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2021 Winter Simulation Conference, WSC 2021

作者： Bijak, Jakub Hilton, Jason Hinsch, Martin Lipscombe, Kim Nurse, Sarah Prike, Toby Smith, Peter W.F. Reinhardt, Oliver Uhrmacher, Adelinde M. Higham, Philip A. Grow, Andre University of Southampton Highfield Campus Department of Social Statistics and Demography SouthamptonSO17 1BJ United Kingdom Institute for Visual and Analytic Computing University of Rostock Rostock18059 Germany School of Psychology University of Southampton Highfield Campus SouthamptonSO17 1BJ United Kingdom Max Planck Institute for Demographic Research Rostock18057 Germany

ISBN: (纸本)9781665433112

The outbreak of the COVID-19 pandemic in 2020 posed unique challenges for academic and professional education, while at the same time offering opportunities related to the mass switching of the delivery of courses to the online mode. In this paper, we share the experience of organizing and delivering an online doctoral-level course on Agent-Based Modeling for Social Research. Our aim was to teach interdisciplinary content on various elements of the modeling process in a coherent and practical way. In the paper, we offer a critical assessment of different aspects of the course, related to content as well as organization and delivery. By looking at the course in the light of the current knowledge on good teaching and learning practices from the educational and psychological literature, and reflecting on the lessons learned, we offer a blueprint for designing and running complex, multi-thread simulation courses in an efficient way. © 2021 IEEE.

关键词： Teaching

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Studying the Influence of Cell Culture Medium Composition on Ciliary Length with Detectcilia: An R Package for Automated Detection and Length Measurement of Primary Cilia

SSRN

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SSRN 2023年

作者： Budde, Kai Krueger, Simone Sehlke, Clemens Lemcke, Heiko Jonitz-Heincke, Anika David, Robert Bader, Rainer Uhrmacher, Adelinde M. Institute for Visual and Analytic Computing University of Rostock Rostock18051 Germany Research Laboratory for Biomechanics and Implant Technology Department of Orthopedics Rostock University Medical Center Rostock18057 Germany Reference and Translation Center for Cardiac Stem Cell Therapy Department of Cardiac Surgery Rostock University Medical Center Rostock18057 Germany Department of Life Light and Matter Interdisciplinary Faculty University of Rostock Rostock18051 Germany

Background and objective: The primary cilium is a cellular protrusion found on most mammalian cell types. This structure is involved in various cell signaling pathways, functioning as a cellular antenna. Therefore, the length of the primary cilium influences its functionality. To investigate the impact of physical or chemical stimuli on the ciliary length, this value is to be determined easily and ***: To automatically and reproducibly detect and measure primary cilia, we have implemented an open-source R package called detectCilia. As a case study, we compare the influence of four different cell culture media compositions on the lengths of primary cilia of human chondrocytes. These media compositions include i) Insulin-Transferrin-Selenium (ITS), ii) ITS and Dexamethasone (Dexa), iii) ITS, Dexa, Insulin-like Growth Factor 1 (IGF-1), and Transforming Growth Factor β⁠1 (TGF-β⁠1), or iv) Fetal Bovine Serum (FBS). The automated detection and length measurement results of detectCilia are also compared with the results of two similar tools: ACDC and ***: Our package provides similar results as the manual evaluation of primary cilia. A comparison with ACDC and CiliaQ shows different advantages of all three tools, which makes detectCilia a valuable addition. In our automatic analysis of our case study, we find that the medium composition has an impact on the ciliary length. The cultivation with ITS and Dexa has led to the longest primary ***: detectCilia is able to automatically and reproducibly detect and measure primary cilia in confocal microscopy images without the need for elaborated user interaction. © 2023, The Authors. All rights reserved.

关键词： Insulin

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AI-Assisted Ethics? Considerations of AI Simulation for the Ethical Assessment and Design of Assistive Technologies

arXiv

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arXiv 2023年

作者： Schicktanz, Silke Welsch, Johannes Schweda, Mark Hein, Andreas Rieger, Jochem W. Kirste, Thomas University Medical Center Göttingen Dept. for Medical Ethics and History of Medicine Germany University of Oldenburg Department of Health Services Research Division for Ethics in Medicine Germany University of Oldenburg Department of Health Services Research Division Assistance Systems and Medical Device Technology Germany University of Oldenburg Applied Neurocognitive Psychology Lab Germany University of Rostock Institute for Visual and Analytic Computing Germany Hanse-Wissenschaftskolleg Institute of Advance Studies Germany

Current ethical debates on the use of artificial intelligence (AI) in health care treat AI as a product of technology in three ways. First, by assessing risks and potential benefits of currently developed AI-enabled products with ethical checklists;second, by proposing ex ante lists of ethical values seen as relevant for the design and development of assisting technology, and third, by promoting AI technology to use moral reasoning as part of the automation process. The dominance of these three perspectives in the discourse is demonstrated by a brief summary of the literature and by findings our own expert interviews regarding their views on intelligent assistive technology in dementia care which is a particular focus of our approach. Subsequently, we propose a fourth approach to AI, namely as a methodological tool to assist ethical reflection. We provide a concept of an AI-simulation informed by three separate elements: 1) stochastic human behavior models based on behavioral data for simulating realistic settings, 2) qualitative empirical data on value statements regarding internal policy, and 3) visualization components that aid in understanding the impact of changes in these variables. The potential of this approach is to inform an interdisciplinary field about anticipated ethical challenges or ethical trade-offs in concrete settings and, hence, to spark a re-evaluation of design and implementation plans. This may be particularly useful for applications that deal with extremely complex values and behavior or with limitations on the communication resources of affected persons (e.g., persons with dementia care or for care of persons with cognitive impairment). Simulation does not replace ethical reflection but does allow for detailed, context-sensitive analysis during the design process and prior to implementation. Finally, we discuss the inherently quantitative methods of analysis afforded by stochastic simulations as well as the potential for ethical discussions

关键词： Stochastic systems

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Teaching a Modeling Process: Reflections From An Online Course

Teaching a Modeling Process: Reflections From An Online Cour...

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Simulation Winter Conference

作者： Jakub Bijak Jason Hilton Martin Hinsch Kim Lipscombe Sarah Nurse Toby Prike Peter W.F. Smith Oliver Reinhardt Adelinde M. Uhrmacher Philip A. Higham André Grow University of Southampton Highfield Campus Southampton UK Institute for Visual and Analytic Computing University of Rostock Rostock GERMANY School of Psychology University of Southampton Highfield Campus Southampton UK Max Planck Institute for Demographic Research Rostock GERMANY

ISBN: (纸本)9781665433129

关键词： COVID-19 Pandemics Education Psychology Switches Organizations Medical services

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Responsive matrix cells: A focus+context approach for exploring and editing multivariate graphs

arXiv

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arXiv 2020年

作者： Horak, Tom Berger, Philip Schumann, Heidrun Dachselt, Raimund Tominski, Christian Interactive Media Lab Technische Universität Dresden Germany Inst. for Visual & Analytic Computing University of Rostock Germany

Matrix visualizations are a useful tool to provide a general overview of a graph’s structure. For multivariate graphs, a remaining challenge is to cope with the attributes that are associated with nodes and edges. Addressing this challenge, we propose responsive matrix cells as a focus+context approach for embedding additional interactive views into a matrix. Responsive matrix cells are local zoomable regions of interest that provide auxiliary data exploration and editing facilities for multivariate graphs. They behave responsively by adapting their visual contents to the cell location, the available display space, and the user task. Responsive matrix cells enable users to reveal details about the graph, compare node and edge attributes, and edit data values directly in a matrix without resorting to external views or tools. We report the general design considerations for responsive matrix cells covering the visual and interactive means necessary to support a seamless data exploration and editing. Responsive matrix cells have been implemented in a web-based prototype based on which we demonstrate the utility of our approach. We describe a walk-through for the use case of analyzing a graph of soccer players and report on insights from a preliminary user feedback session. Copyright © 2020, The Authors. All rights reserved.

关键词： visualization

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A Characterization of Data Exchange between visual analytics Tools

A Characterization of Data Exchange between Visual Analytics...

引用

International Conference on Information visualisation (IV)

作者： Lars Nonnemann Heidrun Schumann Bodo Urban Mario Aehnelt Hans-Jörg Schulz Institute of Visual and Analytic Computing University of Rostock Rostock Germany Competence Center for Visual Assistance Technologies Fraunhofer Institute for Computer Graphics Research Rostock Germany Aarhus University Aarhus Denmark

ISBN: (数字)9781728191348

ISBN: (纸本)9781728191355

Over the past years, the visualization of large and complex data sets brought up various visual analytics (VA) tools in order to solve domain-specific tasks. These VA tools are typically implemented as individual software components in data-flow-oriented models, meaning that data is transferred from one component to the next. While most VA frameworks rely on a monolithic architecture with features for the integration of specialized analysis methods, we consider a loose coupling of independent applications, where autonomous VA tools are used in predefined analysis sequences. To this end, we provide a characterization of the data exchange process among individual VA tools in the form of a taxonomy. This taxonomy can be used as a checklist to identify characteristics and improve the data flow of one's own multi-tool VA setup. For this purpose, we conducted a systematic investigation of the individual aspects of data exchange that are commonly found across different usage scenarios. We apply our taxonomy to three existing multi-tool frameworks, the open-source library ReVize, the toolchain editor AnyProc, and the visualization and monitoring framework Plant@Hand3D.

关键词： Systematics visual analytics Taxonomy Data visualization Tools Data models Task analysis

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Optimizing Discrete Simulations of the Spread of HIV-1 to Handle Billions of Cells on a Workstation 20

Optimizing Discrete Simulations of the Spread of HIV-1 to Ha...

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2020 ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, SIGSIM-PADS 2020

作者： Giabbanelli, Philippe J. Devita, Joshua A. Köster, Till Kohrt, Jared A. Miami University Department of Computer Science and Software Engineering OxfordOH United States Department of Computer Science Northern Illinois University DeKalb IL United States University of Rostock Institute for Visual and Analytic Computing Rostock Germany Furman University Computer Science Department GreenvilleSC United States

ISBN: (纸本)9781450375924

Cellular Automata have been used on many occasions to model the spread of the Human Immunodeficiency Virus (HIV) within a human body. This is in part due to the relative simplicity of crafting their rules and the convenience of visualizing disease dynamics in 2D. Although such models appeared in 2001 and have been extended in dozens of studies, their potential to serve as a virtual laboratory has been limited by their computationally intensive nature. So far, they have been used to simulate at most 0.5 million cells instead of the billion cells that may harbor the virus. Simulating too few cells is a key issue for calibration (the 'small' models are calibrated based on results observed in a much larger space), prevents us from using a sufficient proportion of cells to model latent HIV reservoirs (in which HIV can hide for years), and prohibits even more computationally intensive aspects such as tracking mutations (which is essential to assess drug resistance). In short, the low number of cells prevents these models from answering many of the questions that would make them useful as virtual laboratories. Although the models may be scaled by running on clusters, this is not always an option since interdisciplinary research in discrete models of HIV often takes place on the lab's computer, and patients for whom we seek to provide virtual laboratories may have limited access to computational resources. Given these constraints, we demonstrate how to optimize simulations of HIV on a workstation by combining features such as just-in-time compilation, parallelism at the level of threads, pseudo random number generators, and simplified handling of neighbors in a cellular automaton. Our results demonstrate that, within 10 minutes, we can finish a simulation run for 6.7 billion cells instead of 60,000 cells in an unoptimized simulation. © 2020 Association for computing Machinery.

关键词： Cells

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Multi-display visual analysis: Model, interface, and layout computation

arXiv

引用

arXiv 2019年

作者： Eichner, C. Schumann, H. Tominski, C. Institute for Visual and Analytic Computing University of Rostock Germany

Modern display environments offer great potential for involving multiple users in presentations, discussions, and data analysis sessions. By showing multiple views on multiple displays, information exchange can be improved, several perspectives on the data can be combined, and different analysis strategies can be pursued. In this report, we describe concepts to support display composition, information distribution, and analysis coordination for visual data analysis in multi-display environments. In particular, a basic model for layout modeling is introduced, a graphical interface for interactive generation of the model is presented, and a layout mechanism is described that arranges multiple views on multiple displays automatically. Furthermore, approaches to meta-analysis will be discussed. The developed approaches are demonstrated in a use case that focuses on parameter space analysis for the segmentation of time series data. Copyright © 2019, The Authors. All rights reserved.

关键词： Information analysis

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Improving species distribution models for climate change studies: ecological plausibility and performance metrics

引用

Ecological Modelling 2025年 508卷

作者： Dario Fiorentino Ismael Núñez-Riboni Maria E. Pierce Daniel Oesterwind Anna Akimova Thünen-Institut für Seefischerei Herwigstraße 31 27572 Bremerhaven Germany Thünen-Institut für Ostseefischerei Alter Hafen Süd 2 18069 Rostock Germany Institute for Visual and Analytic Computing University of Rostock Albert-Einstein-Straße 22 Germany

Species Distribution Models (SDMs) are widely used tools for studying potential climate-induced shifts in species distribution to support future marine spatial planning. However, the ecological plausibility of selected models is often neglected, particularly in marine ecosystems, resulting in potentially misleading outcomes, especially when climate effects are of concern. In this study we modeled the distribution of 11 commercial fish species in the North Sea using 57 years of observations and 60 SDMs with various degrees of freedom and aimed to improve the ecological plausibility of SDMs by evaluating common model selection techniques. Model performance was evaluated using deviances obtained with three cross-validation designs, Akaike Information Criterion, median absolute deviation and percentage of local mismatch. We identified top performing models based on consistent good scores of those metrics and assessed the ecological plausibility of all models. Specifically, we tested whether the modeled temperature response curve aligned with the ecological niche concept, i.e. having a bell shape within the plausible temperature range for each species, where the highest habitat suitability should relate to optimal conditions. The tested performance metrics often yielded conflicting outcomes and selected models with implausible temperature response curves that had poor extrapolation skills in temperature space and, thus, may result in unreliable predictions under climate change. Building on our findings, we provide recommendations for future SDM applications to improve their accuracy, ecological plausibility and predictive skills in climate-related studies.

关键词： Fish habitat modeling Model selection Cross-validation Habitat niche Partial plot Climate change

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Towards Accurate visualization and Measurement of Localized Changes in Intraretinal Layer Thickness

Towards Accurate Visualization and Measurement of Localized ...

引用

IEEE Workshop on visual analytics in Healthcare (VAHC)

作者： Martin Röhlig Christoph Schmidt Ruby Kala Prakasam Oliver Stachs Heidrun Schumann Institute of Visual and Analytic Computing University of Rostock Department of Ophthalmology University of Rostock

Optical coherence tomography (OCT) enables high-resolution 3D imaging of intraretinal layers. The layers' thickness are commonly compared to normative data to understand a variety of retinal and systemic disorders. Yet, discovering and measuring localized thickness differences in the complex OCT data is challenging, particularly in an early stage of eye diseases. We combine interactive visualization and automated measurements to support the analysis of abnormal layer thickness. First, the spatial distribution of thickness differences is visualized via precise deviation maps. Second, statistical tests are applied to quantify every point of the visualized data. Third, measurements of significant differences for anatomically distinct areas and selected regions of interest are retrieved. We demonstrate the effectiveness of our solution in detecting abnormal layer thickness in the context of a cross-sectional ophthalmic study.

关键词： Retina Area measurement Thickness measurement Data visualization Diseases Diabetes Image color analysis

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