Maintenance of Strongly Connected Component in Shared-memory Graph

In this paper, we present an on-line fully dynamic algorithm for maintaining strongly connected component of a directed graph in a shared memory architecture. The edges and vertices are added or deleted concurrently by fixed number of threads. To the best of our knowledge, this is the first work to propose using linearizable concurrent directed graph and is build using both ordered and unordered list-based set. We provide an empirical comparison against sequential and coarse-grained. The results show our algorithm's throughput is increased between 3 to 6x depending on different workload distributions and applications. We believe that there are huge applications in the on-line graph. Finally, we show how the algorithm can be extended to community detection in on-line graph.Comment: 29 pages, 4 figures, Accepted in the Conference NETYS-201

Perturbed Timed Automata

We consider timed automata whose clocks are imperfect. For a given perturbation error 0 \u3c ε \u3c 1, the perturbed language of a timed automaton is obtained by letting its clocks change at a rate within the interval [1 - ε, 1 + ε]. We show that the perturbed language of a timed automaton with a single clock can be captured by a deterministic timed automaton. This leads to a decision procedure for the language inclusion problem for systems modeled as products of 1-clock automata with imperfect clocks. We also prove that determinization and decidability of language inclusion are not possible for multi-clock automata, even with perturbation

Limit Synchronization in Markov Decision Processes

Markov decision processes (MDP) are finite-state systems with both strategic and probabilistic choices. After fixing a strategy, an MDP produces a sequence of probability distributions over states. The sequence is eventually synchronizing if the probability mass accumulates in a single state, possibly in the limit. Precisely, for 0 <= p <= 1 the sequence is p-synchronizing if a probability distribution in the sequence assigns probability at least p to some state, and we distinguish three synchronization modes: (i) sure winning if there exists a strategy that produces a 1-synchronizing sequence; (ii) almost-sure winning if there exists a strategy that produces a sequence that is, for all epsilon > 0, a (1-epsilon)-synchronizing sequence; (iii) limit-sure winning if for all epsilon > 0, there exists a strategy that produces a (1-epsilon)-synchronizing sequence. We consider the problem of deciding whether an MDP is sure, almost-sure, limit-sure winning, and we establish the decidability and optimal complexity for all modes, as well as the memory requirements for winning strategies. Our main contributions are as follows: (a) for each winning modes we present characterizations that give a PSPACE complexity for the decision problems, and we establish matching PSPACE lower bounds; (b) we show that for sure winning strategies, exponential memory is sufficient and may be necessary, and that in general infinite memory is necessary for almost-sure winning, and unbounded memory is necessary for limit-sure winning; (c) along with our results, we establish new complexity results for alternating finite automata over a one-letter alphabet

On the decidability and complexity of problems for restricted hierarchical hybrid systems

We study variants of a recently introduced hybrid system model, called a Hierarchical Piecewise Constant Derivative (HPCD). These variants (loosely called Restricted HPCDs) form a class of natural models with similarities to many other well known hybrid system models in the literature such as Stopwatch Automata, Rectangular Automata and PCDs. We study the complexity of reachability and mortality problems for variants of RHPCDs and show a variety of results, depending upon the allowed powers. These models form a useful tool for the study of the complexity of such problems for hybrid systems, due to their connections with existing models. We show that the reachability problem and the mortality problem are co-NP-hard for bounded 3-dimensional RHPCDs (3-RHPCDs). Reachability is shown to be in PSPACE, even for n-dimensional RHPCDs. We show that for an unbounded 3-RHPCD, the reachability and mortality problems become undecidable. For a nondeterministic variant of 2-RHPCDs, the reachability problem is shown to be PSPACE-complete

Long lived transients in gene regulation

Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof

Towards concolic testing for hybrid systems

Hybrid systems exhibit both continuous and discrete behavior. Analyzing hybrid systems is known to be hard. Inspired by the idea of concolic testing (of programs), we investigate whether we can combine random sampling and symbolic execution in order to effectively verify hybrid systems. We identify a sufficient condition under which such a combination is more effective than random sampling. Furthermore, we analyze different strategies of combining random sampling and symbolic execution and propose an algorithm which allows us to dynamically switch between them so as to reduce the overall cost. Our method has been implemented as a web-based checker named HYCHECKER. HYCHECKER has been evaluated with benchmark hybrid systems and a water treatment system in order to test its effectiveness.CPCI-S(ISTP)[email protected]; [email protected]

Fluent temporal logic for discrete-time event-based models

Fluent model checking is an automated technique for verifying that an event-based operational model satisfies some state-based declarative properties. The link between the event-based and state-based formalisms is defined through fluents which are state predicates whose value are determined by the occurrences of initiating and terminating events that make the fluents values become true or false, respectively. The existing fluent temporal logic is convenient for reasoning about untimed event-based models but difficult to use for timed models. The paper extends fluent temporal logic with temporal operators for modelling timed properties of discrete-time event-based models. It presents two approaches that differ on whether the properties model the system state after the occurrence of each event or at a fixed time rate. Model checking of timed properties is made possible by translating them into the existing untimed framework. Copyright 2005 ACM

Model checking the evolution of gene regulatory networks

The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs—an important problem of interest in evolutionary biology—more efficiently than the classical simulation method. We specify the property in linear temporal logic. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights

Verification and Control of Partially Observable Probabilistic Real-Time Systems

We propose automated techniques for the verification and control of probabilistic real-time systems that are only partially observable. To formally model such systems, we define an extension of probabilistic timed automata in which local states are partially visible to an observer or controller. We give a probabilistic temporal logic that can express a range of quantitative properties of these models, relating to the probability of an event's occurrence or the expected value of a reward measure. We then propose techniques to either verify that such a property holds or to synthesise a controller for the model which makes it true. Our approach is based on an integer discretisation of the model's dense-time behaviour and a grid-based abstraction of the uncountable belief space induced by partial observability. The latter is necessarily approximate since the underlying problem is undecidable, however we show how both lower and upper bounds on numerical results can be generated. We illustrate the effectiveness of the approach by implementing it in the PRISM model checker and applying it to several case studies, from the domains of computer security and task scheduling