Related papers: A Model Checking-based Analysis Framework for Syst…
Recent measurements of durations of non-equilibrium processes provide valuable information on microscopic mechanisms and energetics. Comprehensive theory for corresponding experiments so far is well developed for single-particle systems…
Network equilibrium models represent a versatile tool for the analysis of interconnected objects and their relationships. They have been widely employed in both science and engineering to study the behavior of complex systems under various…
The molecular computing has been successfully employed to solve more and more complex computation problems. However, as an important complex problem, the model checking are still far from fully resolved under the circumstance of molecular…
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…
Understanding the oscillating behaviors that govern organisms' internal biological processes requires interdisciplinary efforts combining both biological and computer experiments, as the latter can complement the former by simulating…
Mathematical modelling allows us to concisely describe fundamental principles in biology. Analysis of models can help to both explain known phenomena, and predict the existence of new, unseen behaviours. Model analysis is often a complex…
Model checking is a technique to automatically assess whether a model of the behaviour of a system meets its requirements. Evidence explaining why the behaviour does (not) meet its requirements is essential for the user to understand the…
The development of complex multicellular organisms from a single parent cell is a highly orchestrated process that cells conduct collectively without central guidance, creating intricate dynamic patterns essential for development and…
We introduce a machine learning approach to model checking temporal logic, with application to formal hardware verification. Model checking answers the question of whether every execution of a given system satisfies a desired temporal logic…
Dynamical systems in the life sciences are often composed of complex mixtures of overlapping behavioral regimes. Cellular subpopulations may shift from cycling to equilibrium dynamics or branch towards different developmental fates. The…
Transaction-level modeling with SystemC has been very successful in describing the behavior of embedded systems by providing high-level executable models, in which many of them have inherent probabilistic behaviors, e.g., random data and…
Accurate comparisons between theoretical models and experimental data are critical for scientific progress. However, inferred physical model parameters can vary significantly with the chosen physics model, highlighting the importance of…
Model checkers use automated state exploration in order to prove various properties such as reachability, non-reachability, and bisimulation over state transition systems. While model checkers have proved valuable for locating errors in…
Delays in biological systems may be used to model events for which the underlying dynamics cannot be precisely observed. Mathematical modeling of biological systems with delays is usually based on Delay Differential Equations (DDEs), a kind…
In the field of modeling, the word validation refers to simple comparisons between model outputs and experimental data. Usually, this comparison constitutes plotting the model results against data on the same axes to provide a visual…
This paper presents a method for modeling biological systems which combines formal techniques on intervals, numerical simulations and satisfaction of Signal Temporal Logic (STL) formulas. The main modeling challenge addressed by this…
In this paper, we study model-checking of linear-time properties in multi-valued systems. Safety property, invariant property, liveness property, persistence and dual-persistence properties in multi-valued logic systems are introduced. Some…
We describe a novel procedure for deciding when a mass-action model is incompatible with observed steady-state data that does not require any parameter estimation. Thus, we avoid the difficulties of nonlinear optimization typically…
Computational models and simulations are not just appealing because of their intrinsic characteristics across spatiotemporal scales, scalability, and predictive power, but also because the set of problems in cancer biomedicine that can be…
Parameterizing mathematical models of biological systems often requires fitting to stable periodic data. In cardiac electrophysiology this typically requires converging to a stable action potential through long simulations. We explore this…