摘要翻译：
本文提出了一种基于组件规范的系统行为逻辑规范的方法，并描述了它们之间一类通信“信号通路”的作用。在产生的系统中可以看到路径的动作和效果（语义）的变化。我们展示了如何“丰富”行为的原始组成部分的确切什么是由信号通路提供的。这有可能允许正式证明系统作为一个整体的性质，或者正式诊断为什么通信模块的系统可能不满足期望的规范，以及它是否以及如何可以“修复”。在我们看来，有五个不同的阶段：1。潜在组件之间的连接的描述，潜在模块连接的级别。2.这些模块的具体选择。对不同模块之间的连接到这些不同模块成员之间的连接的“阐述”4。这些连接的语义描述（它们实际上是做什么的）5。步骤2中选择的模块的“填充”，以允许连接的动作（步骤3)，如步骤4所述。形式主义是完全分层的--换句话说，形式主义同样适用于作为一个整体的系统，适用于每个模块，也适用于原始系统是其中一个组成部分的任何更大的系统。事实证明，无论出于什么原因--也许是在正确的抽象层次上的进化优势优化--许多生物系统是分层模块化的，模块通过各种途径进行通信。因此，像这里所提出的那种形式主义可以应用于生物学中的问题。
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英文标题：
《A Model-Theoretic Approach to Modular Implementation, with Application
  to Biological Systems》
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作者：
Leo Marcus
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最新提交年份：
2019
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分类信息：

一级分类：Quantitative Biology        数量生物学
二级分类：Other Quantitative Biology        其他定量生物学
分类描述：Work in quantitative biology that does not fit into the other q-bio classifications
不适合其他q-bio分类的定量生物学工作
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英文摘要：
  We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in the actions and effects (semantics) of the pathways can be seen in the resulting system. We show how to "enrich" the behavior of the original components by exactly what is provided by the signaling pathways. This has the potential to allow a formal proof of a property of the system as a whole, or a formal diagnosis why a system of communicating modules may not satisfy a desired specification, and if and how it can be "fixed." There are five distinct stages in our view: 1. A description of the connections between potential components at the level of which potential modules are connected. 2. Specific choices for those modules 3. An "elaboration" of the connections among different modules to connections among members of those different modules 4. A description of the semantics of those connections (what they actually do) 5. A "padding" of the modules chosen in step 2 to allow for the action of the connections (step 3), as described in step 4. The formalism is completely hierarchical -- in other words, the formalism works equally for the system as a whole, for each of the modules, and for any larger system in which the original system is a component. As it turns out, for whatever reason -- perhaps evolutionary advantage optimization at the right level of abstraction -- many biological systems are hierarchically modular, with the modules communicating via various pathways. Thus, a formalism such as the one presented here could have application to questions in biology.
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PDF链接：
https://arxiv.org/pdf/1907.05529