Automated Benchmarking of Incremental SAT and QBF Solvers

Incremental SAT and QBF solving potentially yields improvements when sequences of related formulas are solved. An incremental application is usually tailored towards some specific solver and decomposes a problem into incremental solver calls. This hinders the independent comparison of different solvers, particularly when the application program is not available. As a remedy, we present an approach to automated benchmarking of incremental SAT and QBF solvers. Given a collection of formulas in (Q)DIMACS format generated incrementally by an application program, our approach automatically translates the formulas into instructions to import and solve a formula by an incremental SAT/QBF solver. The result of the translation is a program which replays the incremental solver calls and thus allows to evaluate incremental solvers independently from the application program. We illustrate our approach by different hardware verification problems for SAT and QBF solvers.Comment: camera-ready version (8 pages + 2 pages appendix), to appear in the proceedings of the 20th International Conference on Logic for Programming, Artificial Intelligence and Reasoning (LPAR), LNCS, Springer, 201

Dependency Schemes in QBF Calculi: Semantics and Soundness

We study the parametrisation of QBF resolution calculi by dependency schemes. One of the main problems in this area is to understand for which dependency schemes the resulting calculi are sound. Towards this end we propose a semantic framework for variable independence based on ‘exhibition’ by QBF models, and use it to express a property of dependency schemes called full exhibition that is known to be sufficient for soundness in Q-resolution. Introducing a generalised form of the long-distance resolution rule, we propose a complete parametrisation of classical long-distance Q-resolution, and show that full exhibition remains sufficient for soundness. We demonstrate that our approach applies to the current research frontiers by proving that the reflexive resolution path dependency scheme is fully exhibited

Dynamic and combinatorial control of gene expression by nuclear retinoic acid receptors (RARs)

Nuclear retinoic acid receptors (RARs) are transcriptional regulators controlling the expression of specific subsets of genes in a ligand-dependent manner. The basic mechanism for switching on transcription of cognate target genes involves RAR binding at specific response elements and a network of interactions with coregulatory protein complexes, the assembly of which is directed by the C-terminal ligand-binding domain of RARs. In addition to this scenario, new roles for the N-terminal domain and the ubiquitin-proteasome system recently emerged. Moreover, the functions of RARs are not limited to the regulation of cognate target genes, as they can transrepress other gene pathways. Finally, RARs are also involved in nongenomic biological activities such as the activation of translation and of kinase cascades. Here we will review these mechanisms, focusing on how kinase signaling and the proteasome pathway cooperate to influence the dynamics of RAR transcriptional activity

DepQBF 6.0: A Search-Based QBF Solver Beyond Traditional QCDCL

We present the latest major release version 6.0 of the quantified Boolean formula (QBF) solver DepQBF, which is based on QCDCL. QCDCL is an extension of the conflict-driven clause learning (CDCL) paradigm implemented in state of the art propositional satisfiability (SAT) solvers. The Q-resolution calculus (QRES) is a QBF proof system which underlies QCDCL. QCDCL solvers can produce QRES proofs of QBFs in prenex conjunctive normal form (PCNF) as a byproduct of the solving process. In contrast to traditional QCDCL based on QRES, DepQBF 6.0 implements a variant of QCDCL which is based on a generalization of QRES. This generalization is due to a set of additional axioms and leaves the original Q-resolution rules unchanged. The generalization of QRES enables QCDCL to potentially produce exponentially shorter proofs than the traditional variant. We present an overview of the features implemented in DepQBF and report on experimental results which demonstrate the effectiveness of generalized QRES in QCDCL.Comment: 12 pages + appendix; to appear in the proceedings of CADE-26, LNCS, Springer, 201

Distribution, habitat associations, and conservation status updates for the pilose crayfish Pacifastacus gambelii (Girard, 1852) and Snake River pilose crayfish Pacifastacus connectens (Faxon, 1914) of the western United States

Our study evaluates the distribution, habitat associations, and current conservation status of the Snake River pilose crayfish Pacifastacus connectens (Faxon, 1914) and pilose crayfish Pacifastacus gambelii (Girard, 1852), two little-studied and data-deficient species endemic to the western United States. We first developed a species distribution model (SDM) for the pilose crayfishes based on their historical occurrence records using boosted regression trees and freshwater GIS data layers. We then sampled 163 sites in the summers of 2016 and 2017 within the distribution of these crayfishes, including 50 where these species were observed historically. We next compared our field results to modeled predictions of suitable habitat from the SDM. Our SDM predicted 73 sites (45%) we sampled as suitable for the pilose crayfishes, with a moderate AUC value of 0.824. The pilose crayfishes were generally predicted to occur in larger streams and rivers with less extreme upstream temperature and precipitation seasonality. We found the pilose crayfishes at only 20 (12%) of the 163 total sites we sampled, 14 (20%) of the 73 sites predicted as suitable for them by our SDM, and 12 (24%) of 50 historical sites that we sampled. We found the invasive virile crayfish Faxonius virilis (Hagen, 1870) at 22 sites total and 12 (24%) historical sites for the pilose crayfishes, and we found the “native invader” signal crayfish Pacifastacus leniusculus (Dana, 1852) at 29 sites total and 6 (12%) historical sites for the pilose crayfishes. We subsequently used a single classification tree to identify factors associated with our high rate of false positives for contemporary pilose crayfish distributions relative to our SDM. This classification tree identified the presence of invasive crayfishes, impairment of the benthic community, and sampling method as some of the factors differentiating false positives relative to true positives for the pilose crayfishes. Our study identified the historical distribution and habitat associations for P. connectens and P. gambelii using an SDM and contrasted this prediction to results of contemporary field sampling. We found that the pilose crayfishes have seemingly experienced substantial range declines, attributable to apparent displacement by invasive crayfishes and impairment or change to stream communities and habitat. We recommend increased conservation and management attention to P. connectens and P. gambelii in response to these findings

dynPARTIX - A Dynamic Programming Reasoner for Abstract Argumentation

The aim of this paper is to announce the release of a novel system for abstract argumentation which is based on decomposition and dynamic programming. We provide first experimental evaluations to show the feasibility of this approach.Comment: The paper appears in the Proceedings of the 19th International Conference on Applications of Declarative Programming and Knowledge Management (INAP 2011

Analysis of Dialogical Argumentation via Finite State Machines

Dialogical argumentation is an important cognitive activity by which agents exchange arguments and counterarguments as part of some process such as discussion, debate, persuasion and negotiation. Whilst numerous formal systems have been proposed, there is a lack of frameworks for implementing and evaluating these proposals. First-order executable logic has been proposed as a general framework for specifying and analysing dialogical argumentation. In this paper, we investigate how we can implement systems for dialogical argumentation using propositional executable logic. Our approach is to present and evaluate an algorithm that generates a finite state machine that reflects a propositional executable logic specification for a dialogical argumentation together with an initial state. We also consider how the finite state machines can be analysed, with the minimax strategy being used as an illustration of the kinds of empirical analysis that can be undertaken.Comment: 10 page

Understanding Gentzen and Frege Systems for QBF

Recently Beyersdorff, Bonacina, and Chew [10] introduced a natural class of Frege systems for quantified Boolean formulas (QBF) and showed strong lower bounds for restricted versions of these systems. Here we provide a comprehensive analysis of the new extended Frege system from [10], denoted EF + ∀red, which is a natural extension of classical extended Frege EF. Our main results are the following: Firstly, we prove that the standard Gentzen-style system G*1 p-simulates EF + ∀red and that G*1 is strictly stronger under standard complexity-theoretic hardness assumptions. Secondly, we show a correspondence of EF + ∀red to bounded arithmetic: EF + ∀red can be seen as the non-uniform propositional version of intuitionistic S12. Specifically, intuitionistic S12 proofs of arbitrary statements in prenex form translate to polynomial-size EF + ∀red proofs, and EF + ∀red is in a sense the weakest system with this property. Finally, we show that unconditional lower bounds for EF + ∀red would imply either a major breakthrough in circuit complexity or in classical proof complexity, and in fact the converse implications hold as well. Therefore, the system EF + ∀red naturally unites the central problems from circuit and proof complexity. Technically, our results rest on a formalised strategy extraction theorem for EF + ∀red akin to witnessing in intuitionistic S12 and a normal form for EF + ∀red proofs

Incrementally Computing Minimal Unsatisfiable Cores of QBFs via a Clause Group Solver API

We consider the incremental computation of minimal unsatisfiable cores (MUCs) of QBFs. To this end, we equipped our incremental QBF solver DepQBF with a novel API to allow for incremental solving based on clause groups. A clause group is a set of clauses which is incrementally added to or removed from a previously solved QBF. Our implementation of the novel API is related to incremental SAT solving based on selector variables and assumptions. However, the API entirely hides selector variables and assumptions from the user, which facilitates the integration of DepQBF in other tools. We present implementation details and, for the first time, report on experiments related to the computation of MUCs of QBFs using DepQBF's novel clause group API.Comment: (fixed typo), camera-ready version, 6-page tool paper, to appear in proceedings of SAT 2015, LNCS, Springe

Encoding argument graphs in logic

International audienceArgument graphs are a common way to model argumentative reasoning. For reasoning or computational purposes, such graphs may have to be encoded in a given logic. This paper aims at providing a systematic approach for this encoding. This approach relies upon a general, principle-based characterization of argumentation semantics