5,108 research outputs found

    Test Derivation from Timed Automata

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    A real-time system is a discrete system whose state changes occur in real-numbered time [AH97]. For testing real-time systems, specification languages must be extended with constructs for expressing real-time constraints, the implementation relation must be generalized to consider the temporal dimension, and the data structures and algorithms used to generate tests must be revised to operate on a potentially infinite set of states

    Computing Multidimensional Persistence

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    The theory of multidimensional persistence captures the topology of a multifiltration -- a multiparameter family of increasing spaces. Multifiltrations arise naturally in the topological analysis of scientific data. In this paper, we give a polynomial time algorithm for computing multidimensional persistence. We recast this computation as a problem within computational algebraic geometry and utilize algorithms from this area to solve it. While the resulting problem is Expspace-complete and the standard algorithms take doubly-exponential time, we exploit the structure inherent withing multifiltrations to yield practical algorithms. We implement all algorithms in the paper and provide statistical experiments to demonstrate their feasibility.Comment: This paper has been withdrawn by the authors. Journal of Computational Geometry, 1(1) 2010, pages 72-100. http://jocg.org/index.php/jocg/article/view/1

    A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks

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    An explosion of high-throughput DNA sequencing in the past decade has led to a surge of interest in population-scale inference with whole-genome data. Recent work in population genetics has centered on designing inference methods for relatively simple model classes, and few scalable general-purpose inference techniques exist for more realistic, complex models. To achieve this, two inferential challenges need to be addressed: (1) population data are exchangeable, calling for methods that efficiently exploit the symmetries of the data, and (2) computing likelihoods is intractable as it requires integrating over a set of correlated, extremely high-dimensional latent variables. These challenges are traditionally tackled by likelihood-free methods that use scientific simulators to generate datasets and reduce them to hand-designed, permutation-invariant summary statistics, often leading to inaccurate inference. In this work, we develop an exchangeable neural network that performs summary statistic-free, likelihood-free inference. Our framework can be applied in a black-box fashion across a variety of simulation-based tasks, both within and outside biology. We demonstrate the power of our approach on the recombination hotspot testing problem, outperforming the state-of-the-art.Comment: 9 pages, 8 figure

    Automatic Margin Computation for Risk-Limiting Audits

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    A risk-limiting audit is a statistical method to create confidence in the correctness of an election result by checking samples of paper ballots. In order to perform an audit, one usually needs to know what the election margin is, i.e., the number of votes that would need to be changed in order to change the election outcome. In this paper, we present a fully automatic method for computing election margins. It is based on the program analysis technique of bounded model checking to analyse the implementation of the election function. The method can be applied to arbitrary election functions without understanding the actual computation of the election result or without even intuitively knowing how the election function works. We have implemented our method based on the model checker CBMC; and we present a case study demonstrating that it can be applied to real-world elections

    Querying the Guarded Fragment

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    Evaluating a Boolean conjunctive query Q against a guarded first-order theory F is equivalent to checking whether "F and not Q" is unsatisfiable. This problem is relevant to the areas of database theory and description logic. Since Q may not be guarded, well known results about the decidability, complexity, and finite-model property of the guarded fragment do not obviously carry over to conjunctive query answering over guarded theories, and had been left open in general. By investigating finite guarded bisimilar covers of hypergraphs and relational structures, and by substantially generalising Rosati's finite chase, we prove for guarded theories F and (unions of) conjunctive queries Q that (i) Q is true in each model of F iff Q is true in each finite model of F and (ii) determining whether F implies Q is 2EXPTIME-complete. We further show the following results: (iii) the existence of polynomial-size conformal covers of arbitrary hypergraphs; (iv) a new proof of the finite model property of the clique-guarded fragment; (v) the small model property of the guarded fragment with optimal bounds; (vi) a polynomial-time solution to the canonisation problem modulo guarded bisimulation, which yields (vii) a capturing result for guarded bisimulation invariant PTIME.Comment: This is an improved and extended version of the paper of the same title presented at LICS 201

    MV3: A new word based stream cipher using rapid mixing and revolving buffers

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    MV3 is a new word based stream cipher for encrypting long streams of data. A direct adaptation of a byte based cipher such as RC4 into a 32- or 64-bit word version will obviously need vast amounts of memory. This scaling issue necessitates a look for new components and principles, as well as mathematical analysis to justify their use. Our approach, like RC4's, is based on rapidly mixing random walks on directed graphs (that is, walks which reach a random state quickly, from any starting point). We begin with some well understood walks, and then introduce nonlinearity in their steps in order to improve security and show long term statistical correlations are negligible. To minimize the short term correlations, as well as to deter attacks using equations involving successive outputs, we provide a method for sequencing the outputs derived from the walk using three revolving buffers. The cipher is fast -- it runs at a speed of less than 5 cycles per byte on a Pentium IV processor. A word based cipher needs to output more bits per step, which exposes more correlations for attacks. Moreover we seek simplicity of construction and transparent analysis. To meet these requirements, we use a larger state and claim security corresponding to only a fraction of it. Our design is for an adequately secure word-based cipher; our very preliminary estimate puts the security close to exhaustive search for keys of size < 256 bits.Comment: 27 pages, shortened version will appear in "Topics in Cryptology - CT-RSA 2007
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