007/978-3-030-35802-0_25},
year = {2019},
publisher = {Springer International Publishing},
pages = {323--336},
author = {Matthias Hummel and Fabian Klute and Soeren Nickel and Martin N\"{o}llenburg},
title = {Maximizing Ink in Partial Edge Drawings of k-plane Graphs},
booktitle = {Lecture Notes in Computer Science}
}

@inproceedings{tarik1,
author = {Crnovrsanin, Tarik and Chu, Jacqueline and Ma, Kwan-Liu},
title = {An Incremental Layout Method for Visualizing Online Dynamic Graphs},
year = {2015},
isbn = {978-3-319-27260-3},
publisher = {Springer-Verlag},
address = {Berlin, Heidelberg},
doi = {10.1007/978-3-319-27261-0_2},
abstract = {Graphs provide a visual means for examining relation data and force-directed methods are often used to lay out graphs for viewing. Making sense of a dynamic graph as it evolves over time is challenging, and previous force-directed methods were designed for static graphs. In this paper, we present an incremental version of a multilevel multi-pole layout method with a refinement scheme incorporated, which enables us to visualize online dynamic networks while maintaining a mental map of the graph structure. We demonstrate the effectiveness of our method and compare it to previous methods using several network data sets.},
booktitle = {Graph Drawing and Network Visualization},
pages = {16–29},
numpages = {14},
keywords = {Graph layout, Dynamic graphs, Streaming data},
location = {Los Angeles
CA
USA}
}

@article{tarik2,
title = {Visualization techniques for categorical analysis of social networks with multiple edge sets},
journal = {Social Networks},
volume = {37},
pages = {56-64},
year = {2014},
issn = {0378-8733},
doi = {10.1016/j.socnet.2013.12.002},
author = {Tarik Crnovrsanin and Chris W. Muelder and Robert Faris and Diane Felmlee and Kwan-Liu Ma},
keywords = {Social networks, Information visualization, Network analytics, Graph layouts},
abstract = {The growing popularity and diversity of social network applications present new opportunities as well as new challenges. The resulting social networks have high value to business intelligence, sociological studies, organizational studies, epidemical studies, etc. The ability to explore and extract information of interest from the networks is thus crucial. However, these networks are often large and composed of multi-categorical nodes and edges, making it difficult to visualize and reason with conventional methods. In this paper, we show how to combine statistical methods with visualization to address these challenges, and how to arrange layouts differently to better bring out different aspects of the networks. We applied our methods to several social networks to demonstrate their effectiveness in characterizing the networks and clarifying the structures of interest, leading to new findings.}
}



@article{tarik3,
  author    = {Tarik Crnovrsanin and
               Shilpika and
               Senthil K. Chandrasegaran and
               Kwan{-}Liu Ma},
  title     = {Staged Animation Strategies for Online Dynamic Networks},
  journal   = {{IEEE} Transactions on Visualization and Computer Graphics},
  volume    = {27},
  number    = {2},
  pages     = {539--549},
  year      = {2021},
  doi       = {10.1109/TVCG.2020.3030385},
  timestamp = {Tue, 01 Jun 2021 09:59:00 +0200},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

@article{tarik4,
  author    = {Oh{-}Hyun Kwon and
               Tarik Crnovrsanin and
               Kwan{-}Liu Ma},
  title     = {What Would a Graph Look Like in this Layout? {A} Machine Learning
               Approach to Large Graph Visualization},
  journal   = {{IEEE} Transactions on Visualization and Computer Graphics},
  volume    = {24},
  number    = {1},
  pages     = {478--488},
  year      = {2018},
  doi       = {10.1109/TVCG.2017.2743858},
  timestamp = {Wed, 14 Nov 2018 10:22:19 +0100},
  biburl    = {https://dblp.org/rec/journals/tvcg/KwonCM18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

@article{tarik5,
  author    = {Tarik Crnovrsanin and
               Isaac Liao and
               Yingcai Wu and
               Kwan{-}Liu Ma},
  title     = {Visual Recommendations for Network Navigation},
  journal   = {Comput. Graph. Forum},
  volume    = {30},
  number    = {3},
  pages     = {1081--1090},
  year      = {2011},
  doi       = {10.1111/j.1467-8659.2011.01957.x},
  timestamp = {Fri, 26 May 2017 22:53:55 +0200},
  biburl    = {https://dblp.org/rec/journals/cgf/CrnovrsaninLWM11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{tarik6,
  author    = {Tarik Crnovrsanin and
               Carlos D. Correa and
               Kwan{-}Liu Ma},
  editor    = {Nasrullah Memon and
               Reda Alhajj},
  title     = {Social Network Discovery Based on Sensitivity Analysis},
  booktitle = {2009 International Conference on Advances in Social Network Analysis
               and Mining, {ASONAM} 2009, 20-22 July 2009, Athens, Greece},
  pages     = {107--112},
  publisher = {{IEEE} Computer Society},
  year      = {2009},
  doi       = {10.1109/ASONAM.2009.56},
  timestamp = {Wed, 16 Oct 2019 14:14:53 +0200},
  biburl    = {https://dblp.org/rec/conf/asunam/CrnovrsaninCM09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

@InProceedings{chimani2006,
author="Chimani, Markus
and Gutwenger, Carsten
and Mutzel, Petra",
editor="{\`A}lvarez, Carme
and Serna, Mar{\'i}a",
title="Experiments on Exact Crossing Minimization Using Column Generation",
booktitle="Experimental Algorithms",
year="2006",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="303--315",
doi="10.1007/11764298_28",
abstract="The crossing number of a graph G is the smallest number of edge crossings in any drawing of G into the plane. Recently, the first branch-and-cut approach for solving the crossing number problem has been presented in [3]. Its major drawback was the huge number of variables out of which only very few were actually used in the optimal solution. This restricted the algorithm to rather small graphs with low crossing number.",
isbn="978-3-540-34598-5"
}

@incollection{Ahmed2020,
doi = {10.1007/978-3-030-68766-3_1},
year = {2020},
publisher = {Springer International Publishing},
pages = {3--17},
author = {Reyan Ahmed and Felice De Luca and Sabin Devkota and Stephen Kobourov and Mingwei Li},
title = {Graph Drawing via Gradient Descent, ({GD})$^2$},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Brsig2020,
doi = {10.1007/978-3-030-68766-3_2},
year = {2020},
publisher = {Springer International Publishing},
pages = {18--25},
author = {Katharina B\"{o}rsig and Ulrik Brandes and Barna Pasztor},
title = {Stochastic Gradient Descent Works Really Well for Stress Minimization},
booktitle = {Lecture Notes in Computer Science}
}

@inproceedings{navlakha2008,
author = {Navlakha, Saket and Rastogi, Rajeev and Shrivastava, Nisheeth},
title = {Graph Summarization with Bounded Error},
year = {2008},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
doi = {10.1145/1376616.1376661},
abstract = {We propose a highly compact two-part representation of a given graph G consisting of a graph summary and a set of corrections. The graph summary is an aggregate graph in which each node corresponds to a set of nodes in G, and each edge represents the edges between all pair of nodes in the two sets. On the other hand, the corrections portion specifies the list of edge-corrections that should be applied to the summary to recreate G. Our representations allow for both lossless and lossy graph compression with bounds on the introduced error. Further, in combination with the MDL principle, they yield highly intuitive coarse-level summaries of the input graph G. We develop algorithms to construct highly compressed graph representations with small sizes and guaranteed accuracy, and validate our approach through an extensive set of experiments with multiple real-life graph data sets.To the best of our knowledge, this is the first work to compute graph summaries using the MDL principle, and use the summaries (along with corrections) to compress graphs with bounded error.},
booktitle = {Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data},
pages = {419–432},
numpages = {14},
keywords = {approximation, graph compression, minimum description length},
location = {Vancouver, Canada},
series = {SIGMOD '08}
}

@article{makinen1990,
author = { Erkki   Mäkinen },
title = {How to draw a hypergraph},
journal = {International Journal of Computer Mathematics},
volume = {34},
number = {3-4},
pages = {177-185},
year  = {1990},
publisher = {Taylor & Francis},
doi = {10.1080/00207169008803875},
}

@article{lhuillier2017,
author = {Lhuillier, A. and Hurter, C. and Telea, A.},
title = {State of the Art in Edge and Trail Bundling Techniques},
journal = {Computer Graphics Forum},
volume = {36},
number = {3},
pages = {619-645},
keywords = {Categories and Subject Descriptors (according to ACM CCS), I.3.3 Computer Graphics: Computing Methodologies—Picture/Image Generation, I.3.6 Computer Graphics: Computing Methodologies—Methodology and Techniques},
doi = {10.1111/cgf.13213},
abstract = {Abstract Bundling techniques provide a visual simplification of a graph drawing or trail set, by spatially grouping similar graph edges or trails. This way, the structure of the visualization becomes simpler and thereby easier to comprehend in terms of assessing relations that are encoded by such paths, such as finding groups of strongly interrelated nodes in a graph, finding connections between spatial regions on a map linked by a number of vehicle trails, or discerning the motion structure of a set of objects by analyzing their paths. In this state of the art report, we aim to improve the understanding of graph and trail bundling via the following main contributions. First, we propose a data-based taxonomy that organizes bundling methods on the type of data they work on (graphs vs trails, which we refer to as paths). Based on a formal definition of path bundling, we propose a generic framework that describes the typical steps of all bundling algorithms in terms of high-level operations and show how existing method classes implement these steps. Next, we propose a description of tasks that bundling aims to address. Finally, we provide a wide set of example applications of bundling techniques and relate these to the above-mentioned taxonomies. Through these contributions, we aim to help both researchers and users to understand the bundling landscape as well as its technicalities.},
year = {2017}
}

@inproceedings{minghim2006,
author = {Minghim, Rosane and Paulovich, Fernando and Lopes, Alneu},
year = {2006},
month = {01},
pages = {60600S},
title = {Content-based text mapping using multi-dimensional projections for exploration of document collections},
volume = {6060},
doi = {10.1117/12.650880},
booktitle = {Visualization and Data Analysis},
}

@INPROCEEDINGS{nguyen2013,
  author={Nguyen, Quan and Eades, Peter and Hong, Seok-Hee},
  booktitle={2013 IEEE Pacific Visualization Symposium (PacificVis)}, 
  title={On the faithfulness of graph visualizations}, 
  year={2013},
  volume={},
  number={},
  pages={209-216},
  doi={10.1109/PacificVis.2013.6596147}}


@InProceedings{hachul2004,
author="Hachul, Stefan
and J{\"u}nger, Michael",
editor="Pach, J{\'a}nos",
title="Drawing Large Graphs with a Potential-Field-Based Multilevel Algorithm",
booktitle="Graph Drawing",
year="2005",
doi={10.1007/978-3-540-31843-9_29},
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="285--295",
abstract="Force-directed graph drawing algorithms are widely used for drawing general graphs. However, these methods do not guarantee a sub-quadratic running time in general. We present a new force-directed method that is based on a combination of an efficient multilevel scheme and a strategy for approximating the repulsive forces in the system by rapidly evaluating potential fields. Given a graph G=(V,E), the asymptotic worst case running time of this method is O(|V|log|V|{\thinspace}+{\thinspace}|E|) with linear memory requirements. In practice, the algorithm generates nice drawings of graphs containing 100000 nodes in less than 5 minutes. Furthermore, it clearly visualizes even the structures of those graphs that turned out to be challenging for some other methods.",
isbn="978-3-540-31843-9"
}

@InProceedings{walshaw2001,
author="Walshaw, C.",
editor="Marks, Joe",
title="A Multilevel Algorithm for Force-Directed Graph Drawing",
booktitle="Graph Drawing",
year="2001",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="171--182",
abstract="We describe a heuristic method for drawing graphs which uses a multilevel technique combined with a force-directed placement algorithm. The multilevel process groups vertices to form clusters, uses the clusters to define a new graph and is repeated until the graph size falls below some threshold. The coarsest graph is then given an initial layout and the layout is successively refined on all the graphs starting with the coarsest and ending with the original. In this way the multilevel algorithm both accelerates and gives a more global quality to the force- directed placement. The algorithm can compute both 2 {\&} 3 dimensional layouts and we demonstrate it on a number of examples ranging from 500 to 225,000 vertices. It is also very fast and can compute a 2D layout of a sparse graph in around 30 seconds for a 10,000 vertex graph to around 10 minutes for the largest graph. This is an order of magnitude faster than recent implementations of force-directed placement algorithms.",
isbn="978-3-540-44541-8"
}

@article{hu2005efficient,
  author = {Hu, Y. F.},
  journal = {The Mathematica Journal},
  keywords = {directed drawing force graph visualization},
  pages = {37-71},
  title = {Efficient and high quality force-directed graph drawing},
  url = {http://www.mathematica-journal.com/issue/v10i1/contents/graph_draw/graph_draw.pdf},
  volume = 10,
  year = 2005
}

@incollection{Bekos2018,
doi = {10.1007/978-3-030-04414-5_19},
year = {2018},
publisher = {Springer International Publishing},
pages = {271--285},
author = {Michael A. Bekos and Henry F\"{o}rster and Christian Geckeler and Lukas Holl\"{a}nder and Michael Kaufmann and Amad\"{a}us M. Spallek and Jan Splett},
title = {A Heuristic Approach Towards Drawings of Graphs with High Crossing Resolution},
booktitle = {Lecture Notes in Computer Science}
}

@incollection{Giovannangeli2021,
doi = {10.1007/978-3-030-92931-2_27},
year = {2021},
publisher = {Springer International Publishing},
pages = {375--390},
author = {Loann Giovannangeli and Frederic Lalanne and David Auber and Romain Giot and Romain Bourqui},
title = {Deep Neural Network for {DrawiNg} Networks},
booktitle = {Lecture Notes in Computer Science}
}

@article{Clancy2019,
doi = {10.7155/jgaa.00487},
year = {2019},
publisher = {Journal of Graph Algorithms and Applications},
volume = {23},
number = {2},
pages = {135--166},
author = {Kieran Clancy and Mıchael Haythorpe and Alex Newcombe},
title = {An effective crossing minimisation heuristic based on star insertion},
journal = {Journal of Graph Algorithms and Applications}
}

@incollection{Gutwenger2004,
doi = {10.1007/978-3-540-24595-7_2},
year = {2004},
publisher = {Springer Berlin Heidelberg},
pages = {13--24},
author = {Carsten Gutwenger and Petra Mutzel},
title = {An Experimental Study of Crossing Minimization Heuristics},
booktitle = {Graph Drawing}
}

@article{DiBattista1997b,
doi = {10.1016/s0925-7721(96)00005-3},
year = {1997},
month = apr,
publisher = {Elsevier {BV}},
volume = {7},
number = {5-6},
pages = {303--325},
author = {Giuseppe Di Battista and Ashim Garg and Giuseppe Liotta and Roberto Tamassia and Emanuele Tassinari and Francesco Vargiu},
title = {An experimental comparison of four graph drawing algorithms},
journal = {Computational Geometry}
}

@article{maddison2007,
author = {Maddison, David and Schulz, Katja and Maddison, Wayne},
year = {2007},
month = {12},
pages = {19-40},
title = {The Tree of Life Web Project*},
volume = {1668},
journal = {Zootaxa},
doi = {10.11646/zootaxa.1668.1.4}
}

@article{gkab301,
author = {Letunic, Ivica and Bork, Peer},
title = "{Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation}",
journal = {Nucleic Acids Research},
volume = {49},
number = {W1},
pages = {W293-W296},
year = {2021},
month = {04},
abstract = "{The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a completely new tree display engine, together with numerous new features. For example, a new dataset type has been added (MEME motifs), while annotation options have been expanded for several existing ones. Node metadata display options have been extended and now also support non-numerical categorical values, as well as multiple values per node. Direct manual annotation is now available, providing a set of basic drawing and labeling tools, allowing users to draw shapes, labels and other features by hand directly onto the trees. Support for tree and dataset scales has been extended, providing fine control over line and label styles. Unrooted tree displays can now use the equal-daylight algorithm, proving a much greater display clarity. The user account system has been streamlined and expanded with new navigation options and currently handles \\>1 million trees from \\>70 000 individual users.}",
issn = {0305-1048},
doi = {10.1093/nar/gkab301},
url = {10.1093/nar/gkab301},
eprint = {https://academic.oup.com/nar/article-pdf/49/W1/W293/38842284/gkab301.pdf},
}

@misc{Jolly_2017, title={Chess game dataset (lichess)}, url={https://www.kaggle.com/datasets/datasnaek/chess?resource=download}, journal={Kaggle}, author={Jolly, Mitchell}, year={2017}, month={Sep}}

@techreport{navigating_numbers,
title = {Navigating the Numbers: Greenhouse Gas Data and International Climate Policy},
author = {Kevin A. Baumert and Timothy Herzog and Jonathan Pershing},
institution = {World Resources Institute (WRI)},
year = {2005},
isbn = {1-56973-599-9},
url = {https://files.wri.org/d8/s3fs-public/pdf/navigating_numbers.pdf},
}

@misc{Kleinberg_2002,
 title={The Structure of Information Networks },
 url={https://www.cs.cornell.edu/courses/cs685/2002fa/},
 author={Kleinberg, Jon},
 year={2002}}

@inproceedings{Klimt2004IntroducingTE,
title={Introducing the Enron Corpus},
author={Bryan Klimt and Yiming Yang},
booktitle={International Conference on Email and Anti-Spam},
year={2004}
}

@article{davis2011,
author = {Davis, Timothy A. and Hu, Yifan},
title = {The University of Florida Sparse Matrix Collection},
year = {2011},
issue_date = {November 2011},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
volume = {38},
number = {1},
issn = {0098-3500},
url = {10.1145/2049662.2049663},
doi = {10.1145/2049662.2049663},
abstract = {We describe the University of Florida Sparse Matrix Collection, a large and actively growing set of sparse matrices that arise in real applications. The Collection is widely used by the numerical linear algebra community for the development and performance evaluation of sparse matrix algorithms. It allows for robust and repeatable experiments: robust because performance results with artificially generated matrices can be misleading, and repeatable because matrices are curated and made publicly available in many formats. Its matrices cover a wide spectrum of domains, include those arising from problems with underlying 2D or 3D geometry (as structural engineering, computational fluid dynamics, model reduction, electromagnetics, semiconductor devices, thermodynamics, materials, acoustics, computer graphics/vision, robotics/kinematics, and other discretizations) and those that typically do not have such geometry (optimization, circuit simulation, economic and financial modeling, theoretical and quantum chemistry, chemical process simulation, mathematics and statistics, power networks, and other networks and graphs). We provide software for accessing and managing the Collection, from MATLAB™, Mathematica™, Fortran, and C, as well as an online search capability. Graph visualization of the matrices is provided, and a new multilevel coarsening scheme is proposed to facilitate this task.},
journal = {ACM Trans. Math. Softw.},
month = {dec},
articleno = {1},
numpages = {25},
keywords = {Graph drawing, sparse matrices, performance evaluation, multilevel algorithms}
}

@InProceedings{gray2023,
author="Gray, Kathryn
and Li, Mingwei
and Ahmed, Reyan
and Kobourov, Stephen",
editor="Angelini, Patrizio
and von Hanxleden, Reinhard",
title="Visualizing Evolving Trees",
booktitle="Graph Drawing and Network Visualization",
year="2023",
doi={10.1007/978-3-031-22203-0_23},
publisher="Springer International Publishing",
address="Cham",
pages="319--335",
isbn="978-3-031-22203-0"
}

@article{ADAI2004179,
title = {LGL: Creating a Map of Protein Function with an Algorithm for Visualizing Very Large Biological Networks},
journal = {Journal of Molecular Biology},
volume = {340},
number = {1},
pages = {179-190},
year = {2004},
issn = {0022-2836},
doi = {10.1016/j.jmb.2004.04.047},
url = {https://www.sciencedirect.com/science/article/pii/S0022283604004851},
author = {Alex T. Adai and Shailesh V. Date and Shannon Wieland and Edward M. Marcotte},
keywords = {network, visualization, protein function, protein map, bioinformatics},
abstract = {Networks are proving to be central to the study of gene function, protein–protein interaction, and biochemical pathway data. Visualization of networks is important for their study, but visualization tools are often inadequate for working with very large biological networks. Here, we present an algorithm, called large graph layout (LGL), which can be used to dynamically visualize large networks on the order of hundreds of thousands of vertices and millions of edges. LGL applies a force-directed iterative layout guided by a minimal spanning tree of the network in order to generate coordinates for the vertices in two or three dimensions, which are subsequently visualized and interactively navigated with companion programs. We demonstrate the use of LGL in visualizing an extensive protein map summarizing the results of ∼21 billion sequence comparisons between 145,579 proteins from 50 genomes. Proteins are positioned in the map according to sequence homology and gene fusions, with the map ultimately serving as a theoretical framework that integrates inferences about gene function derived from sequence homology, remote homology, gene fusions, and higher-order fusions. We confirm that protein neighbors in the resulting map are functionally related, and that distinct map regions correspond to distinct cellular systems, enabling a computational strategy for discovering proteins' functions on the basis of the proteins' map positions. Using the map produced by LGL, we infer general functions for 23 uncharacterized protein families. LGL is freely available (at http://bioinformatics.icmb.utexas.edu/lgl).}
}

@article{Sugiyama1981,
doi = {10.1109/tsmc.1981.4308636},
url = {10.1109/tsmc.1981.4308636},
year = {1981},
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
volume = {11},
number = {2},
pages = {109--125},
author = {Kozo Sugiyama and Shojiro Tagawa and Mitsuhiko Toda},
title = {Methods for Visual Understanding of Hierarchical System Structures},
journal = {{IEEE} Transactions on Systems, Man, and Cybernetics}
}

@ARTICLE{malone1975,
  author={Malone, D.W.},
  journal={Proceedings of the IEEE}, 
  title={An introduction to the application of interpretive structural modeling}, 
  year={1975},
  volume={63},
  number={3},
  pages={397-404},
  doi={10.1109/PROC.1975.9765}}

@article{SUBRAMANIAN2007151,
title = {The WTO promotes trade, strongly but unevenly},
journal = {Journal of International Economics},
volume = {72},
number = {1},
pages = {151-175},
year = {2007},
issn = {0022-1996},
doi = {10.1016/j.jinteco.2006.07.007},
url = {https://www.sciencedirect.com/science/article/pii/S0022199606001140},
author = {Arvind Subramanian and Shang-Jin Wei},
keywords = {GATT, WTO, Gravity model},
}

@book{Knuth_2009, title={The Stanford graphbase: A platform for combinatorial computing}, publisher={Addison-Wesley}, author={Knuth, Donald Ervin}, year={2009}}

@inproceedings{nr, title = {The Network Data Repository with Interactive Graph Analytics and Visualization}, author={Ryan A. Rossi and Nesreen K. Ahmed},  booktitle = {AAAI},  url={http://networkrepository.com},  year={2015} }

@inproceedings{pajek,
title = {Pajek datasets},
author = {Vladimir Batagelj and Andrej Mrvar},
year = {2006},
url = {http://vlado.fmf.uni-lj.si/pub/networks/data/},
}

@misc{snapnets,
author = {Jure Leskovec and Andrej Krevl},
title = {{SNAP Datasets}: {Stanford} Large Network Dataset Collection},
howpublished = {\url{http://snap.stanford.edu/data}},
month = jun,
year = 2014
}

@ARTICLE{zhao2021,
author={Zhao, Ying and Jiang, Haojin and Chen, Qi'an and Qin, Yaqi and Xie, Huixuan and Wu, Yitao and Liu, Shixia and Zhou, Zhiguang and Xia, Jiazhi and Zhou, Fangfang},
journal={IEEE Transactions on Visualization and Computer Graphics},
title={Preserving Minority Structures in Graph Sampling},
year={2021},
volume={27},
number={2},
pages={1698-1708},
doi={10.1109/TVCG.2020.3030428}}

@article{Isenberg:2017:VMC,
  author      = {Petra Isenberg and Florian Heimerl and Steffen Koch and Tobias Isenberg and Panpan Xu and Chad Stolper and Michael Sedlmair and Jian Chen and Torsten M{\"o}ller and John Stasko},
  title       = {vispubdata.org: A Metadata Collection about {IEEE} Visualization ({VIS}) Publications},
  journal     = {IEEE Transactions on Visualization and Computer Graphics},
  year        = {2017},
  volume      = {23},
  number      = {9},
  month       = sep,
  pages       = {2199--2206},
  doi         = {10.1109/TVCG.2016.2615308},
  doi_url     = {10.1109/TVCG.2016.2615308},
  url         = {https://tobias.isenberg.cc/VideosAndDemos/Isenberg2017VMC},
  url2        = {http://www.vispubdata.org/site/vispubdata/},
  pdf         = {https://petra.isenberg.cc/publications/papers/Isenberg_2017_VMC.pdf},
}

@article{heymanncpan2009,
  title={CPAN-explorer, an interactive exploration of the Perl Ecosystem},
  author={Heymann, S},
  journal={Gephi Blog},
  year={2009}, 
  url = {https://gephi.wordpress.com/2009/06/25/cpan-explorer-an-interactive-exploration-of-the-perl-ecosystem/}
}

@inproceedings{leskovec2005,
author = {Leskovec, Jure and Kleinberg, Jon and Faloutsos, Christos},
title = {Graphs over Time: Densification Laws, Shrinking Diameters and Possible Explanations},
year = {2005},
isbn = {159593135X},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
url = {10.1145/1081870.1081893},
doi = {10.1145/1081870.1081893},
abstract = {How do real graphs evolve over time? What are "normal" growth patterns in social, technological, and information networks? Many studies have discovered patterns in static graphs, identifying properties in a single snapshot of a large network, or in a very small number of snapshots; these include heavy tails for in- and out-degree distributions, communities, small-world phenomena, and others. However, given the lack of information about network evolution over long periods, it has been hard to convert these findings into statements about trends over time.Here we study a wide range of real graphs, and we observe some surprising phenomena. First, most of these graphs densify over time, with the number of edges growing super-linearly in the number of nodes. Second, the average distance between nodes often shrinks over time, in contrast to the conventional wisdom that such distance parameters should increase slowly as a function of the number of nodes (like O(log n) or O(log(log n)).Existing graph generation models do not exhibit these types of behavior, even at a qualitative level. We provide a new graph generator, based on a "forest fire" spreading process, that has a simple, intuitive justification, requires very few parameters (like the "flammability" of nodes), and produces graphs exhibiting the full range of properties observed both in prior work and in the present study.},
booktitle = {Proceedings of the Eleventh ACM SIGKDD International Conference on Knowledge Discovery in Data Mining},
pages = {177–187},
numpages = {11},
keywords = {graph mining, densification power laws, heavy-tailed distributions, graph generators, small-world phenomena},
location = {Chicago, Illinois, USA},
series = {KDD '05}
}

@article{leskovec2007,
author = {Leskovec, Jure and Adamic, Lada A. and Huberman, Bernardo A.},
title = {The Dynamics of Viral Marketing},
year = {2007},
issue_date = {May 2007},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
volume = {1},
number = {1},
issn = {1559-1131},
url = {10.1145/1232722.1232727},
doi = {10.1145/1232722.1232727},
abstract = {We present an analysis of a person-to-person recommendation network, consisting of 4 million people who made 16 million recommendations on half a million products. We observe the propagation of recommendations and the cascade sizes, which we explain by a simple stochastic model. We analyze how user behavior varies within user communities defined by a recommendation network. Product purchases follow a ‘long tail’ where a significant share of purchases belongs to rarely sold items. We establish how the recommendation network grows over time and how effective it is from the viewpoint of the sender and receiver of the recommendations. While on average recommendations are not very effective at inducing purchases and do not spread very far, we present a model that successfully identifies communities, product, and pricing categories for which viral marketing seems to be very effective.},
journal = {ACM Trans. Web},
month = {may},
pages = {5–es},
numpages = {39},
keywords = {recommender systems, word-of-mouth, e-commerce, Viral marketing, long tail, network analysis}
}

@Inbook{Boisvert1997,
author="Boisvert, Ronald F.
and Pozo, Roldan
and Remington, Karin
and Barrett, Richard F.
and Dongarra, Jack J.",
editor="Boisvert, Ronald F.",
title="Matrix Market: a web resource for test matrix collections",
bookTitle="Quality of Numerical Software: Assessment and enhancement",
year="1997",
publisher="Springer US",
address="Boston, MA",
pages="125--137",
abstract="We describe a repository of data for the testing of numerical algorithms and mathematical software for matrix computations. The repository is designed to accommodate both dense and sparse matrices, as well as software to generate matrices. It has been seeded with the well-known Harwell-Boeing sparse matrix collection. The raw data files have been augmented with an integrated World Wide Web interface which describes the matrices in the collection quantitatively and visually. For example, each matrix has a Web page which details its attributes, graphically depicts its sparsity pattern, and provides access to the matrix itself in several formats. In addition, a search mechanism is included which allows retrieval of matrices based on a variety of attributes, such as type and size, as well as through free-text search in abstracts. The URL is http://math.nist.gov/MatrizMarket/.",
isbn="978-1-5041-2940-4",
doi="10.1007/978-1-5041-2940-4_9",
url="10.1007/978-1-5041-2940-4_9"
}

@inproceedings{DiBattista1995,
author = {Di Battista, Giuseppe and Garg, Ashim and Liotta, Giuseppe},
title = {An experimental comparison of three graph drawing algorithms (extended abstract)},
year = {1995},
isbn = {0897917243},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
url = {10.1145/220279.220312},
doi = {10.1145/220279.220312},
booktitle = {Proceedings of the Eleventh Annual Symposium on Computational Geometry},
pages = {306–315},
numpages = {10},
location = {Vancouver, British Columbia, Canada},
series = {SCG '95}
}

@article{Clancy2019ASO,
  title={A survey of graphs with known or bounded crossing numbers},
  author={Kieran Clancy and Michael Haythorpe and Alex Newcombe},
  journal={Australas. J Comb.},
  year={2019},
  volume={78},
  pages={209-296},
  url={https://api.semanticscholar.org/CorpusID:119313173}
}

@incollection{Demel2018,
doi = {10.1007/978-3-030-04414-5_20},
year = {2018},
publisher = {Springer International Publishing},
pages = {286--299},
author = {Almut Demel and Dominik D\"{u}rrschnabel and Tamara Mchedlidze and Marcel Radermacher and Lasse Wulf},
title = {A Greedy Heuristic for Crossing-Angle Maximization},
booktitle = {Lecture Notes in Computer Science}
}



@article{KOREN20051867,
title = {Drawing graphs by eigenvectors: theory and practice},
journal = {Computers \& Mathematics with Applications},
volume = {49},
number = {11},
pages = {1867-1888},
year = {2005},
issn = {0898-1221},
doi = {10.1016/j.camwa.2004.08.015},
author = {Y. Koren},
keywords = {Graph drawing, Laplacian, Eigenvectors, Fiedler vector, Force-directed layout, Spectral graph theory},
abstract = {The spectral approach for graph visualization computes the layout of a graph using certain eigenvectors of related matrices. Two important advantages of this approach are an ability to compute optimal layouts (according to specific requirements) and a very rapid computation time. In this paper, we explore spectral visualization techniques and study their properties from different points of view. We also suggest a novel algorithm for calculating spectral layouts resulting in an extremely fast computation by optimizing the layout within a small vector space.}
}

@ARTICLE{frishman2007, author={Frishman, Yaniv and Tal, Ayellet}, journal={IEEE Transactions on Visualization and Computer Graphics}, title={Multi-Level Graph Layout on the GPU}, year={2007}, volume={13}, number={6}, pages={1310-1319}, doi={10.1109/TVCG.2007.70580}}

@InProceedings{chimani2016b,
author =	{Markus Chimani and Tılo Wiedera},
title =	{An {ILP}-based Proof System for the Crossing Number Problem},
booktitle =	{24th Annual European Symposium on Algorithms (ESA 2016)},
pages =	{29:1--29:13},
series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN =	{978-3-95977-015-6},
ISSN =	{1868-8969},
year =	{2016},
volume =	{57},
editor =	{Piotr Sankowski and Christos Zaroliagis},
publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
address =	{Dagstuhl, Germany},
URN =	{urn:nbn:de:0030-drops-63803},
doi =	{10.4230/LIPIcs.ESA.2016.29},
annote =	{Keywords: automatic formal proof, crossing number, integer linear programming}
}

@ARTICLE{dunne2015,  author={Dunne, C. and Ross, S. I. and Shneiderman, B. and Martino, M.},  journal={IBM Journal of Research and Development},   title={Readability metric feedback for aiding node-link visualization designers},   year={2015},  volume={59},  number={2/3},  pages={14:1-14:16},  doi={10.1147/JRD.2015.2411412}}

@article{Buchheim2008,
doi = {10.1016/j.disopt.2007.05.006},
year = {2008},
month = may,
publisher = {Elsevier {BV}},
volume = {5},
number = {2},
pages = {373--388},
author = {Christoph Buchheim and Markus Chimani and Dietmar Ebner and Carsten Gutwenger and Michael J\"{u}nger and Gunnar W. Klau and Petra Mutzel and Ren{\'{e}} Weiskircher},
title = {A branch-and-cut approach to the crossing number problem},
journal = {Discrete Optimization}
}

@InProceedings{Purchase1997WhichAestheticHas,
author="Purchase, Helen",
title="Which aesthetic has the greatest effect on human understanding?",
booktitle="Graph Drawing",
year="1997",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="248--261",
doi={10.1007/3-540-63938-1_67},
abstract="In the creation of graph drawing algorithms and systems, designers claim that by producing layouts that optimise certain aesthetic qualities, the graphs are easier to understand. Such aesthetics include maximise symmetry, minimise edge crosses and minimise bends.",
isbn="978-3-540-69674-2"
}




@article{PURCHASE2002501,
title = {Metrics for Graph Drawing Aesthetics},
journal = {Journal of Visual Languages \& Computing},
volume = {13},
number = {5},
pages = {501-516},
year = {2002},
issn = {1045-926X},
doi = {10.1006/jvlc.2002.0232},
author = {HELEN C. Purchase},
keywords = {Graph drawing, Aesthetics, Metrics},
abstract = {Graph layout algorithms typically conform to one or more aesthetic criteria (e.g. minimizing the number of bends, maximizing orthogonality). Determining the extent to which a graph drawing conforms to an aesthetic criterion tends to be done informally, and varies between different algorithms. This paper presents formal metrics for measuring the aesthetic presence in a graph drawing for seven common aesthetic criteria, applicable to any graph drawing of any size. The metrics are useful for determining the aesthetic quality of a given graph drawing, or for defining a cost function for genetic algorithms or simulated annealing programs. The metrics are continuous, so that aesthetic quality is not stated as a binary conformance decision (i.e. the drawing either conforms to the aesthetic or not), but can be stated as the extent of aesthetic conformance using a number between 0 and 1. The paper presents the seven metric formulae. The application of these metrics is demonstrated through the aesthetic analysis of example graph drawings produced by common layout algorithms.}
}

@inproceedings{di2022six,
  title={Six methods for transforming layered hypergraphs to apply layered graph layout algorithms},
  author={Di~Bartolomeo, Sara and Pister, Alexis and Buono, Paolo and Plaisant, Catherine and Dunne, Cody and Fekete, Jean-Daniel},
  booktitle={Computer Graphics Forum},
  volume={41},
  pages={259--270},
  year={2022},
  organization={Wiley Online Library}
}

@book{tamassia2013handbook,
  title={Handbook of graph drawing and visualization},
  author={Tamassia, Roberto},
  year={2013},
  publisher={CRC press}
}

@Article{Pandey2020CerebrovisDesigningAbstract,
  author   = {Pandey, Aditeya and Shukla, Harsh and Young, Geoffrey S. and Qin, Lei and Zamani, Amir A. and Hsu, Liangge and Huang, Raymond and Dunne, Cody and Borkin, Michelle A.},
  journal  = {IEEE Transactions on Visualization and Computer Graphics},
  title    = {{CerebroVis}: designing an abstract yet spatially contextualized cerebral arteries network visualization},
  year     = {2020},
  note     = {VIS '19. Preprint \& supplemental material: https://osf.io/63y5c},
  pages    = {1-1},
  abstract = {Blood circulation in the human brain is supplied through a network of cerebral arteries. If a clinician suspects a patient has a stroke or other cerebrovascular condition, they order imaging tests. Neuroradiologists visually search the resulting scans for abnormalities. Their visual search tasks correspond to the abstract network analysis tasks of browsing and path following. To assist neuroradiologists in identifying cerebral artery abnormalities, we designed CerebroVis, a novel abstract-yet spatially contextualized-cerebral artery network visualization. In this design study, we contribute a novel framing and definition of the cerebral artery system in terms of network theory and characterize neuroradiologist domain goals as abstract visualization and network analysis tasks. Through an iterative, user-centered design process we developed an abstract network layout technique which incorporates cerebral artery spatial context. The abstract visualization enables increased domain task performance over 3D geometry representations, while including spatial context helps preserve the user's mental map of the underlying geometry. We provide open source implementations of our network layout technique and prototype cerebral artery visualization tool. We demonstrate the robustness of our technique by successfully laying out 61 open source brain scans. We evaluate the effectiveness of our layout through a mixed methods study with three neuroradiologists. In a formative controlled experiment our study participants used CerebroVis and a conventional 3D visualization to examine real cerebral artery imaging data to identify a simulated intracranial artery stenosis. Participants were more accurate at identifying stenoses using CerebroVis (absolute risk difference 13\%). A free copy of this paper, the evaluation stimuli and data, and source code are available at https://osf.io/e5sxt.},
  doi      = {10.1109/TVCG.2019.2934402},
  series   = {VIS/TVCG},
}


@InProceedings{Dunne15VoroGraphVisualizationTools,
  author    = {Dunne, Cody and Muller, Michael and Perra, Nicola and Martino, Mauro},
  title     = {{V}oro{G}raph: visualization tools for epidemic analysis},
  booktitle = {{P}roc. {SIGCHI} {C}onference on {H}uman {F}actors in {C}omputing {S}ystems {E}xtended {A}bstracts},
  year      = {2015},
  series    = {{CHI} {EA}},
  isbn      = {978-1-4503-3146-3},
  pages     = {255--258},
  doi       = {10.1145/2702613.2725459},
  abstract  = {Epidemiologists struggle to integrate complex information about the incidence and spread of disease, in relation to population density and other demographic conditions, at geographical scales ranging from global air travel down to local commuting. A partial solution overlays air travel as arcs above color-coded maps. However, commuting is not shown and it is often challenging to understand changing relationships due to the visual complexity arcs introduce. Moreover, when region sizes and shapes vary their color-codings become difficult to perceive. We introduce three visualizations which combine representations of population, movement, and disease spread at a local scale that is consistent with a zoomable global scale: (1) a map with commuting border encodings, (2) a centroidal Voronoi tessellation morphing technique, and (3) a meta-layout showing commuting alongside air travel. Our work provides mid-level abstractions that expert epidemiologists can use for insights into contagion.},
  file      = {Paper:Dunne15VoroGraphVisualizationTools.pdf:PDF;Demo:https\://www.youtube.com/watch?v=h2A329Yu5fc:URL},
  groups    = {1 PR Conferences, AVST},
  keywords  = {Epidemiology; Emergency Management; Visualization; Graph/Network Data; Geographic/Geospatial Data},
  numpages  = {4},
  owner     = {CGD},
  timestamp = {2015.01.22},
}

@Article{Chaturvedi14GroupinBox,
  author    = {Chaturvedi, Snigdha and Dunne, Cody and Ashktorab, Zahra and Zacharia, Rajan and Shneiderman, Ben},
  title     = {{G}roup-in-a-{B}ox meta-layouts for topological clusters and attribute-based groups: space efficient visualizations of network communities and their ties},
  journal   = {{C}omputer {G}raphics {F}orum},
  year      = {2014},
  series    = {CGF},
  volume    = {33},
  number    = {8},
  pages     = {52--68},
  issn      = {1467-8659},
  doi       = {10.1111/cgf.12400},
  abstract  = {An important part of network analysis is understanding community structures like topological clusters and attribute-based groups. Standard approaches for showing communities using color, shape, rectangular bounding boxes, convex hulls, or force-directed layout algorithms remain valuable, however our Group-in-a-Box meta-layouts add a fresh strategy for presenting community membership, internal structure, and {inter-cluster} relationships. This paper extends the basic Group-in-a-Box meta-layout, which uses a Treemap substrate of rectangular regions whose size is proportional to community size. When there are numerous inter-community relationships, the proposed extensions help users view them more clearly: (1) the Croissant-Donut meta-layout applies empirically determined rules for box arrangement to improve space utilization while still showing inter-community relationships, and (2) the Force-Directed layout arranges community boxes based on their aggregate ties at the cost of additional space. Our free and open source reference implementation in NodeXL includes heuristics to choose what we have found to be the preferable Group-in-a-Box meta-layout to show networks with varying numbers or sizes of communities. Case study examples, a pilot comparative user preference study (9 participants), and a readability measure-based evaluation of 309 Twitter networks demonstrate the utility of the proposed meta-layouts.},
  file      = {Paper:Chaturvedi14GroupinBox.pdf:PDF},
  groups    = {0 PR Journals, AVST, Used},
  keywords  = {information visualization, graphical user interfaces, community structures, group-in-a-box, networks, graph drawing, H.5.2 [Information Interfaces and Presentation (e.g. HCI)]: User Interfaces (D.2.2, H.1.2, I.3.6) Screen design},
  owner     = {CGD},
  timestamp = {2014.04.28},
}

@InProceedings{Blue08VisualizingReal-TimeNetwork,
  author     = {Blue, Ryan and Dunne, Cody and Fuchs, Adam and King, Kyle and Schulman, Aaron},
  title      = {{V}isualizing real-time network resource usage},
  booktitle  = {{P}roc. 5th international workshop on {V}isualization for {C}omputer {S}ecurity},
  year       = {2008},
  series     = {VizSec},
  publisher  = {Springer-Verlag},
  isbn       = {978-3-540-85931-4},
  pages      = {119--135},
  doi        = {10.1007/978-3-540-85933-8_12},
  abstract   = {We present NetGrok, a tool for visualizing computer network usage in real-time. NetGrok combines well-known information visualization techniques--overview, zoom \& filter, details on demand--with network graph and treemap visualizations. NetGrok integrates these tools with a shared data store that can read PCAP-formatted network traces, capture traces from a live interface, and filter the data set dynamically by bandwidth, number of connections, and time. We performed an expert user case study that demonstrates the benefits of applying these techniques to static and real-time streaming packet data. Our user study shows NetGrok serves as an ``excellent real-time diagnostic'', enabling fast understanding of network resource usage and rapid anomaly detection.},
  acceptrate = {66.7% (18/27)},
  address    = {Berlin, Heidelberg},
  file       = {Paper:Blue08VisualizingReal-TimeNetwork.pdf:PDF;Slides:Blue08VisualizingReal-TimeNetwork.ppt:PowerPoint;Homepage:http\://www.cs.umd.edu/projects/netgrok/:URL},
  groups     = {1 PR Conferences, Conference Talks (Dupe), AVST, NetGrok},
  keywords   = {Force-Directed, Network Administration, Real-Time, Treemap},
  numpages   = {17},
  owner      = {CGD},
  review     = {M:
Acceptance Rate: 66.7% (18/27)},
  timestamp  = {2008.06.15},
}


@InProceedings{Dunne13Motifsimplification_improving,
  author     = {Dunne, Cody and Shneiderman, Ben},
  title      = {{M}otif simplification: improving network visualization readability with fan, connector, and clique glyphs},
  booktitle  = {{P}roc. {SIGCHI} {C}onference on {H}uman {F}actors in {C}omputing {S}ystems},
  year       = {2013},
  series     = {CHI},
  isbn       = {978-1-4503-1899-0},
  pages      = {3247--3256},
  doi        = {10.1145/2470654.2466444},
  abstract   = {Analyzing networks involves understanding the complex relationships between entities, as well as any attributes they may have. The widely used node-link diagrams excel at this task, but many are difficult to extract meaning from because of the inherent complexity of the relationships and limited screen space. To help address this problem we introduce a technique called motif simplification, in which common patterns of nodes and links are replaced with compact and meaningful glyphs. Well-designed glyphs have several benefits: they (1) require less screen space and layout effort, (2) are easier to understand in the context of the network, (3) can reveal otherwise hidden relationships, and (4) preserve as much underlying information as possible. We tackle three frequently occurring and high-payoff motifs: fans of nodes with a single neighbor, connectors that link a set of anchor nodes, and cliques of completely connected nodes. We contribute design guidelines for motif glyphs; example glyphs for the fan, connector, and clique motifs; algorithms for detecting these motifs; a free and open source reference implementation; and results from a controlled study of 36 participants that demonstrates the effectiveness of motif simplification.},
  acceptrate = {20.0% (393/1963)},
  file       = {Paper:Dunne13Motifsimplification_improving.pdf:PDF;Demo:http\://youtu.be/mIxbWIHzhQg?hd=1:URL;Demo (MP4):Dunne13Motifsimplification_improving.mp4:MP4 Video},
  groups     = {1 PR Conferences, Conference Talks (Dupe), AVST, IBM JRD RM},
  keywords   = {graph drawing, motif simplification, network visualization, node-link diagram, visual analytics},
  numpages   = {10},
  owner      = {CGD},
  timestamp  = {2012.12.09},
}


@InProceedings{Shneiderman12Interactivenetworkexploration,
  author    = {Shneiderman, Ben and Dunne, Cody},
  title     = {{I}nteractive network exploration to derive insights: {F}iltering, clustering, grouping, and simplification},
  booktitle = {{P}roc. 20th {I}nternational {S}ymposium on {G}raph {D}rawing},
  year      = {2012},
  volume    = {7704},
  series    = {GD},
  note      = {Keynote},
  publisher = {Springer Berlin Heidelberg},
  isbn      = {978-3-642-36762-5},
  pages     = {2-18},
  doi       = {10.1007/978-3-642-36763-2_2},
  abstract  = {The growing importance of network analysis has increased attention on interactive exploration to derive insights and support personal, business, legal, scientific, or national security decisions. Since networks are often complex and cluttered, strategies for effective filtering, clustering, grouping, and simplification are helpful in finding key nodes and links, surprising clusters, important groups, or meaningful patterns. We describe readability metrics and strategies that have been implemented in NodeXL, our free and open source network analysis tool, and show examples from our research. While filtering, clustering, and grouping have been used in many tools, we present several advances on these techniques. We also discuss our recent work on motif simplification, in which common patterns are replaced with compact and meaningful glyphs, thereby improving readability.},
  file      = {Paper:Shneiderman12Interactivenetworkexploration.pdf:PDF;Talk Video:http\://research.microsoft.com/apps/video/default.aspx?id=173332:URL;Talk Video (MP4):Shneiderman12Interactivenetworkexploration.mp4:MP4 Video;Talk Transcript (PDF):Shneiderman12Interactivenetworkexplorationa.pdf:PDF;Talk Transcript (Word):Shneiderman12Interactivenetworkexploration.doc:Word},
  groups    = {1 PR Conferences, Conference Talks (Dupe), AVST, Used, IBM JRD RM},
  keywords  = {Network visualization; visual analytics; readability metrics; dynamic filters; link clustering; attribute grouping; motif simplification},
  owner     = {CGD},
  timestamp = {2012.08.24},
}


@InProceedings{Smith09Analyzingsocialmedia,
  author     = {Smith, Marc and Shneiderman, Ben and Milic-Frayling, Natasa and Rodrigues, Eduarda Mendes and Barash, Vladimir and Dunne, Cody and Capone, Tony and Perer, Adam and Gleave, Eric},
  title      = {{A}nalyzing (social media) networks with {NodeXL}},
  booktitle  = {{P}roc. 4th {I}nternational {C}onference on {C}ommunities and {T}echnologies},
  year       = {2009},
  series     = {C\&T},
  publisher  = {ACM},
  isbn       = {978-1-60558-713-4},
  pages      = {255--264},
  doi        = {10.1145/1556460.1556497},
  abstract   = {In this paper we present NodeXL, an extendible toolkit for network data analysis and visualization, implemented as an add-in to the Microsoft Excel 2007 spreadsheet software. We demonstrate NodeXL features through analysis of a data sample drawn from an enterprise intranet social network, discussion, and wiki. Through a sequence of steps we show how NodeXL leverages and extends the broadly used spreadsheet paradigm to support common operations in network analysis. This ranges from data import to computation of network statistics and refinement of network visualization through a selection of ready-to-use sorting, filtering, and clustering functions.},
  acceptrate = {37.5% (30/80)},
  address    = {New York, NY, USA},
  file       = {Paper:Smith09Analyzingsocialmedia.pdf:PDF;Homepage:http\://nodexl.codeplex.com/:URL;Demo 1:http\://youtu.be/0M3T65Iw3Ac?hd=1:URL;Demo 2:http\://youtu.be/xKhYGRpbwOc?hd=1:URL},
  groups     = {1 PR Conferences, AVST, CGF paper, IBM JRD RM},
  keywords   = {excel, network analysis, social media, social network, spreadsheet, visualization},
  owner      = {CGD},
  review     = {M:
Acceptance Rate: 37.5% (30/80)},
  timestamp  = {2009.03.16},
}

@ARTICLE{BGP,
  author={Raynor, Justin and Crnovrsanin, Tarik and Di~Bartolomeo, Sara and South, Laura and Saffo, David and Dunne, Cody},
  journal={IEEE Transactions on Visualization and Computer Graphics}, 
  title={The State of the Art in {BGP} Visualization Tools: A Mapping of Visualization Techniques to Cyberattack Types}, 
  year={2022},
  volume={},
  number={},
  pages={1-11},
  doi={10.1109/TVCG.2022.3209412}}
  
  @article{likert,
author = {South, Laura and Saffo, David and Vitek, Olga and Dunne, Cody and Borkin, Michelle A.},
title = {Effective Use of {Likert} Scales in Visualization Evaluations: A Systematic Review},
journal = {Computer Graphics Forum},
volume = {41},
number = {3},
pages = {43-55},
keywords = {CCS Concepts, • Human-centered computing → Visualization design and evaluation methods, Empirical studies in visualization},
doi = {10.1111/cgf.14521},
abstract = {Abstract Likert scales are often used in visualization evaluations to produce quantitative estimates of subjective attributes, such as ease of use or aesthetic appeal. However, the methods used to collect, analyze, and visualize data collected with Likert scales are inconsistent among evaluations in visualization papers. In this paper, we examine the use of Likert scales as a tool for measuring subjective response in a systematic review of 134 visualization evaluations published between 2009 and 2019. We find that papers with both objective and subjective measures do not hold the same reporting and analysis standards for both aspects of their evaluation, producing less rigorous work for the subjective qualities measured by Likert scales. Additionally, we demonstrate that many papers are inconsistent in their interpretations of Likert data as discrete or continuous and may even sacrifice statistical power by applying nonparametric tests unnecessarily. Finally, we identify instances where key details about Likert item construction with the potential to bias participant responses are omitted from evaluation methodology reporting, inhibiting the feasibility and reliability of future replication studies. We summarize recommendations from other fields for best practices with Likert data in visualization evaluations, based on the results of our survey. A full copy of this paper and all supplementary material are available at https://osf.io/exbz8/.},
year = {2022}
}

@article{Kucher,
author = {Kucher, Kostiantyn and Paradis, Carita and Kerren, Andreas},
title = {The State of the Art in Sentiment Visualization},
journal = {Computer Graphics Forum},
volume = {37},
number = {1},
pages = {71-96},
doi = {10.1111/cgf.13217},
year = {2018}
}


@article{McNabb2017,
author = {McNabb, Liam and Laramee, Robert S.},
title = {Survey of Surveys ({SoS}) - Mapping The Landscape of Survey Papers in Information Visualization},
journal = {Computer Graphics Forum},
volume = {36},
number = {3},
pages = {589-617},
keywords = {Categories and Subject Descriptors (according to ACM CCS), Human-centered computing: Visualization—Information visualization},
doi = {10.1111/cgf.13212},
abstract = {Abstract Information visualization as a field is growing rapidly in popularity since the first information visualization conference in 1995. However, as a consequence of its growth, it is increasingly difficult to follow the growing body of literature within the field. Survey papers and literature reviews are valuable tools for managing the great volume of previously published research papers, and the quantity of survey papers in visualization has reached a critical mass. To this end, this survey paper takes a quantum step forward by surveying and classifying literature survey papers in order to help researchers understand the current landscape of Information Visualization. It is, to our knowledge, the first survey of survey papers (SoS) in Information Visualization. This paper classifies survey papers into natural topic clusters which enables readers to find relevant literature and develops the first classification of classifications. The paper also enables researchers to identify both mature and less developed research directions as well as identify future directions. It is a valuable resource for both newcomers and experienced researchers in and outside the field of Information Visualization and Visual Analytics.},
year = {2017}
}


@article{Landesberger2011,
author = {von~Landesberger, T. and Kuijper, A. and Schreck, T. and Kohlhammer, J. and van~Wikj, J.J. and Fekete, J.-D. and Fellner, D.W.},
title = {Visual Analysis of Large Graphs: State-of-the-Art and Future Research Challenges},
journal = {Computer Graphics Forum},
volume = {30},
number = {6},
pages = {1719-1749},
keywords = {visual graph analysis, graph visualization, graph interaction, visual analytics, Data Structures E.1: Graphs and Networks, Trees, Mathematics of Computing G.2.2: Discrete Mathematics, Graph Theory H.4: Information Systems: Applications, Information Systems H.5.2: Interfaces and Presentation, User Interfaces},
doi = {10.1111/j.1467-8659.2011.01898.x},
abstract = {Abstract The analysis of large graphs plays a prominent role in various fields of research and is relevant in many important application areas. Effective visual analysis of graphs requires appropriate visual presentations in combination with respective user interaction facilities and algorithmic graph analysis methods. How to design appropriate graph analysis systems depends on many factors, including the type of graph describing the data, the analytical task at hand and the applicability of graph analysis methods. The most recent surveys of graph visualization and navigation techniques cover techniques that had been introduced until 2000 or concentrate only on graph layouts published until 2002. Recently, new techniques have been developed covering a broader range of graph types, such as time-varying graphs. Also, in accordance with ever growing amounts of graph-structured data becoming available, the inclusion of algorithmic graph analysis and interaction techniques becomes increasingly important. In this State-of-the-Art Report, we survey available techniques for the visual analysis of large graphs. Our review first considers graph visualization techniques according to the type of graphs supported. The visualization techniques form the basis for the presentation of interaction approaches suitable for visual graph exploration. As an important component of visual graph analysis, we discuss various graph algorithmic aspects useful for the different stages of the visual graph analysis process. We also present main open research challenges in this field.},
year = {2011}
}

@misc{CGF,
title = {Computer Graphics Forum: All STARs, Surveys, and Reviews},
author = {Computer Graphics Forum},
URL = {https://sites.google.com/site/drminchen/cgf-info/cgf-stars},
howpublished = {Accessed 2023.1},
year = 2023
}

@inproceedings {Beck2014,
booktitle = {EuroVis - STARs},
editor = {R. Borgo and R. Maciejewski and I. Viola},
title = {{The State of the Art in Visualizing Dynamic Graphs}},
author = {Beck, Fabian and Burch, Michael and Diehl, Stephan and Weiskopf, Daniel},
year = {2014},
publisher = {The Eurographics Association},
ISBN = {978-3-03868-028-4},
DOI = {10.2312/eurovisstar.20141174}
}

@ARTICLE{Kerracher2015,
  author={Kerracher, Natalie and Kennedy, Jessie and Chalmers, Kevin},
  journal={IEEE Transactions on Visualization and Computer Graphics}, 
  title={A Task Taxonomy for Temporal Graph Visualisation}, 
  year={2015},
  volume={21},
  number={10},
  pages={1160-1172},
  doi={10.1109/TVCG.2015.2424889}}

@article{Vehlow2017,
author = {Vehlow, Corinna and Beck, Fabian and Weiskopf, Daniel},
title = {Visualizing Group Structures in Graphs: A Survey},
journal = {Computer Graphics Forum},
volume = {36},
number = {6},
pages = {201-225},
keywords = {graph visualization, group visualization, literature survey, Categories and Subject Descriptors (according to ACM CCS): H.5.2 Information Interfaces and Presentation: User Interfaces—Graphical user interfaces (GUI)},
doi = {10.1111/cgf.12872},
abstract = {Abstract Graph visualizations encode relationships between objects. Abstracting the objects into group structures provides an overview of the data. Groups can be disjoint or overlapping, and might be organized hierarchically. However, the underlying graph still needs to be represented for analyzing the data in more depth. This work surveys research in visualizing group structures as part of graph diagrams. A particular focus is the explicit visual encoding of groups, rather than only using graph layout to indicate groups implicitly. We introduce a taxonomy of visualization techniques structuring the field into four main categories: visual node attributes vary properties of the node representation to encode the grouping, juxtaposed approaches use two separate visualizations, superimposed techniques work with two aligned visual layers, and embedded visualizations tightly integrate group and graph representation. The derived taxonomies for group structure and visualization types are also applied to group visualizations of edges. We survey group-only, group–node, group–edge and group–network tasks that are described in the literature as use cases of group visualizations. We discuss results from evaluations of existing visualization techniques as well as main areas of application. Finally, we report future challenges based on interviews we conducted with leading researchers of the field.},
year = {2017}
}

@ARTICLE{Burch2021,
  author={Burch, Michael and Huang, Weidong and Wakefield, Mathew and Purchase, Helen C. and Weiskopf, Daniel and Hua, Jie},
  journal={IEEE Access}, 
  title={The State of the Art in Empirical User Evaluation of Graph Visualizations}, 
  year={2021},
  volume={9},
  number={},
  pages={4173-4198},
  doi={10.1109/ACCESS.2020.3047616}}

  @article{Yoghourdjian2018,
title = {Exploring the limits of complexity: A survey of empirical studies on graph visualisation},
journal = {Visual Informatics},
volume = {2},
number = {4},
pages = {264-282},
year = {2018},
issn = {2468-502X},
doi = {10.1016/j.visinf.2018.12.006},
author = {Vahan Yoghourdjian and Daniel Archambault and Stephan Diehl and Tim Dwyer and Karsten Klein and Helen C. Purchase and Hsiang-Yun Wu},
keywords = {Graph visualisation, Network visualisation, node–link diagrams, Cognitive scalability, Evaluations, Empirical studies}
}