相关论文: Formal Analysis of the Biological Circuits using H…

Logic is playing an increasingly important role in the engineering of real-time, hybrid, and cyber-physical systems, but mostly in the form of posterior verification and high-level analysis. The core methodology in the design of real-world…

Bacteria have been a source of inspiration for the design of evolutionary algorithms. At the beginning of the 20th century synthetic biology was born, a discipline whose goal is the design of biological systems that do not exist in nature,…

Humans and animals exhibit a range of interesting behaviors in dynamic environments, and it is unclear how our brains actively reformat this dense sensory information to enable these behaviors. Experimental neuroscience is undergoing a…

We present a formalization of higher-order logic in the Isabelle proof assistant, building directly on the foundational framework Isabelle/Pure and developed to be as small and readable as possible. It should therefore serve as a good…

There is growing consensus among neuroscientists that neural circuits critical for survival are the result of genomic decompression processes. We introduce SynaptoGen, a novel computational framework--member of the Connectome Models…

Mathematical modelling is a cornerstone of computational biology. While mechanistic models might describe the interactions of interest of a system, they are often difficult to study. On the other hand, abstract models might capture key…

It is customary to assess the reliability of underground oil and gas pipelines in the presence of excessive loading and corrosion effects to ensure a leak-free transport of hazardous materials. The main idea behind this reliability analysis…

The digital transformation of automation places new demands on data acquisition and processing in industrial processes. Logical relationships between acquired data and cyclic process sequences must be correctly interpreted and evaluated. To…

This paper presents a new type of genetic algorithm for the set covering problem. It differs from previous evolutionary approaches first because it is an indirect algorithm, i.e. the actual solutions are found by an external decoder…

A method of discovering how neurons are connected to process information is presented here: Design a simple logic circuit that can perform a single, biologically advantageous function. Engineering concepts can be helpful in choosing the…

It has been experimentally proven that realizing universal quantum gates using higher-radices logic is practically and technologically possible. We developed a Parallel Genetic Algorithm that synthesizes Boolean reversible circuits realized…

We write down a series of basic laws for (strict) higher-order circuit diagrams. More precisely, we define higher-order circuit theories in terms of: (a) nesting, (b) temporal and spatial composition, and (c) equivalence between lower-order…

A central strategy of synthetic biology is to understand the basic processes of living creatures through engineering organisms using the same building blocks. Biological machines described in terms of parts can be studied by computer…

This paper describes a procedure that system developers can follow to translate typical mathematical representations of linearized control systems into logic theories. These theories are then used to verify system requirements and find…

We advocate the use of qualitative models in the analysis of large biological systems. We show how qualitative models are linked to theoretical differential models and practical graphical models of biological networks. A new technique for…

Causal discovery in multi-omic datasets is crucial for understanding the bigger picture of gene regulatory mechanisms, but remains challenging due to high dimensionality, differentiation of direct from indirect relationships, and hidden…

We consider a model for substrate-depletion oscillations in genetic systems, based on a stochastic differential equation with a slowly evolving external signal. We show the existence of critical transitions in the system. We apply two…

We axiomatize the molecular-biology reasoning style, show compliance of the standard reference: Ptashne, A Genetic Switch, and present proof-theory-induced technologies to help infer phenotypes and to predict life cycles from genotypes. The…

Several formal systems, such as resolution and minimal model semantics, provide a framework for logic programming. In this paper, we will survey the use of structural proof theory as an alternative foundation. Researchers have been using…

Many promising quantum algorithms in economics, medical science, and material science rely on circuits that are parameterized by a large number of angles. To ensure that these algorithms are efficient, these parameterized circuits must be…