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

On the complexity of probabilistic trials for hidden satisfiability problems

What is the minimum amount of information and time needed to solve 2SAT? When the instance is known, it can be solved in polynomial time, but is this also possible without knowing the instance? Bei, Chen and Zhang (STOC '13) considered a model where the input is accessed by proposing possible assignments to a special oracle. This oracle, on encountering some constraint unsatisfied by the proposal, returns only the constraint index. It turns out that, in this model, even 1SAT cannot be solved in polynomial time unless P=NP. Hence, we consider a model in which the input is accessed by proposing probability distributions over assignments to the variables. The oracle then returns the index of the constraint that is most likely to be violated by this distribution. We show that the information obtained this way is sufficient to solve 1SAT in polynomial time, even when the clauses can be repeated. For 2SAT, as long as there are no repeated clauses, in polynomial time we can even learn an equivalent formula for the hidden instance and hence also solve it. Furthermore, we extend these results to the quantum regime. We show that in this setting 1QSAT can be solved in polynomial time up to constant precision, and 2QSAT can be learnt in polynomial time up to inverse polynomial precision.Comment: 24 pages, 2 figures. To appear in the 41st International Symposium on Mathematical Foundations of Computer Scienc

An Overview of Backtrack Search Satisfiability Algorithms

Propositional Satisfiability (SAT) is often used as the underlying model for a significan

GRASP: A New Search Algorithm for Satisfiability

This paper introduces GRASP (Generic search Algorithm J3r the Satisfiabilily Problem), an integrated algorithmic J3amework 30r SAT that unifies several previously proposed searchpruning techniques and jcilitates identification of additional ones. GRASP is premised on the inevitability of conflicts during search and its most distinguishingjature is the augmentation of basic backtracking search with a powerful conflict analysis procedure. Analyzing conflicts to determine their causes enables GRASP to backtrack non-chronologically to earlier levels in the search tree, potentially pruning large portions of the search space. In addition, by 'ecording" the causes of conflicts, GRASP can recognize and preempt the occurrence of similar conflicts later on in the search. Einally, straighrward bookkeeping of the causali y chains leading up to conflicts a/lows GRASP to identij) assignments that are necessary jr a solution to be found. Experimental results obtained jom a large number of benchmarks, including many J3om the field of test pattern generation, indicate that application of the proposed conflict analysis techniques to SAT algorithms can be extremely ejctive jr a large number of representative classes of SAT instances