9,431 research outputs found
Paraiso : An Automated Tuning Framework for Explicit Solvers of Partial Differential Equations
We propose Paraiso, a domain specific language embedded in functional
programming language Haskell, for automated tuning of explicit solvers of
partial differential equations (PDEs) on GPUs as well as multicore CPUs. In
Paraiso, one can describe PDE solving algorithms succinctly using tensor
equations notation. Hydrodynamic properties, interpolation methods and other
building blocks are described in abstract, modular, re-usable and combinable
forms, which lets us generate versatile solvers from little set of Paraiso
source codes.
We demonstrate Paraiso by implementing a compressive hydrodynamics solver. A
single source code less than 500 lines can be used to generate solvers of
arbitrary dimensions, for both multicore CPUs and GPUs. We demonstrate both
manual annotation based tuning and evolutionary computing based automated
tuning of the program.Comment: 52 pages, 14 figures, accepted for publications in Computational
Science and Discover
The edge-disjoint path problem on random graphs by message-passing
We present a message-passing algorithm to solve the edge disjoint path
problem (EDP) on graphs incorporating under a unique framework both traffic
optimization and path length minimization. The min-sum equations for this
problem present an exponential computational cost in the number of paths. To
overcome this obstacle we propose an efficient implementation by mapping the
equations onto a weighted combinatorial matching problem over an auxiliary
graph. We perform extensive numerical simulations on random graphs of various
types to test the performance both in terms of path length minimization and
maximization of the number of accommodated paths. In addition, we test the
performance on benchmark instances on various graphs by comparison with
state-of-the-art algorithms and results found in the literature. Our
message-passing algorithm always outperforms the others in terms of the number
of accommodated paths when considering non trivial instances (otherwise it
gives the same trivial results). Remarkably, the largest improvement in
performance with respect to the other methods employed is found in the case of
benchmarks with meshes, where the validity hypothesis behind message-passing is
expected to worsen. In these cases, even though the exact message-passing
equations do not converge, by introducing a reinforcement parameter to force
convergence towards a sub optimal solution, we were able to always outperform
the other algorithms with a peak of 27% performance improvement in terms of
accommodated paths. On random graphs, we numerically observe two separated
regimes: one in which all paths can be accommodated and one in which this is
not possible. We also investigate the behaviour of both the number of paths to
be accommodated and their minimum total length.Comment: 14 pages, 8 figure
`The frozen accident' as an evolutionary adaptation: A rate distortion theory perspective on the dynamics and symmetries of genetic coding mechanisms
We survey some interpretations and related issues concerning the frozen hypothesis due to F. Crick and how it can be explained in terms of several natural mechanisms involving error correction codes, spin glasses, symmetry breaking and the characteristic robustness of genetic networks. The approach to most of these questions involves using elements of Shannon's rate distortion theory incorporating a semantic system which is meaningful for the relevant alphabets and vocabulary implemented in transmission of the genetic code. We apply the fundamental homology between information source uncertainty with the free energy density of a thermodynamical system with respect to transcriptional regulators and the communication channels of sequence/structure in proteins. This leads to the suggestion that the frozen accident may have been a type of evolutionary adaptation
Effective Fitness Landscapes for Evolutionary Systems
In evolution theory the concept of a fitness landscape has played an
important role, evolution itself being portrayed as a hill-climbing process on
a rugged landscape. In this article it is shown that in general, in the
presence of other genetic operators such as mutation and recombination,
hill-climbing is the exception rather than the rule. This descrepency can be
traced to the different ways that the concept of fitness appears --- as a
measure of the number of fit offspring, or as a measure of the probability to
reach reproductive age. Effective fitness models the former not the latter and
gives an intuitive way to understand population dynamics as flows on an
effective fitness landscape when genetic operators other than selection play an
important role. The efficacy of the concept is shown using several simple
analytic examples and also some more complicated cases illustrated by
simulations.Comment: 11 pages, 8 postscript figure
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