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arXiv 2023年

作者： Berger, Philip Beleites, Sebastian Tominski, Christian Institute for Visual & Analytic Computing University of Rostock Germany

visual comparison is an important task in the analysis of multivariate graphs. However, comparison of topological features of a graph with respect to its data attributes for different portions of the data remains challenging because there is no single visual representation that would suit the dynamic nature of comparative analyses. To facilitate the visual comparison in node-link diagrams, we propose the comparison lens as a focus+context approach for dynamic layout adaptation. The core idea is to start with a topology-driven layout and locally inject an attribute-driven layout based on the multivariate similarity of node attributes. This facilitates comparison tasks on a local level while preserving the user's overall mental map of the graph topology. Additional visual enhancements, including color-coding, reduction of edge clutter, and radial guides, further support the comparison. To fit the lens to different comparison situations, it can be configured via user-controllable parameters. To demonstrate the utility of our approach, we use it for comparison in a real-world dataset of soccer players. © 2023, CC BY.

关键词： Lenses

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Creating PROV-DM Graphs from Model Databases 22

Creating PROV-DM Graphs from Model Databases

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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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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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GPU-Accelerated Simulation Ensembles of Stochastic Reaction Networks 22

GPU-Accelerated Simulation Ensembles of Stochastic Reaction ...

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Proceedings of the Winter Simulation Conference

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

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.

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Seamless Simulation-Based Verification and Validation of Event-Driven Software Systems 22

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

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Proceedings of the Winter Simulation Conference

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

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.

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SMOOTHING METHODS FOR AUTOMATIC DIFFERENTIATION ACROSS CONDITIONAL BRANCHES

arXiv

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arXiv 2023年

作者： Kreikemeyer, Justin N. Andelfinger, Philipp Institute for Visual and Analytic Computing University of Rostock Rostock18059 Germany

Programs involving discontinuities introduced by control flow constructs such as conditional branches pose challenges to mathematical optimization methods that assume a degree of smoothness in the objective function’s response surface. Smooth interpretation (SI) is a form of abstract interpretation that approximates the convolution of a program’s output with a Gaussian kernel, thus smoothing its output in a principled manner. Here, we combine SI with automatic differentiation (AD) to efficiently compute gradients of smoothed programs. In contrast to AD across a regular program execution, these gradients also capture the effects of alternative control flow paths. The combination of SI with AD enables the direct gradient-based parameter synthesis for branching programs, allowing for instance the calibration of simulation models or their combination with neural network models in machine learning pipelines. We detail the effects of the approximations made for tractability in SI and propose a novel Monte Carlo estimator that avoids the underlying assumptions by estimating the smoothed programs’ gradients through a combination of AD and sampling. Using DiscoGrad, our tool for automatically translating simple C++ programs to a smooth differentiable form, we perform an extensive evaluation. We compare the combination of SI with AD and our Monte Carlo estimator to existing gradient-free and stochastic methods on four non-trivial and originally discontinuous problems ranging from classical simulation-based optimization to neural network-driven control. While the optimization progress with the SI-based estimator depends on the complexity of the program’s control flow, our Monte Carlo estimator is competitive in all problems, exhibiting the fastest convergence by a substantial margin in our highest-dimensional problem. © 2023, CC BY.

关键词： Optimization

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Promoting Digital Twins of the Baltic Sea 20

Promoting Digital Twins of the Baltic Sea

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20. GI-Fachtagung Informatik und Schule, Informatikmonitor der Gesellschaft fur Informatik, INFOS 2023 - 20th GI Conference on Informatics and Schools, Informatics Monitor of the German Informatics Society, INFOS 2023

作者： von Lukas, Uwe Freiherr Fraunhofer IGD Joachim-Jungius-Str. 11 Rostock18059 Germany University of Rostock Institute for Visual and Analytic Computing Einsteinstr. 22 Rostock18059 Germany

ISBN: (纸本)9783885797302

Digital Twins are a powerful concept - initially intended to support complex technical products over their whole lifecycle, including ramp-up, operation and decommissioning. In recent years this concept has also become more and more popular in the maritime domain. Digital Twins are not only used to accompany maritime assets such as offshore wind plants or port facilities but can also be used to support decision making in marine spatial planning, maintaining marine ecosystems, dealing with marine hazards, or realize potentials of the oceans to mitigate climate change. Based on some general remarks on Digital Twins and some considerations on the Baltic Sea, this paper gives an introduction into the concept of Digital Twins of the Oceans. Based on this foundation, various technology examples are presented to illustrate the contribution of visual and analytic computing to offer powerful Digital Twins. Finally, ties are established to deal with this topic in STEM education. © 2023 Gesellschaft fur Informatik (GI). All rights reserved.

关键词： Decision making

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Simulation-Supported Engineering of Self-Adaptive Software Systems

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

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2021 Winter Simulation Conference, WSC 2021

作者： Meyer, Tom Ruscheinski, Andreas Wilsdorf, Pia Uhrmacher, Adelinde M. Institute for Visual and Analytic Computing University of Rostock Rostock18059 Germany

ISBN: (纸本)9781665433112

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. © 2021 IEEE.

关键词： Diagnosis

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Validation Without Data - Formalizing Stylized Facts Of Time Series

Validation Without Data - Formalizing Stylized Facts Of Time...

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2023 Winter Simulation Conference, WSC 2023

作者： Wilsdorf, Pia Zuska, Marian Andelfinger, Philipp Uhrmacher, Adelinde M. Peters, Florian University of Rostock Institute for Visual and Analytic Computing Albert-Einstein-Str. 22 Rostock18059 Germany University of Rostock Department of Economics Ulmenstraße 69 Rostock18057 Germany

ISBN: (纸本)9798350369663

A stylized fact is a simplified presentation of an empirical finding. When modeling and simulating complex systems and real data are sparse, stylized facts have become a key instrument for building trust in a model as they represent important requirements regarding the model's behavior. However, automatically validating stylized facts has remained limited as they are usually expressed in natural language. Therefore, we develop a formal language with a custom syntax and tailored predicates allowing modelers to unambiguously and succinctly describe important (temporal) characteristics of simulation traces or relationships between multiple traces via statistical tests. The proposed formal language is able to express numerous facts from the literature in different application domains, as well as to automatically check stylized facts. If stylized facts are defined at the beginning of a simulation study, formally expressing and checking them can streamline and guide the development of simulation models and their successive revisions. © 2023 IEEE.

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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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2021 Winter Simulation Conference, WSC 2021

作者： Kreikemeyer, Justin Noah Koster, Till Uhrmacher, Adelinde M. Warnke, Tom Institute for Visual and Analytic Computing University of Rostock Rostock18059 Germany

ISBN: (纸本)9781665433112

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. © 2021 IEEE.

关键词： Stochastic models

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