Related papers: A Process Calculus for Molecular Interaction Maps
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
We advocates here the use of (mathematical) logic for systems biology, as a unified framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these properties. The…
Artificial intelligence (AI) is reshaping computational and network biology by enabling new approaches to decode cellular communication networks. We introduce Hierarchical Molecular Language Models (HMLMs), a novel framework that models…
In this paper we work on (bi)simulation semantics of processes that exhibit both nondeterministic and probabilistic behaviour. We propose a probabilistic extension of the modal mu-calculus and show how to derive characteristic formulae for…
Reaction systems are a computational model inspired by the bio-chemical reactions that happen inside biological cells. They have been and currently are studied for their many nice theoretical properties. They are also a useful modeling tool…
Mathematical modelling and numerical simulations of interaction populations are crucial topics in systems biology. The interactions of ecological models may occur among individuals of the same species or individuals of different species.…
Signalling pathways are abstractions that help life scientists structure the coordination of cellular activity. Cross-talk between pathways accounts for many of the complex behaviours exhibited by signalling pathways and is often critical…
In this paper, we aim to synthesize cell microscopy images under different molecular interventions, motivated by practical applications to drug development. Building on the recent success of graph neural networks for learning molecular…
The Ambient Logic (AL) has been proposed for expressing properties of process mobility in the calculus of Mobile Ambients (MA), and as a basis for query languages on semistructured data. In this paper, we study the expressiveness of AL. We…
Nowadays, data-intensive applications are gaining popularity and, together with this trend, processing-in-memory (PIM)-based systems are being given more attention and have become more relevant. This paper describes an analytical modeling…
Quantum chemical studies of reactivity involve calculations on a large number of molecular structures and comparison of their energies. Already the set-up of these calculations limits the scope of the results that one will obtain, because…
Social media mining has become one of the most popular research areas in Big Data with the explosion of social networking information from Facebook, Twitter, LinkedIn, Weibo and so on. Understanding and representing the structure of a…
In current molecular communication (MC) systems, performing computational operations at the nanoscale remains challenging, restricting their applicability in complex scenarios such as adaptive biochemical control and advanced nanoscale…
Although artificial intelligence (AI) has made significant progress in understanding molecules in a wide range of fields, existing models generally acquire the single cognitive ability from the single molecular modality. Since the hierarchy…
This paper presents the Pi-graphs, a visual paradigm for the modelling and verification of mobile systems. The language is a graphical variant of the Pi-calculus with iterators to express non-terminating behaviors. The operational semantics…
Molecular communication (MC) engineering is inspired by the use of chemical signals as information carriers in cell biology. The biological nature of chemical signaling makes MC a promising methodology for interdisciplinary applications…
While much of the current study on quantum computation employs low-level formalisms such as quantum circuits, several high-level languages/calculi have been recently proposed aiming at structured quantum programming. The current work…
Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…
The dynamic properties and independence structure of stochastic kinetic models (SKMs) are analyzed. An SKM is a highly multivariate jump process used to model chemical reaction networks, particularly those in biochemical and cellular…
We use dialgebras, generalising both algebras and coalgebras, as a complement of the standard coalgebraic framework, aimed at describing the semantics of an interactive system by the means of reaction rules. In this model, interaction is…