9,819 research outputs found
Pattern Matching for sets of segments
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 . 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
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
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
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
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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