112 research outputs found
Reverse Engineering of Middleware for Verification of Robot Control Architectures
We consider the problem of automating the verification of distributed control
software relying on publish-subscribe middleware. In this scenario, the main
challenge is that software correctness depends intrinsically on correct usage
of middleware components, but structured models of such components might not be
available for analysis, e.g., because they are too large and complex to be
described precisely in a cost-effective way. To overcome this problem, we
propose to identify abstract models of middleware as finite-state automata, and
then to perform verification on the combined middleware and control software
models. Both steps are carried out in a computer-assisted way using
state-of-the-art techniques in automata-based identification and verification.
Our main contribution is to show that the combination of identification and
verification is feasible and useful when considering typical issues that arise
in the implementation of distributed control software.Comment: 14 pages, 4 figures. The final version of the article is published in
Proc. of "Simulation, Modeling, and Programming for Autonomous Robots",
SIMPAR 2014 (published by Springer
Efficient Symmetry Reduction and the Use of State Symmetries for Symbolic Model Checking
One technique to reduce the state-space explosion problem in temporal logic
model checking is symmetry reduction. The combination of symmetry reduction and
symbolic model checking by using BDDs suffered a long time from the
prohibitively large BDD for the orbit relation. Dynamic symmetry reduction
calculates representatives of equivalence classes of states dynamically and
thus avoids the construction of the orbit relation. In this paper, we present a
new efficient model checking algorithm based on dynamic symmetry reduction. Our
experiments show that the algorithm is very fast and allows the verification of
larger systems. We additionally implemented the use of state symmetries for
symbolic symmetry reduction. To our knowledge we are the first who investigated
state symmetries in combination with BDD based symbolic model checking
Non-Zero Sum Games for Reactive Synthesis
In this invited contribution, we summarize new solution concepts useful for
the synthesis of reactive systems that we have introduced in several recent
publications. These solution concepts are developed in the context of non-zero
sum games played on graphs. They are part of the contributions obtained in the
inVEST project funded by the European Research Council.Comment: LATA'16 invited pape
Interrupt Timed Automata: verification and expressiveness
We introduce the class of Interrupt Timed Automata (ITA), a subclass of
hybrid automata well suited to the description of timed multi-task systems with
interruptions in a single processor environment. While the reachability problem
is undecidable for hybrid automata we show that it is decidable for ITA. More
precisely we prove that the untimed language of an ITA is regular, by building
a finite automaton as a generalized class graph. We then establish that the
reachability problem for ITA is in NEXPTIME and in PTIME when the number of
clocks is fixed. To prove the first result, we define a subclass ITA- of ITA,
and show that (1) any ITA can be reduced to a language-equivalent automaton in
ITA- and (2) the reachability problem in this subclass is in NEXPTIME (without
any class graph). In the next step, we investigate the verification of real
time properties over ITA. We prove that model checking SCL, a fragment of a
timed linear time logic, is undecidable. On the other hand, we give model
checking procedures for two fragments of timed branching time logic. We also
compare the expressive power of classical timed automata and ITA and prove that
the corresponding families of accepted languages are incomparable. The result
also holds for languages accepted by controlled real-time automata (CRTA), that
extend timed automata. We finally combine ITA with CRTA, in a model which
encompasses both classes and show that the reachability problem is still
decidable. Additionally we show that the languages of ITA are neither closed
under complementation nor under intersection
Improving BDD Based Symbolic Model Checking with Isomorphism Exploiting Transition Relations
Symbolic model checking by using BDDs has greatly improved the applicability
of model checking. Nevertheless, BDD based symbolic model checking can still be
very memory and time consuming. One main reason is the complex transition
relation of systems. Sometimes, it is even not possible to generate the
transition relation, due to its exhaustive memory requirements. To diminish
this problem, the use of partitioned transition relations has been proposed.
However, there are still systems which can not be verified at all. Furthermore,
if the granularity of the partitions is too fine, the time required for
verification may increase. In this paper we target the symbolic verification of
asynchronous concurrent systems. For such systems we present an approach which
uses similarities in the transition relation to get further memory reductions
and runtime improvements. By applying our approach, even the verification of
systems with an previously intractable transition relation becomes feasible.Comment: In Proceedings GandALF 2011, arXiv:1106.081
Decreased transcription-coupled nucleotide excision repair capacity is associated with increased p53- and MLH1-independent apoptosis in response to cisplatin
Abstract
Background
One of the most commonly used classes of anti-cancer drugs presently in clinical practice is the platinum-based drugs, including cisplatin. The efficacy of cisplatin therapy is often limited by the emergence of resistant tumours following treatment. Cisplatin resistance is multi-factorial but can be associated with increased DNA repair capacity, mutations in p53 or loss of DNA mismatch repair capacity.
Methods
RNA interference (RNAi) was used to reduce the transcription-coupled nucleotide excision repair (TC-NER) capacity of several prostate and colorectal carcinoma cell lines with specific defects in p53 and/or DNA mismatch repair. The effect of small inhibitory RNAs designed to target the CSB (Cockayne syndrome group B) transcript on TC-NER and the sensitivity of cells to cisplatin-induced apoptosis was determined.
Results
These prostate and colon cancer cell lines were initially TC-NER proficient and RNAi against CSB significantly reduced their DNA repair capacity. Decreased TC-NER capacity was associated with an increase in the sensitivity of tumour cells to cisplatin-induced apoptosis, even in p53 null and DNA mismatch repair-deficient cell lines.
Conclusion
The present work indicates that CSB and TC-NER play a prominent role in determining the sensitivity of tumour cells to cisplatin even in the absence of p53 and DNA mismatch repair. These results further suggest that CSB represents a potential target for cancer therapy that may be important to overcome resistance to cisplatin in the clinic
Program Verification by Using DISCOVERER
Recent advances in program verification indicate that various verification problems can be reduced to semi-algebraic system (SAS for short) solving. An SAS consists of polynomial equations and polynomial inequalities. Algorithms for quantifier elimination of real closed fields are the general method for those problems. But the general method usually has low efficiency for specific problems. To overcome the bottleneck of program verification with a symbolic approach, one has to combine special techniques with the general method. Based on the work of complete discrimination systems of polynomials [33,31], we invented new theories and algorithms [32,30,35] for SAS solving and partly implemented them as a real symbolic computation tool in Maple named DISCOVERER. In this paper, we first summarize the results that we have done so far both on SAS-solving and program verification with DISCOVERER, and then discuss the future work in this direction, including SAS-solving itself, termination analysis and invariant generation of programs, and reachability computation of hybrid systems etc. ? IFIP International Federation for Information Processing 2008.EI
A Novel Method to Verify Multilevel Computational Models of Biological Systems Using Multiscale Spatio-Temporal Meta Model Checking
Insights gained from multilevel computational models of biological systems can be translated into real-life applications only if the model correctness has been verified first. One of the most frequently employed in silico techniques for computational model verification is model checking. Traditional model checking approaches only consider the evolution of numeric values, such as concentrations, over time and are appropriate for computational models of small scale systems (e.g. intracellular networks). However for gaining a systems level understanding of how biological organisms function it is essential to consider more complex large scale biological systems (e.g. organs). Verifying computational models of such systems requires capturing both how numeric values and properties of (emergent) spatial structures (e.g. area of multicellular population) change over time and across multiple levels of organization, which are not considered by existing model checking approaches. To address this limitation we have developed a novel approximate probabilistic multiscale spatio-temporal meta model checking methodology for verifying multilevel computational models relative to specifications describing the desired/expected system behaviour. The methodology is generic and supports computational models encoded using various high-level modelling formalisms because it is defined relative to time series data and not the models used to generate it. In addition, the methodology can be automatically adapted to case study specific types of spatial structures and properties using the spatio-temporal meta model checking concept. To automate the computational model verification process we have implemented the model checking approach in the software tool Mule (http://mule.modelchecking.org). Its applicability is illustrated against four systems biology computational models previously published in the literature encoding the rat cardiovascular system dynamics, the uterine contractions of labour, the Xenopus laevis cell cycle and the acute inflammation of the gut and lung. Our methodology and software will enable computational biologists to efficiently develop reliable multilevel computational models of biological systems
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