On the Relative Strength of Pebbling and Resolution

The last decade has seen a revival of interest in pebble games in the context of proof complexity. Pebbling has proven a useful tool for studying resolution-based proof systems when comparing the strength of different subsystems, showing bounds on proof space, and establishing size-space trade-offs. The typical approach has been to encode the pebble game played on a graph as a CNF formula and then argue that proofs of this formula must inherit (various aspects of) the pebbling properties of the underlying graph. Unfortunately, the reductions used here are not tight. To simulate resolution proofs by pebblings, the full strength of nondeterministic black-white pebbling is needed, whereas resolution is only known to be able to simulate deterministic black pebbling. To obtain strong results, one therefore needs to find specific graph families which either have essentially the same properties for black and black-white pebbling (not at all true in general) or which admit simulations of black-white pebblings in resolution. This paper contributes to both these approaches. First, we design a restricted form of black-white pebbling that can be simulated in resolution and show that there are graph families for which such restricted pebblings can be asymptotically better than black pebblings. This proves that, perhaps somewhat unexpectedly, resolution can strictly beat black-only pebbling, and in particular that the space lower bounds on pebbling formulas in [Ben-Sasson and Nordstrom 2008] are tight. Second, we present a versatile parametrized graph family with essentially the same properties for black and black-white pebbling, which gives sharp simultaneous trade-offs for black and black-white pebbling for various parameter settings. Both of our contributions have been instrumental in obtaining the time-space trade-off results for resolution-based proof systems in [Ben-Sasson and Nordstrom 2009].Comment: Full-length version of paper to appear in Proceedings of the 25th Annual IEEE Conference on Computational Complexity (CCC '10), June 201

Understanding Space in Proof Complexity: Separations and Trade-offs via Substitutions

For current state-of-the-art DPLL SAT-solvers the two main bottlenecks are the amounts of time and memory used. In proof complexity, these resources correspond to the length and space of resolution proofs. There has been a long line of research investigating these proof complexity measures, but while strong results have been established for length, our understanding of space and how it relates to length has remained quite poor. In particular, the question whether resolution proofs can be optimized for length and space simultaneously, or whether there are trade-offs between these two measures, has remained essentially open. In this paper, we remedy this situation by proving a host of length-space trade-off results for resolution. Our collection of trade-offs cover almost the whole range of values for the space complexity of formulas, and most of the trade-offs are superpolynomial or even exponential and essentially tight. Using similar techniques, we show that these trade-offs in fact extend to the exponentially stronger k-DNF resolution proof systems, which operate with formulas in disjunctive normal form with terms of bounded arity k. We also answer the open question whether the k-DNF resolution systems form a strict hierarchy with respect to space in the affirmative. Our key technical contribution is the following, somewhat surprising, theorem: Any CNF formula F can be transformed by simple variable substitution into a new formula F' such that if F has the right properties, F' can be proven in essentially the same length as F, whereas on the other hand the minimal number of lines one needs to keep in memory simultaneously in any proof of F' is lower-bounded by the minimal number of variables needed simultaneously in any proof of F. Applying this theorem to so-called pebbling formulas defined in terms of pebble games on directed acyclic graphs, we obtain our results.Comment: This paper is a merged and updated version of the two ECCC technical reports TR09-034 and TR09-047, and it hence subsumes these two report

Comparative analysis of rigidity across protein families

We present a comparative study in which 'pebble game' rigidity analysis is applied to multiple protein crystal structures, for each of six different protein families. We find that the main-chain rigidity of a protein structure at a given hydrogen bond energy cutoff is quite sensitive to small structural variations, and conclude that the hydrogen bond constraints in rigidity analysis should be chosen so as to form and test specific hypotheses about the rigidity of a particular protein. Our comparative approach highlights two different characteristic patterns ('sudden' or 'gradual') for protein rigidity loss as constraints are removed, in line with recent results on the rigidity transitions of glassy networks

Applications of Finite Model Theory: Optimisation Problems, Hybrid Modal Logics and Games.

There exists an interesting relationships between two seemingly distinct fields: logic from the field of Model Theory, which deals with the truth of statements about discrete structures; and Computational Complexity, which deals with the classification of problems by how much of a particular computer resource is required in order to compute a solution. This relationship is known as Descriptive Complexity and it is the primary application of the tools from Model Theory when they are restricted to the finite; this restriction is commonly called Finite Model Theory. In this thesis, we investigate the extension of the results of Descriptive Complexity from classes of decision problems to classes of optimisation problems. When dealing with decision problems the natural mapping from true and false in logic to yes and no instances of a problem is used but when dealing with optimisation problems, other features of a logic need to be used. We investigate what these features are and provide results in the form of logical frameworks that can be used for describing optimisation problems in particular classes, building on the existing research into this area. Another application of Finite Model Theory that this thesis investigates is the relative expressiveness of various fragments of an extension of modal logic called hybrid modal logic. This is achieved through taking the Ehrenfeucht-Fraïssé game from Model Theory and modifying it so that it can be applied to hybrid modal logic. Then, by developing winning strategies for the players in the game, results are obtained that show strict hierarchies of expressiveness for fragments of hybrid modal logic that are generated by varying the quantifier depth and the number of proposition and nominal symbols available

Large scale rigidity-based flexibility analysis of biomolecules

KINematics And RIgidity (KINARI) is an on-going project for in silico flexibility analysis of proteins. The new version of the software, Kinari-2, extends the function- ality of our free web server KinariWeb, incorporates advanced web technologies, emphasizes the reproducibility of its experiments, and makes substantially improved tools available to the user. It is designed specifically for large scale experiments, in particular, for (a) very large molecules, including bioassemblies with high degree of symmetry such as viruses and crystals, (b) large collections of related biomolecules, such as those obtained through simulated dilutions, mutations, or conformational changes from various types of dynamics simulations, and (c) is intended to work as seemlessly as possible on the large, idiosyncratic, publicly available repository of biomolecules, the Protein Data Bank. We describe the system design, along with the main data processing, computational, mathematical, and validation challenges under- lying this phase of the KINARI project

A virtual pebble game to ensemble average graph rigidity

Previous works have demonstrated that protein rigidity is related to thermodynamic stability, especially under conditions that favor formation of native structure. Mechanical network rigidity properties of a single conformation are efficiently calculated using the in- teger Pebble Game (PG) algorithm. However, thermodynamic properties require averaging over many samples from the ensemble of accessible conformations, leading to fluctuations within the network. We have developed a mean field Virtual Pebble Game (VPG) that provides a probabilistic description of the interaction network, meaning that sampling is not required. We extensively test the VPG algorithm over a variety of body-bar networks created on disordered lattices, from these calculations we fully characterize the network conditions under which the performance of the VPG offers the best solution. The VPG provides a satisfactory description of the ensemble averaged PG properties, especially in regions removed from the rigidity transition where ensemble fluctuations are greatest. In further experiments, we characterized the VPG across a structurally nonredundant dataset of 272 proteins. Using quantitative and visual assessments of the rigidity characterizations, the VPG results are shown to accurately reflect the ensemble averaged PG properties. That is, the fluctuating interaction network is well represented by a single calculation that re- places density functions with average values, thus speeding up the desired calculation by several orders of magnitude. Finally, we propose a new algorithm that is based on the combination of PG and VPG to balance the amount of sampling and mean field treatment. While offering interesting results, this approach needs to be further optimized to fully lever- age its utility. All these results positions the VPG as an efficient alternative to understand the mechanical role that chemical interactions play in maintaining protein stability