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Houtgast, E.J. (author), Sima, V.M. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)We are rapidly entering the era of genomics. The dramatic cost reduction of DNA sequencing due to the introduction of Next Generation Sequencing (NGS) techniques has resulted in an exponential growth of genetics data. The amount of data generated, and its associated processing into useful information, poses serious computational challenges. Here...abstract 2016
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Bulavintsev, V. (author), Zhdanov, Dmitry D. (author)We propose a generalized method for adapting and optimizing algorithms for efficient execution on modern graphics processing units (GPU). The method consists of several steps. First, build a control flow graph (CFG) of the algorithm. Next, transform the CFG into a tree of loops and merge non-parallelizable loops into parallelizable ones....conference paper 2021
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Sun, W. (author), Katsifodimos, A (author), Hai, R. (author)Recent advances in Graphic Processing Units (GPUs) have facilitated a significant performance boost for database operators, in particular, joins. It has been intensively studied how conventional join implementations, such as hash joins, benefit from the massive parallelism of GPUs. With the proliferation of machine learning, more databases...conference paper 2023
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Park, Seongyeon (author), Kim, Hajin (author), Ahmad, T. (author), Ahmed, N. (author), Al-Ars, Z. (author), Hofstee, H.P. (author), Kim, Youngsok (author), Lee, Jinho (author)Sequence alignment forms an important backbone in many sequencing applications. A commonly used strategy for sequence alignment is an approximate string matching with a two-dimensional dynamic programming approach. Although some prior work has been conducted on GPU acceleration of a sequence alignment, we identify several shortcomings that limit...conference paper 2022
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Ren, S. (author), Ahmed, N. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)In order to improve the accuracy of indel detection, micro-assembly is used in multiple variant callers, such as the GATK HaplotypeCaller to reassemble reads in a specific region of the genome. Assembly is a computationally intensive process that causes runtime bottlenecks. In this paper, we propose a GPU-based de Bruijn graph construction...conference paper 2018
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Houtgast, E.J. (author), Sima, V.M. (author), Marchiori, G. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)Next Generation Sequencing techniques have dramatically reduced the cost of sequencing genetic material, resulting in huge amounts of data being sequenced. The processing of this data poses huge challenges, both from a performance perspective, as well as from a power-efficiency perspective. Heterogeneous computing can help on both fronts, by...conference paper 2016
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Ahmed, N. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)The seeding heuristic is widely used in many DNA analysis applications to speed up the analysis time. In many applications, seeding takes a substantial amount of the total execution time. In this paper, we present an efficient GPU implementation for computing maximal exact matching (MEM) seeds in long DNA reads. We applied various...conference paper 2020
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Miri Rostami, Seyyed Reza (author), Mozaffarzadeh, M. (author), Hariri, Ali (author), Jokerst, Jesse V. (author), Ghaffari-Miab, Mohsen (author)Double-stage delay-multiply-and-sum (DS-DMAS) is one of the algorithms proposed for photoacoustic image reconstruction where a linear-array transducer is used to detect signals. This algorithm provides a higher contrast image in comparison with the conventional delay-multiply-and-sum (DMAS) and delay-and-sum (DAS), but it imposes a high...conference paper 2019
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Knibbe, H.P. (author)The oil and gas industry makes use of computational intensive algorithms to provide an image of the subsurface. The image is obtained by sending wave energy into the subsurface and recording the signal required for a seismic wave to reflect back to the surface from the Earth interfaces that may have different physical properties. A seismic wave...doctoral thesis 2015
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Hasan, L. (author)Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of protein or DNA sequences. An accurate alignment...doctoral thesis 2011
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Schalkwijk, J. (author)De vorige eeuw was getuige van de opkomst van numerieke weer- en klimaatmodellen. Weersvoorspelling, voorheen een empirische procedure gebaseerd op de persoonlijke ervaring van de meteoroloog, ontwikkelde zich tot een wetenschappelijke methode om de toekomstige toestand van de atmosfeer te voorspellen op basis van de huidige toestand en tendens....doctoral thesis 2015
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Gupta, R. (author)In this work we study the implementations of deflation and preconditioning techniques for solving ill-conditioned linear systems using iterative methods. Solving such systems can be a time-consuming process because of the jumps in the coefficients due to large difference in material properties. We have developed implementations of the iterative...doctoral thesis 2015
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Shen, J. (author)Heterogeneous platforms are mixes of different processing units in a compute node (e.g., CPUs+GPUs, CPU+MICs) or a chip package (e.g., APUs). This type of platforms keeps gaining popularity in various computer systems ranging from supercomputers to mobile devices. In this context, improving their efficiency and usability has become increasingly...doctoral thesis 2015
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Xu, S. (author)This thesis deals with two research problems. The first research problem is motivated by the numerical computation involved in the Time Domain Simulation (TDS) of Power Grids. Due to the ever growing size and complexity of Power Grids such as the China National Grid, accelerating TDS has become a stringent need for the online analysis of these...doctoral thesis 2011
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Houtgast, E.J. (author)Developments in sequencing technology have drastically reduced the cost of DNA sequencing. The raw sequencing data being generated requires processing through computationally demanding suites of bioinformatics algorithms called genomics pipelines. The greatly decreased cost of sequencing has resulted in its widespread adoption, and the amount of...doctoral thesis 2019
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Khait, M. (author)Numerical simulation is based on space and time discretization providing a trade-off between accuracy and computational performance. The operator-based Linearization (OBL) approach introduces an additional discretization domain for the physical description of fluid and rock. Delft Advanced Research Terra Simulator (DARTS) is a general-purpose...doctoral thesis 2019
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Bouter, P.A. (author)In recent years, the use of Artificial Intelligence (AI) has become prevalent in a large number of societally relevant, real-world problems, e.g., in the domains of engineering and health care. The field of Evolutionary Computation (EC) can be considered to be a sub-field of AI, concerning optimization using Evolutionary Algorithms (EAs), which...doctoral thesis 2023
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Ren, S. (author)Next generation sequencing (NGS) technologies have transformed the landscape of genomic research. With the significant advances in NGS technologies, DNA sequencing is more affordable and accessible than ever before. Meanwhile, many DNA sequence analysis tools have been developed to derive useful information from the raw sequencing data produced...doctoral thesis 2018
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Aissa, M.H. (author)Design optimization relies heavily on time-consuming simulations, especially when using gradient-free optimization methods. These methods require a large number of simulations in order to get a remarkable improvement over reference designs, which are nowadays based on the accumulated engineering knowledge already quite optimal.<br/>High...doctoral thesis 2017
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Performance modeling and optimization of sparse matrix-vector multiplication on NVIDIA CUDA platformXu, S. (author), Xue, W. (author), Lin, H.X. (author)In this article, we discuss the performance modeling and optimization of Sparse Matrix-Vector Multiplication (SpMV) on NVIDIA GPUs using CUDA. SpMV has a very low computation-data ratio and its performance is mainly bound by the memory bandwidth. We propose optimization of SpMV based on ELLPACK from two aspects: (1) enhanced performance for the...journal article 2011