Good Learning and Implicit Model Enumeration

MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation

k-Step Relative Inductive Generalization

We introduce a new form of SAT-based symbolic model checking. One common idea in SAT-based symbolic model checking is to generate new clauses from states that can lead to property violations. Our previous work suggests applying induction to generalize from such states. While effective on some benchmarks, the main problem with inductive generalization is that not all such states can be inductively generalized at a given time in the analysis, resulting in long searches for generalizable states on some benchmarks. This paper introduces the idea of inductively generalizing states relative to $k$-step over-approximations: a given state is inductively generalized relative to the latest $k$-step over-approximation relative to which the negation of the state is itself inductive. This idea motivates an algorithm that inductively generalizes a given state at the highest level $k$ so far examined, possibly by generating more than one mutually $k$-step relative inductive clause. We present experimental evidence that the algorithm is effective in practice.Comment: 14 page

A Simple and Flexible Way of Computing Small Unsatisfiable Cores in SAT Modulo Theories

Finding small unsatisfiable cores for SAT problems has recently received a lot of interest, mostly for its applications in formal verification. However, propositional logic is often not expressive enough for representing many interesting verification problems, which can be more naturally addressed in the framework of Satisfiability Modulo Theories, SMT. Surprisingly, the problem of finding unsatisfiable cores in SMT has received very little attention in the literature; in particular, we are not aware of any work aiming at producing small unsatisfiable cores in SMT. In this paper we present a novel approach to this problem. The main idea is to combine an SMT solver with an external propositional core extractor: the SMT solver produces the theory lemmas found during the search; the core extractor is then called on the boolean abstraction of the original SMT problem and of the theory lemmas. This results in an unsatisfiable core for the original SMT problem, once the remaining theory lemmas have been removed. The approach is conceptually interesting, since the SMT solver is used to dynamically lift the suitable amount of theory information to the boolean level, and it also has several advantages in practice. In fact, it is extremely simple to implement and to update, and it can be interfaced with every propositional core extractor in a plug-and-play manner, so that to benefit for free of all unsat-core reduction techniques which have been or will be made available. We have evaluated our approach by an extensive empirical test on SMT-LIB benchmarks, which confirms the validity and potential of this approach

Partial Quantifier Elimination

We consider the problem of Partial Quantifier Elimination (PQE). Given formula exists(X)[F(X,Y) & G(X,Y)], where F, G are in conjunctive normal form, the PQE problem is to find a formula F*(Y) such that F* & exists(X)[G] is logically equivalent to exists(X)[F & G]. We solve the PQE problem by generating and adding to F clauses over the free variables that make the clauses of F with quantified variables redundant. The traditional Quantifier Elimination problem (QE) is a special case of PQE where G is empty so all clauses of the input formula with quantified variables need to be made redundant. The importance of PQE is twofold. First, many problems are more naturally formulated in terms of PQE rather than QE. Second, in many cases PQE can be solved more efficiently than QE. We describe a PQE algorithm based on the machinery of dependency sequents and give experimental results showing the promise of PQE

From Quantified CTL to QBF

QCTL extends the temporal logic CTL with quantifications over atomic propositions. This extension is known to be very expressive: QCTL allows us to express complex properties over Kripke structures (it is as expressive as MSO). Several semantics exist for the quantifications: here, we work with the structure semantics, where the extra propositions label the Kripke structure (and not its execution tree), and the model-checking problem is known to be PSPACE-complete in this framework. We propose a model-checking algorithm for QCTL based on a reduction to QBF. We consider several reduction strategies, and we compare them with a prototype (based on the SMT-solver Z3) on several examples