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

Gene expression-based heterogeneity analysis has been extensively conducted. In recent studies, it has been shown that network-based analysis, which takes a system perspective and accommodates the interconnections among genes, can be more…

Here we introduce a new design framework for synthetic biology that exploits the advantages of Bayesian model selection. We will argue that the difference between inference and design is that in the former we try to reconstruct the system…

Certain constructs allowed in Mizar articles cannot be represented in first-order logic but can be represented in higher-order logic. We describe a way to obtain higher-order theorem proving problems from Mizar articles that make use of…

Formal methods have been a successful approach for modelling and verifying the correctness of complex technologies like microprocessor chip design, biological systems and others. This is the main motivation of developing quantum formal…

Network data has become widespread, larger, and more complex over the years. Traditional network data is dyadic, capturing the relations among pairs of entities. With the need to model interactions among more than two entities, significant…

Advances in biology have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. Theoretical biology used to primarily provide a basis to rationally examine the frameworks…

Electric circuits manipulate electric charge and magnetic flux via a small set of discrete components to implement useful functionality over continuous time-varying signals represented by currents and voltages. Much of the same…

Several abilities of biological systems, such as adaptation to natural environment, or of animals to learn patterns when appropriately trained, are features that are extremely useful, if emulated by electronic circuits, in applications…

Nowadays, formal methods are used in various areas for the verification of programs or for code generation from models in order to increase the quality of software and to reduce costs. However, there are still fields in which formal methods…

Many practical engineering systems and their components have multiple performance levels and failure modes. If these systems form a monotonically increasing structure function (system model) with respect to the performance of their…

Networks are a fundamental tool for understanding and modeling complex systems in physics, biology, neuroscience, engineering, and social science. Many networks are known to exhibit rich, lower-order connectivity patterns that can be…

Formal methods refer to rigorous, mathematical approaches to system development and have played a key role in establishing the correctness of safety-critical systems. The main building blocks of formal methods are models and specifications,…

We describe an approach to the verified implementation of transformations on functional programs that exploits the higher-order representation of syntax. In this approach, transformations are specified using the logic of hereditary Harrop…

We study open-ended evolution by focusing on computational and information-processing dynamics underlying major evolutionary transitions. In doing so, we consider biological organisms as hierarchical dynamical systems that generate…

We survey dynamic logics for specifying and verifying properties of dynamical systems, including hybrid systems, distributed hybrid systems, and stochastic hybrid systems. A dynamic logic is a first-order modal logic with a pair of…

This contribution deals with identification of fractional-order dynamical systems. We consider systems whose mathematical description is a three-member differential equation in which the orders of derivatives can be real numbers. We give a…

The concepts and methods of Systems Biology are being extended to neuropharmacology, to test and design drugs against neurological and psychiatric disorders. Computational modeling by integrating compartmental neural modeling technique and…

How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting…

Phase separation, crucial for spatially segregating biomolecules in cells, is well-understood in the simple case of a few components with pairwise interactions. Yet, biological cells challenge the simple picture in at least two ways: First,…

Predicting cellular responses to genetic perturbations represents a fundamental challenge in systems biology, critical for advancing therapeutic discovery and virtual cell modeling. While large language models (LLMs) show promise for…