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Increasing effort is put into the development of methods for learning mechanistic models from data. This task entails not only the accurate estimation of parameters but also a suitable model structure. Recent work on the discovery of dynamical systems formulates this problem as a linear equation system. Here, we explore several simulation-based optimization approaches, which allow much greater freedom in the objective formulation and weaker conditions on the available data. We show that even for relatively small stochastic population models, simultaneous estimation of parameters and structure poses major challenges for optimization procedures. Particularly, we investigate the application of the local stochastic gradient descent method, commonly used for training machine learning models. We demonstrate accurate estimation of models but find that enforcing the inference of parsimonious, interpretable models drastically increases the difficulty. We give an outlook on how this challenge can be overcome., Comment: 5 pages, 2 figures

Simulation has become, in many application areas, a sine-qua-non. Most recently, COVID-19 has underlined the importance of simulation studies and limitations in current practices and methods. We identify four goals of methodological work for addressing these limitations. The first is to provide better support for capturing, representing, and evaluating the context of simulation studies, including research questions, assumptions, requirements, and activities contributing to a simulation study. In addition, the composition of simulation models and other simulation studies' products must be supported beyond syntactical coherence, including aspects of semantics and purpose, enabling their effective reuse. A higher degree of automating simulation studies will contribute to more systematic, standardized simulation studies and their efficiency. Finally, it is essential to invest increased effort into effectively communicating results and the processes involved in simulation studies to enable their use in research and decision-making. These goals are not pursued independently of each other, but they will benefit from and sometimes even rely on advances in other subfields. In the present paper, we explore the basis and interdependencies evident in current research and practice and delineate future research directions based on these considerations.

In macroeconomics, an emerging discussion of alternative monetary systems addresses the dimensions of systemic risk in advanced financial systems. Monetary regime changes with the aim of achieving a more sustainable financial system have already been discussed in several European parliaments and were the subject of a referendum in Switzerland. However, their effectiveness and efficacy concerning macro-financial stability are not well-known. This paper introduces a macroeconomic agent-based model (MABM) in a novel simulation environment to simulate the current monetary system, which may serve as a basis to implement and analyze monetary regime shifts. In this context, the monetary system affects the lending potential of banks and might impact the dynamics of financial crises. MABMs are predestined to replicate emergent financial crisis dynamics, analyze institutional changes within a financial system, and thus measure macro-financial stability. The used simulation environment makes the model more accessible and facilitates exploring the impact of different hypotheses and mechanisms in a less complex way. The model replicates a wide range of stylized economic facts, including simplifying assumptions to reduce model complexity., Comment: 31 pages, 13 Figures, 5 Tables

Simulation experiments are typically conducted repeatedly during the model development process, for example, to re-validate if a behavioral property still holds after several model changes. Approaches for automatically reusing and generating simulation experiments can support modelers in conducting simulation studies in a more systematic and effective manner. They rely on explicit experiment specifications and, so far, on user interaction for initiating the reuse. Thereby, they are constrained to support the reuse of simulation experiments in a specific setting. Our approach now goes one step further by automatically identifying and adapting the experiments to be reused for a variety of scenarios. To achieve this, we exploit provenance graphs of simulation studies, which provide valuable information about the previous modeling and experimenting activities, and contain meta-information about the different entities that were used or produced during the simulation study. We define provenance patterns and associate them with a semantics, which allows us to interpret the different activities, and construct transformation rules for provenance graphs. Our approach is implemented in a Reuse and Adapt framework for Simulation Experiments (RASE) which can interface with various modeling and simulation tools. In the case studies, we demonstrate the utility of our framework for a) the repeated sensitivity analysis of an agent-based model of migration routes, and b) the cross-validation of two models of a cell signaling pathway.

Workflow support typically focuses on single simulation experiments. This is also the case for simulation based on finite element methods. If entire simulation studies shall be supported, flexible means for intertwining revising the model, collecting data, executing and analyzing experiments are required. Artifact-based workflows present one means to support entire simulation studies, as has been shown for stochastic discrete-event simulation. To adapt the approach to finite element methods, the set of artifacts, i.e., conceptual model, requirement, simulation model, and simulation experiment, and the constraints that apply are extended by new artifacts, such as geometrical model, input data, and simulation data. Artifacts, their life cycles, and constraints are revisited revealing features both types of simulation studies share and those they vary in. Also, the potential benefits of exploiting an artifact-based workflow approach are shown based on a concrete simulation study. To those benefits belong guidance to systematically conduct simulation studies, reduction of effort by automatically executing specific steps, e.g., generating and executing convergence tests, and support for the automatic reporting of provenance.

Emergent behavior is a key feature defining a system under study as a complex system. Simulation has been recognized as the only way to deal with the study of the emergency of properties (at a macroscopic level) among groups of system components (at a microscopic level), for the manifestations of emergent structures cannot be deduced from analysing components in isolation. A systems-oriented generalisation must consider the presence of feedback loops (micro components react to macro properties), interaction among components of different classes (modular composition) and layered interaction of subsystems operating at different spatio-temporal scales (hierarchical organisation). In this work we introduce Emergent Behavior-DEVS (EB-DEVS) a Modeling and Simulation (M&S) formalism that permits reasoning about complex systems where emergent behavior is placed at the forefront of the analysis activity. EB-DEVS builds on the DEVS formalism, adding upward/downward communication channels to well-established capabilities for modular and hierarchical M&S of heterogeneous multi-formalism systems. EB-DEVS takes a minimalist stance on expressiveness, introducing a small set of extensions on Classic DEVS that can cope with emergent behavior, and making both formalisms interoperable (the modeler decides which subsystems deserve to be expressed via micro-macro dynamics). We present three case studies: flocks of birds with learning, population epidemics with vaccination and sub-cellular dynamics with homeostasis, through which we showcase how EB-DEVS performs by placing emergent properties at the center of the M&S process., Comment: 38 page document with: original content 25 pages, references 3 pages, appendices 10 pages

Up to now, it is not possible to obtain analytical solutions for complex molecular association processes (e.g. Molecule recognition in Signaling or catalysis). Instead Brownian Dynamics (BD) simulations are commonly used to estimate the rate of diffusional association, e.g. to be later used in mesoscopic simulations. Meanwhile a portfolio of diffusional association (DA) methods have been developed that exploit BD. However, DA methods do not clearly distinguish between modeling, simulation, and experiment settings. This hampers to classify and compare the existing methods with respect to, for instance model assumptions, simulation approximations or specific optimization strategies for steering the computation of trajectories. To address this deficiency we propose FADA (Flexible Architecture for Diffusional Association) - an architecture that allows the flexible definition of the experiment comprising a formal description of the model in SpacePi, different simulators, as well as validation and analysis methods. Based on the NAM (Northrup-Allison-McCammon) method, which forms the basis of many existing DA methods, we illustrate the structure and functioning of FADA. A discussion of future validation experiments illuminates how the FADA can be exploited in order to estimate reaction rates and how validation techniques may be applied to validate additional features of the model.