9,819 research outputs found

    Pattern Matching for sets of segments

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    In this paper we present algorithms for a number of problems in geometric pattern matching where the input consist of a collections of segments in the plane. Our work consists of two main parts. In the first, we address problems and measures that relate to collections of orthogonal line segments in the plane. Such collections arise naturally from problems in mapping buildings and robot exploration. We propose a new measure of segment similarity called a \emph{coverage measure}, and present efficient algorithms for maximising this measure between sets of axis-parallel segments under translations. Our algorithms run in time O(n^3\polylog n) in the general case, and run in time O(n^2\polylog n) for the case when all segments are horizontal. In addition, we show that when restricted to translations that are only vertical, the Hausdorff distance between two sets of horizontal segments can be computed in time roughly O(n^{3/2}{\sl polylog}n). These algorithms form significant improvements over the general algorithm of Chew et al. that takes time O(n4log2n)O(n^4 \log^2 n). In the second part of this paper we address the problem of matching polygonal chains. We study the well known \Frd, and present the first algorithm for computing the \Frd under general translations. Our methods also yield algorithms for computing a generalization of the \Fr distance, and we also present a simple approximation algorithm for the \Frd that runs in time O(n^2\polylog n).Comment: To appear in the 12 ACM Symposium on Discrete Algorithms, Jan 200

    Quantification of reachable attractors in asynchronous discrete dynamics

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    Motivation: Models of discrete concurrent systems often lead to huge and complex state transition graphs that represent their dynamics. This makes difficult to analyse dynamical properties. In particular, for logical models of biological regulatory networks, it is of real interest to study attractors and their reachability from specific initial conditions, i.e. to assess the potential asymptotical behaviours of the system. Beyond the identification of the reachable attractors, we propose to quantify this reachability. Results: Relying on the structure of the state transition graph, we estimate the probability of each attractor reachable from a given initial condition or from a portion of the state space. First, we present a quasi-exact solution with an original algorithm called Firefront, based on the exhaustive exploration of the reachable state space. Then, we introduce an adapted version of Monte Carlo simulation algorithm, termed Avatar, better suited to larger models. Firefront and Avatar methods are validated and compared to other related approaches, using as test cases logical models of synthetic and biological networks. Availability: Both algorithms are implemented as Perl scripts that can be freely downloaded from http://compbio.igc.gulbenkian.pt/nmd/node/59 along with Supplementary Material.Comment: 19 pages, 2 figures, 2 algorithms and 2 table

    Linux kernel compaction through cold code swapping

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    There is a growing trend to use general-purpose operating systems like Linux in embedded systems. Previous research focused on using compaction and specialization techniques to adapt a general-purpose OS to the memory-constrained environment, presented by most, embedded systems. However, there is still room for improvement: it has been shown that even after application of the aforementioned techniques more than 50% of the kernel code remains unexecuted under normal system operation. We introduce a new technique that reduces the Linux kernel code memory footprint, through on-demand code loading of infrequently executed code, for systems that support virtual memory. In this paper, we describe our general approach, and we study code placement algorithms to minimize the performance impact of the code loading. A code, size reduction of 68% is achieved, with a 2.2% execution speedup of the system-mode execution time, for a case study based on the MediaBench II benchmark suite

    Importance of chirality and reduced flexibility of protein side chains: A study with square and tetrahedral lattice models

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    In simple models side chains are often represented implicitly (e.g., by spin-states) or simplified as one atom. We study side chain effects using square lattice and tetrahedral lattice models, with explicitly side chains of two atoms. We distinguish effects due to chirality and effects due to side chain flexibilities, since residues in proteins are L-residues, and their side chains adopt different rotameric states. Short chains are enumerated exhaustively. For long chains, we sample effectively rare events (eg, compact conformations) and obtain complete pictures of ensemble properties of these models at all compactness region. We find that both chirality and reduced side chain flexibility lower the folding entropy significantly for globally compact conformations, suggesting that they are important properties of residues to ensure fast folding and stable native structure. This corresponds well with our finding that natural amino acid residues have reduced effective flexibility, as evidenced by analysis of rotamer libraries and side chain rotatable bonds. We further develop a method calculating the exact side-chain entropy for a given back bone structure. We show that simple rotamer counting often underestimates side chain entropy significantly, and side chain entropy does not always correlate well with main chain packing. Among compact backbones with maximum side chain entropy, helical structures emerges as the dominating configurations. Our results suggest that side chain entropy may be an important factor contributing to the formation of alpha helices for compact conformations.Comment: 16 pages, 15 figures, 2 tables. Accepted by J. Chem. Phy

    Quantitative model checking of continuous-time Markov chains against timed automata specifications

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    We study the following problem: given a continuous-time Markov chain (CTMC) C, and a linear real-time property provided as a deterministic timed automaton (DTA) A, what is the probability of the set of paths of C that are\ud accepted by A (C satisfies A)? It is shown that this set of paths is measurable and computing its probability can be reduced to computing the reachability probability in a piecewise deterministic Markov process (PDP). The reachability probability is characterized as the least solution of a system of integral equations and is shown to be approximated by solving a system of partial differential equations. For the special case of single-clock DTA, the system of integral equations can be transformed into a system of linear equations where the coefficients are solutions of ordinary differential equations
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