Computed microtomography visualization and quantification of mouse ischemic brain lesion by nonionic radio contrast agents.

AIM: To explore the possibility of brain imaging by microcomputed tomography (microCT) using x-ray contrasting methods to visualize mouse brain ischemic lesions after middle cerebral artery occlusion (MCAO). ----- METHODS: Isolated brains were immersed in ionic or nonionic radio contrast agent (RCA) for 5 days and subsequently scanned using microCT scanner. To verify whether ex-vivo microCT brain images can be used to characterize ischemic lesions, they were compared to Nissl stained serial histological sections of the same brains. To verify if brains immersed in RCA may be used afterwards for other methods, subsequent immunofluorescent labeling with anti-NeuN was performed. ----- RESULTS: Nonionic RCA showed better gray to white matter contrast in the brain, and therefore was selected for further studies. MicroCT measurement of ischemic lesion size and cerebral edema significantly correlated with the values determined by Nissl staining (ischemic lesion size: P=0.0005; cerebral edema: P=0.0002). Brain immersion in nonionic RCA did not affect subsequent immunofluorescent analysis and NeuN immunoreactivity. ----- CONCLUSION: MicroCT method was proven to be suitable for delineation of the ischemic lesion from the non-infarcted tissue, and quantification of lesion volume and cerebral edema

Algorithmic Verification of Asynchronous Programs

Asynchronous programming is a ubiquitous systems programming idiom to manage concurrent interactions with the environment. In this style, instead of waiting for time-consuming operations to complete, the programmer makes a non-blocking call to the operation and posts a callback task to a task buffer that is executed later when the time-consuming operation completes. A co-operative scheduler mediates the interaction by picking and executing callback tasks from the task buffer to completion (and these callbacks can post further callbacks to be executed later). Writing correct asynchronous programs is hard because the use of callbacks, while efficient, obscures program control flow. We provide a formal model underlying asynchronous programs and study verification problems for this model. We show that the safety verification problem for finite-data asynchronous programs is expspace-complete. We show that liveness verification for finite-data asynchronous programs is decidable and polynomial-time equivalent to Petri Net reachability. Decidability is not obvious, since even if the data is finite-state, asynchronous programs constitute infinite-state transition systems: both the program stack and the task buffer of pending asynchronous calls can be potentially unbounded. Our main technical construction is a polynomial-time semantics-preserving reduction from asynchronous programs to Petri Nets and conversely. The reduction allows the use of algorithmic techniques on Petri Nets to the verification of asynchronous programs. We also study several extensions to the basic models of asynchronous programs that are inspired by additional capabilities provided by implementations of asynchronous libraries, and classify the decidability and undecidability of verification questions on these extensions.Comment: 46 pages, 9 figure

Polynomial Time Algorithms for Branching Markov Decision Processes and Probabilistic Min(Max) Polynomial Bellman Equations

We show that one can approximate the least fixed point solution for a multivariate system of monotone probabilistic max(min) polynomial equations, referred to as maxPPSs (and minPPSs, respectively), in time polynomial in both the encoding size of the system of equations and in log(1/epsilon), where epsilon > 0 is the desired additive error bound of the solution. (The model of computation is the standard Turing machine model.) We establish this result using a generalization of Newton's method which applies to maxPPSs and minPPSs, even though the underlying functions are only piecewise-differentiable. This generalizes our recent work which provided a P-time algorithm for purely probabilistic PPSs. These equations form the Bellman optimality equations for several important classes of infinite-state Markov Decision Processes (MDPs). Thus, as a corollary, we obtain the first polynomial time algorithms for computing to within arbitrary desired precision the optimal value vector for several classes of infinite-state MDPs which arise as extensions of classic, and heavily studied, purely stochastic processes. These include both the problem of maximizing and mininizing the termination (extinction) probability of multi-type branching MDPs, stochastic context-free MDPs, and 1-exit Recursive MDPs. Furthermore, we also show that we can compute in P-time an epsilon-optimal policy for both maximizing and minimizing branching, context-free, and 1-exit-Recursive MDPs, for any given desired epsilon > 0. This is despite the fact that actually computing optimal strategies is Sqrt-Sum-hard and PosSLP-hard in this setting. We also derive, as an easy consequence of these results, an FNP upper bound on the complexity of computing the value (within arbitrary desired precision) of branching simple stochastic games (BSSGs)

Parikh Image of Pushdown Automata

We compare pushdown automata (PDAs for short) against other representations. First, we show that there is a family of PDAs over a unary alphabet with $n$ states and $p \geq 2n + 4$ stack symbols that accepts one single long word for which every equivalent context-free grammar needs $\Omega(n^2(p-2n-4))$ variables. This family shows that the classical algorithm for converting a PDA to an equivalent context-free grammar is optimal even when the alphabet is unary. Moreover, we observe that language equivalence and Parikh equivalence, which ignores the ordering between symbols, coincide for this family. We conclude that, when assuming this weaker equivalence, the conversion algorithm is also optimal. Second, Parikh's theorem motivates the comparison of PDAs against finite state automata. In particular, the same family of unary PDAs gives a lower bound on the number of states of every Parikh-equivalent finite state automaton. Finally, we look into the case of unary deterministic PDAs. We show a new construction converting a unary deterministic PDA into an equivalent context-free grammar that achieves best known bounds.Comment: 17 pages, 2 figure

Analysis of Probabilistic Basic Parallel Processes

Basic Parallel Processes (BPPs) are a well-known subclass of Petri Nets. They are the simplest common model of concurrent programs that allows unbounded spawning of processes. In the probabilistic version of BPPs, every process generates other processes according to a probability distribution. We study the decidability and complexity of fundamental qualitative problems over probabilistic BPPs -- in particular reachability with probability 1 of different classes of target sets (e.g. upward-closed sets). Our results concern both the Markov-chain model, where processes are scheduled randomly, and the MDP model, where processes are picked by a scheduler.Comment: This is the technical report for a FoSSaCS'14 pape

Towards Efficient Verification of Population Protocols

Population protocols are a well established model of computation by anonymous, identical finite state agents. A protocol is well-specified if from every initial configuration, all fair executions reach a common consensus. The central verification question for population protocols is the well-specification problem: deciding if a given protocol is well-specified. Esparza et al. have recently shown that this problem is decidable, but with very high complexity: it is at least as hard as the Petri net reachability problem, which is EXPSPACE-hard, and for which only algorithms of non-primitive recursive complexity are currently known. In this paper we introduce the class WS3 of well-specified strongly-silent protocols and we prove that it is suitable for automatic verification. More precisely, we show that WS3 has the same computational power as general well-specified protocols, and captures standard protocols from the literature. Moreover, we show that the membership problem for WS3 reduces to solving boolean combinations of linear constraints over N. This allowed us to develop the first software able to automatically prove well-specification for all of the infinitely many possible inputs.Comment: 29 pages, 1 figur