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

Stable Model Counting and Its Application in Probabilistic Logic Programming

Model counting is the problem of computing the number of models that satisfy a given propositional theory. It has recently been applied to solving inference tasks in probabilistic logic programming, where the goal is to compute the probability of given queries being true provided a set of mutually independent random variables, a model (a logic program) and some evidence. The core of solving this inference task involves translating the logic program to a propositional theory and using a model counter. In this paper, we show that for some problems that involve inductive definitions like reachability in a graph, the translation of logic programs to SAT can be expensive for the purpose of solving inference tasks. For such problems, direct implementation of stable model semantics allows for more efficient solving. We present two implementation techniques, based on unfounded set detection, that extend a propositional model counter to a stable model counter. Our experiments show that for particular problems, our approach can outperform a state-of-the-art probabilistic logic programming solver by several orders of magnitude in terms of running time and space requirements, and can solve instances of significantly larger sizes on which the current solver runs out of time or memory.Comment: Accepted in AAAI, 201

Bit-Vector Model Counting using Statistical Estimation

Approximate model counting for bit-vector SMT formulas (generalizing \#SAT) has many applications such as probabilistic inference and quantitative information-flow security, but it is computationally difficult. Adding random parity constraints (XOR streamlining) and then checking satisfiability is an effective approximation technique, but it requires a prior hypothesis about the model count to produce useful results. We propose an approach inspired by statistical estimation to continually refine a probabilistic estimate of the model count for a formula, so that each XOR-streamlined query yields as much information as possible. We implement this approach, with an approximate probability model, as a wrapper around an off-the-shelf SMT solver or SAT solver. Experimental results show that the implementation is faster than the most similar previous approaches which used simpler refinement strategies. The technique also lets us model count formulas over floating-point constraints, which we demonstrate with an application to a vulnerability in differential privacy mechanisms

Parameterized Compilation Lower Bounds for Restricted CNF-formulas

We show unconditional parameterized lower bounds in the area of knowledge compilation, more specifically on the size of circuits in decomposable negation normal form (DNNF) that encode CNF-formulas restricted by several graph width measures. In particular, we show that - there are CNF formulas of size $n$ and modular incidence treewidth $k$ whose smallest DNNF-encoding has size $n^{\Omega(k)}$, and - there are CNF formulas of size $n$ and incidence neighborhood diversity $k$ whose smallest DNNF-encoding has size $n^{\Omega(\sqrt{k})}$. These results complement recent upper bounds for compiling CNF into DNNF and strengthen---quantitatively and qualitatively---known conditional low\-er bounds for cliquewidth. Moreover, they show that, unlike for many graph problems, the parameters considered here behave significantly differently from treewidth

Centrality Heuristics for Exact Model Counting

Model counting is the archetypical #P-complete problem consisting of determining the number of satisfying truth assignments of a given propositional formula. In this short paper, we empirically investigate the potential of employing graph centrality measures as a basis of search heuristics in the context of exact model counting. In particular, we integrate centrality-based heuristics into the search-based exact model counter sharpSAT. Our experiments show that employing centrality information significantly improves the empirical performance of sharpSAT, and also allows for simplifying the search heuristics compared to the current default heuristics of the model counter. In particular, we show that the VSIDS heuristic, which is an integral search heuristic employed in essentially all state-of-the-art conflict-driven clause learning Boolean satisfiability solvers, appears to be of very limited use in the context of model counting.Peer reviewe