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In this paper, we present our view of massively-parallel heterogeneous computing for solving large scientific problems. We start by observing that computing has been the primary driver of major innovations since the beginning of the 21st century. We argue that this is the fruit of decades of progress in computing methods, technology, and systems. A high-level analysis on out-scaling and up-scaling...
In this project, we propose an SoC solution to accelerate the Pair-HMM's forward algorithm which is the key performance bottleneck in the GATK's HaplotypeCaller tool for DNA variant calling. We develop two versions of the Pair-HMM accelerator: one using High Level Synthesis (HLS), and another ring-based manual RTL implementation. We investigate the performance of the manual RTL design and HLS design...
Subsequence similarity search is one of the most common subroutines in time series data mining algorithms. According to previous studies, Dynamic Time Warping (DTW) distance is the best distance measurement in many domains. However, the high computational complexity of DTW distance makes it a critical bottleneck in many subsequence similarity search applications. In some applications, the performance...
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