Relational grounding facilitates development of scientifically useful multiscale models.

C Anthony Hunt, Glen E P Ropella, Tai ning Lam, Andrew D Gewitz
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引用次数: 26

Abstract

We review grounding issues that influence the scientific usefulness of any biomedical multiscale model (MSM). Groundings are the collection of units, dimensions, and/or objects to which a variable or model constituent refers. To date, models that primarily use continuous mathematics rely heavily on absolute grounding, whereas those that primarily use discrete software paradigms (e.g., object-oriented, agent-based, actor) typically employ relational grounding. We review grounding issues and identify strategies to address them. We maintain that grounding issues should be addressed at the start of any MSM project and should be reevaluated throughout the model development process. We make the following points. Grounding decisions influence model flexibility, adaptability, and thus reusability. Grounding choices should be influenced by measures, uncertainty, system information, and the nature of available validation data. Absolute grounding complicates the process of combining models to form larger models unless all are grounded absolutely. Relational grounding facilitates referent knowledge embodiment within computational mechanisms but requires separate model-to-referent mappings. Absolute grounding can simplify integration by forcing common units and, hence, a common integration target, but context change may require model reengineering. Relational grounding enables synthesis of large, composite (multi-module) models that can be robust to context changes. Because biological components have varying degrees of autonomy, corresponding components in MSMs need to do the same. Relational grounding facilitates achieving such autonomy. Biomimetic analogues designed to facilitate translational research and development must have long lifecycles. Exploring mechanisms of normal-to-disease transition requires model components that are grounded relationally. Multi-paradigm modeling requires both hyperspatial and relational grounding.

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关系基础促进了科学上有用的多尺度模型的发展。
我们回顾了影响任何生物医学多尺度模型(MSM)科学有用性的接地问题。接地是变量或模型成分所引用的单位、维度和/或对象的集合。迄今为止,主要使用连续数学的模型严重依赖于绝对基础,而那些主要使用离散软件范例(例如,面向对象的、基于代理的、参与者的)的模型通常使用关系基础。我们审查接地问题,并确定解决这些问题的策略。我们认为接地问题应该在任何MSM项目开始时解决,并且应该在整个模型开发过程中重新评估。我们提出以下几点。接地决策影响模型的灵活性、适应性,从而影响可重用性。接地选择应受测量、不确定性、系统信息和可用验证数据的性质的影响。除非所有模型都是绝对接地的,否则绝对接地会使组合模型形成更大模型的过程变得复杂。关系基础有助于在计算机制中实现引用知识,但需要单独的模型到引用映射。绝对的基础可以通过强制通用单元和通用集成目标来简化集成,但是上下文变化可能需要模型再工程。关系基础支持大型组合(多模块)模型的合成,这些模型对上下文更改具有鲁棒性。由于生物成分具有不同程度的自主性,因此msm中相应的成分也需要这样做。关系根植有助于实现这样的自主。为促进转译研究和开发而设计的仿生类似物必须具有较长的生命周期。探索从正常到疾病转变的机制需要建立关系基础的模型组件。多范式建模需要超空间和关系基础。
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来源期刊
Theoretical Biology and Medical Modelling
Theoretical Biology and Medical Modelling MATHEMATICAL & COMPUTATIONAL BIOLOGY-
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6-12 weeks
期刊介绍: Theoretical Biology and Medical Modelling is an open access peer-reviewed journal adopting a broad definition of "biology" and focusing on theoretical ideas and models associated with developments in biology and medicine. Mathematicians, biologists and clinicians of various specialisms, philosophers and historians of science are all contributing to the emergence of novel concepts in an age of systems biology, bioinformatics and computer modelling. This is the field in which Theoretical Biology and Medical Modelling operates. We welcome submissions that are technically sound and offering either improved understanding in biology and medicine or progress in theory or method.
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