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arXiv 2023年

作者： Röhlig, Martin Nonnemann, Lars Schulz, Hans-Jörg Stachs, Oliver Schumann, Heidrun Institute for Visual and Analytic Computing University of Rostock Germany Department of Computer Science Aarhus University Denmark Department of Ophthalmology Rostock University Medical Center Germany

The visual analysis of retinal data contributes to the understanding of a wide range of eye diseases. For the evaluation of cross-sectional studies, ophthalmologists rely on workflows and toolsets established in their work environment. That is, they know what tools and data are needed at each step of their workflow. Yet, manually operating the various tools, including activation, data handling, or view arrangement, can be cumbersome and time-consuming. We thus introduce a new visualization-supported toolchaining approach that combines workflow, tools, and data. First, we provide access to the tools required for each step of the workflow. Second, we handle the exchange of data between these tools. Third, we organize the views of the tools on screen using suitable layouts. Fourth, we visualize the connection between workflow, tools, and data to support the data analysis. We demonstrate our approach with a use case in ophthalmic research and report on initial feedback from experts. © 2023, CC BY.

关键词： Ophthalmology

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Comparing the Effect of Code Optimizations on Simulation Runtime Across Synchronous Cellular Automata Models of HIV

Comparing the Effect of Code Optimizations on Simulation Run...

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2021 Winter Simulation Conference, WSC 2021

作者： Li, Junjiang Giabbanelli, Philippe J. Koster, Till Miami University Department of Computer Science Software Engineering OH45056 United States Institute for Visual and Analytic Computing University of Rostock Rostock18059 Germany

ISBN: (纸本)9781665433112

Models developed by domain experts occasionally struggle to achieve a sufficient execution speed. Improving performances requires expertise in parallel and distributed simulations, hardware, or time to profile performances to identify bottlenecks. However, end-users in biological simulations of the Human Immunodeficiency Virus (HIV) have repeatedly demonstrated that these resources are either not available or not sought, resulting in models that are developed through user-friendly languages and platforms, then used on workstations. This situation becomes problematic when performances cannot cope with the salient characteristics of the phenomenon that is modeled, as is the case with cellular automata (CA) models of HIV. In this paper, we optimize the Python code of CA models of HIV to scale the number of cells handled by a simulation on a workstation commonly available to end-users. We demonstrate this scalability via five HIV CA models and compare these results to assess how modeling choices can impact runtime. © 2021 IEEE.

关键词： Viruses

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Particle-Wise Higher-Order SPH Field Approximation for DVR

arXiv

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arXiv 2024年

作者： Fischer, Jonathan Schulze, Martin Rosenthal, Paul Linsen, Lars Institute for Visual and Analytic Computing University of Rostock Albert-Einstein-Str. 22 Rostock18059 Germany Institute of Computer Science University of Münster Einsteinstr. 62 Münster48149 Germany

When employing Direct Volume Rendering (DVR) for visualizing volumetric scalar fields, classification is generally performed on a piecewise constant or piecewise linear approximation of the field on a viewing ray. Smoothed Particle Hydrodynamics (SPH) data sets define volumetric scalar fields as the sum of individual particle contributions, at highly varying spatial resolution. We present an approach for approximating SPH scalar fields along viewing rays with piecewise polynomial functions of higher order. This is done by approximating each particle contribution individually and then efficiently summing the results, thus generating a higher-order representation of the field with a resolution adapting to the data resolution in the volume. © 2024, CC BY-SA.

关键词： Volume rendering

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Exploiting Provenance and Ontologies In Supporting Best Practices For Simulation Experiments: A Case Study On Sensitivity Analysis

Exploiting Provenance and Ontologies In Supporting Best Prac...

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Simulation Winter Conference

作者： Pia Wilsdorf Nadine Fischer Fiete Haack Adelinde M. Uhrmacher Institute for Visual and Analytic Computing University of Rostock Rostock GERMANY

ISBN: (纸本)9781665433129

Simulation studies are intricate processes and user support for conducting more consistent, systematic, and efficient simulation studies is needed. Simulation experiments as one crucial part of a simulation study can benefit from semi-automatic method selection, parameterization, and execution. However, this largely depends on the context in which the experiment is conducted. Context information about a simulation study can be provided in form of provenance that documents which artifacts contributed in developing a simulation model. We present an approach that exploits provenance to support best practices for simulation experiments. The approach relies on 1) explicitly specified provenance information, 2) an ontology of methods, 3) best practices rules, and 4) integration with a previously developed experiment generation pipeline. We demonstrate our approach by conducting a sensitivity analysis experiment within a cell biological simulation study.

关键词： analytical models Systematics Sensitivity analysis Biological system modeling Pipelines Ontologies Best practices

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Differentiable agent-based simulation for gradient-guided simulation-based optimization

arXiv

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arXiv 2021年

作者： Andelfinger, Philipp University of Rostock Institute for Visual and Analytic Computing Rostock Germany

Simulation-based optimization using agent-based models is typically carried out under the assumption that the gradient describing the sensitivity of the simulation output to the input cannot be evaluated directly. To still apply gradient-based optimization methods, which efficiently steer the optimization towards a local optimum, gradient estimation methods can be employed. However, many simulation runs are needed to obtain accurate estimates if the input dimension is large. Automatic differentiation (AD) is a family of techniques to compute gradients of general programs directly. Here, we explore the use of AD in the context of time-driven agent-based simulations. By substituting common discrete model elements such as conditional branching with smooth approximations, we obtain gradient information across discontinuities in the model logic. On the example of microscopic traffic models and an epidemics model, we study the fidelity and overhead of the differentiable models, as well as the convergence speed and solution quality achieved by gradient-based optimization compared to gradient-free methods. In traffic signal timing optimization problems with high input dimension, the gradient-based methods exhibit substantially superior performance. Finally, we demonstrate that the approach enables gradient-based training of neural network-controlled simulation entities embedded in the model logic. Copyright © 2021, The Authors. All rights reserved.

关键词： Optimization

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LEARNING SURROGATE EQUATIONS FOR THE ANALYSIS OF AN AGENT-BASED CANCER MODEL

arXiv

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arXiv 2025年

作者： Burrage, Kevin Burrage, Pamela Kreikemeyer, Justin N. Uhrmacher, Adelinde M. Weerasinghe, Hasitha N. School of Mathematical Sciences Queensland University of Technology BrisbaneQLD Australia Department of Computer Science University of Oxford United Kingdom Modelling and Simulation Institute for Visual and Analytic Computing Faculty of Informatics and Electrical Engineering University of Rostock Rostock Germany

In this paper, we adapt a two species agent-based cancer model that describes the interaction between cancer cells and healthy cells on a uniform grid to include the interaction with a third species – namely immune cells. We run six different scenarios to explore the competition between cancer and immune cells and the initial concentration of the immune cells on cancer dynamics. We then use coupled equation learning to construct a population-based reaction model for each scenario. We show how they can be unified into a single surrogate population-based reaction model, whose underlying three coupled ordinary differential equations are much easier to analyse than the original agent-based model. As an example, by finding the single steady state of the cancer concentration, we are able to find a linear relationship between this concentration and the initial concentration of the immune cells. This then enables us to estimate suitable values for the competition and initial concentration to reduce the cancer substantially without performing additional complex and expensive simulations from an agent-based stochastic model. The work shows the importance of performing equation learning from agent-based stochastic data for gaining key insights about the behaviour of complex cellular dynamics. © 2025, CC BY.

关键词： Lung cancer

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Simulation-Supported Engineering of Self-Adaptive Software Systems

Simulation-Supported Engineering of Self-Adaptive Software S...

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Simulation Winter Conference

作者： Tom Meyer Andreas Ruscheinski Pia Wilsdorf Adelinde M. Uhrmacher Institute for Visual and Analytic Computing University of Rostock Rostock GERMANY

ISBN: (纸本)9781665433129

Engineering a self-adaptive software system is challenging. During design- as well as run-time, assurance cases are central for ensuring reliable operation of the software. Simulation, in addition to software verification and testing, is a viable means to provide evidence for assurance cases. So far, little attention has been given to the development of underlying simulation models. Here, we argue that a systematic approach to develop simulation models will enhance the overall engineering process and will contribute to seamless integration of simulation and engineering processes. In our approach, we relate an explicit representation of the conceptual model and simulation experiments to artifacts of the engineering process. We will show first steps of applying our approach in a concrete ongoing software project for medical diagnosis, and discuss the role of components of the conceptual model in designing the software as a self-adaptive software system.

关键词： Systematics Software systems Reliability engineering Software reliability Medical diagnosis Testing

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Inferring Dependency Graphs for Agent-Based Models Using Aspect-Oriented Programming

Inferring Dependency Graphs for Agent-Based Models Using Asp...

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Simulation Winter Conference

作者： Justin Noah Kreikemeyer Till Köster Adelinde M. Uhrmacher Tom Warnke Institute for Visual and Analytic Computing University of Rostock Rostock GERMANY

ISBN: (纸本)9781665433129

Population-based CTMC models can generally be executed efficiently with stochastic simulation algorithms (SSAs). However, the heterogeneity in agent-based models poses a challenge for SSAs. To allow for an efficient simulation, we take SSAs that exploit dependency graphs for population-based models and adapt them to agent-based models. We integrate our approach with object-oriented frameworks for agent-based simulation by detecting dependencies via aspect-oriented programming (AOP). This way, modelers can implement models without manually recording dependency information, while still executing the models with efficient, dependency-aware SSAs. We provide an open-source implementation of our approach for the framework MASON, showing significant speedups in model execution.

关键词： Adaptation models Computer languages Codes Object oriented modeling Biological system modeling Sociology Stochastic processes

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Advanced Tutorial: Parallel and Distributed Methods for Scalable Discrete Simulation

Advanced Tutorial: Parallel and Distributed Methods for Scal...

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Simulation Winter Conference

作者： Philipp Andelfinger Wentong Cai Institute for Visual and Analytic Computing University of Rostock Rostock GERMANY School of Computer Science and Engineering Nanyang Technological University Singapore SINGAPORE

ISBN: (纸本)9781665476621

Discrete simulation is an indispensable approach to investigate systems whose complexity prohibits analytical modeling and for which real-world experimentation is costly or dangerous. To keep pace with system models of increasing levels of detail and scope, a simulator's ability to make full use of the available hardware, typically through parallel and distributed simulation, is a vital concern. Building on well-studied synchronization algorithms, the field's focus has shifted towards aspects such as the avoidance of redundant computations in ensemble studies and the exploitation of heterogeneous hardware platforms. In this tutorial, we describe the fundamental notions of parallel and distributed simulation and summarize the main classes of synchronization algorithms as well their use when applied under the constraints of the domains of transportation and spiking neural networks. Current research directions and challenges are discussed in light of the tension between efficiency through specialization and wide applicability through generalization.

关键词： analytical models Computational modeling Neural networks Buildings Transportation Focusing Tutorials

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Engineering the Interaction of a Humanoid Robot Pepper with Post-Stroke Patients during Training Tasks 21

Engineering the Interaction of a Humanoid Robot Pepper with ...

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13th ACM SIGCHI Symposium on Engineering Interactive computing Systems, EICS 2021

作者： Forbrig, Peter Bundea, Alexandru Bader, Sebastian Dept. of Software Engineering University of Rostock Germany Dept. of CS/Chair of Software Engineering University of Rostock Germany Institute of Visual Chair in Mobile Multimedia Information Systems University of Rostock Institute of Visual and Analytic Computing Germany

ISBN: (纸本)9781450384490

Engineering the dialog of a humanoid robot like Pepper with human beings is challenging. The software from Softbanks allows the programming of spoken sentences and the understanding of specific words for apps on the robot. However, we recognized that the fexibility of the software is limited in this way. Therefore, we developed tools based on state machines that run on a server and communicate with the robot. In this way Pepper becomes a kind of thin robot. The paper discusses the architecture of the software, its advantages and the tools used within our project E-BRAiN (Evidence-Based Robot Assistance in Neurorehabilitation). Additionally, one of our identified interaction patterns is discussed. © 2021 ACM.

关键词： Anthropomorphic robots

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