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WSim4ABM: Agent-based Modelling simulation web service with Message-broker middleware and Annotation processing library

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SOFTWAREX 2025年 30卷

作者： Habtemariam, Duguma Yeshitla Kim, Youngjin Kim, Minsoo Lee, Jihwan Pukyong Natl Univ Dept Ind & Data Engn Major Ind Data Sci & Engn Busan 48513 South Korea

Agent-based modelling is a widely used paradigm for simulating Complex Systems representing real-world phenomena. High-Performance Computing (HPC) resources are essential to model such systems on a large scale. However, many existing Agent-based Modelling Simulation (ABMS) tools do not optimize simultaneous multi-user access to HPC resources because they are often built as monolithic software. An ABMS web service that is deployable on HPC resources is proposed to address this issue using MASON as its simulation core. The outcomes of this research include workflows that include Gradle and Annotation processing which assist the modelling experience of users, integration of message broker for scalability and robustness, and a web interface for managing user accounts, running simulations, and obtaining visualizations.

关键词： Agent-based modelling simulation web service Annotation processing Message broker middleware High-performance computing resource web-based visualization

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Residency Octree: A Hybrid Approach for Scalable web-based Multi-Volume Rendering

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IEEE TRANSACTIONS ON visualization AND COMPUTER GRAPHICS 2024年第1期30卷 1380-1390页

作者： Herzberger, Lukas Hadwiger, Markus Krueger, Robert Sorger, Peter Pfister, Hanspeter Groeller, Eduard Beyer, Johanna TU Wien Vienna Austria King Abdullah Univ Sci & Technol KAUST Thuwal Saudi Arabia Harvard Univ John A Paulson Sch Engn & Appl Sci Cambridge MA USA Harvard Med Sch Cambridge MA USA

We present a hybrid multi-volume rendering approach based on a novel Residency Octree that combines the advantages of out-of-core volume rendering using page tables with those of standard octrees. Octree approaches work by performing hierarchical tree traversal. However, in octree volume rendering, tree traversal and the selection of data resolution are intrinsically coupled. This makes fine-grained empty-space skipping costly. Page tables, on the other hand, allow access to any cached brick from any resolution. However, they do not offer a clear and efficient strategy for substituting missing high-resolution data with lower-resolution data. We enable flexible mixed-resolution out-of-core multi-volume rendering by decoupling the cache residency of multi-resolution data from a resolution-independent spatial subdivision determined by the tree. Instead of one-to-one node-to-brick correspondences, each residency octree node is mapped to a set of bricks from different resolution levels. This makes it possible to efficiently and adaptively choose and mix resolutions, adapt sampling rates, and compensate for cache misses. At the same time, residency octrees support fine-grained empty-space skipping, independent of the data subdivision used for caching. Finally, to facilitate collaboration and outreach, and to eliminate local data storage, our implementation is a web-based, pure client-side renderer using webGPU and webAssembly. Our method is faster than prior approaches and efficient for many data channels with a flexible and adaptive choice of data resolution.

关键词： Volume rendering ray-guided rendering large-scale data out-of-core rendering multi-resolution multi-channel web-based visualization

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The 15-Minute City of Mass Public Transportation in Yogyakarta: Case of Trans Jogja Bus 8

The 15-Minute City of Mass Public Transportation in Yogyakar...

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8th Geoinformation Science Symposium on Geoinformation Science for Sustainable Planet

作者： Susanta, Febrian Fitryanik Muryamto, Rochmad Laksono, Dany Puguh Univ Gadjah Mada Dept Geodet Engn Fac Engn Jl Grafika 2 Yogyakarta 55281 Indonesia

ISBN: (纸本)9781510672697;9781510672703

The Trans Jogja Bus system is an essential urban transportation service in Yogyakarta and its surrounding areas. With numerous bus stops strategically located throughout the Yogyakarta Urban Area, it aims to provide convenient boarding and disembarkation points for passengers. To improve the commuting experience for passengers, it is crucial to ensure that the Trans Jogja shelters are easily accessible and equipped with a comprehensive range of amenities, covering all regions within the urban area. To evaluate the service level of Trans Jogja Bus stops, the service area from each bus stop is modeled as an interactive isochronous service area map. These maps depict the coverage area of each bus stop based on network analysis, considering travel time to the road network. Each bus stop is a single node with four distinct travel time values: 3, 6, 9, 12, and 15 minutes. By employing this interactive modeling approach, the service areas of Trans Jogja bus stops can be presented, along with other variables representing the population in and around these bus stops. The resulting interactive visualization of these isochrone maps showcases the spatial distribution of the bus stop locations and their respective service areas at each travel time interval. This web-based visualization represents the coverage provided by the Trans Jogja bus system across the Yogyakarta urban area. The service area modeling using isochronous service area maps a comprehensive overview of the services offered by Trans Jogja bus stops in Yogyakarta, giving a clear depiction of the accessible amenities around each bus stops. It supports efforts to optimize service accessibility and quality, ensuring a seamless and efficient transportation experience for passengers.

关键词： Trans Jogja Bus Service Area Analysis Isochrone Map web-based visualization

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Topology-aware space distortion for structured visualization spaces

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INFORMATION visualization 2022年第2期21卷 166-181页

作者： Wang, Weihang Badam, Sriram Karthik Elmqvist, Niklas Univ Buffalo Buffalo NY USA Apple Inc Cupertino CA 95014 USA Univ Maryland College Pk MD 20742 USA

We propose topology-aware space distortion (TASD), a family of interactive layout techniques for non-linearly distorting geometric space based on user attention and on the structure of the visual representation. TASD seamlessly adapts the visual substrate of any visualization to give more screen real estate to important regions of the representation at the expense of less important regions. In this paper, we present a concrete TASD technique that we call ZoomHalo for interactively distorting a two-dimensional space based on a degree-of-interest (DOI) function defined for the space. Using this DOI function, ZoomHalo derives several areas of interest, computes the available space around each area in relation to other areas and the current viewport extents, and then dynamically expands (or shrinks) each area given user input. We use our prototype to evaluate the technique in two user studies, as well as showcase examples of TASD for node-link diagrams, word clouds, and geographical maps.

关键词： Topology-aware navigation zooming distortion web-based visualization user study

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The power of interactively linked hierarchy visualizations

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JOURNAL OF visualization 2022年第4期25卷 857-873页

作者： Burch, Michael van de Wetering, Huub Klaassen, Nico Eindhoven Univ Technol Eindhoven Netherlands

This paper describes an interactive web-based tool for visualizing hierarchical data including the recently developed concept of space-reclaiming icicle plots and several more traditional hierarchy visualizations. The tool provides ways to upload, share, explore, and compare hierarchical data using a multitude of different linked hierarchy visualizations. The current version supports up to eight hierarchy visualizations, focusing on user-friendly interactive navigation by a dynamic graphical user interface with a variety of functions while each visualization is interactive by itself. Moreover, color deficiency issues are taken into account in the tool, further improving the usability for this user group. All of the visualizations can be shown in linked views while typical hierarchy parameters and visual variables can be changed on user demand. The interactive tool makes use of OpenGL and Angular, an industry standard JavaScript platform, and runs in a web browser. We illustrate the usefulness of the visualization tool by applying it to the NCBI taxonomy that consists of more than 300,000 hierarchically organized species while filtering for the tetrapoda subhierarchy as an application example. To further test the usability of the tool we did a performance test with increasing sizes of processed hierarchy datasets and even support a GPU implementation. Also user feedback on the eight visualizations was collected. Finally, we explain implementation details and discuss limitations and scalability issues of the linked visualization techniques.

关键词： Hierarchy visualization Multiple coordinated views web-based visualization Interaction techniques GPU support

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COMPUTING ARBITRARILY LARGE MESHES WITH LEVEL-OF-DETAIL SUPPORT FOR CESIUM 3D TILES 7

COMPUTING ARBITRARILY LARGE MESHES WITH LEVEL-OF-DETAIL SUPP...

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7th International Workshop on LowCost 3D - Sensors, Algorithms, Applications

作者： Hillmann, Malte Igelbrink, Felix Wiemann, Thomas Osnabruck Univ Knowledge Based Syst Grp D-49080 Osnabruck Germany DFKI Niedersachsen Plan Based Robot Control D-49080 Osnabruck Germany

In this paper we present an approach to compute arbitrarily sized meshes of large scale environments. The meshes can be reconstructed from laser-scanned point clouds or existing high-resolution meshes. The algorithm automatically builds a level of detail hierarchy in the Cesium 3D Tiles format using an octree partition. The main contribution of this paper is a method that ensures that the generated meshes for each level-of-detail stage are computed in a consistent manner to minimize visual artifacts between different detail levels during rendering. Furthermore, both the reconstruction and simplification algorithm are designed to constrain the memory consumption, which enables to process even very large data sets on consumer-grade hardware. The export into the Cesium 3D Tiles format allows to render such large meshes efficiently in all web-based viewers that support this format. In our experiments we evaluate the method on different datasets and assess the visual quality during the rendering process and analyze the memory footprint as well as the runtime behaviour.

关键词： 3D Surface Reconstruction Mesh Simplification Level-of-Detail Rendering web-based visualization

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FlowDyn: A daily streamflow prediction pipeline for dynamical deep neural network applications

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ENVIRONMENTAL MODELLING & SOFTWARE 2023年 170卷

作者： Tabas, S. Sadeghi Humaira, N. Samadi, S. Hubig, N. C. Clemson Univ Glenn Dept Civil Engn Clemson SC 29634 USA Clemson Univ Sch Comp Clemson SC USA Clemson Univ Dept Agr Sci Clemson SC USA

This paper presents a dynamical neural network framework to understand how catchment systems respond to daily rainfall-runoff processes over time. We developed an interactive Python-based deep neural network (DNN) package called FlowDyn (presented through a JS-based web platform) to simulate and forecast daily streamflow data for >180 gauging stations across the globe. Several DNN models, including long short-term memory (LSTM), Gated Recurrent Unit (GRU), and a hybrid network of convolutional neural network and LSTM (ConvLSTM), as well as an auto encoder (AE) model were developed and integrated into the FlowDyn pipeline to analyze and forecast sequential daily streamflow values that are embedded within a web-based application for demonstration and visualization. Inputs were gathered from different web services, including the catchment attributes and meteorology for large-sample studies (CAMELS), the national climatic data center (NCDC), and the global runoff data center (GRDC). DNN configurations were trained and tested with an average accuracy rating of 0.83 across 183 river basins globally. FlowDyn simulation and performance demonstrated that different DNN models were able to learn both regionally consistent and location-specific hydrological behaviors. Through the findings of this paper, we advocate the merit of applying FlowDyn package in the field of daily rainfall-runoff prediction at both local and global scales.

关键词： Deep neural networks Autoencoders FlowDyn package Streamflow prediction web-based visualization

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KGETCDA: an efficient representation learning framework based on knowledge graph encoder from transformer for predicting circRNA-disease associations

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BRIEFINGS IN BIOINFORMATICS 2023年第5期24卷 bbad292-bbad292页

作者： Wu, Jinyang Ning, Zhiwei Ding, Yidong Wang, Ying Peng, Qinke Fu, Laiyi Xi An Jiao Tong Univ Sch Automat Sci & Engn Xian Peoples R China

Recent studies have demonstrated the significant role that circRNA plays in the progression of human diseases. Identifying circRNA-disease associations (CDA) in an efficient manner can offer crucial insights into disease diagnosis. While traditional biological experiments can be time-consuming and labor-intensive, computational methods have emerged as a viable alternative in recent years. However, these methods are often limited by data sparsity and their inability to explore high-order information. In this paper, we introduce a novel method named Knowledge Graph Encoder from Transformer for predicting CDA (KGETCDA). Specifically, KGETCDA first integrates more than 10 databases to construct a large heterogeneous non-coding RNA dataset, which contains multiple relationships between circRNA, miRNA, lncRNA and disease. Then, a biological knowledge graph is created based on this dataset and Transformer-based knowledge representation learning and attentive propagation layers are applied to obtain high-quality embeddings with accurately captured high-order interaction information. Finally, multilayer perceptron is utilized to predict the matching scores of CDA based on their embeddings. Our empirical results demonstrate that KGETCDA significantly outperforms other state-of-the-art models. To enhance user experience, we have developed an interactive web-based platform named HNRBase that allows users to visualize, download data and make predictions using KGETCDA with ease. The code and datasets are publicly available at .

关键词： CircRNA-disease associations Heterogeneous non-coding RNA database Knowledge graph Transformer web-based visualization

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Medical Data and Mathematically Modeled Implicit Surface Real-Rime visualization in web Browsers

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INTERNATIONAL JOURNAL OF IMAGE AND GRAPHICS 2022年第4期22卷 2250027-2250027页

作者： Zhang, Qi Illinois State Univ Sch Informat Technol 100 North Univ St Normal IL 61761 USA

Raycasting can display volumetric medical data in fine details and reveal crucial inner imaging information, while implicit surface is able to effectively model complex objects with high flexibility, combining these two rendering modalities together will provide comprehensive information of the scene and has wide applications in surgical simulation, image-guided intervention, and medical training. However, medical data rendering is based on texture depth at every sampling point, while mathematically modeled implicit surfaces do not have geometric information in texture space. It is a challenging task to visualize both physical scalar data and virtual implicit surfaces simultaneously. To address this issue, in this paper, we present a new dual-casting ray-based double modality data rendering algorithm and web-based software platform to visualize volumetric medical data and implicit surface in the same browser. The algorithm runs on graphics processing unit and casts two virtual rays from camera to each pixel on the display panel, where one ray travels through the mathematically defined scene for implicit surface rendering and the other one passes the 3D texture space for volumetric data visualization. The proposed algorithm can detect voxel depth information and algebraic surface models along each casting ray and dynamically enhance the visualized dual-modality data with the improved lighting model and transparency adjustment function. Moreover, auxiliary innovative techniques are also presented to enhance the shading and rendering features of interest. Our software platform can seamlessly visualize volumetric medical data and implicit surfaces in the same web browser over Internet.

关键词： web-based visualization volumetric data rendering dual-casting ray implicit surface modeling feature enhancement

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Graphery: a Biological Network Algorithm Tutorial webservice 20

Graphery: a Biological Network Algorithm Tutorial Webservice

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11th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)

作者： Zeng, Heyuan Ritz, Anna Reed Coll Dept Comp Sci Portland OR 97202 USA Reed Coll Dept Biol Portland OR 97202 USA

No abstract available.

ISBN: (纸本)9781450379649

No abstract available.

关键词： Biological networks web-based visualization graph algorithms

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