Related papers: A Model Checking-based Analysis Framework for Syst…
We introduce a framework for analyzing ordinary differential equation (ODE) models of biological networks using statistical model checking (SMC). A key aspect of our work is the modeling of single-cell variability by assigning a probability…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
A central problem in systems biology is to identify parameter values such that a biological model satisfies some behavioral constraints (\eg, time series). In this paper we focus on parameter synthesis for hybrid (continuous/discrete)…
Most available tools propose simulation frameworks to study models of biological systems, but simulation only explores a few of the most probable behaviours of the system. On the contrary, techniques such as model checking, coming from…
Model-based mutation testing uses altered test models to derive test cases that are able to reveal whether a modelled fault has been implemented. This requires conformance checking between the original and the mutated model. This paper…
In this paper we survey recent work on the use of statistical model checking techniques for biological applications. We begin with an overview of the basic modelling techniques for biochemical reactions and their corresponding stochastic…
Understanding control mechanisms in biological systems plays a crucial role in important applications, for instance in cell reprogramming. Boolean modeling allows the identification of possible efficient strategies, helping to reduce the…
The dynamics of systems biological processes are usually modeled by a system of ordinary differential equations (ODEs) with many unknown parameters that need to be inferred from noisy and sparse measurements. Here, we introduce…
Model checking is an established technique to formally verify automation systems which are required to be trusted. However, for sufficiently complex systems model checking becomes computationally infeasible. On the other hand, testing,…
Energy systems optimisation models are a leading tool for informing decisions in the energy transition. However, these models often remain opaque, and results are frequently presented without a clear discussion of their epistemic…
Boolean automata networks, genetic regulation networks, and metabolic networks are just a few examples of biological modelling by discrete dynamical systems (DDS). A major issue in modelling is the verification of the model against the…
Clinical trials are considered as the golden standard for medical device validation. However, many sacrifices have to be made during the design and conduction of the trials due to cost considerations and partial information, which may…
This report proposes a novel framework for a rigorous robustness analysis of stochastic biochemical systems. The technique is based on probabilistic model checking. We adapt the general definition of robustness introduced by Kitano to the…
Fault-tolerant distributed algorithms are central for building reliable spatially distributed systems. Unfortunately, the lack of a canonical precise framework for fault-tolerant algorithms is an obstacle for both verification and…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
Background: Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time…
Mathematical models are indispensable to the system biology toolkit for studying the structure and behavior of intracellular signaling networks. A common approach to modeling is to develop a system of equations that encode the known biology…
Model checking has been successfully applied to verification of computer hardware and software, communication systems and even biological systems. In this paper, we further push the boundary of its applications and show that it can be…
Quantitative properties of stochastic systems are usually specified in logics that allow one to compare the measure of executions satisfying certain temporal properties with thresholds. The model checking problem for stochastic systems with…
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…