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Search Results: 1 - 10 of 125 matches for " Lubo? Brim "
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Platform Dependent Verification: On Engineering Verification Tools for 21st Century
LuboBrim,Ji?í Barnat
Electronic Proceedings in Theoretical Computer Science , 2011, DOI: 10.4204/eptcs.72.1
Abstract: The paper overviews recent developments in platform-dependent explicit-state LTL model checking.
Using Strategy Improvement to Stay Alive
LuboBrim,Jakub Chaloupka
Electronic Proceedings in Theoretical Computer Science , 2010, DOI: 10.4204/eptcs.25.8
Abstract: We design a novel algorithm for solving Mean-Payoff Games (MPGs). Besides solving an MPG in the usual sense, our algorithm computes more information about the game, information that is important with respect to applications. The weights of the edges of an MPG can be thought of as a gained/consumed energy -- depending on the sign. For each vertex, our algorithm computes the minimum amount of initial energy that is sufficient for player Max to ensure that in a play starting from the vertex, the energy level never goes below zero. Our algorithm is not the first algorithm that computes the minimum sufficient initial energies, but according to our experimental study it is the fastest algorithm that computes them. The reason is that it utilizes the strategy improvement technique which is very efficient in practice.
On Expressing and Monitoring Oscillatory Dynamics
Petr Dluho?,LuboBrim,David ?afránek
Electronic Proceedings in Theoretical Computer Science , 2012, DOI: 10.4204/eptcs.92.6
Abstract: To express temporal properties of dense-time real-valued signals, the Signal Temporal Logic (STL) has been defined by Maler et al. The work presented a monitoring algorithm deciding the satisfiability of STL formulae on finite discrete samples of continuous signals. The logic has been used to express and analyse biological systems, but it is not expressive enough to sufficiently distinguish oscillatory properties important in biology. In this paper we define the extended logic STL* in which STL is augmented with a signal-value freezing operator allowing us to express (and distinguish) detailed properties of biological oscillations. The logic is supported by a monitoring algorithm prototyped in Matlab. The monitoring procedure of STL* is evaluated on a biologically-relevant case study.
DiVinE-CUDA - A Tool for GPU Accelerated LTL Model Checking
Ji?í Barnat,LuboBrim,Milan ?e?ka
Electronic Proceedings in Theoretical Computer Science , 2009, DOI: 10.4204/eptcs.14.8
Abstract: In this paper we present a tool that performs CUDA accelerated LTL Model Checking. The tool exploits parallel algorithm MAP adjusted to the NVIDIA CUDA architecture in order to efficiently detect the presence of accepting cycles in a directed graph. Accepting cycle detection is the core algorithmic procedure in automata-based LTL Model Checking. We demonstrate that the tool outperforms non-accelerated version of the algorithm and we discuss where the limits of the tool are and what we intend to do in the future to avoid them.
Computing Optimal Cycle Mean in Parallel on CUDA
Ji?í Barnat,Petr Bauch,LuboBrim,Milan ?e?ka
Electronic Proceedings in Theoretical Computer Science , 2011, DOI: 10.4204/eptcs.72.8
Abstract: Computation of optimal cycle mean in a directed weighted graph has many applications in program analysis, performance verification in particular. In this paper we propose a data-parallel algorithmic solution to the problem and show how the computation of optimal cycle mean can be efficiently accelerated by means of CUDA technology. We show how the problem of computation of optimal cycle mean is decomposed into a sequence of data-parallel graph computation primitives and show how these primitives can be implemented and optimized for CUDA computation. Finally, we report a fivefold experimental speed up on graphs representing models of distributed systems when compared to best sequential algorithms.
BioDiVinE: A Framework for Parallel Analysis of Biological Models
Ji?í Barnat,LuboBrim,Ivana ?erná,Sven Dra?an
Electronic Proceedings in Theoretical Computer Science , 2009, DOI: 10.4204/eptcs.6.3
Abstract: In this paper a novel tool BioDiVinEfor parallel analysis of biological models is presented. The tool allows analysis of biological models specified in terms of a set of chemical reactions. Chemical reactions are transformed into a system of multi-affine differential equations. BioDiVinE employs techniques for finite discrete abstraction of the continuous state space. At that level, parallel analysis algorithms based on model checking are provided. In the paper, the key tool features are described and their application is demonstrated by means of a case study.
Robustness Analysis of Stochastic Biochemical Systems
Milan ?eska, David ?afránek, Sven Dra?an, LuboBrim
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0094553
Abstract: We propose a new framework for rigorous robustness analysis of stochastic biochemical systems that is based on probabilistic model checking techniques. We adapt the general definition of robustness introduced by Kitano to the class of stochastic systems modelled as continuous time Markov Chains in order to extensively analyse and compare robustness of biological models with uncertain parameters. The framework utilises novel computational methods that enable to effectively evaluate the robustness of models with respect to quantitative temporal properties and parameters such as reaction rate constants and initial conditions. We have applied the framework to gene regulation as an example of a central biological mechanism where intrinsic and extrinsic stochasticity plays crucial role due to low numbers of DNA and RNA molecules. Using our methods we have obtained a comprehensive and precise analysis of stochastic dynamics under parameter uncertainty. Furthermore, we apply our framework to compare several variants of two-component signalling networks from the perspective of robustness with respect to intrinsic noise caused by low populations of signalling components. We have successfully extended previous studies performed on deterministic models (ODE) and showed that stochasticity may significantly affect obtained predictions. Our case studies demonstrate that the framework can provide deeper insight into the role of key parameters in maintaining the system functionality and thus it significantly contributes to formal methods in computational systems biology.
Analysing Sanity of Requirements for Avionics Systems (Preliminary Version)
Ji?í Barnat,Petr Bauch,Nikola Bene?,LuboBrim,Jan Beran,Tomá? Kratochvíla
Computer Science , 2015,
Abstract: In the last decade it became a common practice to formalise software requirements to improve the clarity of users' expectations. In this work we build on the fact that functional requirements can be expressed in temporal logic and we propose new sanity checking techniques that automatically detect flaws and suggest improvements of given requirements. Specifically, we describe and experimentally evaluate approaches to consistency and redundancy checking that identify all inconsistencies and pinpoint their exact source (the smallest inconsistent set). We further report on the experience obtained from employing the consistency and redundancy checking in an industrial environment. To complete the sanity checking we also describe a semi-automatic completeness evaluation that can assess the coverage of user requirements and suggest missing properties the user might have wanted to formulate. The usefulness of our completeness evaluation is demonstrated in a case study of an aeroplane control system.
Non-Trivial Linkup of Both Compact-Neutron-Object and Outer-Empty-Space Metrics  [PDF]
Lubo? Neslu?an
International Journal of Astronomy and Astrophysics (IJAA) , 2014, DOI: 10.4236/ijaa.2014.41001
Abstract:

In 2011, Chinese researcher Ni found the solution of the Oppenheimer-Volkoff problem for a stable configuration of stellar object with no internal source of energy. The Ni’s solution is the nonrotating hollow sphere having not only an outer, but an inner physical radius as well. The upper mass of the object is not constrained. In our paper, we contribute to the description of the solution. Specifically, we give the explicit description of metrics inside the object and attempt to link it with that in the corresponding outer Schwarzschild solution of Einstein field equations. This task appears to be non-trivial. We discuss the problem and suggest a way how to achieve the continuous linkup of both object-interior and outer-Schwarzschild metrics. Our suggestion implies an important fundamental consequence: there is no universal relativistic speed limit, but every compact object shapes the adjacent spacetime and this action results in the specific speed limit for the spacetime dominated by the object. Regardless our suggestion will definitively be proved or the successful linkup will also be achieved in else, still unknown way, the success in the linkup represents a constraint for the physical acceptability of the models of compact objects.

Another Way of the Continuous Linkup of Neutron-Star-Body and Surrounding Empty-Space Metrics  [PDF]
Lubo? Neslu?an
International Journal of Astronomy and Astrophysics (IJAA) , 2014, DOI: 10.4236/ijaa.2014.42035
Abstract:

The metrics of the compact objects should be the continuous function of coordinates. The metrics inside every object is set by its internal structure. The metrics in the adjacent empty space is described by the outer Schwarzschild or Kerr solution of the Einstein field equations. It appears that the linkup of both object-interior and empty-space metrics is not continuous at the physical surfaces of the objects for the common, generally (by convention) accepted set of assumptions. We suggest the new way of how to achieve the success in the linkup, which does not assume the higher value of the relativistic speed limit in the empty space governed by the object, in contrast to our previous suggestion. We also give a more detailed explanation of the existence of inner physical surface of compact objects and suggest the way of the linkup of metrics in this surface. To achieve the continuous linkup, we assume a lower value of the speed limit in the object’s interior as well as a new gauging of the outer Schwarzschild solution for the inner empty space of the object. Newly established gauging constants are calculated and the success of the linkup is shown in several examples. The new gauging implies a lower gravitational attraction (lower gravitational constant) in the inner empty space in comparison with that in the outer space, which is measured in the common, observed, gravitational interactions of material objects.

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