相关论文: P versus B: P Systems as a Formal Framework for Co…
Living systems, from single cells to higher vertebrates, receive a continuous stream of non-stationary inputs that they sense, e.g., via cell surface receptors or sensory organs. Integrating these time-varying, multi-sensory, and often…
In this paper, we aim at modelling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modelling framework is based on interconnected logical regulatory networks a la Rene Thomas equipped…
Logical models have been successfully used to describe regulatory and signaling networks without requiring quantitative data. However, existing data is insufficient to adequately define a unique model, rendering the parametrization of a…
The design of a parallel computing system using several thousands or even up to a million processors asks for processing units that are simple and thus small in space, to make as many processing units as possible fit on a single die. The…
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex…
Boolean networks are popular tools for the exploration of qualitative dynamical properties of biological systems. Several dynamical interpretations have been proposed based on the same logical structure that captures the interactions…
The regulation of the cell state is a complex process involving several components. These complex dynamics can be modeled using Boolean networks, allowing us to explain the existence of different cell states and the transition between them.…
The emergence of Context-aware systems in the domains of autonomic, monitoring, and safety-critical applications asks for the definition of methods to formally assess their correctness and dependability properties. Many of these properties…
We address the problem of analysing the complexity of concurrent programs written in Pi-calculus. We are interested in parallel complexity, or span, understood as the execution time in a model with maximal parallelism. A type system for…
Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC…
A new method for the simulation of evolving multi-domains problems has been introduced in a previous work (RealIMotion), Florez et al. (2020). In this article further developments of the model will be presented. The main focus here is a…
Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into…
Boolean automata networks (BANs) are a generalisation of Boolean cellular automata. In such, any theorem describing the way BANs compute information is a strong tool that can be applied to a wide range of models of computation. In this…
The unknown parameters of simulation models often need to be calibrated using observed data. When simulation models are expensive, calibration is usually carried out with an emulator. The effectiveness of the calibration process can be…
There is a growing trend in molecular and synthetic biology of using mechanistic (non machine learning) models to design biomolecular networks. Once designed, these networks need to be validated by experimental results to ensure the…
Control parallelism and data parallelism is mostly reasoned and optimized as separate functions. Because of this, workloads that are irregular, fine-grain and dynamic such as dynamic graph processing become very hard to scale. An…
We introduce the PBS-calculus to represent and reason on quantum computations involving coherent control of quantum operations. Coherent control, and in particular indefinite causal order, is known to enable multiple computational and…
Programmable Logic Controllers (PLCs) are widely used in industrial automation to control physical systems. As PLC applications become increasingly complex, ensuring their correctness is crucial. Existing formal verification techniques…
Recent work has shown that the input-output behavior of some machine learning systems can be captured symbolically using Boolean expressions or tractable Boolean circuits, which facilitates reasoning about the behavior of these systems.…
Discrete modelling frameworks of Biological networks can be divided in two distinct categories: Boolean and Multi-valued. Although Multi-valued networks are more expressive for qualifying the regulatory behaviours modelled by more than two…