Computational modeling, formal analysis, and tools for systems biology

E Bartocci, P Lió - PLoS computational biology, 2016 - journals.plos.org
As the amount of biological data in the public domain grows, so does the range of modeling
and analysis techniques employed in systems biology. In recent years, a number of …

[图书][B] Formal methods for discrete-time dynamical systems

C Belta, B Yordanov, EA Gol - 2017 - Springer
In control theory, complex models of physical processes, such as systems of differential or
difference equations, are usually checked against simple specifications, such as stability …

Comparing different ODE modelling approaches for gene regulatory networks

A Polynikis, SJ Hogan, M Di Bernardo - Journal of theoretical biology, 2009 - Elsevier
A fundamental step in synthetic biology and systems biology is to derive appropriate
mathematical models for the purposes of analysis and design. For example, to synthesize a …

Synthesis of reactive switching protocols from temporal logic specifications

J Liu, N Ozay, U Topcu… - IEEE Transactions on …, 2013 - ieeexplore.ieee.org
We propose formal means for synthesizing switching protocols that determine the sequence
in which the modes of a switched system are activated to satisfy certain high-level …

Temporal logic control of discrete-time piecewise affine systems

B Yordanov, J Tumova, I Cerna… - IEEE Transactions on …, 2011 - ieeexplore.ieee.org
We present a computational framework for automatic synthesis of a feedback control
strategy for a discrete-time piecewise affine (PWA) system from a specification given as a …

From cardiac cells to genetic regulatory networks

R Grosu, G Batt, FH Fenton, J Glimm… - … Aided Verification: 23rd …, 2011 - Springer
A fundamental question in the treatment of cardiac disorders, such as tachycardia and
fibrillation, is under what circumstances does such a disorder arise? To answer to this …

Falsification of LTL safety properties in hybrid systems

E Plaku, LE Kavraki, MY Vardi - International Journal on Software Tools for …, 2013 - Springer
This paper develops a novel approach for the falsification of safety properties given by a
syntactically safe linear temporal logic (LTL) formula ϕ for hybrid systems with nonlinear …

Augmented finite transition systems as abstractions for control synthesis

P Nilsson, N Ozay, J Liu - Discrete Event Dynamic Systems, 2017 - Springer
This work is motivated by the problem of synthesizing switching protocols for continuous
switched systems described by differential or difference equations, in a way that guarantees …

Symbolic models for nonlinear time-delay systems using approximate bisimulations

G Pola, P Pepe, MD Di Benedetto, P Tabuada - Systems & Control Letters, 2010 - Elsevier
In this paper we show that incrementally stable nonlinear time-delay systems admit symbolic
models which are approximately equivalent, in the sense of approximate bisimulation, to the …

Neural abstractions

A Abate, A Edwards… - Advances in Neural …, 2022 - proceedings.neurips.cc
We present a novel method for the safety verification of nonlinear dynamical models that
uses neural networks to represent abstractions of their dynamics. Neural networks have …