arXivDaily arXiv每日学术速递 周一至周五更新
arXiv 2109.06355cs.AR
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基于FPGA的大规模分子相似性搜索加速器优化设计

Optimizing FPGA-based Accelerator Design for Large-Scale Molecular Similarity Search

Hongwu Peng, Shiyang Chen, Zhepeng Wang, Junhuan Yang, Scott A. Weitze, Tong Geng, Ang Li, Jinbo Bi, Minghu Song, Weiwen Jiang, Hang Liu, Caiwen Ding

摘要:

分子相似性搜索技术已广泛应用于药物发现中,以快速从大型分子数据库中识别结构相似的化合物。随着化学库规模的不断扩大,如何有效地加速大规模的相似性搜索越来越受到人们的关注。现有的工作主要集中在CPU和GPU加速计算Tanimoto系数在衡量不同分子指纹图谱之间的两两相似性。在本文中,我们提出并优化了基于FPGA的加速器设计的穷举和近似搜索算法。在使用BitBound和折叠的穷举搜索中,分析了相似度截断和折叠级别与搜索加速比和搜索精度的关系,并提出了一种基于FPGA的可扩展的动态查询引擎,以减少资源利用率和流水线间隔。我们实现了一个查询引擎每秒4.5亿复合处理吞吐量。在近似搜索中,使用了层次导航小世界(HNSW),这是一种流行的高召回率和查询速度的算法。我们提出了一个基于FPGA的图遍历引擎,利用高吞吐量的寄存器阵列的优先级队列和细粒度的距离计算引擎,以提高处理能力。实验结果表明,提出的基于FPGA的HNSW实现具有每秒103385查询(QPS)的Chembl数据库与0.92召回,并实现了35倍的加速比现有的CPU实现平均。据我们所知,我们基于FPGA的实现是第一次尝试在FPGA上加速分子相似性搜索算法,并在现有方法中具有最高的性能。

英文摘要:

Molecular similarity search has been widely used in drug discovery to identify structurally similar compounds from large molecular databases rapidly. With the increasing size of chemical libraries, there is growing interest in the efficient acceleration of large-scale similarity search. Existing works mainly focus on CPU and GPU to accelerate the computation of the Tanimoto coefficient in measuring the pairwise similarity between different molecular fingerprints. In this paper, we propose and optimize an FPGA-based accelerator design on exhaustive and approximate search algorithms. On exhaustive search using BitBound & folding, we analyze the similarity cutoff and folding level relationship with search speedup and accuracy, and propose a scalable on-the-fly query engine on FPGAs to reduce the resource utilization and pipeline interval. We achieve a 450 million compounds-per-second processing throughput for a single query engine. On approximate search using hierarchical navigable small world (HNSW), a popular algorithm with high recall and query speed. We propose an FPGA-based graph traversal engine to utilize a high throughput register array based priority queue and fine-grained distance calculation engine to increase the processing capability. Experimental results show that the proposed FPGA-based HNSW implementation has a 103385 query per second (QPS) on the Chembl database with 0.92 recall and achieves a 35x speedup than the existing CPU implementation on average. To the best of our knowledge, our FPGA-based implementation is the first attempt to accelerate molecular similarity search algorithms on FPGA and has the highest performance among existing approaches.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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