Related papers: Formal Analysis of the Biological Circuits using H…
Systems engineering has developed a mature knowledge on how to design, integrate and manage complex industrial systems, whereas disciplines studying complex systems in nature or society also propose numerous tools for their understanding.…
The rapid advances in the field of optimization methods in many pure and applied science pose the difficulty of keeping track of the developments as well as selecting an appropriate technique that best suits the problem in-hand. From a…
We take an order-theoretic approach to circuit (string diagram) syntax, treating a circuit as a partial order with additional input-output structure. We define morphisms between circuits and prove a factorisation theorem showing that these…
A sound and complete embedding of conditional logics into classical higher-order logic is presented. This embedding enables the application of off-the-shelf higher-order automated theorem provers and model finders for reasoning within and…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
The presented previously indirect optimization method (IOM) developed within biochemical systems theory (BST) provides a versatile and mathematically tractable optimization strategy for biochemical systems. However, due to the local…
Linear implication can represent state transitions, but real transition systems operate under temporal, stochastic or probabilistic constraints that are not directly representable in ordinary linear logic. We propose a general modal…
We describe an approach to modelling and reasoning about data-centric business processes and present a form of general model checking. Our technique extends existing approaches, which explore systems only from concrete initial states.…
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…
Program synthesis is the generation of a program from a specification. Correct synthesis is difficult, and methods that provide formal guarantees suffer from scalability issues. On the other hand, neural networks are able to generate…
The phase reduction technique is essential for studying rhythmic phenomena across various scientific fields. It allows the complex dynamics of high-dimensional oscillatory systems to be expressed by a single phase variable. This paper…
The renormalization group has proven to be a very powerful tool in physics for treating systems with many length scales. Here we show how it can be adapted to provide a new class of algorithms for discrete optimization. The heart of our…
Linear finite dynamical systems play an important role, for example, in coding theory and simulations. Methods for analyzing such systems are often restricted to cases in which the system is defined over a field %and usually strive to…
Network representations often cannot fully account for the structural richness of complex systems spanning multiple levels of organisation. Recently proposed high-order information-theoretic signals are well-suited to capture synergistic…
A central idea in understanding brains and building artificial intelligence is that structure determines function. Yet, how the brain's complex structure arises from a limited set of genetic instructions remains a key question. The ultra…
Reversible logic synthesis is emerging as a major research component for post-CMOS computing devices, in particular Quantum computing. In this work, we link the reversible logic synthesis problem to sorting algorithms. Based on our…
Rule-based reasoning is an essential part of human intelligence prominently formalized in artificial intelligence research via logic programs. Describing complex objects as the composition of elementary ones is a common strategy in computer…
Understanding the high-level conceptual structure of quantum algorithms from their low-level circuit representations is a critical task for verification, debugging, and education. While traditional numerical simulators can calculate output…
Biological networks are pivotal in deciphering the complexity and functionality of biological systems. Causal inference, which focuses on determining the directionality and strength of interactions between variables rather than merely…
Graph Theoretic Process Network Synthesis is described as an introduction to biological networks. Genetic, protein and metabolic systems are considered. The theoretical work of Kauffman is discussed and amplified by critical property…