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Proceedings of the Winter Simulation Conference

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

Documenting the provenance of the main products of a simulation study plays a crucial role in improving the understanding of mechanistic, biological models as well as their reproducibility and credibility. With model databases already an ample collection of simulation models, including metainformation and source files, exists. In this paper, we bridge the gap between the information contained in model databases and the PROV-DM provenance standard, which allows making the diverse products and their relationships formally explicit. We present a procedure for creating PROV-DM graphs from model database entries, and illustrate the approach based on ten different models from the BioModels database. These case studies demonstrate the advantages of having a standardized provenance view in addition to the regular database entries, i.e., enhanced means for visualizing the structure of the simulation study and the curation process.

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GPU-Accelerated Simulation Ensembles of Stochastic Reaction Networks

GPU-Accelerated Simulation Ensembles of Stochastic Reaction ...

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Simulation Winter Conference

作者： Till Köster Leon Herrmann Philipp Andelfinger Adelinde Uhrmacher Institute for Visual and Analytic Computing University of Rostock Rostock GERMANY

ISBN: (纸本)9781665476621

Stochastic Simulation Algorithms are widely used for simulating reaction networks in cellular biology. Due to the stochastic nature of models and the large parameter spaces involved, many simulation runs are frequently needed. We approach the computational challenge by expanding the hardware used for execution by massively parallel graphical processing units (GPUs) to execute these ensembles of runs concurrently in a form of coarse-grained parallelization. Such computing infrastructure in the form of GPUs is readily available in desktop workstations and clusters but is not commonly exploited as part of stochastic simulation studies. Building on the existing literature in the field, we employ state-of-the-art algorithms to study the degree to which GPUs can augment the computation resources available for ensemble studies. Furthermore, the challenge of efficient work assignment given the GPU's synchronous mode of execution is explored. There are several algorithmic tradeoffs to consider for models with different execution characteristics, which we investigate in a performance study across four different models. To explore the limitations of the GPU-based simulators, the performance characteristics when executing large models are compared to those of highly optimized CPU simulators. Our results indicate that for some models adding a typical desktop GPU has a similar effect on performance as up to 40 added CPU cores.

关键词： Computational modeling Biological system modeling Instruction sets Layout Graphics processing units Stochastic processes Hardware

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NBSIMGEN: Jupyter Notebook Extension for Generating Simulation Experiments

NBSIMGEN: Jupyter Notebook Extension for Generating Simulati...

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Simulation Winter Conference

作者： Pia Wilsdorf Anton Willy Kirchhübel Adelinde M. Uhrmacher Institute for Visual and Analytic Computing University of Rostock Rostock Germany

Simulation experiments are crucial in conducting simulation studies. With simulation studies growing increasingly complex, simulation experiments are intertwined with steps of conceptual modeling, model building, analyzing data, and visualizing and interpreting results. Making the products of these various steps (assumptions, requirements, data, model components, and experiments) explicit has been shown to increase the reproducibility of simulation studies. Moreover, using an integrated environment that allows developing, organizing and documenting those products can facilitate their automatic reuse and exploitation. We explore Jupyter Notebook as an all-in-one solution for conducting and documenting a simulation study, and we present nbSimGen. This Jupyter Notebook extension lends support to modelers by automatically specifying and running suitable simulation experiments. It is based on an annotation vocabulary that, during the development of the conceptual model and the simulation model, allows users to mark portions of their notebook deemed relevant to the various simulation experiments to come.

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A Data-Driven Platform for the Coordination of Independent visual analytics Tools

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Computers and Graphics (Pergamon) 2022年 106卷 152-160页

作者： Nonnemann, Lars Hogräfer, Marius Röhlig, Martin Schumann, Heidrun Urban, Bodo Schulz, Hans-Jörg University of Rostock Institute for Visual and Analytic Computing Albert-Einstein-Strasse 22 Rostock18059 Germany University of Aarhus Department of Computer Science Abogade 34 Aarhus8200 Denmark Fraunhofer Institute for Computer Graphics Research Joachim-Jungius-Strasse 11 Rostock18059 Germany

visual analysis of unknown data requires the combined use of various functions that are often part of standalone visual analytics (VA) tools. Performing cross-tool visual analysis with standalone VA tools, however, is a challenging and cumbersome endeavor. Some dedicated frameworks address this issue, yet in order to utilize any of them, a visual analytics tool needs to support their required API or architecture. Contrary to most existing frameworks, we present an approach that does not rely on a single predefined interchange mechanism for the entire ensemble of VA tools. Instead, we propose using any available channel for data exchange between two consecutive VA tools. This allows mixing and matching of different data exchange strategies over the course of a cross-tool analysis. In this paper, we identify the challenges associated with establishing such tool chaining platform for data-driven coordination. We further describe the structure and capabilities of data exchange and explain various functionalities of our platform in detail. Based on a demonstrating example, we discuss the limitations of our approach and elaborate new insight for the coordination of the visual output of multiple VA tools. © 2022 Elsevier Ltd

关键词： Electronic data interchange

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Seamless Simulation-Based Verification and Validation of Event-Driven Software Systems

Seamless Simulation-Based Verification and Validation of Eve...

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Simulation Winter Conference

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

ISBN: (纸本)9781665476621

Verification and validation (V&V) are essential concerns in the development of safety-critical distributed software systems. V&V efforts targeting full system implementations rely on testing, which requires real-world deployments and cumbersome analysis to track down issues across distributed software components. Here, we propose a simulation-based development and testing framework for distributed systems following the event-driven architecture (EDA) paradigm. During development, unmodified software components can be executed in their interaction with a simulated environment, allowing for early testing under envisioned deployments. After introducing the interplay of EDA and discrete-event simulation, we present our framework's architecture and the API offered to software components, which closely follows accepted EDA principles. We demonstrate the use of our framework on a medical software system used in the diagnosis of rare genetic diseases. By observing the system's interaction with simulated laboratories, the feedback loop between diagnoses by laboratories and classifications from the software system is evaluated.

关键词： Target tracking Laboratories Computer architecture Quality of service Production Software systems Middleware

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Conceptual Models in Simulation Studies: Making it Explicit

Conceptual Models in Simulation Studies: Making it Explicit

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Simulation Winter Conference

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

ISBN: (数字)9781728194998

ISBN: (纸本)9781728195001

Conceptual models play an important role in conducting simulation studies. A formal or at least explicit specification of conceptual models is key for effectively exploiting them during simulation studies and thereafter, for interpreting and reusing the simulation results. However, the perception of conceptual models varies strongly and with it possible means for specification. A broad definition of the conceptual model, i.e., as a loose collection of early-stage products of the simulation study, holds the potential to unify existing definitions, but also poses specific challenges for specification. To approach these challenges, without claiming to be exhaustive, we identify a set of products, which includes research question, data, and requirements, and define relations and properties of these products. Based on a cell biological case study and a prototypical implementation, we show how the formal structuring of the conceptual model assists in building a simulation model.

关键词： Biological system modeling Simulation Buildings

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nbSimGen: Jupyter Notebook Extension for Generating Simulation Experiments 23

nbSimGen: Jupyter Notebook Extension for Generating Simulati...

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Proceedings of the Winter Simulation Conference

作者： Pia Wilsdorf Anton Willy Kirchhübel Adelinde M. Uhrmacher Institute for Visual and Analytic Computing University of Rostock Rostock Germany

ISBN: (纸本)9798350369663

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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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Pragmatic Logic-Based Spatio-Temporal Pattern Checking in Particle-Based Models

Pragmatic Logic-Based Spatio-Temporal Pattern Checking in Pa...

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Simulation Winter Conference

作者： Andreas Ruscheinski Anja Wolpers Philipp Henning Tom Warnke Fiete Haack Adelinde M. Uhrmacher Institute for Visual and Analytic Computing University of Rostock Rostock GERMANY

ISBN: (数字)9781728194998

ISBN: (纸本)9781728195001

Particle-based simulation is a powerful approach for modeling systems and processes of entities interacting in continuous space. One way to validate a particle-based simulation is to check for the occurrence of spatio-temporal patterns formed by the particles, for example by statistical model checking. Whereas spatio-temporal logics for describing spatio-temporal patterns exist, they are defined on discrete rather than continuous space. We propose an approach to bridge this gap by automatically translating the output of continuous-space particle-based simulations into an input for discrete-space spatio-temporal logics. The translation is parameterized with information about relevant regions and their development in time. We demonstrate the utility of our approach with a case study in which we successfully apply statistical model-checking to a particle-based cell-biological model. A Java implementation of our approach is available under an open-source license.

关键词： Solid modeling Three-dimensional displays Shape Two dimensional displays Model checking Reliability Pragmatics

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