TY - CONF
AB - We consider weighted automata with both positive and negative integer weights on edges and
study the problem of synchronization using adaptive strategies that may only observe whether
the current weight-level is negative or nonnegative. We show that the synchronization problem is decidable in polynomial time for deterministic weighted automata.
AU - Kretinsky, Jan
AU - Larsen, Kim
AU - Laursen, Simon
AU - Srba, Jiří
ID - 1499
TI - Polynomial time decidability of weighted synchronization under partial observability
VL - 42
ER -
TY - JOUR
AB - We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph algorithms with quadratic complexity to compute the simulation relation. We present an automated technique for assume-guarantee style reasoning for compositional analysis of two-player games by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We show a tight link between two-player games and MDPs, and as a consequence the results for games are lifted to MDPs with qualitative properties. We have implemented our algorithms and show that the compositional analysis leads to significant improvements.
AU - Chatterjee, Krishnendu
AU - Chmelik, Martin
AU - Daca, Przemyslaw
ID - 1501
IS - 2
JF - Formal Methods in System Design
TI - CEGAR for compositional analysis of qualitative properties in Markov decision processes
VL - 47
ER -
TY - CONF
AB - We extend the theory of input-output conformance with operators for merge and quotient. The former is useful when testing against multiple requirements or views. The latter can be used to generate tests for patches of an already tested system. Both operators can combine systems with different action alphabets, which is usually the case when constructing complex systems and specifications from parts, for instance different views as well as newly defined functionality of a~previous version of the system.
AU - Beneš, Nikola
AU - Daca, Przemyslaw
AU - Henzinger, Thomas A
AU - Kretinsky, Jan
AU - Nickovic, Dejan
ID - 1502
SN - 978-1-4503-3471-6
TI - Complete composition operators for IOCO-testing theory
ER -
TY - JOUR
AB - Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time.
AU - Ruess, Jakob
AU - Parise, Francesca
AU - Milias Argeitis, Andreas
AU - Khammash, Mustafa
AU - Lygeros, John
ID - 1538
IS - 26
JF - PNAS
TI - Iterative experiment design guides the characterization of a light-inducible gene expression circuit
VL - 112
ER -
TY - JOUR
AB - Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space.
AU - Ruess, Jakob
ID - 1539
IS - 24
JF - Journal of Chemical Physics
TI - Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space
VL - 143
ER -