Representing a P-complete problem by small trellis automata

A restricted case of the Circuit Value Problem known as the Sequential NOR Circuit Value Problem was recently used to obtain very succinct examples of conjunctive grammars, Boolean grammars and language equations representing P-complete languages (Okhotin, http://dx.doi.org/10.1007/978-3-540-74593-8_23 "A simple P-complete problem and its representations by language equations", MCU 2007). In this paper, a new encoding of the same problem is proposed, and a trellis automaton (one-way real-time cellular automaton) with 11 states solving this problem is constructed

Efficient Instantiation of Parameterised Boolean Equation Systems to Parity Games

Parameterised Boolean Equation Systems (PBESs) are sequences of Boolean fixed point equations with data variables, used for, e.g., verification of modal μ-calculus formulae for process algebraic specifications with data. Solving a PBES is usually done by instantiation to a Parity Game and then solving the game. Practical game solvers exist, but the instantiation step is the bottleneck. We enhance the instantiation in two steps. First, we transform the PBES to a Parameterised Parity Game (PPG), a PBES with each equation either conjunctive or disjunctive. Then we use LTSmin, that offers transition caching, efficient storage of states and both distributed and symbolic state space generation, for generating the game graph. To that end we define a language module for LTSmin, consisting of an encoding of variables with parameters into state vectors, a grouped transition relation and a dependency matrix to indicate the dependencies between parts of the state vector and transition groups. Benchmarks on some large case studies, show that the method speeds up the instantiation significantly and decreases memory usage drastically

ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra

Background: Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, with the goal to gain a better understanding of the system. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. Although there exist sophisticated algorithms to determine the dynamics of discrete models, their implementations usually require labor-intensive formatting of the model formulation, and they are oftentimes not accessible to users without programming skills. Efficient analysis methods are needed that are accessible to modelers and easy to use. Method: By converting discrete models into algebraic models, tools from computational algebra can be used to analyze their dynamics. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Results: A method for efficiently identifying attractors, and the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness, i.e., while the number of nodes in a biological network may be quite large, each node is affected only by a small number of other nodes, and robustness, i.e., small number of attractors

Invariant Generation through Strategy Iteration in Succinctly Represented Control Flow Graphs

We consider the problem of computing numerical invariants of programs, for instance bounds on the values of numerical program variables. More specifically, we study the problem of performing static analysis by abstract interpretation using template linear constraint domains. Such invariants can be obtained by Kleene iterations that are, in order to guarantee termination, accelerated by widening operators. In many cases, however, applying this form of extrapolation leads to invariants that are weaker than the strongest inductive invariant that can be expressed within the abstract domain in use. Another well-known source of imprecision of traditional abstract interpretation techniques stems from their use of join operators at merge nodes in the control flow graph. The mentioned weaknesses may prevent these methods from proving safety properties. The technique we develop in this article addresses both of these issues: contrary to Kleene iterations accelerated by widening operators, it is guaranteed to yield the strongest inductive invariant that can be expressed within the template linear constraint domain in use. It also eschews join operators by distinguishing all paths of loop-free code segments. Formally speaking, our technique computes the least fixpoint within a given template linear constraint domain of a transition relation that is succinctly expressed as an existentially quantified linear real arithmetic formula. In contrast to previously published techniques that rely on quantifier elimination, our algorithm is proved to have optimal complexity: we prove that the decision problem associated with our fixpoint problem is in the second level of the polynomial-time hierarchy.Comment: 35 pages, conference version published at ESOP 2011, this version is a CoRR version of our submission to Logical Methods in Computer Scienc

Computerized logic design of digital circuits

Procedure performs all work required for logic design of digital counters or sequential circuits and simplification of Boolean expressions. Program provides simple, accurate, and comprehensive logic design capability to users both experienced and totally inexperienced in logic desig

Parameter estimation for Boolean models of biological networks

Boolean networks have long been used as models of molecular networks and play an increasingly important role in systems biology. This paper describes a software package, Polynome, offered as a web service, that helps users construct Boolean network models based on experimental data and biological input. The key feature is a discrete analog of parameter estimation for continuous models. With only experimental data as input, the software can be used as a tool for reverse-engineering of Boolean network models from experimental time course data.Comment: Web interface of the software is available at http://polymath.vbi.vt.edu/polynome