Related papers: A Model-Theoretic Approach to Modular Implementati…
Complex systems typically have many different parts and facets, with different characteristics. In a multi-paradigm approach to modeling, formalisms with different natures are used in combination to describe complementary parts and aspects…
Reconfiguration paths express sequences of successive reconfiguration operations within a component-based approach allowing dynamic reconfigurations. We use constructs from regular expressions-pin particular, alternatives-to introduce…
We propose a novel approach for the formal verification of biological systems based on the use of a modal linear logic. We show how such a logic can be used, with worlds as instants of time, as an unified framework to encode both biological…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to…
We propose a method to write and check a specification including quantifiers using behaviors, i.e., input-output pairs. Our method requires the following input from the user: (1) answers to a finite number of queries, each of which presents…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
Biological systems are often modeled as a system of ordinary differential equations (ODEs) with time-invariant parameters. However, cell signaling events or pharmacological interventions may alter the cellular state and induce multi-mode…
The safety of automated driving systems must be justified by convincing arguments and supported by compelling evidence to persuade certification agencies, regulatory entities, and the general public to allow the systems on public roads.…
We recently presented the so-called allagmatic method, which includes a system metamodel providing a framework for describing, modelling, simulating, and interpreting complex systems. Its development and programming was guided by…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
There are two fundamentally different approaches to specifying and verifying properties of systems. The logical approach makes use of specifications given as formulae of temporal or modal logics and relies on efficient model checking…
Computer systems can be found everywhere: in space, in our homes, in our cars, in our pockets, and sometimes even in our own bodies. For concerns of safety, economy, and convenience, it is important that such systems work correctly.…
This paper investigates questions related to the modularity in discrete models of biological interaction networks. We develop a theoretical framework based on the analysis of their asymptotic dynamics. More precisely, we exhibit formal…
Specifying the intended behaviour of autonomous systems is becoming increasingly important but is fraught with many challenges. This technical report provides an overview of existing work on specifications of autonomous systems and places a…
In several applications, including in synthetic biology, one often has input/output data on a system composed of many modules, and although the modules' input/output functions and signals may be unknown, knowledge of the composition…
A notion of biologic system or just a system implies a functional wholeness of comprising system components. Positive and negative feedback are the examples of how the idea to unite anatomical elements in the whole functional structure was…
There is a growing interest in developing goal-oriented dialog systems which serve users in accomplishing complex tasks through multi-turn conversations. Although many methods are devised to evaluate and improve the performance of…
The ability to represent intracellular biochemical dynamics via deterministic and stochastic modelling is one of the crucial components to move biological sciences in the observe-predict-control-design knowledge ladder. Compared to the…
Natural materials achieve adaptive behavior through hierarchical organization and coupled mechanisms across scales. Their translation into engineering, however, remains largely heuristic. What is missing is a formal translation framework…