62,938 research outputs found
Memetic Multilevel Hypergraph Partitioning
Hypergraph partitioning has a wide range of important applications such as
VLSI design or scientific computing. With focus on solution quality, we develop
the first multilevel memetic algorithm to tackle the problem. Key components of
our contribution are new effective multilevel recombination and mutation
operations that provide a large amount of diversity. We perform a wide range of
experiments on a benchmark set containing instances from application areas such
VLSI, SAT solving, social networks, and scientific computing. Compared to the
state-of-the-art hypergraph partitioning tools hMetis, PaToH, and KaHyPar, our
new algorithm computes the best result on almost all instances
Recommended from our members
A survey of behavioral-level partitioning systems
Many approaches have been developed to partition a system's behavioral description before a structural implementation is synthesized. We highlight the foundations and motivations for behavioral partitioning. We survey behavioral partitioning approaches, discussing abstraction levels, goals, major steps, and key assumptions in each
Paradigms for computational nucleic acid design
The design of DNA and RNA sequences is critical for many endeavors, from DNA nanotechnology, to PCR‐based applications, to DNA hybridization arrays. Results in the literature rely on a wide variety of design criteria adapted to the particular requirements of each application. Using an extensively studied thermodynamic model, we perform a detailed study of several criteria for designing sequences intended to adopt a target secondary structure. We conclude that superior design methods should explicitly implement both a positive design paradigm (optimize affinity for the target structure) and a negative design paradigm (optimize specificity for the target structure). The commonly used approaches of sequence symmetry minimization and minimum free‐energy satisfaction primarily implement negative design and can be strengthened by introducing a positive design component. Surprisingly, our findings hold for a wide range of secondary structures and are robust to modest perturbation of the thermodynamic parameters used for evaluating sequence quality, suggesting the feasibility and ongoing utility of a unified approach to nucleic acid design as parameter sets are refined further. Finally, we observe that designing for thermodynamic stability does not determine folding kinetics, emphasizing the opportunity for extending design criteria to target kinetic features of the energy landscape
Multi-core computation of transfer matrices for strip lattices in the Potts model
The transfer-matrix technique is a convenient way for studying strip lattices
in the Potts model since the compu- tational costs depend just on the periodic
part of the lattice and not on the whole. However, even when the cost is
reduced, the transfer-matrix technique is still an NP-hard problem since the
time T(|V|, |E|) needed to compute the matrix grows ex- ponentially as a
function of the graph width. In this work, we present a parallel
transfer-matrix implementation that scales performance under multi-core
architectures. The construction of the matrix is based on several repetitions
of the deletion- contraction technique, allowing parallelism suitable to
multi-core machines. Our experimental results show that the multi-core
implementation achieves speedups of 3.7X with p = 4 processors and 5.7X with p
= 8. The efficiency of the implementation lies between 60% and 95%, achieving
the best balance of speedup and efficiency at p = 4 processors for actual
multi-core architectures. The algorithm also takes advantage of the lattice
symmetry, making the transfer matrix computation to run up to 2X faster than
its non-symmetric counterpart and use up to a quarter of the original space
- …