Efficient parameter search for qualitative models of regulatory networks using symbolic model checking

Investigating the relation between the structure and behavior of complex biological networks often involves posing the following two questions: Is a hypothesized structure of a regulatory network consistent with the observed behavior? And can a proposed structure generate a desired behavior? Answering these questions presupposes that we are able to test the compatibility of network structure and behavior. We cast these questions into a parameter search problem for qualitative models of regulatory networks, in particular piecewise-affine differential equation models. We develop a method based on symbolic model checking that avoids enumerating all possible parametrizations, and show that this method performs well on real biological problems, using the IRMA synthetic network and benchmark experimental data sets. We test the consistency between the IRMA network structure and the time-series data, and search for parameter modifications that would improve the robustness of the external control of the system behavior

Partial Orders for Efficient BMC of Concurrent Software

This version previously deposited at arXiv:1301.1629v1 [cs.LO]The vast number of interleavings that a concurrent program can have is typically identified as the root cause of the difficulty of automatic analysis of concurrent software. Weak memory is generally believed to make this problem even harder. We address both issues by modelling programs' executions with partial orders rather than the interleaving semantics (SC). We implemented a software analysis tool based on these ideas. It scales to programs of sufficient size to achieve first-time formal verification of non-trivial concurrent systems code over a wide range of models, including SC, Intel x86 and IBM Power

A Multi-Core Solver for Parity Games

We describe a parallel algorithm for solving parity games,\ud with applications in, e.g., modal mu-calculus model\ud checking with arbitrary alternations, and (branching) bisimulation\ud checking. The algorithm is based on Jurdzinski's Small Progress\ud Measures. Actually, this is a class of algorithms, depending on\ud a selection heuristics.\ud \ud Our algorithm operates lock-free, and mostly wait-free (except for\ud infrequent termination detection), and thus allows maximum\ud parallelism. Additionally, we conserve memory by avoiding storage\ud of predecessor edges for the parity graph through strictly\ud forward-looking heuristics.\ud \ud We evaluate our multi-core implementation's behaviour on parity games\ud obtained from mu-calculus model checking problems for a set of\ud communication protocols, randomly generated problem instances, and\ud parametric problem instances from the literature.\ud \u

Taming Numbers and Durations in the Model Checking Integrated Planning System

The Model Checking Integrated Planning System (MIPS) is a temporal least commitment heuristic search planner based on a flexible object-oriented workbench architecture. Its design clearly separates explicit and symbolic directed exploration algorithms from the set of on-line and off-line computed estimates and associated data structures. MIPS has shown distinguished performance in the last two international planning competitions. In the last event the description language was extended from pure propositional planning to include numerical state variables, action durations, and plan quality objective functions. Plans were no longer sequences of actions but time-stamped schedules. As a participant of the fully automated track of the competition, MIPS has proven to be a general system; in each track and every benchmark domain it efficiently computed plans of remarkable quality. This article introduces and analyzes the most important algorithmic novelties that were necessary to tackle the new layers of expressiveness in the benchmark problems and to achieve a high level of performance. The extensions include critical path analysis of sequentially generated plans to generate corresponding optimal parallel plans. The linear time algorithm to compute the parallel plan bypasses known NP hardness results for partial ordering by scheduling plans with respect to the set of actions and the imposed precedence relations. The efficiency of this algorithm also allows us to improve the exploration guidance: for each encountered planning state the corresponding approximate sequential plan is scheduled. One major strength of MIPS is its static analysis phase that grounds and simplifies parameterized predicates, functions and operators, that infers knowledge to minimize the state description length, and that detects domain object symmetries. The latter aspect is analyzed in detail. MIPS has been developed to serve as a complete and optimal state space planner, with admissible estimates, exploration engines and branching cuts. In the competition version, however, certain performance compromises had to be made, including floating point arithmetic, weighted heuristic search exploration according to an inadmissible estimate and parameterized optimization