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New automatic sketching method for planetary gear train

PROCEEDINGS OF THE INSTITUTION OF MECHANICAL ENGINEERS PART C-JOURNAL OF MECHANICAL ENGINEERING SCIENCE 2025年第1期239卷 38-54页

作者： Huang, Xuewen Ye, Zhizheng Xu, Haocong Ye, Bingliang Cui, Rongjiang Sun, Liang Zhejiang Sci Tech Univ Sch Mech Engn 928 Second Ave Hangzhou 310018 Peoples R China Hangzhou Vocat & Tech Coll Special Equipment Inst Hangzhou Peoples R China

At present, the synthesis results of planetary gear train are saved in the form of adjacency matrices. Research on the sketching method of gear train mechanism is lacking. Adjacency matrices are not conducive to the kinematic analysis and evaluation of gear train mechanism. This study presents a new method for automatic sketching of planetary gear trains by generating a gear distribution matrix. The sketching rules of gears and planet carriers are established based on the structure characteristics. The gear is reasonably distributed by analyzing the gear meshing path and gear level. Thereafter, an algorithm of sketching for the planet carrier is proposed to avoid the line crossing between the planet carrier and gears. This study is beneficial in improving the design efficiency of planetary gear trains.

关键词： Automatic sketching planetary gear train gear distribution matrix kinematic sketch of mechanism layout algorithm

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SFFSlib: A Python library for optimizing attribute layouts from micro to macro scales in network visualization

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CHINESE PHYSICS B 2025年第5期34卷

作者： Zhang, Ke-Chao Jiang, Sheng-Yue Xiao, Jing Shenzhen Technol Univ Coll Big Data & Internet Shenzhen 518118 Peoples R China Univ Sci & Technol China Sch Cyber Sci & Technol Hefei 230026 Peoples R China Dalian Minzu Univ Coll Informat & Commun Engn Dalian 116600 Peoples R China

Complex network modeling characterizes system relationships and structures, while network visualization enables intuitive analysis and interpretation of these patterns. However, existing network visualization tools exhibit significant limitations in representing attributes of complex networks at various scales, particularly failing to provide advanced visual representations of specific nodes and edges, community affiliation attribution, and global scalability. These limitations substantially impede the intuitive analysis and interpretation of complex network patterns through visual representation. To address these limitations, we propose SFFSlib, a multi-scale network visualization framework incorporating novel methods to highlight attribute representation in diverse network scenarios and optimize structural feature visualization. Notably, we have enhanced the visualization of pivotal details at different scales across diverse network scenarios. The visualization algorithms proposed within SFFSlib were applied to real-world datasets and benchmarked against conventional layout algorithms. The experimental results reveal that SFFSlib significantly enhances the clarity of visualizations across different scales, offering a practical solution for the advancement of network attribute representation and the overall enhancement of visualization quality.

关键词： complex network visualization layout algorithm signed network fuzzy community structure social bot network

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Visualizing the Uncertainty Induced by Graph layout algorithms 10

Visualizing the Uncertainty Induced by Graph Layout Algorith...

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IEEE Pacific Visualization Symposium (IEEE PacificVis)

作者： Yan, Kai Cui, Weiwei Harbin Inst Technol Harbin Heilongjiang Peoples R China Microsoft Res Asia Beijing Peoples R China

ISBN: (纸本)9781509057382

Given a graph structure, different layout algorithms (even different settings of the same algorithm) usually result in different arrangements of vertices, and each layout may reflect certain aspects/parts of the graph more accurately than others. Thus, for high-level graph analysis tasks that rely on the overall arrangement of vertices, drawing conclusions only from one layout is risky. To alleviate the risk, we propose an ensemble framework to capture the commonalities and differences among possible layouts, and help users obtain a comprehensive view of the structure patterns. We leverage a set of layouts that represents the distribution of algorithm outputs. Then, visual features are extracted and analyzed based on various measures of visual similarity. Our framework supports users to analyze individual layouts in the context of the distribution, so that users can quickly identify structures of interest and discover patterns more accurately and comprehensively. We demonstrate the effectiveness of our framework by applying it to three datasets.

关键词： Graph visualization layout uncertainty layout algorithm visual feature graph layout uncertainty visualization

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A generic algorithm for layout of biological networks

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BMC BIOINFORMATICS 2009年第1期10卷 1-12页

作者： Schreiber, Falk Dwyer, Tim Marriott, Kim Wybrow, Michael Leibniz Inst Plant Genet & Crop Plant Res IPK D-06466 Gatersleben Germany Univ Halle Wittenberg Inst Comp Sci D-06120 Halle Germany Microsoft Res Seattle WA USA Monash Univ Clayton Sch Informat Technol Clayton Vic 3800 Australia

Background: Biological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due to the ongoing growth of knowledge in the life sciences. To aid understanding of biological networks several algorithms for laying out and graphically representing networks and network analysis results have been developed. However, current algorithms are specialized to particular layout styles and therefore different algorithms are required for each kind of network and/or style of layout. This increases implementation effort and means that new algorithms must be developed for new layout styles. Furthermore, additional effort is necessary to compose different layout conventions in the same diagram. Also the user cannot usually customize the placement of nodes to tailor the layout to their particular need or task and there is little support for interactive network exploration. Results: We present a novel algorithm to visualize different biological networks and network analysis results in meaningful ways depending on network types and analysis outcome. Our method is based on constrained graph layout and we demonstrate how it can handle the drawing conventions used in biological networks. Conclusion: The presented algorithm offers the ability to produce many of the fundamental popular drawing styles while allowing the exibility of constraints to further tailor these layouts.

关键词： Metabolic Network Biological Network Protein Interaction Network Network Motif layout algorithm

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Research on network topology generation algorithm based on node layout

Research on network topology generation algorithm based on n...

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2017 3rd Workshop on Advanced Research and Technology in Industry Applications(WARTIA 2017)

作者： LI Teng-fei LI Qiang YU Xiang WU Dai-yue Electronic Engineering Institute

Network topology layout is one of the key technologies in the research of network topology structure. How to make the node overlap less and distribute evenly in the layout is an important and key problem in the research of network topological structure. Establishment of network topology generation algorithm based on node layout, design the node layout model, through node location layout and node linkage adjustment to achieve uniform layout, construction network topology generation algorithm, to achieves the effect from the physical topological structure to the logical topology beautiful display. The experiment shows that the network topology generation algorithm based on node layout has lower node coincidence ratio, point-edge crossover rate and better evaluation index, and the layout effect is better than other algorithms.

关键词： Network Topology Node Location Node Contact layout algorithm

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Helium: visualization of large scale plant pedigrees

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BMC BIOINFORMATICS 2014年第1期15卷 1-15页

作者： Shaw, Paul D. Graham, Martin Kennedy, Jessie Milne, Iain Marshall, David F. James Hutton Inst Dundee DD2 5DA Scotland Edinburgh Napier Univ Sch Comp Edinburgh EH10 5DT Midlothian Scotland

Background: Plant breeders use an increasingly diverse range of data types to identify lines with desirable characteristics suitable to be taken forward in plant breeding programmes. There are a number of key morphological and physiological traits, such as disease resistance and yield that need to be maintained and improved upon if a commercial variety is to be successful. Computational tools that provide the ability to integrate and visualize this data with pedigree structure, will enable breeders to make better decisions on the lines that are used in crossings to meet both the demands for increased yield/production and adaptation to climate change. Results: We have used a large and unique set of experimental barley (H. vulgare) data to develop a prototype pedigree visualization system. We then used this prototype to perform a subjective user evaluation with domain experts to guide and direct the development of an interactive pedigree visualization tool called Helium. Conclusions: We show that Helium allows users to easily integrate a number of data types along with large plant pedigrees to offer an integrated environment in which they can explore pedigree data. We have also verified that users were happy with the abstract representation of pedigrees that we have used in our visualization tool.

关键词： Phenotypic Data Plant Line Pedigree Data Plant Breeding Programme layout algorithm

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Design Considerations for Optimizing Storyline Visualizations

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IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2012年第12期18卷 2679-2688页

作者： Tanahashi, Yuzuru Ma, Kwan-Liu Univ Calif Davis ViDi Res Grp Davis CA 95616 USA

Storyline visualization is a technique used to depict the temporal dynamics of social interactions. This visualization technique was first introduced as a hand-drawn illustration in XKCD's "Movie Narrative Charts" [21]. If properly constructed, the visualization can convey both global trends and local interactions in the data. However, previous methods for automating storyline visualizations are overly simple, failing to achieve some of the essential principles practiced by professional illustrators. This paper presents a set of design considerations for generating aesthetically pleasing and legible storyline visualizations. Our layout algorithm is based on evolutionary computation, allowing us to effectively incorporate multiple objective functions. We show that the resulting visualizations have significantly improved aesthetics and legibility compared to existing techniques.

关键词： layout algorithm timeline visualization storyline visualization design study

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CySBGN: A Cytoscape plug-in to integrate SBGN maps

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BMC BIOINFORMATICS 2013年第1期14卷 1-7页

作者： Goncalves, Emanuel van Iersel, Martijn Saez-Rodriguez, Julio EMBL European Bioinformat Inst Cambridge England

Background: A standard graphical notation is essential to facilitate exchange of network representations of biological processes. Towards this end, the Systems Biology Graphical Notation (SBGN) has been proposed, and it is already supported by a number of tools. However, support for SBGN in Cytoscape, one of the most widely used platforms in biology to visualise and analyse networks, is limited, and in particular it is not possible to import SBGN diagrams. Results: We have developed CySBGN, a Cytoscape plug-in that extends the use of Cytoscape visualisation and analysis features to SBGN maps. CySBGN adds support for Cytoscape users to visualize any of the three complementary SBGN languages: Process Description, Entity Relationship, and Activity Flow. The interoperability with other tools (CySBML plug-in and Systems Biology Format Converter) was also established allowing an automated generation of SBGN diagrams based on previously imported SBML models. The plug-in was tested using a suite of 53 different test cases that covers almost all possible entities, shapes, and connections. A rendering comparison with other tools that support SBGN was performed. To illustrate the interoperability with other Cytoscape functionalities, we present two analysis examples, shortest path calculation, and motif identification in a metabolic network. Conclusions: CySBGN imports, modifies and analyzes SBGN diagrams in Cytoscape, and thus allows the application of the large palette of tools and plug-ins in this platform to networks and pathways in SBGN format.

关键词： Process Description System Biology Markup Language layout algorithm Entity Relationship Node Shape

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SPEULER: Semantics-preserving Euler Diagrams

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IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2022年第1期28卷 433-442页

作者： Kehlbeck, Rebecca Goertler, Jochen Wang, Yunhai Deussen, Oliver Univ Konstanz Constance Germany Shandong Univ Jinan Peoples R China

Creating comprehensible visualizations of highly overlapping set-typed data is a challenging task due to its complexity. To facilitate insights into set connectivity and to leverage semantic relations between intersections, we propose a fast two-step layout technique for Euler diagrams that are both well-matched and well-formed. Our method conforms to established form guidelines for Euler diagrams regarding semantics, aesthetics, and readability. First, we establish an initial ordering of the data, which we then use to incrementally create a planar, connected, and monotone dual graph representation. In the next step, the graph is transformed into a circular layout that maintains the semantics and yields simple Euler diagrams with smooth curves. When the data cannot be represented by simple diagrams, our algorithm always falls back to a solution that is not well-formed but still well-matched, whereas previous methods often fail to produce expected results. We show the usefulness of our method for visualizing set-typed data using examples from text analysis and infographics. Furthermore, we discuss the characteristics of our approach and evaluate our method against state-of-the-art methods.

关键词： Data visualization Task analysis Faces Semantics layout Guidelines Visualization Euler diagrams Venn diagrams set visualization layout algorithm

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3DScapeCS: application of three dimensional, parallel, dynamic network visualization in Cytoscape

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BMC BIOINFORMATICS 2013年第1期14卷 1-8页

作者： Wang, Qi Tang, Biao Song, Lifu Ren, Biao Liang, Qun Xie, Feng Zhuo, Ying Liu, Xueting Zhang, Lixin Chinese Acad Sci Inst Microbiol Key Lab Pathogen Microbiol & Immunol Beijing 100190 Peoples R China Fudan Univ Sch Life Sci Dept Microbiol State Key Lab Genet Engn Shanghai 200433 Peoples R China Hamburg Univ Technol Inst Bioproc & Biosyst Engn Hamburg Germany Univ Chinese Acad Sci Beijing 100049 Peoples R China

Background: The exponential growth of gigantic biological data from various sources, such as protein-protein interaction (PPI), genome sequences scaffolding, Mass spectrometry (MS) molecular networking and metabolic flux, demands an efficient way for better visualization and interpretation beyond the conventional, two-dimensional visualization tools. Results: We developed a 3D Cytoscape Client/Server (3DScapeCS) plugin, which adopted Cytoscape in interpreting different types of data, and UbiGraph for three-dimensional visualization. The extra dimension is useful in accommodating, visualizing, and distinguishing large-scale networks with multiple crossed connections in five case studies. Conclusions: Evaluation on several experimental data using 3DScapeCS and its special features, including multilevel graph layout, time-course data animation, and parallel visualization has proven its usefulness in visualizing complex data and help to make insightful conclusions.

关键词： Flux Balance Analysis Network Visualization layout algorithm Graph layout Motion Graph

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