A survey of gene regulatory networks modelling methods: from differential equations, to Boolean and qualitative bioinspired models

R Barbuti, R Gori, P Milazzo, L Nasti - Journal of Membrane Computing, 2020 - Springer
Abstract Gene Regulatory Networks (GRNs) represent the interactions among genes
regulating the activation of specific cell functionalities, such as reception of (chemical) …

Neural jump stochastic differential equations

J Jia, AR Benson - Advances in Neural Information …, 2019 - proceedings.neurips.cc
Many time series are effectively generated by a combination of deterministic continuous
flows along with discrete jumps sparked by stochastic events. However, we usually do not …

Noise in biomolecular systems: Modeling, analysis, and control implications

C Briat, M Khammash - Annual Review of Control, Robotics, and …, 2023 - annualreviews.org
While noise is generally associated with uncertainties and often has a negative connotation
in engineering, living organisms have evolved to adapt to (and even exploit) such …

Neural hybrid automata: Learning dynamics with multiple modes and stochastic transitions

M Poli, S Massaroli, L Scimeca… - Advances in …, 2021 - proceedings.neurips.cc
Effective control and prediction of dynamical systems require appropriate handling of
continuous-time and discrete, event-triggered processes. Stochastic hybrid systems (SHSs) …

Formalizing a notion of concentration robustness for biochemical networks

L Nasti, R Gori, P Milazzo - … Workshops, Toulouse, France, June 25-29 …, 2018 - Springer
The main goal of systems biology is to understand the dynamical properties of biological
systems by investigating the interactions among the components of a biological system. In …

Verifiable biology

S Konur, M Gheorghe… - Journal of the Royal …, 2023 - royalsocietypublishing.org
The formalization of biological systems using computational modelling approaches as an
alternative to mathematical-based methods has recently received much interest because …

Moment analysis of stochastic hybrid systems using semidefinite programming

KR Ghusinga, A Lamperski, A Singh - Automatica, 2020 - Elsevier
This paper proposes a method based on semidefinite programming for estimating moments
of stochastic hybrid systems (SHSs). The class of SHSs considered herein consists of a finite …

The Reasoning Engine: A Satisfiability Modulo Theories-Based Framework for Reasoning About Discrete Biological Models

B Yordanov, S Dunn, C Gravill, H Arora… - Journal of …, 2023 - liebertpub.com
We present a framework called the Reasoning Engine, which implements Satisfiability
Modulo Theories (SMT)-based methods within a unified computational environment to …

Decisiveness of stochastic systems and its application to hybrid models

P Bouyer, T Brihaye, M Randour, C Rivière… - Information and …, 2022 - Elsevier
In 2007, Abdulla et al. introduced the concept of decisiveness, an interesting tool for lifting
good properties of finite Markov chains to denumerable ones. Later, this concept was …

Feller property of regime-switching jump diffusion processes with hybrid jumps

HAP Blom - Stochastic Analysis and Applications, 2024 - Taylor & Francis
The transition kernel of an ℝ n-valued diffusion or jump diffusion process {X t} is known to
satisfy the Feller property if {X t} is the solution of an SDE whose coefficients are Lipschitz …