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

Logic Programming languages and combinational circuit synthesis tools share a common "combinatorial search over logic formulae" background. This paper attempts to reconnect the two fields with a fresh look at Prolog encodings for the…

We propose a novel, fully explainable neural approach to synthesis of combinatorial logic circuits from input-output examples. The carrying advantage of our method is that it readily extends to inductive scenarios, where the set of examples…

Motivation: One of the branches of Systems Biology is focused on a deep understanding of underlying regulatory networks through the analysis of the biomolecules oscillations and their interplay. Synthetic Biology exploits gene or/and…

This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…

Background: Neuro-symbolic methods enhance the reliability of neural network classifiers through logical constraints, but they lack native support for ontologies. Objectives: We aim to develop a neuro-symbolic method that reliably outputs…

Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…

In real-world systems, phase transitions often materialize abruptly, making it difficult to design appropriate controls that help uncover underlying processes. Some agent-based computational models display transformations similar to phase…

We present a new approach to automated reasoning about higher-order programs by endowing symbolic execution with a notion of higher-order, symbolic values. Our approach is sound and relatively complete with respect to a first-order solver…

With the advancement of synthetic biology, several new tools have been conceptualized over the years as alternative treatments for current medical procedures. Most of those applications are applied to various chronic diseases. This work…

We present the Thought Graph as a novel framework to support complex reasoning and use gene set analysis as an example to uncover semantic relationships between biological processes. Our framework stands out for its ability to provide a…

A modern approach to engineering correct-by-construction systems is to synthesize them automatically from formal specifications. Oftentimes, a system can only satisfy its guarantees if certain environment assumptions hold, which motivates…

Digital logic forms the functional basics of most modern electronic equipment and as such the creation of novel digital logic circuits is an active area of computer engineering research. This study demonstrates that genetic algorithms can…

The biologically inspired framework of port-graphs has been successfully used to specify complex systems. It is the basis of the PORGY modelling tool. To facilitate the specification of proof normalisation procedures via graph rewriting, in…

Reversible logic circuits have been historically motivated by theoretical research in low-power electronics as well as practical improvement of bit-manipulation transforms in cryptography and computer graphics. Recently, reversible circuits…

We propose a categorical framework to reason about scientific explanations: descriptions of a phenomenon meant to translate it into simpler terms, or into a context that has been already understood. Our motivating examples come from systems…

An overset grid method was used to investigate the interaction between a particle-laden flow and a circular cylinder. The overset grid method was implemented in the Pencil Code , a high-order finite-difference code for compressible flow…

Many biological functions are executed by molecular machines, which consume energy and convert it into mechanical work. Biological machines have evolved to transport cargo, facilitate folding of proteins and RNA, remodel chromatin and…

We present superconducting quantum circuits which exhibit atomic energy spectrum and selection rules as ladder and lambda three-level configurations designed by means of genetic algorithms. These heuristic optimization techniques are…

Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…

The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…