245,557 research outputs found
Software for Exact Integration of Polynomials over Polyhedra
We are interested in the fast computation of the exact value of integrals of
polynomial functions over convex polyhedra. We present speed ups and extensions
of the algorithms presented in previous work. We present the new software
implementation and provide benchmark computations. The computation of integrals
of polynomials over polyhedral regions has many applications; here we
demonstrate our algorithmic tools solving a challenge from combinatorial voting
theory.Comment: Major updat
An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids
It has been shown that minimum free energy structure for RNAs and RNA-RNA
interaction is often incorrect due to inaccuracies in the energy parameters and
inherent limitations of the energy model. In contrast, ensemble based
quantities such as melting temperature and equilibrium concentrations can be
more reliably predicted. Even structure prediction by sampling from the
ensemble and clustering those structures by Sfold [7] has proven to be more
reliable than minimum free energy structure prediction. The main obstacle for
ensemble based approaches is the computational complexity of the partition
function and base pairing probabilities. For instance, the space complexity of
the partition function for RNA-RNA interaction is and the time
complexity is which are prohibitively large [4,12]. Our goal in this
paper is to give a fast algorithm, based on sparse folding, to calculate an
upper bound on the partition function. Our work is based on the recent
algorithm of Hazan and Jaakkola [10]. The space complexity of our algorithm is
the same as that of sparse folding algorithms, and the time complexity of our
algorithm is for single RNA and for RNA-RNA
interaction in practice, in which is the running time of sparse folding
and () is a sequence dependent parameter
A Machine-Checked Formalization of the Generic Model and the Random Oracle Model
Most approaches to the formal analyses of cryptographic protocols make the perfect cryptography assumption, i.e. the hypothese that there is no way to obtain knowledge about the plaintext pertaining to a ciphertext without knowing the key. Ideally, one would prefer to rely on a weaker hypothesis on the computational cost of gaining information about the plaintext pertaining to a ciphertext without knowing the key. Such a view is permitted by the Generic Model and the Random Oracle Model which provide non-standard computational models in which one may reason about the computational cost of breaking a cryptographic scheme. Using the proof assistant Coq, we provide a machine-checked account of the Generic Model and the Random Oracle Mode
On the enumeration of closures and environments with an application to random generation
Environments and closures are two of the main ingredients of evaluation in
lambda-calculus. A closure is a pair consisting of a lambda-term and an
environment, whereas an environment is a list of lambda-terms assigned to free
variables. In this paper we investigate some dynamic aspects of evaluation in
lambda-calculus considering the quantitative, combinatorial properties of
environments and closures. Focusing on two classes of environments and
closures, namely the so-called plain and closed ones, we consider the problem
of their asymptotic counting and effective random generation. We provide an
asymptotic approximation of the number of both plain environments and closures
of size . Using the associated generating functions, we construct effective
samplers for both classes of combinatorial structures. Finally, we discuss the
related problem of asymptotic counting and random generation of closed
environemnts and closures
Kinetic and Dynamic Delaunay tetrahedralizations in three dimensions
We describe the implementation of algorithms to construct and maintain
three-dimensional dynamic Delaunay triangulations with kinetic vertices using a
three-simplex data structure. The code is capable of constructing the geometric
dual, the Voronoi or Dirichlet tessellation. Initially, a given list of points
is triangulated. Time evolution of the triangulation is not only governed by
kinetic vertices but also by a changing number of vertices. We use
three-dimensional simplex flip algorithms, a stochastic visibility walk
algorithm for point location and in addition, we propose a new simple method of
deleting vertices from an existing three-dimensional Delaunay triangulation
while maintaining the Delaunay property. The dual Dirichlet tessellation can be
used to solve differential equations on an irregular grid, to define partitions
in cell tissue simulations, for collision detection etc.Comment: 29 pg (preprint), 12 figures, 1 table Title changed (mainly
nomenclature), referee suggestions included, typos corrected, bibliography
update
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