Special Algorithm for Stability Analysis of Multistable Biological Regulatory Systems

We consider the problem of counting (stable) equilibriums of an important family of algebraic differential equations modeling multistable biological regulatory systems. The problem can be solved, in principle, using real quantifier elimination algorithms, in particular real root classification algorithms. However, it is well known that they can handle only very small cases due to the enormous computing time requirements. In this paper, we present a special algorithm which is much more efficient than the general methods. Its efficiency comes from the exploitation of certain interesting structures of the family of differential equations.Comment: 24 pages, 5 algorithms, 10 figure

Program Verification in the presence of complex numbers, functions with branch cuts etc

In considering the reliability of numerical programs, it is normal to "limit our study to the semantics dealing with numerical precision" (Martel, 2005). On the other hand, there is a great deal of work on the reliability of programs that essentially ignores the numerics. The thesis of this paper is that there is a class of problems that fall between these two, which could be described as "does the low-level arithmetic implement the high-level mathematics". Many of these problems arise because mathematics, particularly the mathematics of the complex numbers, is more difficult than expected: for example the complex function log is not continuous, writing down a program to compute an inverse function is more complicated than just solving an equation, and many algebraic simplification rules are not universally valid. The good news is that these problems are theoretically capable of being solved, and are practically close to being solved, but not yet solved, in several real-world examples. However, there is still a long way to go before implementations match the theoretical possibilities

Adapting Real Quantifier Elimination Methods for Conflict Set Computation

The satisfiability problem in real closed fields is decidable. In the context of satisfiability modulo theories, the problem restricted to conjunctive sets of literals, that is, sets of polynomial constraints, is of particular importance. One of the central problems is the computation of good explanations of the unsatisfiability of such sets, i.e.\ obtaining a small subset of the input constraints whose conjunction is already unsatisfiable. We adapt two commonly used real quantifier elimination methods, cylindrical algebraic decomposition and virtual substitution, to provide such conflict sets and demonstrate the performance of our method in practice

Polynomial Interrupt Timed Automata

Interrupt Timed Automata (ITA) form a subclass of stopwatch automata where reachability and some variants of timed model checking are decidable even in presence of parameters. They are well suited to model and analyze real-time operating systems. Here we extend ITA with polynomial guards and updates, leading to the class of polynomial ITA (PolITA). We prove the decidability of the reachability and model checking of a timed version of CTL by an adaptation of the cylindrical decomposition method for the first-order theory of reals. Compared to previous approaches, our procedure handles parameters and clocks in a unified way. Moreover, we show that PolITA are incomparable with stopwatch automata. Finally additional features are introduced while preserving decidability