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A simulated annealing algorithm for zoning in planning using parallel computing
(Pergamon Press, 2016)
[Abstract] There is an increasing demand for tools that support land use planning processes, particularly the design of zoning maps, which is one of the most complex tasks in the field. In this task, different land use ...
Implementing Parallel Differential Evolution on Spark
(Springer, 2016-04-02)
[Abstract] Metaheuristics are gaining increased attention as an efficient way of solving hard global optimization problems. Differential Evolution (DE) is one of the most popular algorithms in that class. However, its ...
Prediction of missing sequences and branch lengths in phylogenomic data
(Oxford University Press, 2016-01-05)
[Abstract] Motivation: The presence of missing data in large-scale phylogenomic datasets has negative effects on the phylogenetic inference process. One effect that is caused by alignments with missing per-gene or per-partition ...
Locality-Aware Automatic Parallelization for GPGPU with OpenHMPP Directives
(Springer New York LLC, 2016-06)
[Abstract] The use of GPUs for general purpose computation has increased dramatically in the past years due to the rising demands of computing power and their tremendous computing capacity at low cost. Hence, new programming ...
Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures
(Institute of Electrical and Electronics Engineers, 2016-08)
[Abstract] Development of new methods to detect pairwise epistasis, such as SNP-SNP interactions, in Genome-Wide Association Studies is an important task in bioinformatics as they can help to explain genetic influences on ...
Does the choice of nucleotide substitution models matter topologically?
(BioMed Central Ltd., 2016-03-24)
[Abstract] Background: In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available an open-source code for testing all ...
ParDRe: faster parallel duplicated reads removal tool for sequencing studies
(Oxford University Press, 2016)
[Abstract] Summary: Current next generation sequencing technologies often generate duplicated or near-duplicated reads that (depending on the application scenario) do not provide any interesting biological information but ...
Novel parallelization of simulated annealing and Hooke & Jeeves search algorithms for multicore systems with application to complex fisheries stock assessment models
(Elsevier Ltd, 2016-11)
[Abstract] Estimating parameters of a statistical fisheries assessment model typically involves a comparison of disparate datasets to a forward simulation model through a likelihood function. In all but trivial cases the ...
Reducing the overhead of an MPI application-level migration approach
(Elsevier BV * North-Holland, 2016)
[Abstract] Process migration provides many benefits for parallel environments including dynamic load balance, data access locality, or fault tolerance. This work proposes a solution that reduces the memory and I/O overhead ...
Towards cloud-based parallel metaheuristics: A case study in computational biology with Differential Evolution and Spark
(Sage Publications Ltd., 2016-11-28)
[Abstract]
Many key problems in science and engineering can be formulated and solved using global optimization techniques. In the particular case of computational biology, the development of dynamic (kinetic) models is ...